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Extracellular proteases, such as chitinases secreted by Arthrobotrys oligospora (A. oligospora), play a crucial role in the process of nematode infection. However, post-transcriptional regulation of gene expression involving microRNAs (miRNAs) in A. oligospora remains scarcely described. Hereto, transcriptome sequencing was carried out to analyze the expression profiles of chitin-responsive miRNAs in A. oligospora. Based on the RNA-seq data, the differential expression of miRNAs (DEmiRNAs) in response to chitin was screened, identified and characterized in A. oligospora. Meanwhile, the potential target genes were predicted by the online tools miRanda and Targetscan, respectively. Furthermore, the interaction of DEmiRNA with it’s target gene was validated by a dual-luciferase reporter assay system. Among 85 novel miRNAs identified, 25 miRNAs displayed significant differences in expression in A. oligospora in response to chitin. Gene Ontology (GO) analysis showed that the potential genes targeted by DEmiRNAs were enriched in the biological processes such as bio-degradation, extracellular components and cell cycle. KEGG analysis revealed that the target genes were mainly involved in Hippo, carbon and riboflavin metabolic pathway. Outstandingly, chitinase AOL_s00004g379, which is involved in the hydrolysis metabolic pathway of chitin, was confirmed to be a target gene of differential miR_70. These findings suggest that chitin-responsive miRNAs are involved in the regulation of cell proliferation, predator hyphae growth and chitinase expression through the mechanisms of post-transcriptional regulation, which provides a new perspective to the molecular mechanisms underlying miRNAs-mediated control of gene expression in A. oligospora. [ABSTRACT FROM AUTHOR]

Valproic acid (valproate, VA) has been widely used as an antiepileptic agent for several decades, as well as in the treatment of bipolar affective disorder. For many years, the ability of VA to stop different types of epileptic seizures has been associated with increased GABAergic neurotransmission, inhibition of glutamatergic neurotransmission and a general decrease in CNS hyperactivity by acting on ion channels. However, precise mechanisms of VA anticonvulsant effects are still not clear. Over time, the effects of VA on other neurotransmitter systems, enzymes and intracellular signalling pathways have been revealed, however they do not explain the effectiveness of the drug as an anticonvulsant and mood stabilizer, but only expand its pharmacological profile. Over the past 10 years, the focus of interest in valproate research has changed due to its ability to alter gene expression both by inhibiting histone deacetylases and by changing levels of DNA methylation. These new studies reveal alternative mechanisms of valproate action rather than trying to test and confirm hypotheses previously put forward. [ABSTRACT FROM AUTHOR]

Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome—the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system. [ABSTRACT FROM AUTHOR]

Genetic transformation of higher eukaryote mitochondria in vivo is an unresolved and important problem. For efficient expression of foreign genetic material in mitochondria, it is necessary to select regulatory elements that provide a high level of transcription and transcript stability. This work is aimed at studying the effectiveness of regulatory elements of mitochondrial genes flanking exogenous DNA using the phenomenon of natural competence of plant mitochondria. For this purpose, genetic constructs carrying the GFP gene under the control of the promoter regions of the RRN26 or COX1 genes and one of the two 3'-untranslated regions (3'-UTR) of mitochondrial genes were imported into isolated Arabidopsis mitochondria, followed by transcription in organello. It was shown that the level of GFP expression under the control of promoters of the RRN26 or COX1 genes in organello correlates with the level of transcription of these genes observed in vivo. At the same time, the presence of the tRNATrp sequence in the 3'-UTR leads to a higher level of the GFP transcript than the presence in this region of the 3'-UTR of the NAD4 gene containing the binding site of the MTSF1 protein. The results we obtained open prospects for creating a system for efficient transformation of the mitochondrial genome. [ABSTRACT FROM AUTHOR]

Using a mutant of Mycobacterium smegmatis lacking the major aa3 cytochrome c oxidase of the electron transport chain (Δaa3), we demonstrated that inhibition of the respiratory electron transport chain led to an increase in antibiotic resistance of M. smegmatis to isoniazid, rifampicin, ethambutol, and tetracycline. The alternative sigma factors SigB and SigE were shown to be involved in an increase in rifampicin resistance of M. smegmatis induced under respiration-inhibitory conditions. As in Mycobacterium tuberculosis, SigE and SigB form a hierarchical regulatory pathway in M. smegmatis through SigE-dependent transcription of sigB. Expression of sigB and sigE was demonstrated to increase in the Δaa3 mutant, leading to upregulation of the SigB-dependent genes in the mutant. The pho U2 (MSMEG_1605) gene implicated in a phosphate-signaling pathway and the MSMEG_1097 gene encoding a putative glycosyltransferase were identified to be involved in the SigB-dependent enhancement of rifampicin resistance observed for the Δaa3 mutant of M. smegmatis. The significance of this study is that the direct link between the functionality of the respiratory electron transport chain and antibiotic resistance in mycobacteria was demonstrated for the first time using an electron transport chain mutant rather than inhibitors of electron transport chain. [ABSTRACT FROM AUTHOR]

Purpose: Long non-coding RNAs (lncRNAs) control gene expression at multiple levels. By interacting with microRNAs (miRNAs), they regulate their mRNA targets creating dynamic regulatory networks involved in different cellular processes. Their role in follicle development and oocyte maturation has recently emerged. lncRNA deregulation has been found associated with different pathological conditions. In this study, we identified differentially expressed lncRNAs in cumulus cells (CCs) isolated from MII oocytes of advanced maternal age women and proposed ceRNA-networks involved in signaling pathways crucial in ovarian folliculogenesis and female germ cell maturation. Methods: We performed a high-throughput analysis of the expression profile of 68 lncRNAs from CCs of aged and young women by using NanoString technology. By miRNet, TarPmiR, miRTarBase, OKdb, and KEGG we predicted some ceRNA-networks involving the differentially expressed (DE) lncRNAs, miRNA interactors, and their mRNA target genes. Results: We identified 28 lncRNAs down-regulated in CC samples from aged women. The analysis revealed that the miRNAs binding 11 of the DE lncRNAs and their mRNA targets are included in ceRNA-networks involved in the regulation of the PI3K-Akt, FOXO, and p53 signaling pathways. Conclusion: We proposed that the lncRNA down-regulation in CCs from aged women could influence the expression of genes encoding proteins deregulated in reproductive aging. A better understanding of the interplay of lncRNA-miRNA-mRNA networks in human CCs could increase our knowledge about the mechanisms of regulation of gene expression involved in aging, lead to the development of novel therapeutics, and improve reproductive outcomes in aged women. [ABSTRACT FROM AUTHOR]

Freezing tolerance of triticale is a major trait contributing to its winter hardiness. The identification of genomic regions — quantitative trait loci (QTL) and molecular markers associated with freezing tolerance in winter hexaploid triticale — was the aim of this study. For that purpose, a new genetic linkage map was developed for the population of 92 doubled haploid lines derived from 'Hewo' × 'Magnat' F1 hybrid. Those lines, together with parents were subjected to freezing tolerance test three times during two winter seasons. Plants were grown and cold-hardened under natural fall/winter conditions and then subjected to freezing in controlled conditions. Freezing tolerance was assessed as the plants recovery (REC), the electrolyte leakage (EL) from leaves and chlorophyll fluorescence parameters (JIP) after freezing. Three consistent QTL for several fluorescence parameters, electrolyte leakage, and the percentage of the survived plants were identified with composite interval mapping (CIM) and single marker analysis (SMA). The first locus Qfr.hm-7A.1 explained 9% of variation of both electrolyte leakage and plants recovery after freezing. Two QTL explaining up to 12% of variation in plants recovery and shared by selected chlorophyll fluorescence parameters were found on 4R and 5R chromosomes. Finally, main locus Qchl.hm-5A.1 was detected for chlorophyll fluorescence parameters that explained up to 19.6% of phenotypic variation. The co-located QTL on chromosomes 7A.1, 4R and 5R, clearly indicated physiological and genetic relationship of the plant survival after freezing with the ability to maintain optimal photochemical activity of the photosystem II and preservation of the cell membranes integrity. The genes located in silico within the identified QTL include those encoding BTR1-like protein, transmembrane helix proteins like potassium channel, and phosphoric ester hydrolase involved in response to osmotic stress as well as proteins involved in the regulation of the gene expression, chloroplast RNA processing, and pyrimidine salvage pathway. Additionally, our results confirm that the JIP test is a valuable tool to evaluate freezing tolerance of triticale under unstable winter environments. [ABSTRACT FROM AUTHOR]

Key message: GhDRP1 acts as a negatively regulator to participate in response to drought stress possibly by modulating ABA signaling pathway and flavonoid biosynthesis pathway which affects stomata movement and thus water loss, ROS scavenging enzymes, and proline accumulation in cotton. Type-2C protein phosphatases (PP2C) may play important roles in plant stress signal transduction. Here, we show the evidence that a cotton PP2C protein GhDRP1 participates in plant response to drought stress. GhDRP1 gene encodes an active type-2C protein phosphatase (PP2C) and its expression is significantly induced in cotton by drought stress. Compared with wild type, the GhDRP1 overexpression (OE) transgenic cotton and Arabidopsis displayed reduced drought tolerance, whereas GhDRP1-silenced (RNAi) cotton showed enhanced drought tolerance. Under drought stress, malondialdehyde content was lower, whereas superoxide dismutase and peroxidase activities, proline content, stomata closure and relative water content were higher in GhDRP1 RNAi plants compared with those in wild type. In contrast, GhDRP1 OE plants showed the opposite phenotype under the same conditions. Expression levels of some stress-related and flavonoid biosynthesis-related genes were altered in GhDRP1 transgenic plants under drought stress. Additionally, GhDRP1 protein could interact with other proteins such as PYLs, SNF1-related protein kinase and GLK1-like protein. Collectively, these data suggest that GhDRP1 participates in plant response to drought stress possibly by modulating ABA signaling pathway and flavonoid biosynthesis pathway which affects stomata movement and thus water loss, ROS scavenging enzymes, and proline accumulation in cotton. [ABSTRACT FROM AUTHOR]

Cell metabolism depends, to a large extent, on correct regulation of gene expression. One of the mechanisms of regulation is the formation of nucleic acid secondary structures, among which guanine quadruplexes (G-quadruplexes, or G4) are of particular importance. G-quadruplexes are dynamic structures whose stability is determined by their size, ionic composition, and the nature of the nucleic acids forming them. They are regulated by various protein factors. Guanine quadruplexes play an important role in the regulation of many processes occurring in DNA and RNA, from maintaining telomere homeostasis to determining the ribosome landing site on mRNA. Therefore, these structures are considered a promising target for antitumor therapy, and their detailed study is important to modern biology. This review is focused on the structure and thermodynamic properties of G-quadruplexes together with their interaction with some nuclear proteins. [ABSTRACT FROM AUTHOR]

Rapidly occurring advancements in molecular genetics, such as recent developments in epigenetics, are challenging traditional genetics as it is taught at schools. For example, the adoption of epigenetics—which provides molecular mechanisms for the environment to directly alter phenotypic variation—would mean that pivotal tenets in genetics instruction, such as the central dogma, will require revision. Despite the important implications of epigenetic mechanisms in human health and biological evolution, it is seldom considered at secondary school. The aim of this research was to evaluate the possibility of introducing epigenetics to secondary school students, to foresee the conceptual barriers that might arise and, accordingly, to give some clues which might guide instruction. A short introductory lecture on epigenetics, followed by an open-ended question based in a real case showed that more than half of the students (424 students in 12 schools) were able to understand that environmental factors influence differential gene expression, and over 25% of the students at grade 12 mentioned also some epigenetic molecular mechanisms. However, the students held some conceptual barriers likely hindering comprehension of epigenetics: lack of basic genetic knowledge, genetic determinism, and misunderstanding of the process of adaptation to the environment. The results of this research suggest that it is feasible to introduce epigenetics in secondary school curriculum: at lower levels, special attention should be paid to avoid inducing misconceptions that can work as conceptual barriers to complex genetic concepts exceeding linear determinism; the explicit teaching of technical details might better be addressed at later, post-obligatory levels. [ABSTRACT FROM AUTHOR]

The termination of transcription is a complex process that substantially contributes to gene regulation in eukaryotes. Previously, it was noted that a single cytosine deletion at the position + 32 bp relative to the single polyadenylation signal AAUAAA (hereafter the dC mutation) causes a 2-fold increase in the transcription level of the upstream eGFP reporter in mouse embryonic stem cells. Here, we analyzed the conservation of this phenomenon in immortalized mouse, human and drosophila cell lines and the influence of the dC mutation on the choice of the pre-mRNA cleavage sites. We have constructed dual-reporter plasmids to accurately measure the effect of the dC and other nearby located mutations on eGFP mRNA level by RT-qPCR. In this way, we found that the dC mutation leads to a 2-fold increase in the expression level of the upstream eGFP reporter gene in cultured mouse and human, but not in drosophila cells. In addition, 3′ RACE analysis demonstrated that eGFP pre-mRNAs are cut at multiple positions between + 14 to + 31, and that the most proximal cleavage site becomes almost exclusively utilized in the presence of the dC mutation. We also identified new short sequence variations located within positions + 25.. + 40 and + 33.. + 48 that increase eGFP expression up to ~2-4-fold. Altogether, the positive effect of the dC mutation seems to be conserved in mouse embryonic stem cells, mouse embryonic 3T3 fibroblasts and human HEK293T cells. In the latter cells, the dC mutation appears to be involved in regulating pre-mRNA cleavage site selection. Finally, a multiplexed approach is proposed to identify motifs located downstream of cleavage site(s) that are essential for transcription termination. [ABSTRACT FROM AUTHOR]

In silico analysis of the promoter region of the At4g01870 gene of Arabidopsis thaliana (L.) Heynh. showed the presence of ABRE, W-box, RAV1-A, MYB, and LFY cis-elements in the sequence. These regulatory motifs bind the transcription factors involved in responses to abscisic acid (ABA) and stresses. Stable transgenic plants carrying the β-glucuronidase gene under the control of the 5'-deletion fragments of the At4g01870 promoter were obtained. According to the results of histochemical staining of transformants, gene expression was induced by abiotic stress and was most significant in the conductive tissues of the root, leaves, and sepals as well as in flowers. The study of At4g01870 gene expression by RT-PCR confirmed that the gene transcript content increased after the exposure of plants to a solution of NaCl or at 37°C and after ABA treatment; however, hypothermia almost unchanged the level of accumulation of the transcripts. Along with ABA, expression of the At4g01870 gene was induced by indolylacetic and salicylic acids and ethylene precursor 1-aminocyclopropane-1-carboxylic acid; it was hardly regulated by methyl jasmonate and inhibited by cytokinin. The TolB-like protein, encoded by the At4g01870 gene, functions as a type of platform, based on which protein complexes are assembled. Given the previously identified ABA-binding properties of the protein At4g01870 and the presence of the ABA-dependent cis-elements in the promoter of its coding gene, it can be assumed that the protein encoded by the At4g01870 gene allows to control the hormonal signals in the cell, providing a structural platform for the interaction of specific effector proteins, trans-factors and ion channels. [ABSTRACT FROM AUTHOR]

Microorganisms produce various volatile compounds, including volatile organic compounds and complex combinations of volatile compounds. The ecological and functional role of these compounds is presently the subject of intense study. Volatile organic compounds of microbial origin may possess antimicrobial properties, suppress or stimulate plant growth, and act as signals for long-distance communication between organisms (infochemicals), which propagate in the air and in aquatic solutions. Chemical diversity of volatile organic compounds of microbial origin provides a source of new compounds which may find application in medicine, biotechnology, and agriculture. Presently known bacterial volatile compounds, their structure, biosynthesis, and biological activity are discussed, with special emphasis on organic volatile compounds and their effect on bacteria. [ABSTRACT FROM AUTHOR]

Over the past decade, there has been an active study of the interactions between the population of transposable elements (TEs) and the rest of the genome. Many regulatory sequences of TEs have been used for different genes regulation and genome organization. These regulatory sequences can be transcription factor binding sites, enhancers, and insulators. TEs may contain promoters that can be domesticated during substitution of original gene promoters or during de novo formation of long noncoding RNAs. In addition, there are many examples of domestication of TE-encoded proteins, for example, transposases, proteases, and Gag proteins. This review highlights the role of TEs in the evolution of gene regulatory networks and the principles determining it. [ABSTRACT FROM AUTHOR]

Immunotherapy targeting the PD-L1/PD-1 pathway using antibodies is effective in the clinical treatment of a multitude of cancers. This makes research of the regulatory mechanisms of PD-1 expression in cancer cells intriguing. PD-L1 expression can be categorized into inducible expression, attributed to extrinsic factors in the microenvironment, and constitutive expression, attributed to intrinsic cancer-driving gene alteration. The mechanisms of PD-L1 expression in cancer cells operate at multiple levels, including gene amplification, chromatin modification, transcription, posttranscription, translation and posttranslation. Moreover, some open questions in this field that need to be answered in future research are proposed. Studies of regulatory mechanisms of PD-L1 expression pave the way for the application of more effective approaches in the future of cancer immunotherapy. [ABSTRACT FROM AUTHOR]

Translation factor eIF5A participates in protein synthesis at the stage of polypeptide chain elongation. Two eIF5A isoforms are known that are encoded by related genes whose expression varies significantly in different tissues. The eIF5A1 isoform is a constitutively and ubiquitously expressed gene, while the eIF5A2 isoform is expressed in few normal tissues and is an oncogene by a number of parameters. Unique feature of eIF5A isoforms is that they are the only two proteins that contain amino acid hypusine. Modification with hypusine is critical requirement for eIF5A activity. Another distinctive feature of eIF5A is its involvement in the translation of only a subset of the total population of cell mRNAs. The genes for which mRNAs translation requires eIF5A are the members of certain functional groups and are involved in cell proliferation, apoptosis, inflammatory processes, and regulation of transcription and RNA metabolism. The involvement of eIF5A is necessary for the translation of proteins containing oligoproline fragments and some other structures. Modification of eIF5A by hypusine is implemented by two highly specialized enzymes, deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH), which are not involved in other biochemical reactions. Intracellular activity of these enzymes is closely associated with systems of protein acetylation, polyamine metabolism and other biochemical processes. Inhibition of DHS and DOHH activity provides the possibility of pharmacological control of eIF5A activity and expression of eIF5A-dependent genes. [ABSTRACT FROM AUTHOR]

A dramatic increase in drug-resistant forms of tuberculosis (TB) stimulates a search for novel anti- TB drugs and studies of the drug resistance acquisition. One of the possible causes is a phenotypic resistance or drug tolerance which is not associated with genomic changes. The majority of anti-TB drugs eliminate 99% of MTB cells in 3-5 days, but the remaining subpopulation becomes unsusceptible to treatment and capable for long-term persistence with ability to resuscitate once the external adverse factor is removed. This evasion of the stress factor facilitates selection of resistant forms, thus warranting long-term treatment with at least four antibacterial drugs in TB. The review considers the main mechanisms of bacterial tolerance that are due to alterations in the cell wall, activation of efflux pumps, induction of transcriptional regulons, changes in metabolic flows, and modification of molecular machineries. [ABSTRACT FROM AUTHOR]

DNA and machinery for gene expression have been discovered in chloroplasts during the 1960s. It was soon evident that the chloroplast genome is relatively small, that most genes for chloroplast-localized proteins reside in the nucleus and that chloroplast membranes, ribosomes, and protein complexes are composed of proteins encoded in both the chloroplast and the nuclear genome. This situation has made the existence of mechanisms highly probable that coordinate the gene expression in plastids and nucleus. In the 1970s, the first evidence for plastid signals controlling nuclear gene expression was provided by studies on plastid ribosome deficient mutants with reduced amounts and/or activities of nuclear-encoded chloroplast proteins including the small subunit of Rubisco, ferredoxin NADP+ reductase, and enzymes of the Calvin cycle. This review describes first models of plastid-to-nucleus signaling and their discovery. Today, many plastid signals are known. They do not only balance gene expression in chloroplasts and nucleus during developmental processes but are also generated in response to environmental changes sensed by the organelles. [ABSTRACT FROM AUTHOR]

Bronchial asthma is a chronic inflammatory disease of the airways that is characterized by episodes of shortness of breath, expiratory dyspnea, cough, wheezing, and pulmonary emphysema. At the present time, asthma is a global public health problem and affects about 5% of the worldwide population. Although a wide range of anti-inflammatory drugs is available, uncontrolled or poorly controlled asthma is still a problem, requiring the development of novel therapeutic approaches. Intense studies of the molecular mechanisms of asthma in transgenic animals performed since the 1990s implicated cytokines, such as IL-4, IL-5, and IL-13, and their receptors in the initiation and maintenance of asthma. These findings led to anticytokine therapy as a novel approach for bronchial asthma treatment. To date, many preclinical and clinical studies have been performed in this field especially with drugs based on humanized monoclonal antibodies, soluble receptors, peptide inhibitors, etc. The review summarizes the data from preclinical and clinical studies of anti-cytokine therapeutics in humans. [ABSTRACT FROM AUTHOR]

Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications. [ABSTRACT FROM AUTHOR]

The term 'epigenetics' is critically analyzed basing on the differential concept of variability. A strict definition of epigenetic processes is proposed. The widely accepted tradition to oppose the words 'genetic' and 'epigenetic' is shown to be incorrect. An adequate antonym for the term 'epigenetics' is proposed. Optimization of current genetic terminology due to epigenetics redefining is discussed. [ABSTRACT FROM AUTHOR]

Small regulatory RNA (sRNA) is a unique noncoding RNA involved in regulation of gene expression in both eukaryotic and bacterial cells. This short review discusses examples of positive and negative translation regulation by sRNAs in bacteria and participation of Hfq in these processes. The importance of structure investigation of nucleotide-protein and RNA-protein complexes for designing a model of Hfq interaction with both mRNA and sRNA simultaneously is demonstrated. [ABSTRACT FROM AUTHOR]

The study of prokaryotic small RNAs is one of the most important directions in modern molecular biology. In the last decade, multiple short regulatory transcripts have been found in prokaryotes, and for some of them functional roles have been elucidated. Bacterial small RNAs are implicated in the regulation of transcription and translation, and they affect mRNA stability and gene expression via different mechanisms, including changes in mRNA conformation and interaction with proteins. Most small RNAs are expressed in response to external factors, and they help bacteria to adapt to changing environmental conditions. Bacterial infections of various origins remain a serious medical problem, despite significant progress in fighting them. Discovery of mechanisms that bacteria employ to survive in infected organisms and ways to block these mechanisms is promising for finding new treatments for bacterial infections. Regulation of pathogenesis with small RNAs is an attractive example of such mechanisms. This review considers the role of bacterial small RNAs in adaptation to stress conditions. We pay special attention to the role of small RNAs in Mycobacterium tuberculosis infection, in particular during establishment and maintenance of latent infection. [ABSTRACT FROM AUTHOR]

The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response. [ABSTRACT FROM AUTHOR]

The review presents currently available data on the biological role of 8-oxo-2'-deoxyguanosine. This compound for a long time has been used successfully as a biomarker of oxidative stress and diseases associated with it. However, in recent years, an increasing number of publications has appeared reporting that biological role of 8-oxo-dG is not only a mutagenic one; it also is involved in the regulation of gene expression, in some processes of DNA repair, in the control of inflammatory and autoimmune reactions, and in the activation of antioxidant systems. Probably, 8-oxo-2'-deoxyguanosine could prospectively be used as a drug. [ABSTRACT FROM AUTHOR]

In prokaryotic genomes, the neighboring genes are often located on the complementary DNA strands and adjoin each other by their 5′- or 3′-ends, or even overlap with their open reading frames. It was suggested that this gene topology has a functional purpose of regulating their expression. For the genes that overlap by their coding 3′-end encoding regions, this assumption has not been confirmed experimentally. In a broad group of bacteria that belong to proteobacteria, this convergent gene arrangement is typical for functionally connected quorum sensing-related genes ' I' and ' R,' which encode synthases of autoinducers, such as N-acyl homoserine lactones and their sensors, respectively. In the present study on the example of overlapping quorum sensing-related genes of plant pathogenic bacterium Pectobacterium atrosepticum SCRI1043, expI, and expR, it was shown that the topology of these genes determines the regulation of their expression. [ABSTRACT FROM AUTHOR]

Low temperature, drought and salinity are major abiotic stresses that influence survival, productivity and geographical distribution of many important crops across the globe. The C-repeat/dehydration-responsive element binding transcription factors (CBF/DREB) are important proteins involved in response to abiotic stresses in plants. In this study, twenty-one CBF genes were identified in cotton ( Gossypium hirsutum) by bioinformatic approach. The twenty-one CBF genes (named as GhCBF1 - GhCBF21) were characterized to encode proteins that share high similarity with those plant cold stress-related CBF proteins, which contain the classic AP2 domain of 58 amino acid residues. Phylogenetic analysis revealed that the isolated cotton CBF genes can be classified into 4 groups: GhCBF I, GhCBF II, GhCBF III and GhCBF IV. RT-PCR analysis indicated that GhCBF genes were up-regulated in cotton plants under cold stress. Furthermore, four GhCBF genes were up-regulated in cotton under salinity and drought treatments. Our data provided valuable information for further exploring the roles of the CBF genes in cotton development and in response to cold stress. [ABSTRACT FROM AUTHOR]

Background: Net rates of biosynthesis and mineral deposition are needed to understand the physiology and molecular biology of growth and plant responses to environmental variation. Many popular models ignore cell expansion and displacement. In contrast, the continuity equation, used with empirical data on growth velocity and concentration, allows computation of biosynthesis and deposition rates in growing tissue. Scope: This article describes data and methods needed to calculate deposition rates and reviews some insights into environmental physiology and molecular biology. Conclusions: Growth zones actively and strongly deposit mineral elements, even though local concentrations may not be changing in time. Deposition rate profiles give important insight into the mechanism of plant responses to drought and salinity, and they clarify many aspects of nitrogen metabolism in roots and leaves. This approach is also essential to understand molecular regulation of growth. A pioneering study determined transcript densities and calculated rates of change in gene expression; this study revealed how Actin 11 is highly regulated by a balance of transcription and decay during growth of roots. New technologies ( in planta cytometry, coupled with powerful computational routines and real-time confocal microscopy) will allow determination of deposition rates in growing organs and advancement in understanding of gene regulation. [ABSTRACT FROM AUTHOR]

In Drosophila melanogaster differentiation of the male germ cells is accompanied by chromatin rearrangement and activation of the specific genes. These processes are regulated by few transcription factors that belong to two classes, can and aly that form distinct functional complexes. Mechanisms of action of aly and can class transcription factors on gene expression and chromatin state remain unclear. To investigate this question we have built the whole genome binding profile of transcription factor Comr belonging to aly class using the tissue-specific DamID method. Resulting data were correlated with gene expression in comr ( aly class) and can ( can class) mutant testes. It was shown that Comr is a direct activator for about 300 testis-specific genes. Furthermore a set of genes revealed decreased expression in comr mutants but did not bind Comr protein, suggesting the existence of secondary regulation. Indeed, among the Comr gene targets we found a gene coding an uncharacterized transcription factor that could be a secondary participant in the genetic pathway in spermatocytes. These date allowed us to advance a model of gene activation needed for male gametes differentiation in D. melanogaster. [ABSTRACT FROM AUTHOR]

The CBL-CIPK signaling pathway represents a central and critical signaling system involved in plant response to abiotic stress and hormone signaling. In this study, we focused on AtCIPK6 gene, which have been shown to be required for development and salt tolerance in Arabidopsis, but the transcriptional regulatory mechanism of AtCIPK6 gene and whether it plays a role in ABA signaling is still unknown. Here, we showed that in addition to its expression induced by salt and drought stress, the transcripts of AtCIPK6 gene were largely accumulated in abscisic acid treated seedling, compared to basal level expression. Moreover, promoter sequence analysis revealed that there are some elements involved in stress and hormone response detected in the promoter region of AtCIPK6. AtCIPK6p: GUS transgenic assays unraveled that AtCIPK6 promoter is salt/osmotic stress- and ABA-inducible. Overexpression of AtCIPK6 gene in Arabidopsis increased plant tolerance to salt stress, but sensitivity to ABA. Our results contribute to the understanding of transcriptional regulatory mechanism of AtCIPK6 gene and may also provide a good stress-inducible promoter candidate for transgenic engineering. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are low-molecular-weight defense polypeptides produced in all living organisms either constitutively or upon perception of signals from pathogenic microorganisms. They are important components of the immune system in both animals and plants. AMPs differ in structure and mode of action. Most of them belong to the cysteine-rich peptides; their molecules contain even numbers of cysteine residues involved in the formation of disulfide bonds, which stabilize the peptide structure. A number of families of plant AMPs have been isolated on the basis of amino acid sequence similarity and 3D structure. Plant AMP genes can be used in engineering of disease resistance in crops and development of novel antibiotics and antimycotics. We provide a concise review of properties and gene structures of major AMP families discovered by the authors in Triticum kiharae seeds, including glycine-rich peptides, defensins, hevein-like peptides, and the so-called 4-Cys peptides. [ABSTRACT FROM AUTHOR]