4,379 results on '"Prokaryotic Cells"'
Search Results
2. Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes
- Author
-
Yoon, Peter H, Skopintsev, Petr, Shi, Honglue, Chen, LinXing, Adler, Benjamin A, Al-Shimary, Muntathar, Craig, Rory J, Loi, Kenneth J, DeTurk, Evan C, Li, Zheng, Amerasekera, Jasmine, Trinidad, Marena, Nisonoff, Hunter, Chen, Kai, Lahiri, Arushi, Boger, Ron, Jacobsen, Steve, Banfield, Jillian F, and Doudna, Jennifer A
- Subjects
Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Genetics ,Biological Sciences ,Biotechnology ,1.1 Normal biological development and functioning ,Bacteria ,DNA Transposable Elements ,Endonucleases ,Prokaryotic Cells ,Transposases ,Evolution ,Molecular ,Eukaryotic Cells ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and a TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12s. In eukaryotes, TnpB homologs occur as two distinct types, Fanzor1s and Fanzor2s. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, which revealed that both Fanzor1s and Fanzor2s stem from a single lineage of IS607 TnpBs with unusual active site arrangement. The widespread nature of Fanzors implies that the properties of this particular lineage of IS607 TnpBs were particularly suited to adaptation in eukaryotes. Biochemical analysis of an IS607 TnpB and Fanzor1s revealed common strategies employed by TnpBs and Fanzors to co-evolve with their cognate transposases. Collectively, our results provide a new model of sequential evolution from IS607 TnpBs to Fanzor2s, and Fanzor2s to Fanzor1s that details how genes of prokaryotic origin evolve to give rise to new protein families in eukaryotes.
- Published
- 2023
3. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
- Author
-
Eme, Laura, Tamarit, Daniel, Caceres, Eva F, Stairs, Courtney W, De Anda, Valerie, Schön, Max E, Seitz, Kiley W, Dombrowski, Nina, Lewis, William H, Homa, Felix, Saw, Jimmy H, Lombard, Jonathan, Nunoura, Takuro, Li, Wen-Jun, Hua, Zheng-Shuang, Chen, Lin-Xing, Banfield, Jillian F, John, Emily St, Reysenbach, Anna-Louise, Stott, Matthew B, Schramm, Andreas, Kjeldsen, Kasper U, Teske, Andreas P, Baker, Brett J, and Ettema, Thijs JG
- Subjects
Genetics ,Biotechnology ,Generic health relevance ,Archaea ,Eukaryota ,Eukaryotic Cells ,Phylogeny ,Prokaryotic Cells ,Datasets as Topic ,Gene Duplication ,Evolution ,Molecular ,General Science & Technology - Abstract
In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
- Published
- 2023
4. Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean
- Author
-
Winder, Johanna C, Boulton, William, Salamov, Asaf, Eggers, Sarah Lena, Metfies, Katja, Moulton, Vincent, and Mock, Thomas
- Subjects
Microbiology ,Biochemistry and Cell Biology ,Biological Sciences ,Genetics ,Generic health relevance ,Life Below Water ,Prokaryotic Cells ,Carrier Proteins ,Protein Domains ,Seawater ,Oceans and Seas ,Arctic Ocean ,DUF3494 ,MAGs ,MOSAiC expedition ,domain shuffling ,ice-binding proteins ,metagenomics ,polar genomics - Abstract
Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.
- Published
- 2023
5. Prokaryotic microvesicles Ortholog of eukaryotic extracellular vesicles in biomedical fields
- Author
-
Halimeh Mobarak, Farzin Javid, Maryam Taghavi Narmi, Narges Mardi, Fatemeh Sadeghsoltani, Parisa Khanicheragh, Samaneh Narimani, Mahdi Mahdipour, Emel Sokullu, Ferzane Valioglu, and Reza Rahbarghazi
- Subjects
Exosomes ,Bacterial microvesicles ,Prokaryotic cells ,Eukaryotic cells ,Biological properties ,Biomedical applications ,Medicine ,Cytology ,QH573-671 - Abstract
Abstract Every single cell can communicate with other cells in a paracrine manner via the production of nano-sized extracellular vesicles. This phenomenon is conserved between prokaryotic and eukaryotic cells. In eukaryotic cells, exosomes (Exos) are the main inter-cellular bioshuttles with the potential to carry different signaling molecules. Likewise, bacteria can produce and release Exo-like particles, namely microvesicles (MVs) into the extracellular matrix. Bacterial MVs function with diverse biological properties and are at the center of attention due to their inherent therapeutic properties. Here, in this review article, the comparable biological properties between the eukaryotic Exos and bacterial MVs were highlighted in terms of biomedical application. Video Abstract
- Published
- 2024
- Full Text
- View/download PDF
6. Prokaryotic microvesicles Ortholog of eukaryotic extracellular vesicles in biomedical fields.
- Author
-
Mobarak, Halimeh, Javid, Farzin, Narmi, Maryam Taghavi, Mardi, Narges, Sadeghsoltani, Fatemeh, Khanicheragh, Parisa, Narimani, Samaneh, Mahdipour, Mahdi, Sokullu, Emel, Valioglu, Ferzane, and Rahbarghazi, Reza
- Subjects
- *
EXTRACELLULAR vesicles , *EXTRACELLULAR matrix , *EUKARYOTIC cells , *EXOSOMES - Abstract
Every single cell can communicate with other cells in a paracrine manner via the production of nano-sized extracellular vesicles. This phenomenon is conserved between prokaryotic and eukaryotic cells. In eukaryotic cells, exosomes (Exos) are the main inter-cellular bioshuttles with the potential to carry different signaling molecules. Likewise, bacteria can produce and release Exo-like particles, namely microvesicles (MVs) into the extracellular matrix. Bacterial MVs function with diverse biological properties and are at the center of attention due to their inherent therapeutic properties. Here, in this review article, the comparable biological properties between the eukaryotic Exos and bacterial MVs were highlighted in terms of biomedical application. A6C5tqvMEGCcUFjLK3Zi8K Video Abstract [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
7. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms
- Author
-
Decker, Katherine T, Gao, Ye, Rychel, Kevin, Bulushi, Tahani Al, Chauhan, Siddharth M, Kim, Donghyuk, Cho, Byung-Kwan, and Palsson, Bernhard O
- Subjects
Biotechnology ,Genetics ,Human Genome ,1.1 Normal biological development and functioning ,Underpinning research ,Generic health relevance ,Binding Sites ,Chromatin ,Chromatin Immunoprecipitation ,Databases ,Genetic ,Genome ,Prokaryotic Cells ,Protein Binding ,Transcription Factors ,Environmental Sciences ,Biological Sciences ,Information and Computing Sciences ,Developmental Biology - Abstract
The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.
- Published
- 2022
8. 卵细胞质内单精子注射后多原核发生率对胚胎发育和妊娠结局的影响.
- Author
-
倪丹玉, 杨烨, 谢奇君, 姜薇, and 凌秀凤
- Abstract
Objective: To explore the impact of poly-pronucleus (PN) incidence on the embryonic development and pregnancy outcome after intracytoplasmic sperm injection (ICSI). Methods: This is a retrospective cohort study, analyzing the clinical data of patients after ICSI between January 2016 and December 2021. The objects of study were divided into three groups according to the proportion of poly-PN: the control group (the proportion of poly-PN=0%, n=333), the low-frequency poly-PN group (0%<the proportion of poly-PN<20%, n=80) and the high -frequency poly -PN group (the proportion of poly -PN ≥20%, n =31). The embryonic development and pregnancy outcomes were compared among the groups, respectively. Results: The numbers of oocytes retrieved and available embryos on day 3 (D3) were higher in the low-frequency poly-PN group than those in the control group, but the rates of normal fertilization and high -scoring blastocyst formation were lower than those in the control group (all P<0.017). Compared with the control group and the low-frequency poly-PN group, the high-frequency poly-PN group had lower rate of normal fertilization rate, lower number of available embryos on D3 (all P<0.017), and low rate of biochemical pregnancy and high miscarriage rate (but P>0.017). Multifactorial Logistic analysis showed that patients in the high-frequency poly-PN group had significantly lower biochemical pregnancy rate and live birth rate when compared with the control group (aOR=0.402, 95%CI: 0.186-0.870, aP=0.021; aOR=0.247, 95%CI: 0.068-0.901, aP=0.034). Conclusions: In the ICSI cycles, the incidence of poly-PN may reflect oocyte quality, and the incidence of poly -PN ≥20% may predict the poor embryo development, lower biochemical pregnancy rate and lower live birth rate. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
9. Grounding cognition: heterarchical control mechanisms in biology
- Author
-
Bechtel, William and Bich, Leonardo
- Subjects
Behavioral and Social Science ,Basic Behavioral and Social Science ,Underpinning research ,1.1 Normal biological development and functioning ,Generic health relevance ,Cognition ,Eukaryotic Cells ,Prokaryotic Cells ,decision-making ,production mechanisms ,control mechanisms ,chemotaxis ,circadian rhythms ,Biological Sciences ,Medical and Health Sciences ,Evolutionary Biology - Abstract
We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable-controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.
- Published
- 2021
10. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes
- Author
-
Liu, Ying, Demina, Tatiana A, Roux, Simon, Aiewsakun, Pakorn, Kazlauskas, Darius, Simmonds, Peter, Prangishvili, David, Oksanen, Hanna M, and Krupovic, Mart
- Subjects
Microbiology ,Biological Sciences ,Infectious Diseases ,Genetics ,Infection ,Archaeal Viruses ,Biological Evolution ,DNA ,DNA ,Viral ,Genetic Variation ,Genome ,Viral ,Host Specificity ,Mutation ,Phylogeny ,Prokaryotic Cells ,Viral Proteins ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Developmental Biology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
- Published
- 2021
11. Roadmap for naming uncultivated Archaea and Bacteria
- Author
-
Murray, Alison E, Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T, Lane, Christopher E, Papke, R Thane, Parks, Donovan H, Rossello-Mora, Ramon, Stott, Matthew B, Sutcliffe, Iain C, Thrash, J Cameron, Venter, Stephanus N, Whitman, William B, Acinas, Silvia G, Amann, Rudolf I, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J, Barco, Roman A, Bode, Helge B, Boyd, Eric S, Brady, Carrie L, Carini, Paul, Chain, Patrick SG, Colman, Daniel R, DeAngelis, Kristen M, de los Rios, Maria Asuncion, Estrada-de los Santos, Paulina, Dunlap, Christopher A, Eisen, Jonathan A, Emerson, David, Ettema, Thijs JG, Eveillard, Damien, Girguis, Peter R, Hentschel, Ute, Hollibaugh, James T, Hug, Laura A, Inskeep, William P, Ivanova, Elena P, Klenk, Hans-Peter, Li, Wen-Jun, Lloyd, Karen G, Löffler, Frank E, Makhalanyane, Thulani P, Moser, Duane P, Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander J, Smits, Theo HM, Steen, Andrew D, Steenkamp, Emma T, Spang, Anja, Stewart, Frank J, Tiedje, James M, Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Yarza, Pablo, Hedlund, Brian P, and Reysenbach, Anna-Louise
- Subjects
Microbiology ,Biological Sciences ,Ecology ,Archaea ,Bacteria ,DNA ,Bacterial ,Metagenome ,Phylogeny ,Prokaryotic Cells ,Sequence Analysis ,DNA ,Terminology as Topic ,Medical Microbiology - Abstract
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
- Published
- 2020
12. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
- Author
-
Norsigian, Charles J, Fang, Xin, Seif, Yara, Monk, Jonathan M, and Palsson, Bernhard O
- Subjects
Biological Sciences ,Genetics ,Genomics ,Metabolomics ,Models ,Biological ,Molecular Sequence Annotation ,Prokaryotic Cells ,Sequence Analysis ,Workflow ,Chemical Sciences ,Medical and Health Sciences ,Bioinformatics - Abstract
Genome-scale models (GEMs) of bacterial strains' metabolism have been formulated and used over the past 20 years. Recently, with the number of genome sequences exponentially increasing, multi-strain GEMs have proved valuable to define the properties of a species. Here, through four major stages, we extend the original Protocol used to generate a GEM for a single strain to enable multi-strain GEMs: (i) obtain or generate a high-quality model of a reference strain; (ii) compare the genome sequence between a reference strain and target strains to generate a homology matrix; (iii) generate draft strain-specific models from the homology matrix; and (iv) manually curate draft models. These multi-strain GEMs can be used to study pan-metabolic capabilities and strain-specific differences across a species, thus providing insights into its range of lifestyles. Unlike the original Protocol, this procedure is scalable and can be partly automated with the Supplementary Jupyter notebook Tutorial. This Protocol Extension joins the ranks of other comparable methods for generating models such as CarveMe and KBase. This extension of the original Protocol takes on the order of weeks to multiple months to complete depending on the availability of a suitable reference model.
- Published
- 2020
13. DABs are inorganic carbon pumps found throughout prokaryotic phyla
- Author
-
Desmarais, John J, Flamholz, Avi I, Blikstad, Cecilia, Dugan, Eli J, Laughlin, Thomas G, Oltrogge, Luke M, Chen, Allen W, Wetmore, Kelly, Diamond, Spencer, Wang, Joy Y, and Savage, David F
- Subjects
Emerging Infectious Diseases ,Biotechnology ,Vaccine Related ,Genetics ,Infectious Diseases ,Prevention ,Rare Diseases ,Biodefense ,1.1 Normal biological development and functioning ,Underpinning research ,Archaea ,Bacillus anthracis ,Bacteria ,Bacterial Proteins ,Carbon ,Carbon Dioxide ,Carbonic Anhydrases ,Carrier Proteins ,DNA Transposable Elements ,Diazonium Compounds ,Genes ,Bacterial ,Genes ,Essential ,Halothiobacillus ,Mutagenesis ,Operon ,Prokaryotic Cells ,Sulfanilic Acids ,Vibrio cholerae ,Microbiology ,Medical Microbiology - Abstract
Bacterial autotrophs often rely on CO2 concentrating mechanisms (CCMs) to assimilate carbon. Although many CCM proteins have been identified, a systematic screen of the components of CCMs is lacking. Here, we performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the γ-proteobacterium Halothiobacillus neapolitanus. Screening revealed that the CCM comprises at least 17 and probably no more than 25 genes, most of which are encoded in 3 operons. Two of these operons (DAB1 and DAB2) contain a two-gene locus that encodes a domain of unknown function (Pfam: PF10070) and a putative cation transporter (Pfam: PF00361). Physiological and biochemical assays demonstrated that these proteins-which we name DabA and DabB, for DABs accumulate bicarbonate-assemble into a heterodimeric complex, which contains a putative β-carbonic anhydrase-like active site and functions as an energy-coupled inorganic carbon (Ci) pump. Interestingly, DAB operons are found in a diverse range of bacteria and archaea. We demonstrate that functional DABs are present in the human pathogens Bacillus anthracis and Vibrio cholerae. On the basis of these results, we propose that DABs constitute a class of energized Ci pumps and play a critical role in the metabolism of Ci throughout prokaryotic phyla.
- Published
- 2019
14. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
- Author
-
Bin Jang, Ho, Bolduc, Benjamin, Zablocki, Olivier, Kuhn, Jens H, Roux, Simon, Adriaenssens, Evelien M, Brister, J Rodney, Kropinski, Andrew M, Krupovic, Mart, Lavigne, Rob, Turner, Dann, and Sullivan, Matthew B
- Subjects
Microbiology ,Biological Sciences ,Biotechnology ,Genetics ,Human Genome ,Infection ,Bacteriophages ,Classification ,Gene Regulatory Networks ,Genome ,Viral ,Metagenome ,Metagenomics ,Phylogeny ,Prokaryotic Cells ,Viruses - Abstract
Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.
- Published
- 2019
15. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
- Author
-
Brunk, Elizabeth, Chang, Roger L, Xia, Jing, Hefzi, Hooman, Yurkovich, James T, Kim, Donghyuk, Buckmiller, Evan, Wang, Harris H, Cho, Byung-Kwan, Yang, Chen, Palsson, Bernhard O, Church, George M, and Lewis, Nathan E
- Subjects
Biotechnology ,Human Genome ,Genetics ,Escherichia coli ,Gene Editing ,Metabolic Engineering ,Prokaryotic Cells ,Protein Processing ,Post-Translational ,Proteins ,Workflow ,systems biology ,posttranslational modifications ,metabolism ,protein chemistry ,omics data - Abstract
Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coli Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.
- Published
- 2018
16. Cellular structure and molecular functions of plants, animals, bacteria, and viruses
- Author
-
Hamid kheyrodin, Raheba Jami, and Fazal Rehman
- Subjects
cell wall ,bacterial structure ,fungi ,eukaryotic cells ,prokaryotic cells ,dna ,Medicine - Abstract
Plant cells are the basic unit of life in organisms of the kingdom Plantae. These organisms as eukaryotic cells have a true nucleus along with particular structures called organelles that perform various functions. The plant cell wall can provide a structural framework to support plant growth and defense the cells against various viral and bacterial pathogens. The cell wall can retain flexibility, also when subjected to developmental, biotic, abiotic stimuli, and stresses it can be efficiently remodeled in response. Genes encoding enzymes are able to fabricate or hydrolyze substances of the plant cell wall exhibit differential expression when subjected to different stresses, suggesting they may facilitate stress tolerance such as heavy metals, dust accumulation, and salty medium through changes in cell composition wall. Bacteria are small single-celled organisms that get the nutrients they need from their environment. Sometimes, this environment can be your child or any other living thing. Bacteria are very small and cannot be seen under a microscope. Bacteria help the digestive system and prevent harmful bacteria from entering the human body as well as some other bacteria are also applied to produce drugs and vaccines. A cell wall as the non-living component can cover the outmost layer of a cell. According to the type of organism, the cell envelope has a different composition. The cell envelope separates the interior contents of the cell from the exterior environment. In addition, it provides shape, support, and protection to the cell and its organelles. However, this cellular component is present exclusively in eukaryotic plants, fungi, and a few prokaryotic organisms. Compounds found in plant cells are absent in animal cells, and DNA base sequences reflect this. Moreover, plant DNA is often larger than animal DNA. In this mini-review, we concluded that the differences between plant and animal DNA defendant on the sequence of bases in the helix.
- Published
- 2022
- Full Text
- View/download PDF
17. The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species
- Author
-
Wu, Linhuan, McCluskey, Kevin, Desmeth, Philippe, Liu, Shuangjiang, Hideaki, Sugawara, Yin, Ye, Moriya, Ohkuma, Itoh, Takashi, Kim, Cha Young, Lee, Jung-Sook, Zhou, Yuguang, Kawasaki, Hiroko, Hazbón, Manzour Hernando, Robert, Vincent, Boekhout, Teun, Lima, Nelson, Evtushenko, Lyudmila, Boundy-Mills, Kyria, Bunk, Boyke, Moore, Edward RB, Eurwilaichitr, Lily, Ingsriswang, Supawadee, Shah, Heena, Yao, Su, Jin, Tao, Huang, Jinqun, Shi, Wenyu, Sun, Qinglan, Fan, Guomei, Li, Wei, Li, Xian, Kurtböke, İpek, and Ma, Juncai
- Subjects
Human Genome ,Genetics ,Biotechnology ,Bacteria ,Fungi ,Genomics ,Prokaryotic Cells ,Reproducibility of Results ,Sequence Analysis ,DNA ,phylogenomics ,taxonomy ,biodiversity ,whole-genome sequencing ,type strains ,bacteria ,Archaea ,fungi - Abstract
Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.
- Published
- 2018
18. A comparative evaluation of genome assembly reconciliation tools
- Author
-
Alhakami, Hind, Mirebrahim, Hamid, and Lonardi, Stefano
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Algorithms ,Chromosome Mapping ,Contig Mapping ,Eukaryota ,Genome ,High-Throughput Nucleotide Sequencing ,Prokaryotic Cells ,Sequence Analysis ,DNA ,Software ,De novo genome assembly ,Genomics ,Assembly reconciliation ,Environmental Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundThe majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation.ResultsSeveral assembly reconciliation tools have been proposed in the literature, but their strengths and weaknesses have never been compared on a common dataset. We fill this need with this work, in which we report on an extensive comparative evaluation of several tools. Specifically, we evaluate contiguity, correctness, coverage, and the duplication ratio of the merged assembly compared to the individual assemblies provided as input.ConclusionsNone of the tools we tested consistently improved the quality of the input GAGE and synthetic assemblies. Our experiments show an increase in contiguity in the consensus assembly when the original assemblies already have high quality. In terms of correctness, the quality of the results depends on the specific tool, as well as on the quality and the ranking of the input assemblies. In general, the number of misassemblies ranges from being comparable to the best of the input assembly to being comparable to the worst of the input assembly.
- Published
- 2017
19. Bacteriophage–prokaryote dynamics and interaction within anaerobic digestion processes across time and space
- Author
-
Zhang, Junyu, Gao, Qun, Zhang, Qiuting, Wang, Tengxu, Yue, Haowei, Wu, Linwei, Shi, Jason, Qin, Ziyan, Zhou, Jizhong, Zuo, Jiane, and Yang, Yunfeng
- Subjects
Microbiology ,Biological Sciences ,Anaerobiosis ,Bacteriophages ,Biofuels ,Phylogeny ,Prokaryotic Cells ,Seasons ,Sequence Analysis ,DNA ,Wastewater ,Water Purification ,Microbiome ,Anaerobic digestion ,Time dynamics ,GeoChip ,Ecology ,Medical Microbiology ,Evolutionary biology - Abstract
BackgroundBacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage-host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells.ResultsEquipped with high-throughput, cutting-edge environmental genomics techniques, we examined phage and prokaryotic community composition of four anaerobic digesters in full-scale wastewater treatment plants across China. Despite the relatively stable process performance in biogas production, phage and prokaryotic groups fluctuated monthly over a year of study period, showing significant correlations between those two groups at the α- and β-diversity levels. Strikingly, phages explained 40.6% of total variations of the prokaryotic community composition, much higher than the explanatory power by abiotic factors (14.5%). Consequently, phages were significantly (P
- Published
- 2017
20. Hierarchical complexity and the size limits of life
- Author
-
Heim, Noel A, Payne, Jonathan L, Finnegan, Seth, Knope, Matthew L, Kowalewski, Michał, Lyons, S Kathleen, McShea, Daniel W, Novack-Gottshall, Philip M, Smith, Felisa A, and Wang, Steve C
- Subjects
Biological Evolution ,Earth ,Planet ,Eukaryota ,Prokaryotic Cells ,body size ,evolution ,hierarchy ,complexity ,macroecology ,macroevolution ,Biological Sciences ,Agricultural and Veterinary Sciences ,Medical and Health Sciences - Abstract
Over the past 3.8 billion years, the maximum size of life has increased by approximately 18 orders of magnitude. Much of this increase is associated with two major evolutionary innovations: the evolution of eukaryotes from prokaryotic cells approximately 1.9 billion years ago (Ga), and multicellular life diversifying from unicellular ancestors approximately 0.6 Ga. However, the quantitative relationship between organismal size and structural complexity remains poorly documented. We assessed this relationship using a comprehensive dataset that includes organismal size and level of biological complexity for 11 172 extant genera. We find that the distributions of sizes within complexity levels are unimodal, whereas the aggregate distribution is multimodal. Moreover, both the mean size and the range of size occupied increases with each additional level of complexity. Increases in size range are non-symmetric: the maximum organismal size increases more than the minimum. The majority of the observed increase in organismal size over the history of life on the Earth is accounted for by two discrete jumps in complexity rather than evolutionary trends within levels of complexity. Our results provide quantitative support for an evolutionary expansion away from a minimal size constraint and suggest a fundamental rescaling of the constraints on minimal and maximal size as biological complexity increases.
- Published
- 2017
21. Beyond the Triplet Code: Context Cues Transform Translation
- Author
-
Brar, Gloria A
- Subjects
Biological Sciences ,Genetics ,Codon ,Eukaryota ,Molecular Imaging ,Prokaryotic Cells ,Protein Biosynthesis ,RNA ,Messenger ,RNA ,Transfer ,Ribosomes ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
The elucidation of the genetic code remains among the most influential discoveries in biology. While innumerable studies have validated the general universality of the code and its value in predicting and analyzing protein coding sequences, established and emerging work has also suggested that full genome decryption may benefit from a greater consideration of a codon's neighborhood within an mRNA than has been broadly applied. This Review examines the evidence for context cues in translation, with a focus on several recent studies that reveal broad roles for mRNA context in programming translation start sites, the rate of translation elongation, and stop codon identity.
- Published
- 2016
22. Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast
- Author
-
Skjoedt, Mette L, Snoek, Tim, Kildegaard, Kanchana R, Arsovska, Dushica, Eichenberger, Michael, Goedecke, Tobias J, Rajkumar, Arun S, Zhang, Jie, Kristensen, Mette, Lehka, Beata J, Siedler, Solvej, Borodina, Irina, Jensen, Michael K, and Keasling, Jay D
- Subjects
Generic health relevance ,Biosensing Techniques ,Prokaryotic Cells ,Protein Engineering ,Saccharomyces cerevisiae ,Transcription Factors ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Biochemistry & Molecular Biology - Abstract
Whole-cell biocatalysts have proven a tractable path toward sustainable production of bulk and fine chemicals. Yet the screening of libraries of cellular designs to identify best-performing biocatalysts is most often a low-throughput endeavor. For this reason, the development of biosensors enabling real-time monitoring of production has attracted attention. Here we applied systematic engineering of multiple parameters to search for a general biosensor design in the budding yeast Saccharomyces cerevisiae based on small-molecule binding transcriptional activators from the prokaryote superfamily of LysR-type transcriptional regulators (LTTRs). We identified a design supporting LTTR-dependent activation of reporter gene expression in the presence of cognate small-molecule inducers. As proof of principle, we applied the biosensors for in vivo screening of cells producing naringenin or cis,cis-muconic acid at different levels, and found that reporter gene output correlated with production. The transplantation of prokaryotic transcriptional activators into the eukaryotic chassis illustrates the potential of a hitherto untapped biosensor resource useful for biotechnological applications.
- Published
- 2016
23. Optimization of Interleukin-5 Protein Expression in BL21 Strain of Escherichia Coli
- Author
-
mina Jamalvandi, Hossein Khanahmad, Shiva Irani, and Sayad Bastaminejad
- Subjects
gene expression ,interleukin-5 ,prokaryotic cells ,escherichia coli ,Medicine ,Medicine (General) ,R5-920 - Abstract
Background: In asthma, the relationship between number of eosinophils and severity of this disease supports the hypothesis that eosinophil is the major effector cell in inflammation of airway. Evolution of eosinophils is regulated by interlukin-5 (IL-5). Therefore, by blocking IL-5, at least one major reason of asthma would be prevented. To produce antagonists against IL-5 (like aptamer), it is necessary to have this protein in large scale and high purity. This study aimed to optimize IL-5 protein expression of BL21 strain of Escherichia coli (E. coli) to be used instead of antibody. Methods: At first, complementary DNA (cDNA) construct encoding IL-5 was designed, and was ordered to be produced in pET28a vector. Expression vector was transformed into competent E. coli Bl21 (DE3) origami. Then, protein expression was optimized by altering temperature, incubation time, and the amount of isopropyl β-d-1-thiogalactopyranoside (IPTG). Protein expression was assessed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot in different levels of the test. Findings: The optimum conditions for protein expression were gained when the density of bacteria at the OD600 reached to 0.6 to 0.8, and culturing was done at 29 °C for 18 hours and 150 rpm, andinduction with 1mM IPTG. There was a 13-kDa protein band on SDS-PAGE and western blot that confirmed the expression of IL-5 protein. Conclusion: This protein can be used for producing aptamers against IL-5 and enzyme-linked immunosorbent assay (ELISA) kit for measuring IL-5. In all these process, there is no need to perfect folding of the protein. Therefore, the expression can be done in prokaryotic system, as it has high efficiency.
- Published
- 2020
- Full Text
- View/download PDF
24. Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes
- Author
-
Schlessinger, Avner [Icahn School of Medicine at Mount Sinai, New York, NY (United States)]
- Published
- 2016
- Full Text
- View/download PDF
25. The Epigenomic Landscape of Prokaryotes.
- Author
-
Blow, Matthew J, Clark, Tyson A, Daum, Chris G, Deutschbauer, Adam M, Fomenkov, Alexey, Fries, Roxanne, Froula, Jeff, Kang, Dongwan D, Malmstrom, Rex R, Morgan, Richard D, Posfai, Janos, Singh, Kanwar, Visel, Axel, Wetmore, Kelly, Zhao, Zhiying, Rubin, Edward M, Korlach, Jonas, Pennacchio, Len A, and Roberts, Richard J
- Subjects
Prokaryotic Cells ,DNA Restriction-Modification Enzymes ,Methyltransferases ,Evolution ,Molecular ,Phylogeny ,DNA Methylation ,DNA Replication ,Gene Expression Regulation ,Conserved Sequence ,Substrate Specificity ,Multigene Family ,Genome ,Epigenomics ,Molecular Sequence Annotation ,Nucleotide Motifs ,Evolution ,Molecular ,Human Genome ,Genetics ,Generic Health Relevance ,Developmental Biology - Abstract
DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.
- Published
- 2016
26. Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure.
- Author
-
Beulig, Felix, Urich, Tim, Nowak, Martin, Trumbore, Susan E, Gleixner, Gerd, Gilfillan, Gregor D, Fjelland, Kristine E, and Küsel, Kirsten
- Subjects
Prokaryotic Cells ,Carbon Dioxide ,Soil Microbiology ,Wetlands ,Eukaryota ,Carbon Cycle ,Microbiota - Abstract
There is only limited understanding of the impact of high p(CO2) on soil biomes. We have studied a floodplain wetland where long-term emanations of temperate volcanic CO2 (mofettes) are associated with accumulation of carbon from the Earth's mantle. With an integrated approach using isotope geochemistry, soil activity measurements and multi-omics analyses, we demonstrate that high (nearly pure) CO2 concentrations have strongly affected pathways of carbon production and decomposition and therefore carbon turnover. In particular, a promotion of dark CO2 fixation significantly increased the input of geogenic carbon in the mofette when compared to a reference wetland soil exposed to normal levels of CO2. Radiocarbon analysis revealed that high quantities of mofette soil carbon originated from the assimilation of geogenic CO2 (up to 67%) via plant primary production and subsurface CO2 fixation. However, the preservation and accumulation of almost undegraded organic material appeared to be facilitated by the permanent exclusion of meso- to macroscopic eukaryotes and associated physical and/or ecological traits rather than an impaired biochemical potential for soil organic matter decomposition. Our study shows how CO2-induced changes in diversity and functions of the soil community can foster an unusual biogeochemical profile.
- Published
- 2016
27. A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses.
- Author
-
Weinmaier, Thomas, Probst, Alexander J, La Duc, Myron T, Ciobanu, Doina, Cheng, Jan-Fang, Ivanova, Natalia, Rattei, Thomas, and Vaishampayan, Parag
- Subjects
Prokaryotic Cells ,Humans ,Viruses ,RNA ,Ribosomal ,16S ,Environmental Microbiology ,Environment ,Controlled ,Microbial Viability ,Metagenome ,Metagenomics ,Eukaryota ,Microbiota ,Indoor microbiome ,PMA ,Viability ,Comparative metagenomics ,Spacecraft ,Cleanroom ,Bacteria ,Fungi ,RNA ,Ribosomal ,16S ,Environment ,Controlled ,Genetics ,Human Genome ,Infection ,Ecology ,Microbiology ,Medical Microbiology - Abstract
BackgroundRecent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microorganisms when inferring impact on human health.ResultsReported here are the results of a viability-linked metagenomics assay, which (1) unveil a remarkably complex community profile for bacteria, fungi, and viruses and (2) bolster the detection of underrepresented taxa by eliminating biases resulting from extraneous DNA. This approach enabled, for the first time ever, the elucidation of viral genomes from a cleanroom environment. Upon comparing the viable biomes and distribution of phylotypes within a cleanroom and adjoining (uncontrolled) gowning enclosure, the rigorous cleaning and stringent control countermeasures of the former were observed to select for a greater presence of anaerobes and spore-forming microflora. Sequence abundance and correlation analyses suggest that the viable indoor microbiome is influenced by both the human microbiome and the surrounding ecosystem(s).ConclusionsThe findings of this investigation constitute the literature's first ever account of the indoor metagenome derived from DNA originating solely from the potential viable microbial population. Results presented in this study should prove valuable to the conceptualization and experimental design of future studies on indoor microbiomes aimed at inferring impact on human health.
- Published
- 2015
28. Adaptive response of prokaryotic communities to extreme pollution flooding in a Paleolithic rock art cave (Pindal Cave, northern Spain).
- Author
-
Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Gonzalez-Pumariega M, Elez J, Duarte E, de la Rasilla M, Canaveras JC, Saiz-Jimenez C, and Sanchez-Moral S
- Subjects
- Animals, Cattle, Spain, Floods, Prokaryotic Cells, Nitrogen, Mammals, Ecosystem, Microbiota
- Abstract
A flood event affecting Pindal Cave, a UNESCO World Heritage site, introduced a substantial amount of external sediments and waste into the cave. This event led to the burial of preexisting sediments, altering the biogeochemical characteristics of the cave ecosystem by introducing heightened levels of organic matter, nitrogen compounds, phosphorus, and heavy metals. The sediments included particulate matter and waste from a cattle farm located within the water catchment area of the cavity, along with diverse microorganisms, reshaping the cave microbial community. This study addresses the ongoing influence of a cattle farm on the cave ecosystem and aims to understand the adaptive responses of the underground microbial community to the sudden influx of waste allochthonous material. Here, we show that the flood event had an immediate and profound effect on the cave microbial community, marked by a significant increase in methanogenic archaea, denitrifying bacteria, and other microorganisms commonly associated with mammalian intestinal tracts. Furthermore, our findings reveal that one year after the flood, microorganisms related to the flood decreased, while the increase in inorganic forms of ammonium and nitrate suggests potential nitrification, aligning with increased abundances of corresponding functional genes involved in nitrogen cycling. The results reveal that the impact of pollution was neither recent nor isolated, and it was decisive in stopping livestock activity near the cave. The influence of the cattle farm has persisted since its establishment over the impluvium area, and this influence endures even a year after the flood. Our study emphasizes the dynamic interplay between natural events, anthropogenic activities, and microbial communities, offering insights into the resilience of cave ecosystems. Understanding microbial adaptation in response to environmental disturbances, as demonstrated in this cave ecosystem, has implications for broader ecological studies and underscores the importance of considering temporal dynamics in conservation efforts., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
29. Light Control in Microbial Systems.
- Author
-
Elahi Y and Baker MAB
- Subjects
- Archaea genetics, Optical Tweezers, Prokaryotic Cells, Nanoparticles
- Abstract
Light is a key environmental component influencing many biological processes, particularly in prokaryotes such as archaea and bacteria. Light control techniques have revolutionized precise manipulation at molecular and cellular levels in recent years. Bacteria, with adaptability and genetic tractability, are promising candidates for light control studies. This review investigates the mechanisms underlying light activation in bacteria and discusses recent advancements focusing on light control methods and techniques for controlling bacteria. We delve into the mechanisms by which bacteria sense and transduce light signals, including engineered photoreceptors and light-sensitive actuators, and various strategies employed to modulate gene expression, protein function, and bacterial motility. Furthermore, we highlight recent developments in light-integrated methods of controlling microbial responses, such as upconversion nanoparticles and optical tweezers, which can enhance the spatial and temporal control of bacteria and open new horizons for biomedical applications.
- Published
- 2024
- Full Text
- View/download PDF
30. Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland.
- Author
-
Cubillos CF, Aguilar P, Moreira D, Bertolino P, Iniesto M, Dorador C, and López-García P
- Subjects
- Biodiversity, Prokaryotic Cells, Bacteria genetics, Fungi, Ecosystem, Wetlands
- Abstract
Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
31. Bacterial symbionts of the precious coral Corallium rubrum are differentially distributed across colony-specific compartments and differ among colormorphs.
- Author
-
van de Water JAJM, Allemand D, and Ferrier-Pagès C
- Subjects
- Animals, RNA, Ribosomal, 16S genetics, Bacteria genetics, Prokaryotic Cells, Anthozoa, Gammaproteobacteria genetics
- Abstract
Corals engage in symbioses with micro-organisms that provide nutrients and protect the host. Where the prokaryotic microbes perform their symbiotic functions within a coral is, however, poorly understood. Here, we studied the tissue-specific microbiota of the coral Corallium rubrum by dissecting its tissues from the skeleton and separating the white polyps from the red-coloured coenenchyme, followed by 16S rRNA gene metabarcoding of the three fractions. Dissection was facilitated by incubating coral fragments in RNAlater, which caused tissues to detach from the skeleton. Our results show compartmentalisation of the microbiota. Specifically, Endozoicomonas, Parcubacteria and a Gammaproteobacteria were primarily located in polyps, whereas Nitrincolaceae and one Spirochaeta phylotype were found mainly in the coenenchyme. The skeleton-associated microbiota was distinct from the microbiota in the tissues. Given the difference in tissue colour and microbiota of the polyps and coenenchyme, we analysed the microbiota of three colormorphs of C. rubrum (red, pink, white), finding that the main difference was a very low abundance of Spirochaeta in white colormorphs. While the functions of C. rubrum's symbionts are unknown, their localisation within the colony suggests that microhabitats exist, and the presence of Spirochaeta appears to be linked to the colour of C. rubrum., (© 2024 The Authors. Environmental Microbiology Reports published by Applied Microbiology International and John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
32. "Recombinant Host Cells And Methods For The Production Of Isobutyric Acid" in Patent Application Approval Process (USPTO 20240167063).
- Abstract
Lygos Inc., a company based in Berkeley, California, has filed a patent application for a method of producing isobutyric acid using recombinant host cells and microbial fermentation. Isobutyric acid is a chemical used in the production of various products, and the company's method aims to reduce costs and environmental impact compared to traditional methods. The patent application outlines the specific genes and enzymes involved in the production process, as well as the optimal conditions for culturing the host cells. The application also includes claims for specific genes and proteins related to the biosynthetic pathway. [Extracted from the article]
- Published
- 2024
33. Hydrogen Tunneling in a Prokaryotic Lipoxygenase
- Author
-
Carr, Cody A Marcus and Klinman, Judith P
- Subjects
Chemical Sciences ,Physical Chemistry ,Catalytic Domain ,Hydrogen ,Lipoxygenase ,Prokaryotic Cells ,Thermodynamics ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Medical Biochemistry and Metabolomics ,Biochemistry & Molecular Biology ,Biochemistry and cell biology ,Medical biochemistry and metabolomics ,Medicinal and biomolecular chemistry - Abstract
A bacterial lipoxygenase (LOX) shows a deuterium kinetic isotope effect (KIE) that is similar in magnitude and temperature dependence to the very large KIE of eukaryotic LOXs. This occurs despite the evolutionary distance, an ~25% smaller catalytic domain, and an increase in Ea of ~11 kcal/mol. Site-specific mutagenesis leads to a protein variant with an Ea similar to that of the prototypic plant LOX, providing possible insight into the origin of evolutionary differences. These findings, which extend the phenomenon of hydrogen tunneling to a prokaryotic LOX, are discussed in the context of a role for protein size and/or flexibility in enzymatic hydrogen tunneling.
- Published
- 2014
34. Lipid dependencies, biogenesis and cytoplasmic micellar forms of integral membrane sugar transport proteins of the bacterial phosphotransferase system
- Author
-
Aboulwafa, Mohammad and Saier, Milton H
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Cell Membrane ,Cytoplasm ,Lipid Metabolism ,Macromolecular Substances ,Membrane Transport Proteins ,Phosphoenolpyruvate Sugar Phosphotransferase System ,Prokaryotic Cells ,Protein Multimerization ,Microbiology - Abstract
Permeases of the prokaryotic phosphoenolpyruvate-sugar phosphotransferase system (PTS) catalyse sugar transport coupled to sugar phosphorylation. The lipid composition of a membrane determines the activities of these enzyme/transporters as well as the degree of coupling of phosphorylation to transport. We have investigated mechanisms of PTS permease biogenesis and identified cytoplasmic (soluble) forms of these integral membrane proteins. We found that the catalytic activities of the soluble forms differ from those of the membrane-embedded forms. Transport via the latter is much more sensitive to lipid composition than to phosphorylation, and some of these enzymes are much more sensitive to the lipid environment than others. While the membrane-embedded PTS permeases are always dimeric, the cytoplasmic forms are micellar, either monomeric or dimeric. Scattered published evidence suggests that other integral membrane proteins also exist in cytoplasmic micellar forms. The possible functions of cytoplasmic PTS permeases in biogenesis, intracellular sugar phosphorylation and permease storage are discussed.
- Published
- 2013
35. Considering Protonation as a Posttranslational Modification Regulating Protein Structure and Function
- Author
-
Schönichen, André, Webb, Bradley A, Jacobson, Matthew P, and Barber, Diane L
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Generic health relevance ,Animals ,Disease ,Eukaryotic Cells ,Humans ,Hydrogen-Ion Concentration ,Prokaryotic Cells ,Protein Conformation ,Protein Processing ,Post-Translational ,Protons ,pH sensor ,protonation ,intracellular pH ,posttranslational modification ,coincidence detection ,conformational change ,ionization ,histidine ,Medicinal and Biomolecular Chemistry ,Chemical Engineering ,Biophysics ,Biochemistry and cell biology ,Medicinal and biomolecular chemistry - Abstract
Posttranslational modification is an evolutionarily conserved mechanism for regulating protein activity, binding affinity, and stability. Compared with established posttranslational modifications such as phosphorylation or ubiquitination, posttranslational modification by protons within physiological pH ranges is a less recognized mechanism for regulating protein function. By changing the charge of amino acid side chains, posttranslational modification by protons can drive dynamic changes in protein conformation and function. Addition and removal of a proton is rapid and reversible and, in contrast to most other posttranslational modifications, does not require an enzyme. Signaling specificity is achieved by only a minority of sites in proteins titrating within the physiological pH range. Here, we examine the structural mechanisms and functional consequences of proton posttranslational modification of pH-sensing proteins regulating different cellular processes.
- Published
- 2013
36. POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy.
- Author
-
Hölzer M
- Subjects
- Reproducibility of Results, Genome, Bacterial, Prokaryotic Cells, Software
- Abstract
Summary: Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies., Availability and Implementation: The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository., (© The Author(s) 2024. Published by Oxford University Press.)
- Published
- 2024
- Full Text
- View/download PDF
37. Oxygen-dependent biofilm dynamics in leaf decay: an in vitro analysis.
- Author
-
Karačić S, Palmer B, Gee CT, and Bierbaum G
- Subjects
- RNA, Ribosomal, 16S genetics, Prokaryotic Cells, Plant Leaves, Biofilms, Bacteria genetics
- Abstract
Biofilms are important in the natural process of plant tissue degradation. However, fundamental knowledge of biofilm community structure and succession on decaying leaves under different oxygen conditions is limited. Here, we used 16S rRNA and ITS gene amplicon sequencing to investigate the composition, temporal dynamics, and community assembly processes of bacterial and fungal biofilms on decaying leaves in vitro. Leaves harvested from three plant species were immersed in lake water under aerobic and anaerobic conditions in vitro for three weeks. Biofilm-covered leaf samples were collected weekly and investigated by scanning electron microscopy. The results showed that community composition differed significantly between biofilm samples under aerobic and anaerobic conditions, though not among plant species. Over three weeks, a clear compositional shift of the bacterial and fungal biofilm communities was observed. The alpha diversity of prokaryotes increased over time in aerobic assays and decreased under anaerobic conditions. Oxygen availability and incubation time were found to be primary factors influencing the microbial diversity of biofilms on different decaying plant species in vitro. Null models suggest that stochastic processes governed the assembly of biofilm communities of decaying leaves in vitro in the early stages of biofilm formation and were further shaped by niche-associated factors., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
38. Speeding genomic island discovery through systematic design of reference database composition.
- Author
-
Yu SL, Mageeney CM, Shormin F, Ghaffari N, and Williams KP
- Subjects
- Genomics, Bacteria genetics, Prokaryotic Cells, Prophages genetics, Genomic Islands, Genome, Bacterial
- Abstract
Background: Genomic islands (GIs) are mobile genetic elements that integrate site-specifically into bacterial chromosomes, bearing genes that affect phenotypes such as pathogenicity and metabolism. GIs typically occur sporadically among related bacterial strains, enabling comparative genomic approaches to GI identification. For a candidate GI in a query genome, the number of reference genomes with a precise deletion of the GI serves as a support value for the GI. Our comparative software for GI identification was slowed by our original use of large reference genome databases (DBs). Here we explore smaller species-focused DBs., Results: With increasing DB size, recovery of our reliable prophage GI calls reached a plateau, while recovery of less reliable GI calls (FPs) increased rapidly as DB sizes exceeded ~500 genomes; i.e., overlarge DBs can increase FP rates. Paradoxically, relative to prophages, FPs were both more frequently supported only by genomes outside the species and more frequently supported only by genomes inside the species; this may be due to their generally lower support values. Setting a DB size limit for our SMAll Ranked Tailored (SMART) DB design speeded runtime ~65-fold. Strictly intra-species DBs would tend to lower yields of prophages for small species (with few genomes available); simulations with large species showed that this could be partially overcome by reaching outside the species to closely related taxa, without an FP burden. Employing such taxonomic outreach in DB design generated redundancy in the DB set; as few as 2984 DBs were needed to cover all 47894 prokaryotic species., Conclusions: Runtime decreased dramatically with SMART DB design, with only minor losses of prophages. We also describe potential utility in other comparative genomics projects., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Yu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2024
- Full Text
- View/download PDF
39. Structural basis for plasmid restriction by SMC JET nuclease.
- Author
-
Roisné-Hamelin F, Liu HW, Taschner M, Li Y, and Gruber S
- Subjects
- Plasmids genetics, Prokaryotic Cells, Cell Cycle Proteins metabolism, DNA metabolism, Endonucleases
- Abstract
DNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of plasmids through DNA cleavage, yet the mechanisms for plasmid recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET nuclease cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as molecular signature for plasmid recognition and non-self DNA elimination. We moreover elucidate key elements of SMC loop extrusion, including the motor direction and the structure of a DNA-holding state., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
40. Functional Roles and Genomic Impact of Miniature Inverted-Repeat Transposable Elements (MITEs) in Prokaryotes.
- Author
-
Minnick MF
- Subjects
- Prokaryotic Cells, Bacteria genetics, Archaea genetics, DNA Transposable Elements genetics, Genomics
- Abstract
Prokaryotic genomes are dynamic tapestries that are strongly influenced by mobile genetic elements (MGEs), including transposons (Tn's), plasmids, and bacteriophages. Of these, miniature inverted-repeat transposable elements (MITEs) are undoubtedly the least studied MGEs in bacteria and archaea. This review explores the diversity and distribution of MITEs in prokaryotes and describes what is known about their functional roles in the host and involvement in genomic plasticity and evolution.
- Published
- 2024
- Full Text
- View/download PDF
41. Life, its definition, origin, evolution, and four-dimensional hierarchical structure.
- Author
-
Mikhailovsky GE
- Subjects
- Thermodynamics, Prokaryotic Cells, Biological Evolution, Eukaryota
- Abstract
The main unique features of biological systems are reviewed, and four necessary and sufficient attributes of life are formulated, based on the ideas of Ervin Bauer. The possibility of the occurrence of each of these attributes during the origin of life is analyzed. As a result, different scenarios for the origin of life are presented, with their pros and cons. Next, the mainstream of biological evolution is discussed, considering it as a special case of general complexification, and structuredness is defined as a quantitative measure of structural complexity. By introducing the concepts of post-dissipative structure and ratcheting process based on "frozen" patterns, their role in the generation of biological structures underlying biological evolution is demonstrated. Furthermore, it is proposed that all living things can be divided into micro- (unicellular) and macro- (multicellular) creatures, which differ from each other even more radically than the difference between prokaryotes and unicellular eukaryotes. Then the fifth, sufficient, but not necessary attribute of life, hierarchicality, is formulated, which is fully applicable only to macrolife. It is also shown that living organisms are primarily chemodynamic rather than thermodynamic systems, and three basic laws of biochemodynamics are formulated. Finally, fifteen basic features of living beings, grouped into four basic blocks, are summarized., Competing Interests: Declaration of competing interest The author declare that he has no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
42. Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean.
- Author
-
Balmonte JP, Giebel HA, Arnosti C, Simon M, and Wietz M
- Subjects
- Pacific Ocean, Prokaryotic Cells, Glucose, Seawater microbiology, Alginates, Alteromonadaceae
- Abstract
The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions., (© 2024 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
43. Virus-prokaryote infection pairs associated with prokaryotic production in a freshwater lake.
- Author
-
Shen S, Tominaga K, Tsuchiya K, Matsuda T, Yoshida T, and Shimizu Y
- Subjects
- Lakes chemistry, Prokaryotic Cells, Japan, Viruses genetics, Bacteriophages genetics
- Abstract
Viruses infect and kill prokaryotic populations in a density- or frequency-dependent manner and affect carbon cycling. However, the effects of the stratification transition, including the stratified and de-stratified periods, on the changes in prokaryotic and viral communities and their interactions remain unclear. We conducted a monthly survey of the surface and deep layers of a large and deep freshwater lake (Lake Biwa, Japan) for a year and analyzed the prokaryotic production and prokaryotic and viral community composition. Our analysis revealed that, in the surface layer, 19 prokaryotic species, accounting for approximately 40% of the total prokaryotic abundance, could potentially contribute to the majority of prokaryotic production, which is the highest during the summer and is suppressed by viruses. This suggests that a small fraction of prokaryotes and phages were the key infection pairs during the peak period of prokaryotic activity in the freshwater lake. We also found that approximately 50% of the dominant prokaryotic and viral species in the deep layer were present throughout the study period. This suggests that the "kill the winner" model could explain the viral impact on prokaryotes in the surface layer, but other dynamics may be at play in the deep layer. Furthermore, we found that annual vertical mixing could result in a similar rate of community change between the surface and deep layers. These findings may be valuable in understanding how communities and the interaction among them change when freshwater lake stratification is affected by global warming in the future.IMPORTANCEViral infection associated with prokaryotic production occurs in a density- or frequency-dependent manner and regulates the prokaryotic community. Stratification transition and annual vertical mixing in freshwater lakes are known to affect the prokaryotic community and the interaction between prokaryotes and viruses. By pairing measurements of virome analysis and prokaryotic production of a 1-year survey of the depths of surface and deep layers, we revealed (i) the prokaryotic infection pairs associated with prokaryotic production and (ii) the reset in prokaryotic and viral communities through annual vertical mixing in a freshwater lake. Our results provide a basis for future work into changes in stratification that may impact the biogeochemical cycling in freshwater lakes., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
44. Diverse genetic contexts of HicA toxin domains propose a role in anti-phage defense.
- Author
-
Gerdes K
- Subjects
- Bacteria metabolism, Prokaryotic Cells, Bacterial Proteins metabolism, Toxins, Biological genetics, Antitoxins metabolism
- Abstract
Toxin-antitoxin (TA) modules are prevalent in prokaryotic genomes, often in substantial numbers. For instance, the Mycobacterium tuberculosis genome alone harbors close to 100 TA modules, half of which belong to a singular type. Traditionally ascribed multiple biological roles, recent insights challenge these notions and instead indicate a predominant function in phage defense. TAs are often located within Defense Islands, genomic regions that encode various defense systems. The analysis of genes within Defense Islands has unveiled a wide array of systems, including TAs that serve in anti-phage defense. Prokaryotic cells are equipped with anti-phage Viperins that, analogous to their mammalian counterparts, inhibit viral RNA transcription. Additionally, bacterial Structural Maintenance of Chromosome (SMC) proteins combat plasmid intrusion by recognizing foreign DNA signatures. This study undertakes a comprehensive bioinformatics analysis of genetic elements encoding the HicA double-stranded RNA-binding domain, complemented by protein structure modeling. The HicA toxin domains are found in at least 14 distinct contexts and thus exhibit a remarkable genetic diversity. Traditional bicistronic TA operons represent eight of these contexts, while four are characterized by monocistronic operons encoding fused HicA domains. Two contexts involve hicA adjacent to genes that encode bacterial Viperins. Notably, genes encoding RelE toxins are also adjacent to Viperin genes in some instances. This configuration hints at a synergistic enhancement of Viperin-mediated anti-phage action by HicA and RelE toxins. The discovery of a HicA domain merged with an SMC domain is compelling, prompting further investigation into its potential roles.IMPORTANCEProkaryotic organisms harbor a multitude of toxin-antitoxin (TA) systems, which have long puzzled scientists as "genes in search for a function." Recent scientific advancements have shed light on the primary role of TAs as anti-phage defense mechanisms. To gain an overview of TAs it is important to analyze their genetic contexts that can give hints on function and guide future experimental inquiries. This article describes a thorough bioinformatics examination of genes encoding the HicA toxin domain, revealing its presence in no fewer than 14 unique genetic arrangements. Some configurations notably align with anti-phage activities, underscoring potential roles in microbial immunity. These insights robustly reinforce the hypothesis that HicA toxins are integral components of the prokaryotic anti-phage defense repertoire. The elucidation of these genetic contexts not only advances our understanding of TAs but also contributes to a paradigm shift in how we perceive their functionality within the microbial world., Competing Interests: The author declares no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
45. On the ever-growing functional versatility of the CRISPR-Cas13 system.
- Author
-
Montagud-Martínez R, Márquez-Costa R, Heras-Hernández M, Dolcemascolo R, and Rodrigo G
- Subjects
- RNA, Ribonucleoproteins, Synthetic Biology, CRISPR-Cas Systems, Prokaryotic Cells
- Abstract
CRISPR-Cas systems evolved in prokaryotes to implement a powerful antiviral immune response as a result of sequence-specific targeting by ribonucleoproteins. One of such systems consists of an RNA-guided RNA endonuclease, known as CRISPR-Cas13. In very recent years, this system is being repurposed in different ways in order to decipher and engineer gene expression programmes. Here, we discuss the functional versatility of the CRISPR-Cas13 system, which includes the ability for RNA silencing, RNA editing, RNA tracking, nucleic acid detection and translation regulation. This functional palette makes the CRISPR-Cas13 system a relevant tool in the broad field of systems and synthetic biology., (© 2024 The Authors. Microbial Biotechnology published by Applied Microbiology International and John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
46. The population genetics of prokaryotic pangenomes.
- Author
-
Domingo-Sananes MR and Meehan CJ
- Subjects
- Phylogeny, Genetics, Population, Prokaryotic Cells
- Published
- 2024
- Full Text
- View/download PDF
47. Preventing toxicity in toxin-antitoxin systems: An overview of regulatory mechanisms.
- Author
-
Bonabal S and Darfeuille F
- Subjects
- Bacteria genetics, Bacteria metabolism, Prokaryotic Cells, Bacterial Proteins genetics, Bacterial Proteins metabolism, Toxin-Antitoxin Systems genetics, Toxins, Biological genetics, Toxins, Biological metabolism, Antitoxins genetics, Antitoxins metabolism
- Abstract
Toxin-antitoxin systems (TAs) are generally two-component genetic modules present in almost every prokaryotic genome. The production of the free and active toxin is able to disrupt key cellular processes leading to the growth inhibition or death of its host organism in absence of its cognate antitoxin. The functions attributed to TAs rely on this lethal phenotype ranging from mobile genetic elements stabilization to phage defense. Their abundance in prokaryotic genomes as well as their lethal potential make them attractive targets for new antibacterial strategies. The hijacking of TAs requires a deep understanding of their regulation to be able to design such approach. In this review, we summarize the accumulated knowledge on how bacteria cope with these toxic genes in their genome. The characterized TAs can be grouped based on the way they prevent toxicity. Some systems rely on a tight control of the expression to prevent the production of the toxin while others control the activity of the toxin at the post-translational level., (Copyright © 2023 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
48. Large language models improve annotation of prokaryotic viral proteins.
- Author
-
Flamholz ZN, Biller SJ, and Kelly L
- Subjects
- Genomics, Capsid Proteins genetics, Metagenomics, Viral Proteins genetics, Prokaryotic Cells
- Abstract
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
- Published
- 2024
- Full Text
- View/download PDF
49. Chromosome structure modeling tools and their evaluation in bacteria.
- Author
-
Liu T, Qiu QT, Hua KJ, and Ma BG
- Subjects
- Prokaryotic Cells, Chromosomes, Bacterial genetics, Algorithms, Escherichia coli genetics, Chromosome Structures, Bacteria
- Abstract
The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms., (© The Author(s) 2024. Published by Oxford University Press.)
- Published
- 2024
- Full Text
- View/download PDF
50. An ANI gap within bacterial species that advances the definitions of intra-species units.
- Author
-
Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, and Konstantinidis KT
- Subjects
- Prokaryotic Cells, Phylogeny, Sequence Analysis, DNA, Genome, Bacterial, Bacteria genetics
- Abstract
Importance: Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.