255 results on '"overlapping genes"'
Search Results
2. Conditional splicing system for tight control of viral overlapping genes.
- Author
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Qing Yang, Jinlin Wang, and Zhiwei Chen
- Subjects
- *
GENETIC vectors , *VIRAL genes , *GENE expression , *RNA splicing , *VIRAL genomes , *HIV , *DNA vaccines - Abstract
Viral genomes frequently harbor overlapping genes, complicating the development of virus-vectored vaccines and gene therapies. This study introduces a novel conditional splicing system to precisely control the expression of such overlapping genes through recombinase-mediated conditional splicing. We refined site-specific recombinase (SSR) conditional splicing systems and explored their mechanisms. The systems demonstrated exceptional inducibility (116,700-fold increase) with negligible background expression, facilitating the conditional expression of overlapping genes in adenovirus-associated virus (AAV) and human immunodeficiency virus type 1. Notably, this approach enabled the establishment of stable AAV producer cell lines, encapsulating all necessary packaging genes. Our findings underscore the potential of the SSR-conditional splicing system to significantly advance vector engineering, enhancing the efficacy and scalability of viral-vector-based therapies and vaccines. IMPORTANCE Regulating overlapping genes is vital for gene therapy and vaccine development using viral vectors. The regulation of overlapping genes presents challenges, including cytotoxicity and impacts on vector capacity and genome stability, which restrict stable packaging cell line development and broad application. To address these challenges, we present a "loxp-splice-loxp"-based conditional splicing system, offering a novel solution for conditional expression of overlapping genes and stable cell line establishment. This system may also regulate other cytotoxic genes, representing a significant advancement in cell engineering and gene therapy as well as biomass production. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene.
- Author
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Karlin, David G.
- Subjects
- *
PARVOVIRUS B19 , *PHOSPHOLIPASES , *PHOSPHOLIPASE A2 , *PROTEINS , *DNA viruses , *GENES - Abstract
Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet, overlapping genes are often overlooked during genome annotation, in particular in DNA viruses. Here we looked for the presence of overlapping genes likely to encode a functional protein in human parvovirus B19 (genus Erythroparvovirus), using an experimentally validated software, Synplot2. Synplot2 detected an open reading frame, X, conserved in all erythroparvoviruses, which overlaps the VP1 capsid gene and is under highly significant selection pressure. In a related virus, human parvovirus 4 (genus Tetraparvovirus), Synplot2 also detected an open reading frame under highly significant selection pressure, ARF1, which overlaps the VP1 gene and is conserved in all tetraparvoviruses. These findings provide compelling evidence that the X and ARF1 proteins must be expressed and functional. X and ARF1 have the exact same location (they overlap the region of the VP1 gene encoding the phospholipase A2 domain), are both in the same frame (+1) with respect to the VP1 frame, and encode proteins with similar predicted properties, including a central transmembrane region. Further studies will be needed to determine whether they have a common origin and similar function. X and ARF1 are probably translated either from a polycistronic mRNA by a non-canonical mechanism, or from an unmapped monocistronic mRNA. Finally, we also discovered proteins predicted to be expressed from a frame overlapping VP1 in other species related to parvovirus B19: porcine parvovirus 2 (Z protein) and bovine parvovirus 3 (X-like protein). [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
4. Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair.
- Author
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Bukhnikashvili, Lasha
- Subjects
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HUMAN genome , *HUMAN genes , *CIRCADIAN rhythms , *STOP codons , *HUMAN DNA , *SINGLE nucleotide polymorphisms , *CLOCK genes - Abstract
For several decades, it has been known that a substantial number of genes within human DNA exhibit overlap; however, the biological and evolutionary significance of these overlaps remain poorly understood. This study focused on investigating specific instances of overlap where the overlapping DNA region encompasses the coding DNA sequences (CDSs) of protein-coding genes. The results revealed that proteins encoded by overlapping CDSs exhibit greater disorder than those from nonoverlapping CDSs. Additionally, these DNA regions were identified as GC-rich. This could be partially attributed to the absence of stop codons from two distinct reading frames rather than one. Furthermore, these regions were found to harbour fewer single-nucleotide polymorphism (SNP) sites, possibly due to constraints arising from the overlapping state where mutations could affect two genes simultaneously. While elucidating these properties, the NR1D1-THRA gene pair emerged as an exceptional case with highly structured proteins and a distinctly conserved sequence across eutherian mammals. Both NR1D1 and THRA are nuclear receptors lacking a ligand-binding domain at their C-terminus, which is the region where these gene pairs overlap. The NR1D1 gene is involved in the regulation of circadian rhythm, while the THRA gene encodes a thyroid hormone receptor, and both play crucial roles in various physiological processes. This study suggests that, in addition to their well-established functions, the specifically overlapping CDS regions of these genes may encode protein segments with additional, yet undiscovered, biological roles. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. The most exposed regions of SARS-CoV-2 structural proteins are subject to strong positive selection and gene overlap may locally modify this behavior
- Author
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Alejandro Rubio, Maria de Toro, and Antonio J. Pérez-Pulido
- Subjects
SARS-CoV-2 ,selection pressure ,Ka/Ks ratio ,overlapping genes ,Microbiology ,QR1-502 - Abstract
ABSTRACTThe SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic that emerged in 2019 has been an unprecedented event in international science, as it has been possible to sequence millions of genomes, tracking their evolution very closely. This has enabled various types of secondary analyses of these genomes, including the measurement of their sequence selection pressure. In this work, we have been able to measure the selective pressure of all the described SARS-CoV-2 genes, even analyzed by sequence regions, and we show how this type of analysis allows us to separate the genes between those subject to positive selection (usually those that code for surface proteins or those exposed to the host immune system) and those subject to negative selection because they require greater conservation of their structure and function. We have also seen that when another gene with an overlapping reading frame appears within a gene sequence, the overlapping sequence between the two genes evolves under a stronger purifying selection than the average of the non-overlapping regions of the main gene. We propose this type of analysis as a useful tool for locating and analyzing all the genes of a viral genome when an adequate number of sequences are available.IMPORTANCEWe have analyzed the selection pressure of all severe acute respiratory syndrome coronavirus 2 genes by means of the nonsynonymous (Ka) to synonymous (Ks) substitution rate. We found that protein-coding genes are exposed to strong positive selection, especially in the regions of interaction with other molecules (host receptor and genome of the virus itself). However, overlapping coding regions are more protected and show negative selection. This suggests that this measure could be used to study viral gene function as well as overlapping genes.
- Published
- 2024
- Full Text
- View/download PDF
6. Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty.
- Author
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Ardern, Zachary
- Subjects
- *
AMINO acid sequence , *GENETIC code , *MOLECULAR biology , *DNA sequencing - Abstract
Protein-coding DNA sequences can be translated into completely different amino acid sequences if the nucleotide triplets used are shifted by a non-triplet amount on the same DNA strand or by translating codons from the opposite strand. Such "alternative reading frames" of protein-coding genes are a major contributor to the evolution of novel protein products. Recent studies demonstrating this include examples across the three domains of cellular life and in viruses. These sequences increase the number of trials potentially available for the evolutionary invention of new genes and also have unusual properties which may facilitate gene origin. There is evidence that the structure of the standard genetic code contributes to the features and gene-likeness of some alternative frame sequences. These findings have important implications across diverse areas of molecular biology, including for genome annotation, structural biology, and evolutionary genomics. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
7. Orthoparamyxovirinae C Proteins Have a Common Origin and a Common Structural Organization.
- Author
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Roy, Ada, Chan Mine, Emeric, Gaifas, Lorenzo, Leyrat, Cédric, Volchkova, Valentina A., Baudin, Florence, Martinez-Gil, Luis, Volchkov, Viktor E., Karlin, David G., Bourhis, Jean-Marie, and Jamin, Marc
- Subjects
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PROTEIN C , *VIRAL proteins , *PROTEIN fractionation , *QUORUM sensing , *SENDAI virus , *NIPAH virus - Abstract
The protein C is a small viral protein encoded in an overlapping frame of the P gene in the subfamily Orthoparamyxovirinae. This protein, expressed by alternative translation initiation, is a virulence factor that regulates viral transcription, replication, and production of defective interfering RNA, interferes with the host-cell innate immunity systems and supports the assembly of viral particles and budding. We expressed and purified full-length and an N-terminally truncated C protein from Tupaia paramyxovirus (TupV) C protein (genus Narmovirus). We solved the crystal structure of the C-terminal part of TupV C protein at a resolution of 2.4 Å and found that it is structurally similar to Sendai virus C protein, suggesting that despite undetectable sequence conservation, these proteins are homologous. We characterized both truncated and full-length proteins by SEC-MALLS and SEC-SAXS and described their solution structures by ensemble models. We established a mini-replicon assay for the related Nipah virus (NiV) and showed that TupV C inhibited the expression of NiV minigenome in a concentration-dependent manner as efficiently as the NiV C protein. A previous study found that the Orthoparamyxovirinae C proteins form two clusters without detectable sequence similarity, raising the question of whether they were homologous or instead had originated independently. Since TupV C and SeV C are representatives of these two clusters, our discovery that they have a similar structure indicates that all Orthoparamyxovirine C proteins are homologous. Our results also imply that, strikingly, a STAT1-binding site is encoded by exactly the same RNA region of the P/C gene across Paramyxovirinae, but in different reading frames (P or C), depending on which cluster they belong to. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
8. Transcriptional analysis in bacteriophage Fc02 of Pseudomonas aeruginosa revealed two overlapping genes with exclusion activity.
- Author
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Ramírez-Sánchez, Irais, Magos-Castro, Marco, and Guarneros, Gabriel
- Subjects
PSEUDOMONAS aeruginosa ,GENE regulatory networks ,BACTERIOPHAGES ,GENETIC regulation ,LYTIC cycle ,GENES - Abstract
Little is known about the gene expression program during the transition from lysogenic to lytic cycles of temperate bacteriophages in Pseudomonas aeruginosa. To investigate this issue, we developed a thermo-sensitive repressor mutant in a lysogen and analyzed the phage transcriptional program by strand-specific RNASeq before and after thermo-induction. As expected, the repressor gene located on the phage DNA forward strand is transcribed in the lysogen at the permissive temperature of 30°C. Upstream the repressor gene, we noticed the presence of two overlapped ORFs apparently in the same transcript. One ORF is a gene that encodes a protein of 7.9 kDa mediating the exclusion of various super-infecting phages. The other ORF, placed in an alternate reading frame with a possible AUG initiation codon at 25 nucleotide downstream of the AUG of the first gene, is expected to encode a 20.7 kDa polypeptide of yet an unknown function. Upon lifting repression at 40°C, the transcription of an operon which is involved in the lytic cycle is started from a promoter on the reverse phage DNA strand. The first gene in the operon is a homolog of the antirepresor ner, a common gene in the lysis-lysogeny regulation region of other phages. Interestingly, the next gene after ner is gene 10 that on the reverse strand overlaps the overlapped gene olg1 on the forward strand. Curiously, gene 10 expression also shows superinfection exclusion. Strand-specific RNA-Seq also has uncovered the transcription succession of gene modules expressed during the phage lytic stage. The conservation of overlapped genes with similar functions may be evolutionarily selected. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
9. Role of ferroptosis-related genes in coronary atherosclerosis and identification of key genes: integration of bioinformatics analysis and experimental validation
- Author
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Qingwen Meng, Yiqian Xu, Xuebin ling, Huajiang Liu, Shun Ding, Haolin Wu, Dongming Yan, Xingyue Fang, Tianfa Li, and Qibing Liu
- Subjects
Coronary atherosclerosis ,Ferroptosis ,Overlapping genes ,Bioinformatics analysis ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Abstract Background Coronary atherosclerosis (CA) is the most common type of atherosclerosis. However, the inherent pathogenesis and mechanisms of CA are unclear, and the relationship with ferroptosis-related genes (FRGs) has not been reported. The purpose of this study was to use bioinformatics techniques to evaluate potential therapeutic targets for CA.Please provide the given name for author “Dingshun”.Please provide the given name for author “Dingshun”. Methods First, the GSE132651 dataset was acquired from the Gene Expression Omnibus database. Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and Protein–Protein interaction network were successively conducted. Next, overlapping genes between hub genes and CA genes were found. FRGs were found when comparing the CA group with the normal group. The correlation between overlapping genes and FRGs was further analyzed. At last, we performed Elisa to validate the expression of these genes in human blood specimens. Mice aortic tissues were used for western blot to detect the expression of proteins. Results Based on the GSE132651 dataset, 102 differentially expressed genes were identified. Five overlapping genes between hub genes and CA genes were found (CCNA2, RRM2, PBK, PCNA, CDK1). TFRC and GPX4 were found to be FRGs. TFRC was positively correlated with CCNA2, PBK, PCNA, CDK1, RRM2, with CDK1 being the strongest correlation. GPX4 was negatively correlated with these genes, among which CCNA2 was the strongest correlation. The ELISA results showed that CCNA2, CDK1, and TFRC expression were markedly increased in serum of the CA samples compared with controls, while GPX4 expression was markedly decreased in the CA samples. The western blot results show that GPX4 expression was lower in the model group, TFRC, CDK1, and CCNA2 protein expression were high in the model group. Conclusions Ferroptosis-related genes GPX4 and TFRC were closely correlated with the identified overlapping genes CCNA2 and CDK1, which may serve as targeted therapies for the treatment of CA.
- Published
- 2022
- Full Text
- View/download PDF
10. Transcriptional analysis in bacteriophage Fc02 of Pseudomonas aeruginosa revealed two overlapping genes with exclusion activity
- Author
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Irais Ramírez-Sánchez, Marco Magos-Castro, and Gabriel Guarneros
- Subjects
strand-specific RNA-Seq ,overlapping genes ,superinfection exclusion ,Pseudomonas aeruginosa ,beetreviruses ,Microbiology ,QR1-502 - Abstract
Little is known about the gene expression program during the transition from lysogenic to lytic cycles of temperate bacteriophages in Pseudomonas aeruginosa. To investigate this issue, we developed a thermo-sensitive repressor mutant in a lysogen and analyzed the phage transcriptional program by strand-specific RNA-Seq before and after thermo-induction. As expected, the repressor gene located on the phage DNA forward strand is transcribed in the lysogen at the permissive temperature of 30°C. Upstream the repressor gene, we noticed the presence of two overlapped ORFs apparently in the same transcript. One ORF is a gene that encodes a protein of 7.9 kDa mediating the exclusion of various super-infecting phages. The other ORF, placed in an alternate reading frame with a possible AUG initiation codon at 25 nucleotide downstream of the AUG of the first gene, is expected to encode a 20.7 kDa polypeptide of yet an unknown function. Upon lifting repression at 40°C, the transcription of an operon which is involved in the lytic cycle is started from a promoter on the reverse phage DNA strand. The first gene in the operon is a homolog of the antirepresor ner, a common gene in the lysis–lysogeny regulation region of other phages. Interestingly, the next gene after ner is gene 10 that on the reverse strand overlaps the overlapped gene olg1 on the forward strand. Curiously, gene 10 expression also shows superinfection exclusion. Strand-specific RNA-Seq also has uncovered the transcription succession of gene modules expressed during the phage lytic stage. The conservation of overlapped genes with similar functions may be evolutionarily selected.
- Published
- 2023
- Full Text
- View/download PDF
11. Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933
- Author
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Franziska Graf, Barbara Zehentner, Lea Fellner, Siegfried Scherer, and Klaus Neuhaus
- Subjects
overlapping genes ,EHEC O157:H7 ,protein ,prokaryotic genomes ,competitive growth assays ,phenotype ,Microbiology ,QR1-502 - Abstract
ABSTRACT The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes.
- Published
- 2023
- Full Text
- View/download PDF
12. Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes
- Author
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Majid Mehravar, Fatemeh Ghaemimanesh, and Ensieh M. Poursani
- Subjects
Overlapping genes ,Exon sharing ,Intron sharing ,Pouf51 ,OCT4, Tcf19 ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Overlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the advantage and biological significance of overlapping genes is still unclear. Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome. Results By using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share two exons and one intron enclosed, at the same positions, between OCT4B3 and TCF19-D splice variants. Conclusions This new form of overlapping gene expands our previous perception of splicing events and may shed more light on the complexity of gene regulation in higher organisms. Additional such genes might be detected by ESTs analysis also of other organisms.
- Published
- 2021
- Full Text
- View/download PDF
13. Role of ferroptosis-related genes in coronary atherosclerosis and identification of key genes: integration of bioinformatics analysis and experimental validation.
- Author
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Meng, Qingwen, Xu, Yiqian, ling, Xuebin, Liu, Huajiang, Ding, Shun, Wu, Haolin, Yan, Dongming, Fang, Xingyue, Li, Tianfa, and Liu, Qibing
- Subjects
ANIMAL experimentation ,PROGNOSIS ,BIOINFORMATICS ,CORONARY artery disease ,GENES ,RESEARCH funding ,ANIMALS ,MICE - Abstract
Background: Coronary atherosclerosis (CA) is the most common type of atherosclerosis. However, the inherent pathogenesis and mechanisms of CA are unclear, and the relationship with ferroptosis-related genes (FRGs) has not been reported. The purpose of this study was to use bioinformatics techniques to evaluate potential therapeutic targets for CA.Please provide the given name for author "Dingshun".Please provide the given name for author "Dingshun".Methods: First, the GSE132651 dataset was acquired from the Gene Expression Omnibus database. Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and Protein-Protein interaction network were successively conducted. Next, overlapping genes between hub genes and CA genes were found. FRGs were found when comparing the CA group with the normal group. The correlation between overlapping genes and FRGs was further analyzed. At last, we performed Elisa to validate the expression of these genes in human blood specimens. Mice aortic tissues were used for western blot to detect the expression of proteins.Results: Based on the GSE132651 dataset, 102 differentially expressed genes were identified. Five overlapping genes between hub genes and CA genes were found (CCNA2, RRM2, PBK, PCNA, CDK1). TFRC and GPX4 were found to be FRGs. TFRC was positively correlated with CCNA2, PBK, PCNA, CDK1, RRM2, with CDK1 being the strongest correlation. GPX4 was negatively correlated with these genes, among which CCNA2 was the strongest correlation. The ELISA results showed that CCNA2, CDK1, and TFRC expression were markedly increased in serum of the CA samples compared with controls, while GPX4 expression was markedly decreased in the CA samples. The western blot results show that GPX4 expression was lower in the model group, TFRC, CDK1, and CCNA2 protein expression were high in the model group.Conclusions: Ferroptosis-related genes GPX4 and TFRC were closely correlated with the identified overlapping genes CCNA2 and CDK1, which may serve as targeted therapies for the treatment of CA. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
14. Identification of Key Genes and Pathways Associated with PIEZO1 in Bone-Related Disease Based on Bioinformatics.
- Author
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Zhou, Yuanyuan, Zhang, Chen, Zhou, Zhongguo, Zhang, Chao, and Wang, Jiali
- Subjects
- *
ION channels , *GENES , *GENE ontology , *PROTEIN-protein interactions , *BIOINFORMATICS , *CELLULAR signal transduction , *FEMUR - Abstract
PIEZO1 is a mechano-sensitive ion channel that can sense various forms of mechanical stimuli and convert them into biological signals, affecting bone-related diseases. The present study aimed to identify key genes and signaling pathways in Piezo1-regulated bone-related diseases and to explain the potential mechanisms using bioinformatic analysis. The differentially expressed genes (DEGs) in tendon, femur, and humerus bone tissue; cortical bone; and bone-marrow-derived macrophages were identified with the criteria of |log2FC| > 1 and adjusted p-value < 0.05 analysis based on a dataset from GSE169261, GSE139121, GSE135282, and GSE133069, respectively, and visualized in a volcano plot. Venn diagram analyses were performed to identify the overlapping DEGs expressed in the above-mentioned tissues. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, protein–protein interaction (PPI) analysis, and module analysis were also conducted. Furthermore, qRT-PCR was performed to validate the above results using primary chondrocytes. As a result, a total of 222 overlapping DEGs and 12 mostly overlapping DEGs were identified. Key Piezo1-related genes, such as Lcn2, Dkk3, Obscn, and Tnnt1, were identified, and pathways, such as Wnt/β-catenin and PI3k-Akt, were also identified. The present informatic study provides insight, for the first time, into the potential therapeutic targets of Piezo1-regulated bone-related diseases [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
15. Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene
- Author
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Karlin, David and Karlin, David
- Abstract
Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet, overlapping genes are often overlooked during genome annotation, in particular in DNA viruses. Here we looked for the presence of overlapping genes likely to encode a functional protein in human parvovirus B19 (genus Erythroparvovirus), using an experimentally validated software, Synplot2. Synplot2 detected an open reading frame, X, conserved in all erythroparvoviruses, which overlaps the VP1 capsid gene and is under highly significant selection pressure. In a related virus, human parvovirus 4 (genus Tetraparvovirus), Synplot2 also detected an open reading frame under highly significant selection pressure, ARF1, which overlaps the VP1 gene and is conserved in all tetraparvoviruses. These findings provide compelling evidence that the X and ARF1 proteins must be expressed and functional. X and ARF1 have the exact same location (they overlap the region of the VP1 gene encoding the phospholipase A2 domain), are both in the same frame (+1) with respect to the VP1 frame, and encode proteins with similar predicted properties, including a central transmembrane region. Further studies will be needed to determine whether they have a common origin and similar function. X and ARF1 are probably translated either from a polycistronic mRNA by a non-canonical mechanism, or from an unmapped monocistronic mRNA. Finally, we also discovered proteins predicted to be expressed from a frame overlapping VP1 in other species related to parvovirus B19: porcine parvovirus 2 (Z protein) and bovine parvovirus 3 (X-like protein)., Peer Reviewed
- Published
- 2024
16. The most exposed regions of SARS-CoV-2 structural proteins are subject to strong positive selection and gene overlap may locally modify this behavior
- Author
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Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Rubio, Alejandro [0000-0002-6736-6141], Toro, María de [0000-0003-3329-0203], Pérez-Pulido, Antonio J. [0000-0003-3343-2822], Rubio, Alejandro, Toro, María de, Pérez-Pulido, Antonio J., Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Rubio, Alejandro [0000-0002-6736-6141], Toro, María de [0000-0003-3329-0203], Pérez-Pulido, Antonio J. [0000-0003-3343-2822], Rubio, Alejandro, Toro, María de, and Pérez-Pulido, Antonio J.
- Abstract
The SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic that emerged in 2019 has been an unprecedented event in international science, as it has been possible to sequence millions of genomes, tracking their evolution very closely. This has enabled various types of secondary analyses of these genomes, including the measurement of their sequence selection pressure. In this work, we have been able to measure the selective pressure of all the described SARS-CoV-2 genes, even analyzed by sequence regions, and we show how this type of analysis allows us to separate the genes between those subject to positive selection (usually those that code for surface proteins or those exposed to the host immune system) and those subject to negative selection because they require greater conservation of their structure and function. We have also seen that when another gene with an overlapping reading frame appears within a gene sequence, the overlapping sequence between the two genes evolves under a stronger purifying selection than the average of the non-overlapping regions of the main gene. We propose this type of analysis as a useful tool for locating and analyzing all the genes of a viral genome when an adequate number of sequences are available.IMPORTANCEWe have analyzed the selection pressure of all severe acute respiratory syndrome coronavirus 2 genes by means of the nonsynonymous (Ka) to synonymous (Ks) substitution rate. We found that protein-coding genes are exposed to strong positive selection, especially in the regions of interaction with other molecules (host receptor and genome of the virus itself). However, overlapping coding regions are more protected and show negative selection. This suggests that this measure could be used to study viral gene function as well as overlapping genes.
- Published
- 2024
17. Functional and structural segregation of overlapping helices in HIV-1
- Author
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Maliheh Safari, Bhargavi Jayaraman, Henni Zommer, Shumin Yang, Cynthia Smith, Jason D Fernandes, and Alan D Frankel
- Subjects
HIV-1 ,overlapping genes ,overprinting ,Env ,Rev ,lentivirus ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Overlapping coding regions balance selective forces between multiple genes. One possible division of nucleotide sequence is that the predominant selective force on a particular nucleotide can be attributed to just one gene. While this arrangement has been observed in regions in which one gene is structured and the other is disordered, we sought to explore how overlapping genes balance constraints when both protein products are structured over the same sequence. We use a combination of sequence analysis, functional assays, and selection experiments to examine an overlapped region in HIV-1 that encodes helical regions in both Env and Rev. We find that functional segregation occurs even in this overlap, with each protein spacing its functional residues in a manner that allows a mutable non-binding face of one helix to encode important functional residues on a charged face in the other helix. Additionally, our experiments reveal novel and critical functional residues in Env and have implications for the therapeutic targeting of HIV-1.
- Published
- 2022
- Full Text
- View/download PDF
18. Comprehensive Analysis of Key Genes, Signaling Pathways and miRNAs in Human Knee Osteoarthritis: Based on Bioinformatics
- Author
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Liang Chang, Hao Yao, Zhi Yao, Kevin Ki-Wai Ho, Michael Tim-Yun Ong, Bingyang Dai, Wenxue Tong, Jiankun Xu, and Ling Qin
- Subjects
osteoarthiritis ,overlapping genes ,signaling pathways ,miRNAs ,bioinformatics ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Background: Osteoarthritis (OA) is one of the main causes of disability in the elderly population, accompanied by a series of underlying pathologic changes, such as cartilage degradation, synovitis, subchondral bone sclerosis, and meniscus injury. The present study aimed to identify key genes, signaling pathways, and miRNAs in knee OA associated with the entire joint components, and to explain the potential mechanisms using computational analysis.Methods: The differentially expressed genes (DEGs) in cartilage, synovium, subchondral bone, and meniscus were identified using the Gene Expression Omnibus 2R (GEO2R) analysis based on dataset from GSE43923, GSE12021, GSE98918, and GSE51588, respectively and visualized in Volcano Plot. Venn diagram analyses were performed to identify the overlapping DEGs (overlapping DEGs) that expressed in at least two types of tissues mentioned above. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, protein-protein interaction (PPI) analysis, and module analysis were conducted. Furthermore, qRT-PCR was performed to validate above results using our clinical specimens.Results: As a result, a total of 236 overlapping DEGs were identified, of which 160 were upregulated and 76 were downregulated. Through enrichment analysis and constructing the PPI network and miRNA-mRNA network, knee OA-related key genes, such as HEY1, AHR, VEGFA, MYC, and CXCL12 were identified. Clinical validation by qRT-PCR experiments further supported above computational results. In addition, knee OA-related key miRNAs such as miR-101, miR-181a, miR-29, miR-9, and miR-221, and pathways such as Wnt signaling, HIF-1 signaling, PI3K-Akt signaling, and axon guidance pathways were also identified. Among above identified knee OA-related key genes, pathways and miRNAs, genes such as AHR, HEY1, MYC, GAP43, and PTN, pathways like axon guidance, and miRNAs such as miR-17, miR-21, miR-155, miR-185, and miR-1 are lack of research and worthy for future investigation.Conclusion: The present informatic study for the first time provides insight to the potential therapeutic targets of knee OA by comprehensively analyzing the overlapping genes differentially expressed in multiple joint components and their relevant signaling pathways and interactive miRNAs.
- Published
- 2021
- Full Text
- View/download PDF
19. Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes.
- Author
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Mehravar, Majid, Ghaemimanesh, Fatemeh, and Poursani, Ensieh M.
- Subjects
GENETIC regulation ,GENES ,HUMAN genome ,HUMAN genes ,SHARING - Abstract
Background: Overlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the advantage and biological significance of overlapping genes is still unclear. Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome. Results: By using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share two exons and one intron enclosed, at the same positions, between OCT4B3 and TCF19-D splice variants. Conclusions: This new form of overlapping gene expands our previous perception of splicing events and may shed more light on the complexity of gene regulation in higher organisms. Additional such genes might be detected by ESTs analysis also of other organisms. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
20. Comprehensive Analysis of Key Genes, Signaling Pathways and miRNAs in Human Knee Osteoarthritis: Based on Bioinformatics.
- Author
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Chang, Liang, Yao, Hao, Yao, Zhi, Ho, Kevin Ki-Wai, Ong, Michael Tim-Yun, Dai, Bingyang, Tong, Wenxue, Xu, Jiankun, and Qin, Ling
- Subjects
KNEE osteoarthritis ,KNEE ,MICRORNA ,MENISCUS (Anatomy) ,DRUG target ,GENES ,MENISCUS injuries - Abstract
Background: Osteoarthritis (OA) is one of the main causes of disability in the elderly population, accompanied by a series of underlying pathologic changes, such as cartilage degradation, synovitis, subchondral bone sclerosis, and meniscus injury. The present study aimed to identify key genes, signaling pathways, and miRNAs in knee OA associated with the entire joint components, and to explain the potential mechanisms using computational analysis. Methods: The differentially expressed genes (DEGs) in cartilage, synovium, subchondral bone, and meniscus were identified using the Gene Expression Omnibus 2R (GEO2R) analysis based on dataset from GSE43923, GSE12021, GSE98918, and GSE51588, respectively and visualized in Volcano Plot. Venn diagram analyses were performed to identify the overlapping DEGs (overlapping DEGs) that expressed in at least two types of tissues mentioned above. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, protein-protein interaction (PPI) analysis, and module analysis were conducted. Furthermore, qRT-PCR was performed to validate above results using our clinical specimens. Results: As a result, a total of 236 overlapping DEGs were identified, of which 160 were upregulated and 76 were downregulated. Through enrichment analysis and constructing the PPI network and miRNA-mRNA network, knee OA-related key genes, such as HEY1 , AHR , VEGFA , MYC , and CXCL12 were identified. Clinical validation by qRT-PCR experiments further supported above computational results. In addition, knee OA-related key miRNAs such as miR-101, miR-181a, miR-29, miR-9, and miR-221, and pathways such as Wnt signaling, HIF-1 signaling, PI3K-Akt signaling, and axon guidance pathways were also identified. Among above identified knee OA-related key genes, pathways and miRNAs, genes such as AHR , HEY1 , MYC , GAP43 , and PTN , pathways like axon guidance, and miRNAs such as miR-17, miR-21, miR-155, miR-185, and miR-1 are lack of research and worthy for future investigation. Conclusion: The present informatic study for the first time provides insight to the potential therapeutic targets of knee OA by comprehensively analyzing the overlapping genes differentially expressed in multiple joint components and their relevant signaling pathways and interactive miRNAs. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
21. Engineering and characterizing porcine reproductive and respiratory syndrome virus with separated and tagged genes encoding the minor glycoproteins.
- Author
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Zhang, Minze, Qian, Bang, and Veit, Michael
- Subjects
- *
PORCINE reproductive & respiratory syndrome , *GLYCOPROTEINS , *WESTERN immunoblotting , *CYTOSKELETAL proteins , *GENES - Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major pathogen affecting pigs and belongs to the enveloped plus-stranded RNA virus family Arteriviridae. A unique feature of Arteriviruses is that the genes encoding the structural proteins overlap at their 3' and 5' ends. This impedes mutagenesis opportunities and precludes the binding of short peptides for antibody detection, as this would alter the amino acids encoded by the overlapping gene. In this study, we aimed to generate infectious PRRSV variants with separated genes encoding the minor glycoproteins Gp2, Gp3, and Gp4, accompanied by appended tags for detection. All recombinant genomes facilitate the release of infectious virus particles into the supernatant of transfected 293 T cells, as evidenced by immunofluorescence of infected MARC-145 cells using anti-nucleocapsid antibodies. Furthermore, expression of Gp2-Myc and Gp3-HA was confirmed through immunofluorescence and western blot analysis with tag-specific antibodies. However, after two passages of Gp2-Myc and Gp3-HA viruses, the appended tags were completely removed as indicated by sequencing the viral genome. Recombinant viruses with separated Gp2 and Gp3 genes remained stable for at least nine passages, while those with Gp3 and Gp4 genes separated reverted to wild type after only four passages. Notably, this virus exhibited significantly reduced titers in growth assays. Furthermore, we introduced a tag to the C-terminus of Gp4. The Gp4-HA virus was consistently stable for at least 10 passages, and the HA-tag was detectable by western blotting and immunofluorescence. • Most genes encoding the structural proteins are overlapping in the PRRSV genome. • We separated the genes encoding Gp2, Gp3 and Gp4 of PRRSV-2 and added small tags. • Although initially viable, recombinant Gp2-Myc and Gp3-HA viruses lose the tags. • Even viruses with separated genes rapidly reverted to the wild-type sequence. • ORF4 does not overlap with the subsequent genes and Gp4-HA virus is stable. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
22. Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions
- Author
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Paweł Wawrzyniak, Agnieszka Sobolewska-Ruta, Piotr Zaleski, Natalia Łukasiewicz, Paulina Kabaj, Piotr Kierył, Agata Gościk, Anna Bierczyńska-Krzysik, Piotr Baran, Anna Mazurkiewicz-Pisarek, Andrzej Płucienniczak, and Dariusz Bartosik
- Subjects
Overlapping genes ,Plasmid replication ,Replication system ,Rep protein ,In-frame proteins ,Transcription regulation ,Microbiology ,QR1-502 - Abstract
Abstract Background Gene overlapping is a frequent phenomenon in microbial genomes. Excluding so-called “trivial overlapping”, there are significant implications of such genetic arrangements, including regulation of gene expression and modification of protein activity. It is also postulated that, besides gene duplication, the appearance of overlapping genes (OGs) is one of the most important factors promoting a genome’s novelty and evolution. OGs coding for in-frame proteins with different functions are a particularly interesting case. In this study we identified and characterized two in-frame proteins encoded by OGs on plasmid pIGRK from Klebsiella pneumoniae, a representative of the newly distinguished pHW126 plasmid family. Results A single repR locus located within the replication system of plasmid pIGRK encodes, in the same frame, two functional polypeptides: a full-length RepR protein and a RepR’ protein (with N-terminal truncation) translated from an internal START codon. Both proteins form homodimers, and interact with diverse DNA regions within the plasmid replication origin and repR promoter operator. Interestingly, RepR and RepR’ have opposing functions – RepR is crucial for initiation of pIGRK replication, while RepR’ is a negative regulator of this process. Nevertheless, both proteins act cooperatively as negative transcriptional regulators of their own expression. Conclusions Regulation of the initiation of pIGRK replication is a complex process in which a major role is played by two in-frame proteins with antagonistic functions. In-frame encoded Rep proteins are uncommon, having been described in only a few plasmids. This is the first description of such proteins in a plasmid of the pHW126 family.
- Published
- 2019
- Full Text
- View/download PDF
23. ERCC1 及其重叠基因 3’端非编码区多态性与结直肠癌发病 风险关联的病例对照研究.
- Author
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张靖悦, 张倩也, 陈信桢, 张国培, 肖明扬, and 逯晓波
- Abstract
Copyright of Journal of China Medical University is the property of Journal of China Medical University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2021
24. Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic
- Author
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Chase W Nelson, Zachary Ardern, Tony L Goldberg, Chen Meng, Chen-Hao Kuo, Christina Ludwig, Sergios-Orestis Kolokotronis, and Xinzhu Wei
- Subjects
genome annotation ,natural selection ,ORF3d ,overlapping genes ,pandemic ,SARS-CoV-2 ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.
- Published
- 2020
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- View/download PDF
25. Gene Overlapping as a Modulator of Begomovirus Evolution
- Author
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Iván Martín-Hernández and Israel Pagán
- Subjects
overlapping genes ,rate of evolution ,begomoviruses ,ssDNA viruses ,Biology (General) ,QH301-705.5 - Abstract
In RNA viruses, which have high mutation—and fast evolutionary— rates, gene overlapping (i.e., genomic regions that encode more than one protein) is a major factor controlling mutational load and therefore the virus evolvability. Although DNA viruses use host high-fidelity polymerases for their replication, and therefore should have lower mutation rates, it has been shown that some of them have evolutionary rates comparable to those of RNA viruses. Notably, these viruses have large proportions of their genes with at least one overlapping instance. Hence, gene overlapping could be a modulator of virus evolution beyond the RNA world. To test this hypothesis, we use the genus Begomovirus of plant viruses as a model. Through comparative genomic approaches, we show that terminal gene overlapping decreases the rate of virus evolution, which is associated with lower frequency of both synonymous and nonsynonymous mutations. In contrast, terminal overlapping has little effect on the pace of virus evolution. Overall, our analyses support a role for gene overlapping in the evolution of begomoviruses and provide novel information on the factors that shape their genetic diversity.
- Published
- 2022
- Full Text
- View/download PDF
26. Properties and abundance of overlapping genes in viruses.
- Author
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Schlub, Timothy E and Holmes, Edward C
- Subjects
VIRAL genes ,VIRUSES ,GENOMES ,RNA ,SINGLE-stranded DNA ,DOUBLE-stranded RNA ,DNA - Abstract
Overlapping genes are commonplace in viruses and play an important role in their function and evolution. However, aside from studies on specific groups of viruses, relatively little is known about the extent and nature of gene overlap and its determinants in viruses as a whole. Here, we present an extensive characterisation of gene overlap in viruses through an analysis of reference genomes present in the NCBI virus genome database. We find that over half the instances of gene overlap are very small, covering <10 nt, and 84 per cent are <50 nt in length. Despite this, 53 per cent of all viruses still contained a gene overlap of 50 nt or larger. We also investigate several predictors of gene overlap such as genome structure (single- and double-stranded RNA and DNA), virus family, genome length, and genome segmentation. This revealed that gene overlap occurs more frequently in DNA viruses than in RNA viruses, and more frequently in single-stranded viruses than in double-stranded viruses. Genome segmentation is also associated with gene overlap, particularly in single-stranded DNA viruses. Notably, we observed a large range of overlap frequencies across families of all genome types, suggesting that it is a common evolutionary trait that provides flexible genome structures in all virus families. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
27. A case for a negative-strand coding sequence in a group of positive-sense RNA viruses.
- Author
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Dinan, Adam M, Lukhovitskaya, Nina I, Olendraite, Ingrida, and Firth, Andrew E
- Subjects
POSITIVE-strand RNA viruses ,EUKARYOTES ,GENOMES ,NEGATIVE-strand RNA viruses ,RNA viruses ,LEVIVIRIDAE - Abstract
Positive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (∼1,000-codon) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae , form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
28. An Improved Method for Eliminating or Creating Intragenic Bacterial Promoters.
- Author
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Trofimova E, Logel DY, and Jaschke PR
- Subjects
- Promoter Regions, Genetic, RNA, DNA, Transcription, Genetic, Bacteria genetics, Genomics
- Abstract
Recent advances in genomic refactoring have been hindered by the ever-present complication of internal or cryptic transcriptional regulation. Typical approaches to these features have been to randomize or perform mass alterations to the gene sequences thought to contain the regulatory motifs; however, this approach can cause problems by altering translational speeds, introducing long distance DNA-DNA interaction effects, and inducing RNA toxicity. Previously, we developed a rational design approach named COdon Restrained Promoter SilEncing (CORPSE) which takes externally identified promoter sequences and uses position-specific scoring matrices as proxy promoter strengths to make minimal changes to promoter sequences to disable their activity. Additionally, through inverting our system we were also able to modify weak internal promoters to increase their activity. In this chapter, we augment our previous process with the biophysical model Promoter Calculator v1.0 developed by LaFleur et al. to combine promoter identification and activity prediction, with our algorithm to silently modify promoter sequences, to provide more robust promoter elimination and creation., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2024
- Full Text
- View/download PDF
29. Towards Automatic Detecting of Overlapping Genes - Clustered BLAST Analysis of Viral Genomes
- Author
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Neuhaus, Klaus, Oelke, Daniela, Fürst, David, Scherer, Siegfried, Keim, Daniel A., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Pizzuti, Clara, editor, Ritchie, Marylyn D., editor, and Giacobini, Mario, editor
- Published
- 2010
- Full Text
- View/download PDF
30. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora.
- Author
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Huei-Jiun Su, Barkman, Todd J., Weilong Hao, Jones, Samuel S., Naumann, Julia, Skippington, Elizabeth, Wafula, Eric K., Jer-Ming Hu, Palmer, Jeffrey D., and dePamphilis, Claude W.
- Subjects
- *
GENOMES , *PLASTIDS , *BALANOPHORACEAE , *PROTEIN synthesis , *GENES - Abstract
Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size andwith only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
31. Viral Genome Compression
- Author
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Ilie, Lucian, Tinta, Liviu, Popescu, Cristian, Hill, Kathleen A., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Mao, Chengde, editor, and Yokomori, Takashi, editor
- Published
- 2006
- Full Text
- View/download PDF
32. Tobamovirus 3′-Terminal Gene Overlap May be a Mechanism for within-Host Fitness Improvement
- Author
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Yuri L. Dorokhov, Ekaterina V. Sheshukova, and Tatiana V. Komarova
- Subjects
overlapping genes ,plant virus ,virus genome ,evolution ,tobamovirus ,movement protein ,Microbiology ,QR1-502 - Abstract
Overlapping genes (OGs) are a universal phenomenon in all kingdoms, and viruses display a high content of OGs combined with a high rate of evolution. It is believed that the mechanism of gene overlap is based on overprinting of an existing gene. OGs help virus genes compress a maximum amount of information into short sequences, conferring viral proteins with novel features and thereby increasing their within-host fitness. Analysis of tobamovirus 3′-terminal genes reveals at least two modes of OG organization and mechanisms of interaction with the host. Originally isolated from Solanaceae species, viruses (referred to as Solanaceae-infecting) such as tobacco mosaic virus do not show 3′-terminal overlap between movement protein (MP) and coat protein (CP) genes but do contain open reading frame 6 (ORF6), which overlaps with both genes. Conversely, tobamoviruses, originally isolated from Brassicaceae species (referred to as Brassicaceae-infecting) and also able to infect Solanaceae plants, have no ORF6 but are characterized by overlapping MP and CP genes. Our analysis showed that the MP/CP overlap of Brassicaceae-infecting tobamoviruses results in the following: (i) genome compression and strengthening of subgenomic promoters; (ii) CP gene early expression directly from genomic and dicistronic MP subgenomic mRNA using an internal ribosome entry site (IRES) and a stable hairpin structure in the overlapping region; (iii) loss of ORF6, which influences the symptomatology of Solanaceae-infecting tobamoviruses; and (iv) acquisition of an IRES polypurine-rich region encoding an MP nuclear localization signal. We believe that MP/CP gene overlap may constitute a mechanism for host range expansion and virus adjustment to Brassicaceae plants.
- Published
- 2017
- Full Text
- View/download PDF
33. Gene Overlapping as a Modulator of Begomovirus Evolution
- Author
-
Martín-Hernández, Iván, Pagán, Israel, Martín-Hernández, Iván, and Pagán, Israel
- Abstract
In RNA viruses, which have high mutation—and fast evolutionary— rates, gene overlapping (i.e., genomic regions that encode more than one protein) is a major factor controlling mutational load and therefore the virus evolvability. Although DNA viruses use host high-fidelity polymerases for their replication, and therefore should have lower mutation rates, it has been shown that some of them have evolutionary rates comparable to those of RNA viruses. Notably, these viruses have large proportions of their genes with at least one overlapping instance. Hence, gene overlapping could be a modulator of virus evolution beyond the RNA world. To test this hypothesis, we use the genus Begomovirus of plant viruses as a model. Through comparative genomic approaches, we show that terminal gene overlapping decreases the rate of virus evolution, which is associated with lower frequency of both synonymous and nonsynonymous mutations. In contrast, terminal overlapping has little effect on the pace of virus evolution. Overall, our analyses support a role for gene overlapping in the evolution of begomoviruses and provide novel information on the factors that shape their genetic diversity. View Full-Text
- Published
- 2022
34. Gene Overlapping as a Modulator of Begomovirus Evolution
- Author
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Ministerio de Economía y Competitividad (España), Martín-Hernández, Iván, Pagán, Israel, Ministerio de Economía y Competitividad (España), Martín-Hernández, Iván, and Pagán, Israel
- Abstract
In RNA viruses, which have high mutation-and fast evolutionary- rates, gene overlapping (i.e., genomic regions that encode more than one protein) is a major factor controlling mutational load and therefore the virus evolvability. Although DNA viruses use host high-fidelity polymerases for their replication, and therefore should have lower mutation rates, it has been shown that some of them have evolutionary rates comparable to those of RNA viruses. Notably, these viruses have large proportions of their genes with at least one overlapping instance. Hence, gene overlapping could be a modulator of virus evolution beyond the RNA world. To test this hypothesis, we use the genus Begomovirus of plant viruses as a model. Through comparative genomic approaches, we show that terminal gene overlapping decreases the rate of virus evolution, which is associated with lower frequency of both synonymous and nonsynonymous mutations. In contrast, terminal overlapping has little effect on the pace of virus evolution. Overall, our analyses support a role for gene overlapping in the evolution of begomoviruses and provide novel information on the factors that shape their genetic diversity.
- Published
- 2022
35. Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH- III Shows SERAT3;2 Promoter is Nested Within the IDH- III Promoter.
- Author
-
Raipuria, Ritesh, Kumar, Vajinder, Guruprasad, Kadur, and Bhat, Shripad
- Abstract
Intergenic regions of divergent gene pairs show bidirectional promoter activity but whether regulatory sequences for gene expression in opposite directions are shared is not established. In this study, promoters of divergently arranged gene pair At4g35640- At4g35650 ( SERAT3;2- IDH- III) of Arabidopsis thaliana were analyzed to identify overlapping regulatory regions. Both genes showed the highest expression in flower buds and flowers. 5′ RACE experiments extended the intergenic region from 161 bp shown in TAIR annotation to 512 bp. GUS analysis of transgenic A. thaliana plants carrying the 691 bp fragment (512 bp intergenic region plus 5′ UTR of both the genes) linked to uidA gene revealed that SERAT3;2 promoter drives gene expression in the tapetum, whereas IDH- III promoter functions specifically in microspores/pollen. Serial 5′ deletion of the 691 bp fragment showed SERAT3;2 promoter extends up to −355 position, whereas IDH- III promoter encompasses the 512 bp intergenic region. In transgenics, uidA transcript levels were lower than native SERAT3;2 and IDH- III transcripts indicating presence of additional cis regulatory elements beyond the 691 bp fragment. The present study demonstrated for the first time occurrence of a nested promoter in plants and identified a novel bidirectional promoter capable of driving gene expression in tapetum and microspores/pollen. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
36. Tobamovirus 3'-Terminal Gene Overlap May be a Mechanism for within-Host Fitness Improvement.
- Author
-
Dorokhov, Yuri L., Sheshukova, Ekaterina V., and Komarova, Tatiana V.
- Subjects
TOBAMOVIRUSES ,VIRAL proteins ,BRASSICACEAE - Abstract
Overlapping genes (OGs) are a universal phenomenon in all kingdoms, and viruses display a high content of OGs combined with a high rate of evolution. It is believed that the mechanism of gene overlap is based on overprinting of an existing gene. OGs help virus genes compress a maximum amount of information into short sequences, conferring viral proteins with novel features and thereby increasing their within-host fitness. Analysis of tobamovirus 3'-terminal genes reveals at least two modes of OG organization and mechanisms of interaction with the host. Originally isolated from Solanaceae species, viruses (referred to as Solanaceae-infecting) such as tobacco mosaic virus do not show 3'-terminal overlap between movement protein (MP) and coat protein (CP) genes but do contain open reading frame 6 (ORF6), which overlaps with both genes. Conversely, tobamoviruses, originally isolated from Brassicaceae species (referred to as Brassicaceae-infecting) and also able to infect Solanaceae plants, have no ORF6 but are characterized by overlapping MP and CP genes. Our analysis showed that the MP/CP overlap of Brassicaceae-infecting tobamoviruses results in the following: (i) genome compression and strengthening of subgenomic promoters; (ii) CP gene early expression directly fromgenomic and dicistronicMP subgenomicmRNA using an internal ribosome entry site (IRES) and a stable hairpin structure in the overlapping region; (iii) loss of ORF6, which influences the symptomatology of Solanaceae-infecting tobamoviruses; and (iv) acquisition of an IRES polypurine-rich region encoding an MP nuclear localization signal. We believe that MP/CP gene overlap may constitute a mechanism for host range expansion and virus adjustment to Brassicaceae plants. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
37. Gene Overlapping as a Modulator of Begomovirus Evolution
- Author
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Iván Martín Hernández, JESUS ISRAEL PAGAN MUÑOZ, and Ministerio de Economía y Competitividad (España)
- Subjects
Microbiology (medical) ,Begomoviruses ,Overlapping genes ,Virology ,viruses ,Rate of evolution ,Microbiology ,overlapping genes ,rate of evolution ,begomoviruses ,ssDNA viruses - Abstract
15 pags., 4 figs., 1 tab., In RNA viruses, which have high mutation-and fast evolutionary- rates, gene overlapping (i.e., genomic regions that encode more than one protein) is a major factor controlling mutational load and therefore the virus evolvability. Although DNA viruses use host high-fidelity polymerases for their replication, and therefore should have lower mutation rates, it has been shown that some of them have evolutionary rates comparable to those of RNA viruses. Notably, these viruses have large proportions of their genes with at least one overlapping instance. Hence, gene overlapping could be a modulator of virus evolution beyond the RNA world. To test this hypothesis, we use the genus Begomovirus of plant viruses as a model. Through comparative genomic approaches, we show that terminal gene overlapping decreases the rate of virus evolution, which is associated with lower frequency of both synonymous and nonsynonymous mutations. In contrast, terminal overlapping has little effect on the pace of virus evolution. Overall, our analyses support a role for gene overlapping in the evolution of begomoviruses and provide novel information on the factors that shape their genetic diversity., This research was funded by Plan Nacional I + D + i, Ministerio de Economía y Competitividad (Agencia Estatal de Investigación), Spain [PID2019-109579RB-I00] to IP.
- Published
- 2022
38. Subcellular localization and detection of Tobacco mosaic virus ORF6 protein by immunoelectron microscopy.
- Author
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Erokhina, T., Lazareva, E., Richert-Pöggeler, K., Sheval, E., Solovyev, A., and Morozov, S.
- Subjects
- *
TOBACCO mosaic virus , *OPEN reading frames (Genetics) , *IMMUNOELECTRON microscopy , *RNA viruses , *RNA polymerases - Abstract
Members of the genus Tobamovirus represent one of the best-characterized groups of plant positive, single stranded RNA viruses. Previous studies have shown that genomes of some tobamoviruses contain not only genes coding for coat protein, movement protein, and the cistron coding for different domains of RNA-polymerase, but also a gene, named ORF6, coding for a poorly conserved small protein. The amino acid sequences of ORF6 proteins encoded by different tobamoviruses are highly divergent. The potential role of ORF6 proteins in replication of tobamoviruses still needs to be elucidated. In this study, using biochemical and immunological methods, we have shown that ORF6 peptide is accumulated after infection in case of two isolates of Tobacco mosaic virus strain U1 (TMV-U1 common and TMV-U1 isolate A15). Unlike virus particles accumulating in the cytoplasm, the product of the ORF6 gene is found mainly in nuclei, which correlates with previously published data about transient expression of ORF6 isolated from TMV-U1. Moreover, we present new data showing the presence of ORF6 genes in genomes of several tobamoviruses. For example, in the genomes of other members of the tobamovirus subgroup 1, including Rehmannia mosaic virus, Paprika mild mottle virus, Tobacco mild green mosaic virus, Tomato mosaic virus, Tomato mottle mosaic virus, and Nigerian tobacco latent virus, sequence comparisons revealed the existence of a similar open reading frame like ORF6 of TMV. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
39. Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic.
- Author
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Cassan, Elodie, Arigon-Chifolleau, Anne-Muriel, Mesnard, Jean-Michel, Gross, Antoine, and Gascuel, Olivier
- Subjects
- *
ANTISENSE peptides , *PEPTIDES , *HIV , *PANDEMICS , *PROTEINS - Abstract
Recent experiments provide sound arguments in favor of the in vivo expression of the AntiSense Protein (ASP) of HIV-1. This putative protein is encoded on the antisense strand of the provirus genome and entirely overlapped by the env gene with reading frame -2. The existence of ASP was suggested in 1988, but is still controversial, and its function has yet to be determined. We used a large dataset of ~23,000 HIV-1 and SIV sequences to study the origin, evolution, and conservation of the asp gene. We found that the ASP ORF is specific to group M of HIV-1, which is responsible for the human pandemic. Moreover, the correlation between the presence of asp and the prevalence of HIV-1 groups and M subtypes appeared to be statistically significant. We then looked for evidence of selection pressure acting on asp. Using computer simulations, we showed that the conservation of the ASP ORF in the group M could not be due to chance. Standard methods were ineffective in disentangling the two selection pressures imposed by both the Env and ASP proteins--an expected outcome with overlaps in frame -2. We thus developed a method based on careful evolutionary analysis of the presence/absence of stop codons, revealing that ASP does impose significant selection pressure. All of these results support the idea that asp is the 10th gene of HIV-1 groupMand indicate a correlation with the spread of the pandemic. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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- View/download PDF
40. Transcriptional Interference Promotes Rapid Expression Divergence of Drosophila Nested Genes.
- Author
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Assis, Raquel
- Subjects
- *
EUKARYOTIC genomes , *INTRONS , *EXONS (Genetics) , *NESTED clade analysis , *CHROMOSOMES - Abstract
Nested genes are the most common form of protein-coding overlap in eukaryotic genomes. Previous studies have shown that nested genes accumulate rapidly over evolutionary time, typically via the insertion of short young duplicate genes into long introns. However, the evolutionary relationship between nested genes remains unclear. Here, I compare RNA-seqexpression profiles of nested, proximal intra-chromosomal, intermediate intra-chromosomal, distant intra-chromosomal, and inter-chromosomal gene pairs in two Drosophila species. I find that expression profiles of nested genes are more divergent than those of any other class of genes, supporting the hypothesis that concurrent expression of nested genes is deleterious due to transcriptional interference. Further analysis reveals that expression profiles of derived nested genes are more divergent than those of their ancestral un-nested orthologs, which are more divergent than those of un-nested genes with similar genomic features. Thus, gene expression divergence between nested genes is likely caused by selection against nesting of genes with insufficiently divergent expression profiles, as well as by continued expression divergence after nesting. Moreover, expression divergence and sequence evolutionary rates are elevated in young nested genes and reduced in old nested genes, indicating that a burst of rapid evolution occurs after nesting. Together, these findings suggest that similarity between expression profiles of nested genes is deleterious due to transcriptional interference, and that natural selection addresses this problem both by eradicating highly deleterious nestings and by enabling rapid expression divergence of surviving nested genes, thereby quickly limiting or abolishing transcriptional interference. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
41. Seamless editing of the chloroplast genome in plants.
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Avila, Elena Martin, Gisby, Martin F., and Day, Anil
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- *
GENOME editing , *CHLOROPLAST DNA , *HOMOLOGOUS chromosomes , *HOMOGRAFTS , *PLANT fibers - Abstract
Background: Gene editing technologies enable the precise insertion of favourable mutations and performance enhancing trait genes into chromosomes whilst excluding all excess DNA from modified genomes. The technology gives rise to a new class of biotech crops which is likely to have widespread applications in agriculture. Despite progress in the nucleus, the seamless insertions of point mutations and non-selectable foreign genes into the organelle genomes of crops have not been described. The chloroplast genome is an attractive target to improve photosynthesis and crop performance. Current chloroplast genome engineering technologies for introducing point mutations into native chloroplast genes leave DNA scars, such as the target sites for recombination enzymes. Seamless editing methods to modify chloroplast genes need to address reversal of site-directed point mutations by template mediated repair with the vast excess of wild type chloroplast genomes that are present early in the transformation process. Results: Using tobacco, we developed an efficient two-step method to edit a chloroplast gene by replacing the wild type sequence with a transient intermediate. This was resolved to the final edited gene by recombination between imperfect direct repeats. Six out of 11 transplastomic plants isolated contained the desired intermediate and at the second step this was resolved to the edited chloroplast gene in five of six plants tested. Maintenance of a single base deletion mutation in an imperfect direct repeat of the native chloroplast rbcL gene showed the limited influence of biased repair back to the wild type sequence. The deletion caused a frameshift, which replaced the five C-terminal amino acids of the Rubisco large subunit with 16 alternative residues resulting in a ~30-fold reduction in its accumulation. We monitored the process in vivo by engineering an overlapping gusA gene downstream of the edited rbcL gene. Translational coupling between the overlapping rbcL and gusA genes resulted in relatively high GUS accumulation (~0.5 % of leaf protein). Conclusions: Editing chloroplast genomes using transient imperfect direct repeats provides an efficient method for introducing point mutations into chloroplast genes. Moreover, we describe the first synthetic operon allowing expression of a downstream overlapping gene by translational coupling in chloroplasts. Overlapping genes provide a new mechanism for co-ordinating the translation of foreign proteins in chloroplasts. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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- View/download PDF
42. Overlapping genes: A significant genomic correlate of prokaryotic growth rates.
- Author
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Saha, Deeya, Podder, Soumita, Panda, Arup, and Ghosh, Tapash Chandra
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- *
GENES , *GROWTH rate , *BACTERIAL genomes , *BACTERIAL growth , *GENOME size , *TRANSFER RNA genetics - Abstract
Elucidating the genomic features influencing prokaryotic growth rates has always been a study of interest. Previously, it was observed that overlapping genes (OGs) play a crucial role in the prokaryotic genome size reduction. This study is focused to explore whether OGs act as a potential correlate of prokaryotic growth rates. For this purpose, we compiled a dataset of 25 archaeal and 117 eubacterial genomes and analyzed the inter-correlation between the proportion of overlapping regions in these genomes with their growth rates. Here, we observed that the proportion of overlapping region holds a significant negative correlation with generation time in archaeal domain, whereas no correlation was observed in the eubacterial domain. However, after masking the effect of tRNA, rRNA multiplicity and environmental diversity, OGs show an independent effect over growth rates in the eubacterial domain as well as in the archaeal domain. Moreover, the influence of OGs on prokaryotic growth rates provides different delineations in archaeal and eubacterial domains. In archaea, both long overlap frequency (LOF) and short overlap frequency (SOF) influence the growth rates by increasing the degree of operonization. On the contrary, in the case of bacteria, neither SOF nor LOF plays any significant role in achieving faster growth rates. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
43. No Expression Divergence despite Transcriptional Interference between Nested Protein-Coding Genes in Mammals
- Author
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Raquel Assis
- Subjects
nested genes ,Transcription, Genetic ,QH426-470 ,Interference (genetic) ,Article ,Divergence ,Evolution, Molecular ,Gene expression ,Genetics ,Animals ,Humans ,Drosophila (subgenus) ,Gene ,Genetics (clinical) ,Mammals ,Genome ,biology ,Microarray analysis techniques ,Intron ,biology.organism_classification ,Nested gene ,Alternative Splicing ,transcriptional interference ,Evolutionary biology ,overlapping genes ,gene expression - Abstract
Nested protein-coding genes accumulated throughout metazoan evolution, with early analyses of human and Drosophila microarray data indicating that this phenomenon was simply due to the presence of large introns. However, a recent study employing RNA-seq data uncovered evidence of transcriptional interference driving rapid expression divergence between Drosophila nested genes, illustrating that accurate expression estimation of overlapping genes can enhance detection of their relationships. Hence, here I apply an analogous approach to strand-specific RNA-seq data from human and mouse to revisit the role of transcriptional interference in the evolution of mammalian nested genes. A genomic survey reveals that whereas mammalian nested genes indeed accrued over evolutionary time, they are retained at lower frequencies than in Drosophila. Though several properties of mammalian nested genes align with observations in Drosophila and with expectations under transcriptional interference, contrary to both, their expression divergence is not statistically different from that between unnested genes, and also does not increase after nesting. Together, these results support the hypothesis that lower selection efficiencies limit rates of gene expression evolution in mammals, leading to their reliance on immediate eradication of deleterious nested genes to avoid transcriptional interference.
- Published
- 2021
44. Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions.
- Author
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Yan-Cong Zhang and Kui Lin
- Subjects
- *
BACTERIAL genomes , *PHYLOGENY , *PROTEOBACTERIA , *GENOME size , *PROKARYOTIC genomes , *GENOMES - Abstract
Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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45. Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers.
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Perrin, Elena, Fondi, Marco, Maida, Isabel, Mengoni, Alessio, Chiellini, Carolina, Mocali, Stefano, Cocchi, Priscilla, Campana, Silvia, Taccetti, Giovanni, Vaneechoutte, Mario, and Fani, Renato
- Subjects
- *
BACTERIAL typing , *MOLECULAR genetics , *GENETIC markers , *MICROBIAL genomes , *POLYMERASE chain reaction , *NUCLEIC acid isolation methods - Abstract
The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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- View/download PDF
46. Creating De Novo Overlapped Genes.
- Author
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Logel DY and Jaschke PR
- Subjects
- Amino Acid Sequence, Open Reading Frames, Sequence Alignment, Proteins
- Abstract
Future applications of synthetic biology will rely on deploying engineered cells outside of lab environments for long periods of time. Currently, a significant roadblock to this application is the potential for deactivating mutations in engineered genes. A recently developed method to protect engineered coding sequences from mutation is called Constraining Adaptive Mutations using Engineered Overlapping Sequences (CAMEOS). In this chapter we provide a workflow for utilizing CAMEOS to create synthetic overlaps between two genes, one essential (infA) and one non-essential (aroB), to protect the non-essential gene from mutation and loss of protein function. In this workflow we detail the methods to collect large numbers of related protein sequences, produce multiple sequence alignments (MSAs), use the MSAs to generate hidden Markov models and Markov random field models, and finally generate a library of overlapping coding sequences through CAMEOS scripts. To assist practitioners with basic coding skills to try out the CAMEOS method, we have created a virtual machine containing all the required packages already installed that can be downloaded and run locally., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2023
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47. Translational coupling of nas ST expression in Azotobacter vinelandii prevents overexpression of the nasT gene.
- Author
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Wang, Baomin, Rensing, Christopher, Pierson, Leland S., Zhao, Hui, and Kennedy, Christina
- Subjects
- *
GENETIC overexpression , *AZOTOBACTER vinelandii , *GENE expression in bacteria , *NITRATE reductase , *BACTERIAL operons - Abstract
The nas ST operon encodes the transcriptional regulators of assimilatory nitrate reductase operons in phylogenetically diverse bacteria. NasT is a RNA-binding antiterminator and helps RNA polymerase read through the regulatory terminator sequences upstream of the structural genes. NasS senses nitrate and nitrite and regulates the activity of NasT through stoichiometric interaction. In this study, we analyzed the nas ST sequence in Azotobacter vinelandii and revealed that the nasS and nasT genes overlap by 19 nucleotides. Our genetic analyses suggested that translational initiation of NasT was coupled with NasS translation, a regulatory mechanism that prevents overproduction of NasT. The significance of tight control of nasT expression was demonstrated in a nasT-overexpression strain, where expression of the assimilatory nitrate reductase operon was deregulated. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
48. Gene expression profile analysis for different idiopathic interstitial pneumonias subtypes.
- Author
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Chen, Hanzhang, Fang, Xia, Zhu, Hailong, Li, Shuai, He, Jian, Gu, Pan, Fan, Deshen, Han, Fei, Zeng, Yu, Yu, Xiaotin, Luo, Benfang, Xu, Haodong, and Yi, Xianghua
- Subjects
- *
GENE expression , *IDIOPATHIC interstitial pneumonias , *FIBROSIS , *MICROARRAY technology , *PROTEIN-protein interactions , *DIAGNOSIS , *THERAPEUTICS - Abstract
Objective: Idiopathic interstitial pneumonias (IIPs) are a group of diffuse parenchymal lung diseases of unknown etiology characterized by the presence of various degrees of inflammation and fibrosis. We aimed to screen the differences among IIPs subtypes in the gene level by using the microarray expression profiles of normal lung tissue and IIPs tissue for the key genes associated with early diagnosis and treatment of IIPs. Methods: The gene expression profile of six kinds of IIPs (GSE 32537) subtypes tissue and normal lung tissues were downloaded. The differentially expressed genes (DEGs) in different IIPs subtypes were selected by using the expression profiling. In addition, the screened DEGs were further analyzed by function annotation, pathway analysis, and interaction network analysis to reveal the differences among these subtypes. Results: The gene expression analysis showed that nine genes including SERPINA3, IL1R2, CBS, MGAM, SLCO4A1, S100A12, FPR1, SDR16C5, and MT1X in six subtypes of IIPs were significantly increased. There were significant differences in DEGs among six subtypes of IIPs, and the DEGs of some IIPs subtypes involved in immune, inflammatory response and cell adhesion processes. Moreover, the PPI network analysis indicated that SERPINA3 played an important role in the molecular mechanisms of IIPs. Conclusion: This comprehensive description of altered gene expression in different subtypes of IIPs underscores the complex biological processes characteristic of different subtypes of IIPs and may provide a foundation for future research into this devastating disease. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
49. Overlapping genes: a window on gene evolvability.
- Author
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Huvet, Maxime and Stumpf, Michael P. H.
- Abstract
Background: The forces underlying genome architecture and organization are still only poorly understood in detail. Overlapping genes (genes partially or entirely overlapping) represent a genomic feature that is shared widely across biological organisms ranging from viruses to multi-cellular organisms. In bacteria, a third of the annotated genes are involved in an overlap. Despite the widespread nature of this arrangement, its evolutionary origins and biological ramifications have so far eluded explanation. Results: Here we present a comparative approach using information from 699 bacterial genomes that sheds light on the evolutionary dynamics of overlapping genes. We show that these structures exhibit high levels of plasticity. Conclusions: We propose a simple model allowing us to explain the observed properties of overlapping genes based on the importance of initiation and termination of transcriptional and translational processes. We believe that taking into account the processes leading to the expression of protein-coding genes hold the key to the understanding of overlapping genes structures. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
50. Computational design of proteins and enzymes
- Author
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Opuu, Vaitea, Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique de Paris, Thomas Simonson, and STAR, ABES
- Subjects
[PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] ,[SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,[PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] ,Ingénierie de protéines ,Gènes chevauchants ,[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,Overlapping genes ,Molecular mechanics ,[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation ,Protein engineering ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Mécanique moléculaire ,Interactions protéine ligand ,Protein/ligand binding ,[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] - Abstract
We propose a set of methods to design molecular systems. We start from naturally optimized components, namely proteins. Proteins can act as structural components, information transporters, or catalysts. We use computational methods to complement experiments and design protein systems.First, we fully redesigned a PDZ domain involved in metabolic pathways. We used a physics-based approach combining molecular mechanics, continuum electrostatics, and Monte Carlo sampling. Thousands of variants predicted to adopt the PDZ fold were selected. Three were validated experimentally. Two showed binding of the natural peptide ligand.Next, we redesigned the active site of the methionyl-tRNA synthetase enzyme (MetRS). We used an adaptive Monte Carlo method to select variants for methionine (Met) binding. Out of 17 predicted variants that were tested experimentally, 17 were found to be active. We extended the method to transition state binding to select mutants directly according to their catalytic power.We redesigned the MetRS binding site to obtain activity towards two β-amino acids, in order to expand the genetic code. These unnatural amino acids can enhance the structural repertoire of proteins. 20 predicted mutants were tested. Although none had increased β-Met activity, three had a gain in selectivity for β-Met. We then implemented a method to select optimal positions for design and applied it to β-Met and β-Val. Around 20 variants are being experimental tested.Finally, in vivo protein modifications raise the question of their eventual drift away from the original design. We introduce here a design approach for overlapping genes coding PDZ domains. This overlap would reduce genetic drift and provide bio-confinement. We computationally produced almost 2000 pairs of overlapping PDZ domains. One was validated by 2 microsecond molecular dynamic simulations. Experiments are underway., Nous proposons un ensemble de méthodes pour la conception de systèmes moléculaires. Notre stratégie consiste à utiliser comme modèle des machines naturellement optimisées, les protéines. Les protéines peuvent être des briques structurales, des transporteurs d'informations ou des catalyseurs chimiques. Nous utilisons ici des approches computationnelles, complémentaires aux voies expérimentales, pour concevoir de tels systèmes.Nous avons d'abord entièrement redessiné un domaine PDZ impliqué dans des voies métaboliques. Nous utilisons une approche physics-based basée sur la mécanique moléculaire, un modèle de solvant implicite et un échantillonnage Monte Carlo. Parmi plusieurs milliers de variants prédits pour adopter le repliement PDZ, trois ont été sélectionnés et montrent un repliement correct. Deux ont une affinité détectable pour les ligands peptidiques naturels.Nous avons ensuite re-dessiné le site actif de l'enzyme méthionyl-ARNt synthétase (MetRS). En utilisant un algorithme de type Monte Carlo adaptatif, nous avons sélectionné des variants pour l'affinité MetRS/méthionine (Met). Sur 17 variants testés expérimentalement, 17 sont actifs. La méthode a été ensuite appliquée à l'état de transition pour sélectionner des variants directement sur leur efficacité catalytique.Nous avons étudié la possibilité de modifier la MetRS pour étendre son activitéaux acides aminés β, afin d'étendre le code génétique. Ces acides aminésnon-naturels permettraient d'enrichir le répertoire structural des protéines. 20variants MetRS obtenus à partir de prédictions d'affinité MetRS/β-Met ont ététestés. Aucun n'augmente l'activité mais trois ont amélioré la sélectivité enfaveur de la β-Met. Nous avons implémenté une méthode de sélection de positionsd'intérêt et production de variants pour β-Met et β-Val. Une vingtaine deprédictions sont en cours de tests expérimentaux.Enfin, la modification de protéines in vivo pose la question de leur dérive génétique. Nous introduisons ici une méthode de conception de paires de gènes chevauchants pour des domaines PDZ. Ce codage permettrait de limiter la dérive génétique. Nous avons produit près de 2000 paires de domaines PDZ au codage chevauchant, dont une a été validées par 2 microsecondes de dynamique moléculaire. Des tests expérimentaux sont en cours.
- Published
- 2020
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