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Vakirlis N, Kupczok A. Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins. Genome Res 2024; 34:888-903. [PMID: 38977308 DOI: 10.1101/gr.278977.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024]
Abstract
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.
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Affiliation(s)
- Nikolaos Vakirlis
- Institute For Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming," Vari 166 72, Greece;
- Institute for General Microbiology, Kiel University, 24118 Kiel, Germany
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, 6700 PB Wageningen, The Netherlands
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2
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Lanza A, Kimura S, Hirono I, Yoshitake K, Kinoshita S, Asakawa S. Transcriptome analysis of Edwardsiella piscicida during intracellular infection reveals excludons are involved with the activation of a mitochondrion-like energy generation program. mBio 2024; 15:e0352623. [PMID: 38349189 PMCID: PMC10936155 DOI: 10.1128/mbio.03526-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 03/14/2024] Open
Abstract
Phylogenetic evidence suggests a shared ancestry between mitochondria and modern Proteobacteria, a phylum including several genera of intracellular pathogens. Studying these diverse pathogens, particularly during intracellular infection of their hosts, can reveal characteristics potentially representative of the mitochondrial-Proteobacterial ancestor by identifying traits shared with mitochondria. While transcriptomic approaches can provide global insights into intracellular acclimatization by pathogens, they are often limited by excess host RNAs in extracts. Here, we developed a method employing magnetic nanoparticles to enrich RNA from an intracellular Gammaproteobacterium, Edwardsiella piscicida, within zebrafish, Danio rerio, fin fibroblasts, enabling comprehensive exploration of the bacterial transcriptome. Our findings revealed that the intracellular E. piscicida transcriptome reflects a mitochondrion-like energy generation program characterized by the suppression of glycolysis and sugar transport, coupled with upregulation of the tricarboxylic acid (TCA) cycle and alternative import of simple organic acids that directly flux into TCA cycle intermediates or electron transport chain donors. Additionally, genes predicted to be members of excludons, loci of gene pairs antagonistically co-regulated by overlapping antisense transcription, are significantly enriched in the set of all genes with perturbed sense and antisense transcription, suggesting a general but important involvement of excludons with intracellular acclimatization. Notably, genes involved with the activation of the mitochondrion-like energy generation program, specifically with metabolite import and glycolysis, are also members of predicted excludons. Other intracellular Proteobacterial pathogens appear to employ a similar mitochondrion-like energy generation program, suggesting a potentially conserved mechanism for optimized energy acquisition from hosts centered around the TCA cycle.IMPORTANCEPhylogenetic evidence suggests that mitochondria and Proteobacteria, a phylum encompassing various intracellular pathogens, share a common ancestral lineage. In this study, we developed a novel method employing magnetic nanoparticles to explore the transcriptome of an aquatic Gammaproteobacterium, Edwardsiella piscicida, during intracellular infection of host cells. We show that the strategy E. piscicida uses to generate energy strikingly mirrors the function of mitochondria-energy generators devoid of glycolytic processes. Notably, several implicated genes are members of excludons-gene pairs antagonistically co-regulated by overlapping antisense transcription. Other intracellular Proteobacterial pathogens appear to adopt a similar mitochondrion-like energy generation program, indicating a possibly conserved strategy for optimized energy acquisition from hosts centered around the tricarboxylic acid cycle.
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Affiliation(s)
- Andre Lanza
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Satoshi Kimura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ikuo Hirono
- Department of Marine Biosciences, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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3
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Bhardwaj K, Kalita A, Verma N, Prakash A, Thakur R, Dutta D. Rho-dependent termination enables cellular pH homeostasis. J Bacteriol 2024; 206:e0035623. [PMID: 38169297 PMCID: PMC10810219 DOI: 10.1128/jb.00356-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
The termination factor Rho, an ATP-dependent RNA translocase, preempts pervasive transcription processes, thereby rendering genome integrity in bacteria. Here, we show that the loss of Rho function raised the intracellular pH to >8.0 in Escherichia coli. The loss of Rho function upregulates tryptophanase-A (TnaA), an enzyme that catabolizes tryptophan to produce indole, pyruvate, and ammonia. We demonstrate that the enhanced TnaA function had produced the conjugate base ammonia, raising the cellular pH in the Rho-dependent termination defective strains. On the other hand, the constitutively overexpressed Rho lowered the cellular pH to about 6.2, independent of cellular ammonia levels. Since Rho overexpression may increase termination activities, the decrease in cellular pH could result from an excess H+ ion production during ATP hydrolysis by overproduced Rho. Furthermore, we performed in vivo termination assays to show that the efficiency of Rho-dependent termination was increased at both acidic and basic pH ranges. Given that the Rho level remained unchanged, the alkaline pH increases the termination efficiency by stimulating Rho's catalytic activity. We conducted the Rho-mediated RNA release assay from a stalled elongation complex to show an efficient RNA release at alkaline pH, compared to the neutral or acidic pH, that supports our in vivo observation. Whereas acidic pH appeared to increase the termination function by elevating the cellular level of Rho. This study is the first to link Rho function to the cellular pH homeostasis in bacteria. IMPORTANCE The current study shows that the loss or gain of Rho-dependent termination alkalizes or acidifies the cytoplasm, respectively. In the case of loss of Rho function, the tryptophanase-A enzyme is upregulated, and degrades tryptophan, producing ammonia to alkalize cytoplasm. We hypothesize that Rho overproduction by deleting its autoregulatory DNA portion increases termination function, causing excessive ATP hydrolysis to produce H+ ions and cytoplasmic acidification. Therefore, this study is the first to unravel a relationship between Rho function and intrinsic cellular pH homeostasis. Furthermore, the Rho level increases in the absence of autoregulation, causing cytoplasmic acidification. As intracellular pH plays a critical role in enzyme function, such a connection between Rho function and alkalization will have far-reaching implications for bacterial physiology.
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Affiliation(s)
- Kanika Bhardwaj
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Arunima Kalita
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Neha Verma
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anand Prakash
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Ruchika Thakur
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Dipak Dutta
- CSIR Institute of Microbial Technology, Chandigarh, India
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4
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Grandchamp A, Czuppon P, Bornberg-Bauer E. Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster. Nucleic Acids Res 2024; 52:274-287. [PMID: 38000384 PMCID: PMC10783523 DOI: 10.1093/nar/gkad1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to as de novo transcripts. De novo transcripts have been shown to play a major role in genomic innovations. However, little is known about the rates at which de novo transcripts are gained and lost in individuals of the same species. Here, we address this gap and estimate the de novo transcript turnover rate with an evolutionary model. We use DNA long reads and RNA short reads from seven geographically remote samples of inbred individuals of Drosophila melanogaster to detect de novo transcripts that are gained on a short evolutionary time scale. Overall, each sampled individual contains around 2500 unspliced de novo transcripts, with most of them being sample specific. We estimate that around 0.15 transcripts are gained per year, and that each gained transcript is lost at a rate around 5× 10-5 per year. This high turnover of transcripts suggests frequent exploration of new genomic sequences within species. These rate estimates are essential to comprehend the process and timescale of de novo gene birth.
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Affiliation(s)
- Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Peter Czuppon
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
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5
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Hare PJ, Gonzalez JR, Quelle RM, Wu YI, Mok WWK. Metabolic and transcriptional activities underlie stationary-phase Pseudomonas aeruginosa sensitivity to Levofloxacin. Microbiol Spectr 2024; 12:e0356723. [PMID: 38078717 PMCID: PMC10896071 DOI: 10.1128/spectrum.03567-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The bacterial pathogen Pseudomonas aeruginosa is responsible for a variety of chronic human infections. Even in the absence of identifiable resistance mutations, this pathogen can tolerate lethal antibiotic doses through phenotypic strategies like biofilm formation and metabolic quiescence. In this study, we determined that P. aeruginosa maintains greater metabolic activity in the stationary phase compared to the model organism, Escherichia coli, which has traditionally been used to study fluoroquinolone antibiotic tolerance. We demonstrate that hallmarks of E. coli fluoroquinolone tolerance are not conserved in P. aeruginosa, including the timing of cell death and necessity of the SOS DNA damage response for survival. The heightened sensitivity of stationary-phase P. aeruginosa to fluoroquinolones is attributed to maintained transcriptional and reductase activity. Our data suggest that perturbations that suppress transcription and respiration in P. aeruginosa may actually protect the pathogen against this important class of antibiotics.
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Affiliation(s)
- Patricia J Hare
- Department of Molecular Biology & Biophysics, UConn Health , Farmington, Connecticut, USA
- School of Dental Medicine, UConn Health , Farmington, Connecticut, USA
| | - Juliet R Gonzalez
- Department of Molecular Biology & Biophysics, UConn Health , Farmington, Connecticut, USA
| | - Ryan M Quelle
- Department of Molecular Biology & Biophysics, UConn Health , Farmington, Connecticut, USA
| | - Yi I Wu
- Richard D. Berlin Center for Cell Analysis and Modeling, UConn Health , Farmington, Connecticut, USA
| | - Wendy W K Mok
- Department of Molecular Biology & Biophysics, UConn Health , Farmington, Connecticut, USA
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6
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Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods Mol Biol 2024; 2802:347-393. [PMID: 38819565 DOI: 10.1007/978-1-0716-3838-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Over the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large-scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible non-coding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of non-coding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Bioinformatics and Computational Biology research group, University of Vienna, Vienna, Austria
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
- Universidad National de Colombia, Bogotá, Colombia.
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.
- Santa Fe Institute, Santa Fe, NM, USA.
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7
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Agarwal R, T RR, Smith JC. Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. J Chem Inf Model 2023; 63:7444-7452. [PMID: 37972310 DOI: 10.1021/acs.jcim.3c01533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Structure-based virtual high-throughput screening is used in early-stage drug discovery. Over the years, docking protocols and scoring functions for protein-ligand complexes have evolved to improve the accuracy in the computation of binding strengths and poses. In the past decade, RNA has also emerged as a target class for new small-molecule drugs. However, most ligand docking programs have been validated and tested for proteins and not RNA. Here, we test the docking power (pose prediction accuracy) of three state-of-the-art docking protocols on 173 RNA-small molecule crystal structures. The programs are AutoDock4 (AD4) and AutoDock Vina (Vina), which were designed for protein targets, and rDock, which was designed for both protein and nucleic acid targets. AD4 performed relatively poorly. For RNA targets for which a crystal structure of a bound ligand used to limit the docking search space is available and for which the goal is to identify new molecules for the same pocket, rDock performs slightly better than Vina, with success rates of 48% and 63%, respectively. However, in the more common type of early-stage drug discovery setting, in which no structure of a ligand-target complex is known and for which a larger search space is defined, rDock performed similarly to Vina, with a low success rate of ∼27%. Vina was found to have bias for ligands with certain physicochemical properties, whereas rDock performs similarly for all ligand properties. Thus, for projects where no ligand-protein structure already exists, Vina and rDock are both applicable. However, the relatively poor performance of all methods relative to protein-target docking illustrates a need for further methods refinement.
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Affiliation(s)
- Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
| | - Rajitha Rajeshwar T
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
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8
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Liehrmann A, Delannoy E, Launay-Avon A, Gilbault E, Loudet O, Castandet B, Rigaill G. DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection. NAR Genom Bioinform 2023; 5:lqad098. [PMID: 37954572 PMCID: PMC10632193 DOI: 10.1093/nargab/lqad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along annotated patterns (such as genes). These annotations are typically incomplete, leading to errors in the differential expression analysis. To address this issue, we present DiffSegR - an R package that enables the discovery of transcriptome-wide expression differences between two biological conditions using RNA-Seq data. DiffSegR does not require prior annotation and uses a multiple changepoints detection algorithm to identify the boundaries of differentially expressed regions in the per-base log2 fold change. In a few minutes of computation, DiffSegR could rightfully predict the role of chloroplast ribonuclease Mini-III in rRNA maturation and chloroplast ribonuclease PNPase in (3'/5')-degradation of rRNA, mRNA and tRNA precursors as well as intron accumulation. We believe DiffSegR will benefit biologists working on transcriptomics as it allows access to information from a layer of the transcriptome overlooked by the classical differential expression analysis pipelines widely used today. DiffSegR is available at https://aliehrmann.github.io/DiffSegR/index.html.
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Affiliation(s)
- Arnaud Liehrmann
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry,91037, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
| | - Alexandra Launay-Avon
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
| | - Elodie Gilbault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Benoît Castandet
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Gif sur Yvette, 91190, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, CNRS, INRAE, Gif sur Yvette, 91190, France
- Laboratoire de Mathématiques et de Modélisation d’Evry (LaMME), Université d’Evry-Val-d’Essonne, UMR CNRS 8071, ENSIIE, USC INRAE, Evry,91037, France
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9
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Zehentner B, Scherer S, Neuhaus K. Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers. BMC Microbiol 2023; 23:243. [PMID: 37653502 PMCID: PMC10469882 DOI: 10.1186/s12866-023-02988-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.
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Affiliation(s)
- Barbara Zehentner
- Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
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10
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Li Y, Shi R, Yuan R, Jiang Y. Comprehensive transcriptional analysis of pig facial skin development. PeerJ 2023; 11:e15955. [PMID: 37663277 PMCID: PMC10470455 DOI: 10.7717/peerj.15955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Background Skin development is a complex process that is influenced by many factors. Pig skin is used as an ideal material for xenografts because it is more anatomically and physiologically similar to human skin. It has been shown that the skin development of different pig breeds is different, and some Chinese pig breeds have the characteristics of skin thickness and facial skin folds, but the specific regulatory mechanism of this skin development is not yet clear. Methods In this study, the facial skin of Chenghua sows in the four developmental stages of postnatal Day 3 (D3) , Day 90 (D90) , Day 180 (D180), and Year 3 (Y3) were used as experimental materials, and RNA sequencing (RNA-seq) analysis was used to explore the changes in RNA expression in skin development at the four developmental stages, determine the differentially expressed messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), and perform functional analysis of related genes by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results A pairwise comparison of the four developmental stages identified several differentially expressed genes (DEGs) and found that the number of differentially expressed RNAs (DE RNAs) increased with increasing developmental time intervals. Elastin (ELN) is an important component of the skin. Its content affects the relaxation of the epidermis and dermal connection, and its expression is continuously downregulated during the four developmental stages. The functions of DEGs at different developmental stages were examined by performing GO and KEGG analyses, and the GO terms and enrichment pathways of mRNAs, lncRNAs, miRNAs, and circRNAs highly overlapped, among which the PPAR signaling pathway, a classical pathway for skin development, was enriched by DEGs of D3 vs. D180, D90 vs. D180 and D180 vs. Y3. In addition, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA interaction networks and found genes that may be associated with skin development, but their interactions need further study. Conclusions We identified a number of genes associated with skin development, performed functional analyses on some important DEGs and constructed interaction networks that facilitate further studies of skin development.
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Affiliation(s)
- Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
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11
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Fitzgerald DM, Stringer AM, Smith C, Lapierre P, Wade JT. Genome-Wide Mapping of the Escherichia coli PhoB Regulon Reveals Many Transcriptionally Inert, Intragenic Binding Sites. mBio 2023; 14:e0253522. [PMID: 37067422 PMCID: PMC10294691 DOI: 10.1128/mbio.02535-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/23/2023] [Indexed: 04/18/2023] Open
Abstract
Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert and hence are tolerated as genomic "noise." IMPORTANCE Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the Escherichia coli genome, revealing that the majority of PhoB binding sites are within genes. We show that PhoB binding sites within genes are not associated with regulation of the overlapping genes. Indeed, our data suggest that bacteria tolerate the presence of large numbers of nonregulatory, intragenic binding sites for transcription factors and that these binding sites are not under selective pressure.
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Affiliation(s)
- Devon M. Fitzgerald
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Anne M. Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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12
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Hueso-Gil A, Calles B, de Lorenzo V. In Vivo Sampling of Intracellular Heterogeneity of Pseudomonas putida Enables Multiobjective Optimization of Genetic Devices. ACS Synth Biol 2023; 12:1667-1676. [PMID: 37196337 PMCID: PMC10278179 DOI: 10.1021/acssynbio.3c00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Indexed: 05/19/2023]
Abstract
The inner physicochemical heterogeneity of bacterial cells generates three-dimensional (3D)-dependent variations of resources for effective expression of given chromosomally located genes. This fact has been exploited for adjusting the most favorable parameters for implanting a complex device for optogenetic control of biofilm formation in the soil bacterium Pseudomonas putida. To this end, a DNA segment encoding a superactive variant of the Caulobacter crescendus diguanylate cyclase PleD expressed under the control of the cyanobacterial light-responsive CcaSR system was placed in a mini-Tn5 transposon vector and randomly inserted through the chromosome of wild-type and biofilm-deficient variants of P. putida lacking the wsp gene cluster. This operation delivered a collection of clones covering a whole range of biofilm-building capacities and dynamic ranges in response to green light. Since the phenotypic output of the device depends on a large number of parameters (multiple promoters, RNA stability, translational efficacy, metabolic precursors, protein folding, etc.), we argue that random chromosomal insertions enable sampling the intracellular milieu for an optimal set of resources that deliver a preset phenotypic specification. Results thus support the notion that the context dependency can be exploited as a tool for multiobjective optimization, rather than a foe to be suppressed in Synthetic Biology constructs.
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Affiliation(s)
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus
de Cantoblanco, Madrid 28049, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus
de Cantoblanco, Madrid 28049, Spain
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13
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Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Res 2023; 33:872-890. [PMID: 37442576 PMCID: PMC10519401 DOI: 10.1101/gr.277482.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Novel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related sister genomes. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating genomes. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few neORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore, transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate, are rapidly purged, but surviving neORFs spread neutrally through populations and within genomes.
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Affiliation(s)
- Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
| | - Lucas Kühl
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Marie Lebherz
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Kathrin Brüggemann
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Munich, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
- Max Planck Institute for Biology Tübingen, Department of Protein Evolution, 72076 Tübingen, Germany
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14
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Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E. RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Cell 2023; 186:2425-2437.e21. [PMID: 37196657 PMCID: PMC10515295 DOI: 10.1016/j.cell.2023.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023]
Abstract
Ribonuclease HII (RNaseHII) is the principal enzyme that removes misincorporated ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural, biochemical, and genetic evidence demonstrating that ribonucleotide excision repair (RER) is directly coupled to transcription. Affinity pull-downs and mass-spectrometry-assisted mapping of in cellulo inter-protein cross-linking reveal the majority of RNaseHII molecules interacting with RNA polymerase (RNAP) in E. coli. Cryoelectron microscopy structures of RNaseHII bound to RNAP during elongation, with and without the target rNMP substrate, show specific protein-protein interactions that define the transcription-coupled RER (TC-RER) complex in engaged and unengaged states. The weakening of RNAP-RNaseHII interactions compromises RER in vivo. The structure-functional data support a model where RNaseHII scans DNA in one dimension in search for rNMPs while "riding" the RNAP. We further demonstrate that TC-RER accounts for a significant fraction of repair events, thereby establishing RNAP as a surveillance "vehicle" for detecting the most frequently occurring replication errors.
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Affiliation(s)
- Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sergey Proshkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA.
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15
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Middlemiss AD, Warman EA, Forrest D, Haycocks JRJ, Grainger DC. An unexpected abundance of bidirectional promoters within Salmonella Typhimurium plasmids. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001339. [PMID: 37204130 PMCID: PMC10268837 DOI: 10.1099/mic.0.001339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
Transcription of the DNA template, to generate an RNA message, is the first step in gene expression. The process initiates at DNA sequences called promoters. Conventionally, promoters have been considered to drive transcription in a specific direction. However, in recent work, we showed that many prokaryotic promoters can drive divergent transcription. This is a consequence of key DNA sequences for transcription initiation being inherently symmetrical. Here, we used global transcription start site mapping to determine the prevalence of such bidirectional promoters in Salmonella Typhimurium. Surprisingly, bidirectional promoters occur three times more frequently in plasmid components of the genome compared to chromosomal DNA. Implications for the evolution of promoter sequences are discussed.
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Affiliation(s)
| | - Emily A. Warman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - James R. J. Haycocks
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David C. Grainger
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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16
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Mohamadzadeh O, Hajinouri M, Moammer F, Tamehri Zadeh SS, Omid Shafiei G, Jafari A, Ostadian A, Talaei Zavareh SA, Hamblin MR, Yazdi AJ, Sheida A, Mirzaei H. Non-coding RNAs and Exosomal Non-coding RNAs in Traumatic Brain Injury: the Small Player with Big Actions. Mol Neurobiol 2023; 60:4064-4083. [PMID: 37020123 DOI: 10.1007/s12035-023-03321-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023]
Abstract
Nowadays, there is an increasing concern regarding traumatic brain injury (TBI) worldwide since substantial morbidity is observed after it, and the long-term consequences that are not yet fully recognized. A number of cellular pathways related to the secondary injury in brain have been identified, including free radical production (owing to mitochondrial dysfunction), excitotoxicity (regulated by excitatory neurotransmitters), apoptosis, and neuroinflammatory responses (as a result of activation of the immune system and central nervous system). In this context, non-coding RNAs (ncRNAs) maintain a fundamental contribution to post-transcriptional regulation. It has been shown that mammalian brains express high levels of ncRNAs that are involved in several brain physiological processes. Furthermore, altered levels of ncRNA expression have been found in those with traumatic as well non-traumatic brain injuries. The current review highlights the primary molecular mechanisms participated in TBI that describes the latest and novel results about changes and role of ncRNAs in TBI in both clinical and experimental research.
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Affiliation(s)
- Omid Mohamadzadeh
- Department of Neurological Surgery, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsasadat Hajinouri
- Department of Psychiatry, Roozbeh Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Moammer
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | | | | | - Ameneh Jafari
- Advanced Therapy Medicinal Product (ATMP) Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirreza Ostadian
- Department of Laboratory Medicine, School of Allied Medical Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
| | | | - Amirhossein Sheida
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
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17
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Stiens J, Tan YY, Joyce R, Arnvig KB, Kendall SL, Nobeli I. Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data. Mol Microbiol 2023; 119:381-400. [PMID: 36924313 DOI: 10.1111/mmi.15055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
A whole genome co-expression network was created using Mycobacterium tuberculosis transcriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the 'hub' elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This data set provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation.
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Affiliation(s)
- Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Yen Yi Tan
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Rosanna Joyce
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Kristine B Arnvig
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sharon L Kendall
- Royal Veterinary College, Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Hatfield, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
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18
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Fitzgerald D, Stringer A, Smith C, Lapierre P, Wade JT. Genome-wide mapping of the Escherichia coli PhoB regulon reveals many transcriptionally inert, intragenic binding sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527549. [PMID: 36798257 PMCID: PMC9934606 DOI: 10.1101/2023.02.07.527549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert, and hence are tolerated as genomic "noise". IMPORTANCE Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the Escherichia coli genome, revealing that the majority of PhoB binding sites are within genes. We show that PhoB binding sites within genes are not associated with regulation of the overlapping genes. Indeed, our data suggest that bacteria tolerate the presence of large numbers of non-regulatory, intragenic binding sites for transcription factors, and that these binding sites are not under selective pressure.
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Affiliation(s)
- Devon Fitzgerald
- Wadsworth Center, New York State Department of Health, Albany, New York, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Anne Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA.,Corresponding author:
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19
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Yu J, Jiang W, Zhu SB, Liao Z, Dou X, Liu J, Guo FB, Dong C. Prediction of protein-coding small ORFs in multi-species using integrated sequence-derived features and the random forest model. Methods 2023; 210:10-19. [PMID: 36621557 DOI: 10.1016/j.ymeth.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023] Open
Abstract
Proteins encoded by small open reading frames (sORFs) can serve as functional elements playing important roles in vivo. Such sORFs also constitute the potential pool for facilitating the de novo gene birth, driving evolutionary innovation and species diversity. Therefore, their theoretical and experimental identification has become a critical issue. Herein, we proposed a protein-coding sORFs prediction method merely based on integrative sequence-derived features. Our prediction performance is better or comparable compared with other nine prevalent methods, which shows that our method can provide a relatively reliable research tool for the prediction of protein-coding sORFs. Our method allows users to estimate the potential expression of a queried sORF, which has been demonstrated by the correlation analysis between our possibility estimation and codon adaption index (CAI). Based on the features that we used, we demonstrated that the sequence features of the protein-coding sORFs in the two domains have significant differences implying that it might be a relatively hard task in terms of cross-domain prediction, hence domain-specific models were developed, which allowed users to predict protein-coding sORFs both in eukaryotes and prokaryotes. Finally, a web-server was developed and provided to boost and facilitate the study of the related field, which is freely available at http://guolab.whu.edu.cn/codingCapacity/index.html.
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Affiliation(s)
- Jiafeng Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Wenwen Jiang
- Department of Bioinformatics, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Sen-Bin Zhu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Zhen Liao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xianghua Dou
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Feng-Biao Guo
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Chuan Dong
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
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20
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Gómez-Liñán C, Gómez-Díaz E, Ceballos-Pérez G, Fernández-Moya S, Estévez AM. The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes. Nucleic Acids Res 2022; 50:12251-12265. [PMID: 36454008 PMCID: PMC9757043 DOI: 10.1093/nar/gkac1123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
In-depth analysis of the transcriptomes of several model organisms has revealed that genomes are pervasively transcribed, giving rise to an abundance of non-canonical and mainly antisense RNA polymerase II-derived transcripts that are produced from almost any genomic context. Pervasive RNAs are degraded by surveillance mechanisms, but the repertoire of proteins that control the fate of these non-productive transcripts is still incomplete. Trypanosomes are single-celled eukaryotes that show constitutive RNA polymerase II transcription and in which initiation and termination of transcription occur at a limited number of sites per chromosome. It is not known whether pervasive transcription exists in organisms with unregulated RNA polymerase II activity, and which factors could be involved in the process. We show here that depletion of RBP33 results in overexpression of ∼40% of all annotated genes in the genome, with a marked accumulation of sense and antisense transcripts derived from silenced regions. RBP33 loss does not result in a significant increase in chromatin accessibility. Finally, we have found that transcripts that increase in abundance upon RBP33 knockdown are significantly more stable in RBP33-depleted trypanosomes, and that the exosome complex is responsible for their degradation. Our results provide strong evidence that RBP33 dampens non-productive transcription in trypanosomes.
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Affiliation(s)
- Claudia Gómez-Liñán
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Gloria Ceballos-Pérez
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Sandra M Fernández-Moya
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Antonio M Estévez
- To whom correspondence should be addressed. Tel: +34 958 181652; Fax: +34 958 181632;
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21
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Portela R, A. Faria N, Mwangi M, Miragaia M, de Lencastre H, Tomasz A, Gonçalves Sobral R. Analysis of a Cell Wall Mutant Highlights Rho-Dependent Genome Amplification Events in Staphylococcus aureus. Microbiol Spectr 2022; 10:e0248321. [PMID: 36094182 PMCID: PMC9603463 DOI: 10.1128/spectrum.02483-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/06/2022] [Indexed: 01/04/2023] Open
Abstract
In a study of antibiotic resistance in Staphylococcus aureus, specific cell wall mutants were previously generated for the peptidoglycan biosynthesis gene murF, by the insertion of an integrative plasmid. A collection of 30 independent mutants was obtained, and all harbored a variable number of copies of the inserted plasmid, arranged in tandem in the chromosome. Of the 30 mutants, only 3, F9, F20 and F26, with a lower number of plasmid copies, showed an altered peptidoglycan structure, lower resistance to β-lactams and a different loss-of-function mutation in rho gene, that encodes a transcription termination factor. The rho mutations were found to correlate with the level of oxacillin resistance, since genetic complementation with rho gene reestablished the resistance and cell wall parental profile in F9, F20 and F26 strains. Furthermore, complementation with rho resulted in the amplification of the number of plasmid tandem repeats, suggesting that Rho enabled events of recombination that favored a rearrangement in the chromosome in the region of the impaired murF gene. Although the full mechanism of reversion of the cell wall damage was not fully elucidated, we showed that Rho is involved in the recombination process that mediates the tandem amplification of exogeneous DNA fragments inserted into the chromosome. IMPORTANCE The cell wall of bacteria, namely, peptidoglycan, is the target of several antibiotic classes such as β-lactams. Staphylococcus aureus is well known for its capacity to adapt to antibiotic stress and develop resistance strategies, namely, to β-lactams. In this context, the construction of cell wall mutants provides useful models to study the development of such resistance mechanisms. Here, we characterized a collection of independent mutants, impaired in the same peptidoglycan biosynthetic step, obtained through the insertion of a plasmid in the coding region of murF gene. S. aureus demonstrated the capacity to overcome the cell wall damage by amplifying the copy number of the inserted plasmid, through an undescribed mechanism that involves the Rho transcription termination factor.
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Affiliation(s)
- Raquel Portela
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Laboratory of Molecular Microbiology of Bacterial Pathogens, UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Nuno A. Faria
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Michael Mwangi
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, New York, USA
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Alexander Tomasz
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Rita Gonçalves Sobral
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Laboratory of Molecular Microbiology of Bacterial Pathogens, UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
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22
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Khemka N, Rajkumar MS, Garg R, Jain M. Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea. PLANTA 2022; 256:79. [PMID: 36094579 DOI: 10.1007/s00425-022-03986-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The integrated transcriptome data analyses suggested the plausible roles of lncRNAs during seed development in chickpea. The candidate lncRNAs associated with QTLs and those involved in miRNA-mediated seed size/weight determination in chickpea have been identified. Long non-coding RNAs (lncRNAs) are important regulators of various biological processes. Here, we identified lncRNAs at seven successive stages of seed development in small-seeded and large-seeded chickpea cultivars. In total, 4751 lncRNAs implicated in diverse biological processes were identified. Most of lncRNAs were conserved between the two cultivars, whereas only a few of them were conserved in other plants, suggesting their species-specificity. A large number of lncRNAs differentially expressed between the two chickpea cultivars associated with seed development-related processes were identified. The lncRNAs acting as precursors of miRNAs and those mimicking target protein-coding genes of miRNAs involved in seed size/weight determination, including HAIKU1, BIG SEEDS1, and SHB1, were also revealed. Further, lncRNAs located within seed size/weight associated quantitative trait loci were also detected. Overall, we present a comprehensive resource and identified candidate lncRNAs that may play important roles during seed development and seed size/weight determination in chickpea.
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Affiliation(s)
- Niraj Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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23
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Kushwaha SK, Narasimhan LP, Chithananthan C, Marathe SA. Clustered regularly interspaced short palindromic repeats-Cas system: diversity and regulation in Enterobacteriaceae. Future Microbiol 2022; 17:1249-1267. [PMID: 36006039 DOI: 10.2217/fmb-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Insights into the arms race between bacteria and invading mobile genetic elements have revealed the intricacies of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system and the counter-defenses of bacteriophages. Incredible spacer diversity but significant spacer conservation among species/subspecies dictates the specificity of the CRISPR-Cas system. Researchers have exploited this feature to type/subtype the bacterial strains, devise targeted antimicrobials and regulate gene expression. This review focuses on the nuances of the CRISPR-Cas systems in Enterobacteriaceae that predominantly harbor type I-E and I-F CRISPR systems. We discuss the systems' regulation by the global regulators, H-NS, LeuO, LRP, cAMP receptor protein and other regulators in response to environmental stress. We further discuss the regulation of noncanonical functions like DNA repair pathways, biofilm formation, quorum sensing and virulence by the CRISPR-Cas system. The review comprehends multiple facets of the CRISPR-Cas system in Enterobacteriaceae including its diverse attributes, association with genetic features, regulation and gene regulatory mechanisms.
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Affiliation(s)
- Simran K Kushwaha
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Lakshmi P Narasimhan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Chandrananthi Chithananthan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Sandhya A Marathe
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
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24
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Regulatory Interplay between RNase III and Antisense RNAs in E. coli: the Case of AsflhD and FlhD, Component of the Master Regulator of Motility. mBio 2022; 13:e0098122. [PMID: 36000733 PMCID: PMC9600491 DOI: 10.1128/mbio.00981-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to respond to ever-changing environmental cues, bacteria display resilient regulatory mechanisms controlling gene expression. At the post-transcriptional level, this is achieved by a combination of RNA-binding proteins, such as ribonucleases (RNases), and regulatory RNAs, including antisense RNAs (asRNAs). Bound to their complementary mRNA, asRNAs are primary targets for the double-strand-specific endoribonuclease, RNase III. Taking advantage of our own and previously published transcriptomic data sets obtained in strains inactivated for RNase III, we selected several candidate asRNAs and confirmed the existence of RNase III-sensitive asRNAs for crp, ompR, phoP, and flhD genes, all encoding global regulators of gene expression in Escherichia coli. Using FlhD, a component of the master regulator of motility (FlhD4C2), as our model, we demonstrate that the asRNA AsflhD, transcribed from the coding sequence of flhD, is involved in the fine-tuning of flhD expression and thus participates in the control of motility.
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25
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Pervasive transcription enhances the accessibility of H-NS-silenced promoters and generates bistability in Salmonella virulence gene expression. Proc Natl Acad Sci U S A 2022; 119:e2203011119. [PMID: 35858437 PMCID: PMC9335307 DOI: 10.1073/pnas.2203011119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In Escherichia coli and Salmonella, many genes silenced by the nucleoid structuring protein H-NS are activated upon inhibiting Rho-dependent transcription termination. This response is poorly understood and difficult to reconcile with the view that H-NS acts mainly by blocking transcription initiation. Here we have analyzed the basis for the up-regulation of H-NS-silenced Salmonella pathogenicity island 1 (SPI-1) in cells depleted of Rho-cofactor NusG. Evidence from genetic experiments, semiquantitative 5' rapid amplification of complementary DNA ends sequencing (5' RACE-Seq), and chromatin immunoprecipitation sequencing (ChIP-Seq) shows that transcription originating from spurious antisense promoters, when not stopped by Rho, elongates into a H-NS-bound regulatory region of SPI-1, displacing H-NS and rendering the DNA accessible to the master regulator HilD. In turn, HilD's ability to activate its own transcription triggers a positive feedback loop that results in transcriptional activation of the entire SPI-1. Significantly, single-cell analyses revealed that this mechanism is largely responsible for the coexistence of two subpopulations of cells that either express or do not express SPI-1 genes. We propose that cell-to-cell differences produced by stochastic spurious transcription, combined with feedback loops that perpetuate the activated state, can generate bimodal gene expression patterns in bacterial populations.
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26
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Fan X, Yang Y, Chen C, Wang Z. Pervasive translation of circular RNAs driven by short IRES-like elements. Nat Commun 2022; 13:3751. [PMID: 35768398 PMCID: PMC9242994 DOI: 10.1038/s41467-022-31327-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/09/2022] [Indexed: 12/30/2022] Open
Abstract
Some circular RNAs (circRNAs) were found to be translated through IRES-driven mechanism, however the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we develop a cell-based system to screen random sequences and identify 97 overrepresented hexamers that drive cap-independent circRNA translation. These IRES-like short elements are significantly enriched in endogenous circRNAs and sufficient to drive circRNA translation. We further identify multiple trans-acting factors that bind these IRES-like elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides are identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which are experimentally validated. Consistently, mutations of the IRES-like element in one circRNA reduce its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in translation control. Unbiased screen of random sequences identified many short IRES-like elements to drive circular RNA translation and hundreds of rolling circle translation events, suggesting a pervasive cap-independent translation in human transcriptome.
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Affiliation(s)
- Xiaojuan Fan
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yun Yang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,CirCode BioMedicine, Pudong, Shanghai, China
| | - Chuyun Chen
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China
| | - Zefeng Wang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China. .,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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27
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Tombácz D, Kakuk B, Torma G, Csabai Z, Gulyás G, Tamás V, Zádori Z, Jefferson VA, Meyer F, Boldogkői Z. In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing. Viruses 2022; 14:v14061289. [PMID: 35746760 PMCID: PMC9229804 DOI: 10.3390/v14061289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
In this work, a long-read sequencing (LRS) technique based on the Oxford Nanopore Technology MinION platform was used for quantifying and kinetic characterization of the poly(A) fraction of bovine alphaherpesvirus type 1 (BoHV-1) lytic transcriptome across a 12-h infection period. Amplification-based LRS techniques frequently generate artefactual transcription reads and are biased towards the production of shorter amplicons. To avoid these undesired effects, we applied direct cDNA sequencing, an amplification-free technique. Here, we show that a single promoter can produce multiple transcription start sites whose distribution patterns differ among the viral genes but are similar in the same gene at different timepoints. Our investigations revealed that the circ gene is expressed with immediate–early (IE) kinetics by utilizing a special mechanism based on the use of the promoter of another IE gene (bicp4) for the transcriptional control. Furthermore, we detected an overlap between the initiation of DNA replication and the transcription from the bicp22 gene, which suggests an interaction between the two molecular machineries. This study developed a generally applicable LRS-based method for the time-course characterization of transcriptomes of any organism.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
| | - Vivien Tamás
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary; (V.T.); (Z.Z.)
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, 1143 Budapest, Hungary; (V.T.); (Z.Z.)
| | - Victoria A. Jefferson
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (F.M.)
| | - Florencia Meyer
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, 408 Dorman P.O. Box 9655, 32 Creelman St., Starkville, MS 39762, USA; (V.A.J.); (F.M.)
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, 6720 Szeged, Hungary; (D.T.); (B.K.); (G.T.); (Z.C.); (G.G.)
- Correspondence:
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28
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Łabędzka-Dmoch K, Rażew M, Gapińska M, Piątkowski J, Kolondra A, Salmonowicz H, Wenda JM, Nowotny M, Golik P. The Pet127 protein is a mitochondrial 5'-to-3' exoribonuclease from the PD-(D/E)XK superfamily involved in RNA maturation and intron degradation in yeasts. RNA (NEW YORK, N.Y.) 2022; 28:711-728. [PMID: 35197365 PMCID: PMC9014873 DOI: 10.1261/rna.079083.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/31/2022] [Indexed: 06/01/2023]
Abstract
Pet127 is a mitochondrial protein found in multiple eukaryotic lineages, but absent from several taxa, including plants and animals. Distant homology suggests that it belongs to the divergent PD-(D/E)XK superfamily which includes various nucleases and related proteins. Earlier yeast genetics experiments suggest that it plays a nonessential role in RNA degradation and 5' end processing. Our phylogenetic analysis suggests that it is a primordial eukaryotic invention that was retained in diverse groups, and independently lost several times in the evolution of other organisms. We demonstrate for the first time that the fungal Pet127 protein in vitro is a processive 5'-to-3' exoribonuclease capable of digesting various substrates in a sequence nonspecific manner. Mutations in conserved residues essential in the PD-(D/E)XK superfamily active site abolish the activity of Pet127. Deletion of the PET127 gene in the pathogenic yeast Candida albicans results in a moderate increase in the steady-state levels of several transcripts and in accumulation of unspliced precursors and intronic sequences of three introns. Mutations in the active site residues result in a phenotype identical to that of the deletant, confirming that the exoribonuclease activity is related to the physiological role of the Pet127 protein. Pet127 activity is, however, not essential for maintaining the mitochondrial respiratory activity in C. albicans.
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Affiliation(s)
- Karolina Łabędzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Michal Rażew
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Marta Gapińska
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Jakub Piątkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Hanna Salmonowicz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
- Laboratory of Metabolic Quality Control, IMOL, Polish Academy of Sciences, Warsaw 00-783, Poland
| | - Joanna M Wenda
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Paweł Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw 02-106, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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29
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Bharati BK, Gowder M, Zheng F, Alzoubi K, Svetlov V, Kamarthapu V, Weaver JW, Epshtein V, Vasilyev N, Shen L, Zhang Y, Nudler E. Crucial role and mechanism of transcription-coupled DNA repair in bacteria. Nature 2022; 604:152-159. [PMID: 35355008 PMCID: PMC9370829 DOI: 10.1038/s41586-022-04530-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 02/07/2022] [Indexed: 01/11/2023]
Abstract
Transcription-coupled DNA repair (TCR) is presumed to be a minor sub-pathway of nucleotide excision repair (NER) in bacteria. Global genomic repair is thought to perform the bulk of repair independently of transcription. TCR is also believed to be mediated exclusively by Mfd-a DNA translocase of a marginal NER phenotype1-3. Here we combined in cellulo cross-linking mass spectrometry with structural, biochemical and genetic approaches to map the interactions within the TCR complex (TCRC) and to determine the actual sequence of events that leads to NER in vivo. We show that RNA polymerase (RNAP) serves as the primary sensor of DNA damage and acts as a platform for the recruitment of NER enzymes. UvrA and UvrD associate with RNAP continuously, forming a surveillance pre-TCRC. In response to DNA damage, pre-TCRC recruits a second UvrD monomer to form a helicase-competent UvrD dimer that promotes backtracking of the TCRC. The weakening of UvrD-RNAP interactions renders cells sensitive to genotoxic stress. TCRC then recruits a second UvrA molecule and UvrB to initiate the repair process. Contrary to the conventional view, we show that TCR accounts for the vast majority of chromosomal repair events; that is, TCR thoroughly dominates over global genomic repair. We also show that TCR is largely independent of Mfd. We propose that Mfd has an indirect role in this process: it participates in removing obstructive RNAPs in front of TCRCs and also in recovering TCRCs from backtracking after repair has been completed.
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Affiliation(s)
- Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Fangfang Zheng
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Khaled Alzoubi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Venu Kamarthapu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Jacob W Weaver
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Liqiang Shen
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA. .,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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30
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Martinez B, Bharati BK, Epshtein V, Nudler E. Pervasive Transcription-coupled DNA repair in E. coli. Nat Commun 2022; 13:1702. [PMID: 35354807 PMCID: PMC8967931 DOI: 10.1038/s41467-022-28871-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Global Genomic Repair (GGR) and Transcription-Coupled Repair (TCR) have been viewed, respectively, as major and minor sub-pathways of the nucleotide excision repair (NER) process that removes bulky lesions from the genome. Here we applied a next generation sequencing assay, CPD-seq, in E. coli to measure the levels of cyclobutane pyrimidine dimer (CPD) lesions before, during, and after UV-induced genotoxic stress, and, therefore, to determine the rate of genomic recovery by NER at a single nucleotide resolution. We find that active transcription is necessary for the repair of not only the template strand (TS), but also the non-template strand (NTS), and that the bulk of TCR is independent of Mfd – a DNA translocase that is thought to be necessary and sufficient for TCR in bacteria. We further show that repair of both TS and NTS is enhanced by increased readthrough past Rho-dependent terminators. We demonstrate that UV-induced genotoxic stress promotes global antitermination so that TCR is more accessible to the antisense, intergenic, and other low transcribed regions. Overall, our data suggest that GGR and TCR are essentially the same process required for complete repair of the bacterial genome. Transcription-Coupled DNA repair has been classically defined as the preferential repair of the template strand (TS) over the non-template strand (NTS). Here the authors challenge this classic model of TCR by using a genome-wide repair assay, CPD-seq, as well as RNA-seq, to show that TCR occurs across the entire E. coli genome – including NTS and intergenic regions.
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Affiliation(s)
- Britney Martinez
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA.,Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA. .,Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, New York, 10016, USA.
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31
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Smith C, Canestrari JG, Wang AJ, Champion MM, Derbyshire KM, Gray TA, Wade JT. Pervasive translation in Mycobacterium tuberculosis. eLife 2022; 11:e73980. [PMID: 35343439 PMCID: PMC9094748 DOI: 10.7554/elife.73980] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Most bacterial ORFs are identified by automated prediction algorithms. However, these algorithms often fail to identify ORFs lacking canonical features such as a length of >50 codons or the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. The newly described ORFs are predominantly short, with many encoding proteins of ≤50 amino acids. Codon usage of the newly discovered ORFs suggests that most have not been subject to purifying selection, and hence are unlikely to contribute to cell fitness. Nevertheless, we identify 90 new ORFs (median length of 52 codons) that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs in Mycobacterium tuberculosis serves as a rich source for the evolution of new functional proteins.
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Affiliation(s)
- Carol Smith
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Jill G Canestrari
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Archer J Wang
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre DameNotre DameUnited States
| | - Keith M Derbyshire
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
| | - Todd A Gray
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
| | - Joseph T Wade
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
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32
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Miguel-Arribas A, Wu LJ, Michaelis C, Yoshida KI, Grohmann E, Meijer WJJ. Conjugation Operons in Gram-Positive Bacteria with and without Antitermination Systems. Microorganisms 2022; 10:microorganisms10030587. [PMID: 35336162 PMCID: PMC8955417 DOI: 10.3390/microorganisms10030587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
Genes involved in the same cellular process are often clustered together in an operon whose expression is controlled by an upstream promoter. Generally, the activity of the promoter is strictly controlled. However, spurious transcription undermines this strict regulation, particularly affecting large operons. The negative effects of spurious transcription can be mitigated by the presence of multiple terminators inside the operon, in combination with an antitermination system. Antitermination systems modify the transcription elongation complexes and enable them to bypass terminators. Bacterial conjugation is the process by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugation involves many genes that are mostly organized in one or a few large operons. It has recently been shown that many conjugation operons present on plasmids replicating in Gram-positive bacteria possess a bipartite antitermination system that allows not only many terminators inside the conjugation operon to be bypassed, but also the differential expression of a subset of genes. Here, we show that some conjugation operons on plasmids belonging to the Inc18 family of Gram-positive broad host-range plasmids do not possess an antitermination system, suggesting that the absence of an antitermination system may have advantages. The possible (dis)advantages of conjugation operons possessing (or not) an antitermination system are discussed.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Medical Faculty, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK;
| | - Claudia Michaelis
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
| | - Elisabeth Grohmann
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
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33
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Pinatel E, Calcagnile M, Talà A, Damiano F, Siculella L, Peano C, De Benedetto GE, Pennetta A, De Bellis G, Alifano P. Interplay between non-coding RNA transcription, stringent phenotype and antibiotic production in Streptomyces. J Biotechnol 2022:S0168-1656(22)00029-3. [PMID: 35182607 DOI: 10.1016/j.jbiotec.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
While in recent years the key role of non-coding RNAs (ncRNAs) in regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces, and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: i.) the wild type strain; ii.) an isogenic pirA-defective mutant with central carbon metabolism imbalance, "relaxed" phenotype, and repression of antibiotic production; iii.) a pirA-derivative strain harboring a "stringent" RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.
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Affiliation(s)
- Eva Pinatel
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Luisa Siculella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Clelia Peano
- Genomic Unit, IRCCS Humanitas Clinical and Research Center, Rozzano, Milan, Italy; Institute of Genetic and Biomedical Research, UoS of Milan, National Research Council, Rozzano, Milan, Italy
| | | | - Antonio Pennetta
- Department of Cultural Heritage, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy.
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34
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Choi G, Jeon J, Lee H, Zhou S, Lee YH. Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection. BMC Genomics 2022; 23:132. [PMID: 35168559 PMCID: PMC8845233 DOI: 10.1186/s12864-022-08380-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/09/2022] [Indexed: 12/05/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play essential roles in developmental processes and disease development at the transcriptional and post-transcriptional levels across diverse taxa. However, only few studies have profiled fungal lncRNAs in a genome-wide manner during host infection. Results Infection-associated lncRNAs were identified using lncRNA profiling over six stages of host infection (e.g., vegetative growth, pre-penetration, biotrophic, and necrotrophic stages) in the model pathogenic fungus, Magnaporthe oryzae. We identified 2,601 novel lncRNAs, including 1,286 antisense lncRNAs and 980 intergenic lncRNAs. Among the identified lncRNAs, 755 were expressed in a stage-specific manner and 560 were infection-specifically expressed lncRNAs (ISELs). To decipher the potential roles of lncRNAs during infection, we identified 365 protein-coding genes that were associated with 214 ISELs. Analysis of the predicted functions of these associated genes suggested that lncRNAs regulate pathogenesis-related genes, including xylanases and effectors. Conclusions The ISELs and their associated genes provide a comprehensive view of lncRNAs during fungal pathogen-plant interactions. This study expands new insights into the role of lncRNAs in the rice blast fungus, as well as other plant pathogenic fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08380-4.
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Affiliation(s)
- Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea.,Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hyunjun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Shenxian Zhou
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea. .,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea. .,Center for Plant Microbiome Research, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
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35
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Lato DF, Zeng Q, Golding GB. Genomic inversions in Escherichia coli alter gene expression and are associated with nucleoid protein binding sites. Genome 2022; 65:287-299. [DOI: 10.1139/gen-2021-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomic reorganization, like rearrangements and inversions, influence how genetic information is organized within bacterial genomes. Inversions in particular, facilitate genome evolution through gene gain and loss, and can alter gene expression. Previous studies investigating the impact inversions have on gene expression induced inversions targeting specific genes or examine inversions between distantly related species. This fails to encompass a genome wide perspective on naturally occurring inversions and their post adaptation impact on gene expression. Here we use bioinformatic techniques and multiple RNA-seq datasets to investigate the short- and long-range impact inversions have on genomic gene expression within <i>Escherichia coli</i>. We observed differences in gene expression between homologous inverted and non-inverted genes, even after long term exposure to adaptive selection. In 4% of inversions representing 33 genes, differential gene expression between inverted and non-inverted homologs was detected, with nearly two thirds (71%) of differentially expressed inverted genes having 9.4-85.6 fold higher gene expression. The identified inversions had more overlap than expected with nucleoid associated protein binding sites, which assist in genomic gene expression regulation. Some inversions can drastically impact gene expression even between different strains of <i>E.coli</i>, and could provide a mechanism for the diversification of genetic content through controlled expression changes.
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Affiliation(s)
| | - Qing Zeng
- McMaster University, Department of Biology, Hamilton, Ontario, Canada,
| | - G. Brian Golding
- McMaster University, Department of Biology, 1280 Main Street West, Hamilton, Ontario, Canada, L8S 4K1,
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36
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Regulation of Heterogenous LexA Expression in Staphylococcus aureus by an Antisense RNA Originating from Transcriptional Read-Through upon Natural Mispairings in the sbrB Intrinsic Terminator. Int J Mol Sci 2022; 23:ijms23010576. [PMID: 35009002 PMCID: PMC8745188 DOI: 10.3390/ijms23010576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial genomes are pervasively transcribed, generating a wide variety of antisense RNAs (asRNAs). Many of them originate from transcriptional read-through events (TREs) during the transcription termination process. Previous transcriptome analyses revealed that the lexA gene from Staphylococcus aureus, which encodes the main SOS response regulator, is affected by the presence of an asRNA. Here, we show that the lexA antisense RNA (lexA-asRNA) is generated by a TRE on the intrinsic terminator (TTsbrB) of the sbrB gene, which is located downstream of lexA, in the opposite strand. Transcriptional read-through occurs by a natural mutation that destabilizes the TTsbrB structure and modifies the efficiency of the intrinsic terminator. Restoring the mispairing mutation in the hairpin of TTsbrB prevented lexA-asRNA transcription. The level of lexA-asRNA directly correlated with cellular stress since the expressions of sbrB and lexA-asRNA depend on the stress transcription factor SigB. Comparative analyses revealed strain-specific nucleotide polymorphisms within TTsbrB, suggesting that this TT could be prone to accumulating natural mutations. A genome-wide analysis of TREs suggested that mispairings in TT hairpins might provide wider transcriptional connections with downstream genes and, ultimately, transcriptomic variability among S. aureus strains.
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37
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Zardoni L, Nardini E, Brambati A, Lucca C, Choudhary R, Loperfido F, Sabbioneda S, Liberi G. Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions. Nucleic Acids Res 2021; 49:12769-12784. [PMID: 34878142 PMCID: PMC8682787 DOI: 10.1093/nar/gkab1146] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Uncoordinated clashes between replication forks and transcription cause replication stress and genome instability, which are hallmarks of cancer and neurodegeneration. Here, we investigate the outcomes of head-on replication-transcription collisions, using as a model system budding yeast mutants for the helicase Sen1, the ortholog of human Senataxin. We found that RNA Polymerase II accumulates together with RNA:DNA hybrids at sites of head-on collisions. The replication fork and RNA Polymerase II are both arrested during the clash, leading to DNA damage and, in the long run, the inhibition of gene expression. The inactivation of RNA Polymerase II elongation factors, such as the HMG-like protein Spt2 and the DISF and PAF complexes, but not alterations in chromatin structure, allows replication fork progression through transcribed regions. Attenuation of RNA Polymerase II elongation rescues RNA:DNA hybrid accumulation and DNA damage sensitivity caused by the absence of Sen1, but not of RNase H proteins, suggesting that such enzymes counteract toxic RNA:DNA hybrids at different stages of the cell cycle with Sen1 mainly acting in replication. We suggest that the main obstacle to replication fork progression is the elongating RNA Polymerase II engaged in an R-loop, rather than RNA:DNA hybrids per se or hybrid-associated chromatin modifications.
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Affiliation(s)
- Luca Zardoni
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,Scuola Universitaria Superiore IUSS, 27100 Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Alessandra Brambati
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | | | | | - Federica Loperfido
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,IFOM Foundation, 20139 Milan, Italy
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Evguenieva-Hackenberg E. Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1696. [PMID: 34651439 DOI: 10.1002/wrna.1696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022]
Abstract
Gene expression strategies ensuring bacterial survival and competitiveness rely on cis- and trans-acting RNA-regulators (riboregulators). Among the cis-acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans-acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome-dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans-acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA-containing, antibiotic-dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA-based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, Ziganshin R, Kovalchuk S, Kharlampieva D, Lazarev V, Taliansky M, Koonin EV. A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic Acids Res 2021; 49:10328-10346. [PMID: 34570232 DOI: 10.1093/nar/gkab816] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/17/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Pervasive transcription of eukaryotic genomes results in expression of long non-coding RNAs (lncRNAs) most of which are poorly conserved in evolution and appear to be non-functional. However, some lncRNAs have been shown to perform specific functions, in particular, transcription regulation. Thousands of small open reading frames (smORFs, <100 codons) located on lncRNAs potentially might be translated into peptides or microproteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of lncRNAs-smORFs from the moss Physcomitrium patens across transcriptomes of 479 plant species. Although thousands of smORFs are subject to substantial purifying selection, the majority of the smORFs appear to be evolutionary young and could represent a major pool for functional innovation. Using nanopore RNA sequencing, we show that, on average, the transcriptional level of conserved smORFs is higher than that of non-conserved smORFs. Proteomic analysis confirmed translation of 82 novel species-specific smORFs. Numerous conserved smORFs containing low complexity regions (LCRs) or transmembrane domains were identified, the biological functions of a selected LCR-smORF were demonstrated experimentally. Thus, microproteins encoded by smORFs are a major, functionally diverse component of the plant proteome.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Andrey Knyazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Anna Glushkevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Rustam Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergey Kovalchuk
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Daria Kharlampieva
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation
| | - Vassili Lazarev
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region, 141701, Russian Federation
| | - Michael Taliansky
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation.,The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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40
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Ling X, Lu J, Yang J, Qin H, Zhao X, Zhou P, Zheng S, Zhu P. Non-Coding RNAs: Emerging Therapeutic Targets in Spinal Cord Ischemia-Reperfusion Injury. Front Neurol 2021; 12:680210. [PMID: 34566835 PMCID: PMC8456115 DOI: 10.3389/fneur.2021.680210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/09/2021] [Indexed: 01/01/2023] Open
Abstract
Paralysis or paraplegia caused by transient or permanent spinal cord ischemia–reperfusion injury (SCIRI) remains one of the most devastating post-operative complications after thoracoabdominal aortic surgery, even though perioperative strategies and surgical techniques continue to improve. Uncovering the molecular and cellular pathophysiological processes in SCIRI has become a top priority. Recently, the expression, function, and mechanism of non-coding RNAs (ncRNAs) in various diseases have drawn wide attention. Non-coding RNAs contain a variety of biological functions but do not code for proteins. Previous studies have shown that ncRNAs play a critical role in SCIRI. However, the character of ncRNAs in attenuating SCIRI has not been systematically summarized. This review article will be the first time to assemble the knowledge of ncRNAs regulating apoptosis, inflammation, autophagy, and oxidative stress to attenuate SCIRI. A better understanding of the functional significance of ncRNAs following SCIRI could help us to identify novel therapeutic targets and develop potential therapeutic strategies. All the current research about the function of nRNAs in SCIRI will be summarized one by one in this review.
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Affiliation(s)
- Xiao Ling
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jun Lu
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jun Yang
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hanjun Qin
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xingqi Zhao
- Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Pengyu Zhou
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shaoyi Zheng
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Zhu
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Lioy VS, Lorenzi JN, Najah S, Poinsignon T, Leh H, Saulnier C, Aigle B, Lautru S, Thibessard A, Lespinet O, Leblond P, Jaszczyszyn Y, Gorrichon K, Varoquaux N, Junier I, Boccard F, Pernodet JL, Bury-Moné S. Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation. Nat Commun 2021; 12:5221. [PMID: 34471117 PMCID: PMC8410849 DOI: 10.1038/s41467-021-25462-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria of the genus Streptomyces are prolific producers of specialized metabolites, including antibiotics. The linear chromosome includes a central region harboring core genes, as well as extremities enriched in specialized metabolite biosynthetic gene clusters. Here, we show that chromosome structure in Streptomyces ambofaciens correlates with genetic compartmentalization during exponential phase. Conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends tend to be transcriptionally quiescent compartments with different structural features. The onset of metabolic differentiation is accompanied by a rearrangement of chromosome architecture, from a rather 'open' to a 'closed' conformation, in which highly expressed specialized metabolite biosynthetic genes form new boundaries. Thus, our results indicate that the linear chromosome of S. ambofaciens is partitioned into structurally distinct entities, suggesting a link between chromosome folding, gene expression and genome evolution.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Jean-Noël Lorenzi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Soumaya Najah
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Thibault Poinsignon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Hervé Leh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Corinne Saulnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Sylvie Lautru
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Olivier Lespinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Kevin Gorrichon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nelle Varoquaux
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Ivan Junier
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean-Luc Pernodet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphanie Bury-Moné
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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Peng Peng, Yu H, Yongjin Li, Huang J, Yao S, Xing C, Liu W, Zhang B, Feng S. The emerging role of circular RNAs in spinal cord injury. J Orthop Translat 2021; 30:1-5. [PMID: 34401327 PMCID: PMC8326601 DOI: 10.1016/j.jot.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/02/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023] Open
Abstract
Spinal cord injury (SCI) is one kind of severe diseases with high mortality and morbidity worldwide, and lacks effective therapeutic interventions currently, which leads to not only permanent neurological impairments but also heavy social and economic burden. Recent studies have proved that circRNAs are highly expressed in neural tissues, regulating the neuronal and synaptic functions. What's more, significantly altered circRNAs expression profiles are closely associated with the pathophysiology of SCI. In this review, we summarize the current advance on the role of circRNAs in SCI, which may provide a better understanding of pathogenesis and therapeutic strategies of SCI. THE TRANSLATIONAL POTENTIAL OF THIS ARTICLE The Translational potential of this article is that A further understanding of circRNAs in the pathogenesis of SCI will promote the circRNA-based clinical applications.
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Affiliation(s)
- Peng Peng
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Hao Yu
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yongjin Li
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Jingyuan Huang
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Shengyu Yao
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Cong Xing
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Weixiao Liu
- Department of Orthopedics, Kuancheng Manzu Autonomous Country Hospital, Chengde, China
| | - Bin Zhang
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Shiqing Feng
- Department of Orthopedics, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin, 300052, China
- International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury,Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
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Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria? mBio 2021; 12:e0104121. [PMID: 34372700 PMCID: PMC8406224 DOI: 10.1128/mbio.01041-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene regulation in a diversity of genetic backgrounds. In the model GammaproteobacteriaEscherichia coli and Salmonella, the regulatory RNA chaperone Hfq appears to play a global role in gene regulation, directly controlling ∼20 to 25% of the entire transcriptome. While the model FirmicutesBacillus subtilis and Staphylococcus aureus encode a Hfq homologue, its role has been significantly depreciated. These bacteria also have marked differences in RNA turnover. E. coli and Salmonella degrade RNA through internal endonucleolytic and 3′→5′ exonucleolytic cleavage that appears to allow transient accumulation of mRNA 3′ UTR cleavage fragments that contain stabilizing 3′ structures. In contrast, B. subtilis and S. aureus are able to exonucleolytically attack internally cleaved RNA from both the 5′ and 3′ ends, efficiently degrading mRNA 3′ UTR fragments. Here, we propose that the lack of 5′→3′ exoribonuclease activity in Gammaproteobacteria has allowed the accumulation of mRNA 3′ UTR ends as the “default” setting. This in turn may have provided a larger pool of unconstrained RNA sequences that has fueled the expansion of Hfq function and small RNA (sRNA) regulation in E. coli and Salmonella. Conversely, the exoribonuclease RNase J may be a significant barrier to the evolution of 3′ UTR sRNAs in B. subtilis and S. aureus that has limited the pool of RNA ligands available to Hfq and other sRNA chaperones, depreciating their function in these model Firmicutes.
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44
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Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens. Antibiotics (Basel) 2021; 10:antibiotics10080947. [PMID: 34438997 PMCID: PMC8388888 DOI: 10.3390/antibiotics10080947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 11/25/2022] Open
Abstract
While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, “relaxed” phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a “stringent” RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.
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45
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Łabędzka-Dmoch K, Kolondra A, Karpińska MA, Dębek S, Grochowska J, Grochowski M, Piątkowski J, Hoang Diu Bui T, Golik P. Pervasive transcription of the mitochondrial genome in Candida albicans is revealed in mutants lacking the mtEXO RNase complex. RNA Biol 2021; 18:303-317. [PMID: 34229573 PMCID: PMC8677008 DOI: 10.1080/15476286.2021.1943929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The mitochondrial genome of the pathogenic yeast Candida albicans displays a typical organization of several (eight) primary transcription units separated by noncoding regions. Presence of genes encoding Complex I subunits and the stability of its mtDNA sequence make it an attractive model to study organellar genome expression using transcriptomic approaches. The main activity responsible for RNA degradation in mitochondria is a two-component complex (mtEXO) consisting of a 3ʹ-5ʹ exoribonuclease, in yeasts encoded by the DSS1 gene, and a conserved Suv3p helicase. In C. albicans, deletion of either DSS1 or SUV3 gene results in multiple defects in mitochondrial genome expression leading to the loss of respiratory competence. Transcriptomic analysis reveals pervasive transcription in mutants lacking the mtEXO activity, with evidence of the entire genome being transcribed, whereas in wild-type strains no RNAs corresponding to a significant fraction of the noncoding genome can be detected. Antisense (‘mirror’) transcripts, absent from normal mitochondria are also prominent in the mutants. The expression of multiple mature transcripts, particularly those translated from bicistronic mRNAs, as well as those that contain introns is affected in the mutants, resulting in a decreased level of proteins and reduced respiratory complex activity. The phenotype is most severe in the case of Complex IV, where a decrease of mature COX1 mRNA level to ~5% results in a complete loss of activity. These results show that RNA degradation by mtEXO is essential for shaping the mitochondrial transcriptome and is required to maintain the functional demarcation between transcription units and non-coding genome segments.
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Affiliation(s)
- Karolina Łabędzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena A Karpińska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Sonia Dębek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Joanna Grochowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Maciej Grochowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Piątkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Thi Hoang Diu Bui
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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46
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An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium. Proc Natl Acad Sci U S A 2021; 118:2103579118. [PMID: 34131082 PMCID: PMC8237595 DOI: 10.1073/pnas.2103579118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The gram-positive human pathogen Clostridioides difficile has emerged as the leading cause of antibiotic-associated diarrhea. However, little is known about the bacterium's transcriptome architecture and mechanisms of posttranscriptional control. Here, we have applied transcription start site and termination mapping to generate a single-nucleotide-resolution RNA map of C. difficile 5' and 3' untranslated regions, operon structures, and noncoding regulators, including 42 sRNAs. Our results indicate functionality of many conserved riboswitches and predict cis-regulatory RNA elements upstream of multidrug resistance (MDR)-type ATP-binding cassette (ABC) transporters and transcriptional regulators. Despite growing evidence for a role of Hfq in RNA-based gene regulation in C. difficile, the functions of Hfq-based posttranscriptional regulatory networks in gram-positive pathogens remain controversial. Using Hfq immunoprecipitation followed by sequencing of bound RNA species (RIP-seq), we identify a large cohort of transcripts bound by Hfq and show that absence of Hfq affects transcript stabilities and steady-state levels. We demonstrate sRNA expression during intestinal colonization by C. difficile and identify infection-related signals impacting its expression. As a proof of concept, we show that the utilization of the abundant intestinal metabolite ethanolamine is regulated by the Hfq-dependent sRNA CDIF630nc_085. Overall, our study lays the foundation for understanding clostridial riboregulation with implications for the infection process and provides evidence for a global role of Hfq in posttranscriptional regulation in a gram-positive bacterium.
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47
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Miguel-Arribas A, Val-Calvo J, Gago-Córdoba C, Izquierdo JM, Abia D, Wu LJ, Errington J, Meijer WJJ. A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria. Nucleic Acids Res 2021; 49:5553-5567. [PMID: 33999173 PMCID: PMC8191782 DOI: 10.1093/nar/gkab360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulation allows adaptive and coordinated gene expression, and is essential for life. Processive antitermination systems alter the transcription elongation complex to allow the RNA polymerase to read through multiple terminators in an operon. Here, we describe the discovery of a novel bipartite antitermination system that is widespread among conjugative elements from Gram-positive bacteria, which we named conAn. This system is composed of a large RNA element that exerts antitermination, and a protein that functions as a processivity factor. Besides allowing coordinated expression of very long operons, we show that these systems allow differential expression of genes within an operon, and probably contribute to strict regulation of the conjugation genes by minimizing the effects of spurious transcription. Mechanistic features of the conAn system are likely to decisively influence its host range, with important implications for the spread of antibiotic resistance and virulence genes.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa", (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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48
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Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. Best practices on the differential expression analysis of multi-species RNA-seq. Genome Biol 2021; 22:121. [PMID: 33926528 PMCID: PMC8082843 DOI: 10.1186/s13059-021-02337-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
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Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vincent M Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - José F Muñoz
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Greenebaum Cancer Center, University of Maryland, Baltimore, MD, 21201, USA.
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49
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O’Connor NJ, Bordoy AE, Chatterjee A. Engineering Transcriptional Interference through RNA Polymerase Processivity Control. ACS Synth Biol 2021; 10:737-748. [PMID: 33710852 DOI: 10.1021/acssynbio.0c00534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Antisense transcription is widespread in all kingdoms of life and has been shown to influence gene expression through transcriptional interference (TI), a phenomenon in which one transcriptional process negatively influences another in cis. The processivity, or uninterrupted transcription, of an RNA polymerase (RNAP) is closely tied to levels of antisense transcription in bacterial genomes, but its influence on TI, while likely important, is not well-characterized. Here, we show that TI can be tuned through processivity control via three distinct antitermination strategies: the antibiotic bicyclomycin, phage protein Psu, and ribosome-RNAP coupling. We apply these methods toward TI and tune ribosome-RNAP coupling to produce 38-fold transcription-level gene repression due to both RNAP collisions and antisense RNA interference. We then couple protein roadblock and TI to design minimal genetic NAND and NOR logic gates. Together, these results show the importance of processivity control for strong TI and demonstrate TI's potential for synthetic biology.
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Affiliation(s)
- Nolan J. O’Connor
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Antoni E. Bordoy
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Antimicrobial Regeneration Consortium, Boulder, Colorado 80301, United States
- Sachi Bioworks, Inc., Boulder, Colorado 80301, United States
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50
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Goszczynski DE, Halstead MM, Islas-Trejo AD, Zhou H, Ross PJ. Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage. Genome Res 2021; 31:732-744. [PMID: 33722934 PMCID: PMC8015843 DOI: 10.1101/gr.267336.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/01/2021] [Indexed: 01/04/2023]
Abstract
Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and contains a low number of transcripts in comparison to human and mouse. By using the RAMPAGE approach, this study identified transcription start sites at high resolution in a large collection of bovine tissues. We found several known and novel transcription start sites attributed to promoters of protein-coding and lncRNA genes that were validated through experimental and in silico evidence. With these findings, the annotation of transcription start sites in cattle reached a level comparable to the mouse and human genome annotations. In addition, we identified and characterized transcription start sites for antisense transcripts derived from bidirectional promoters, potential lncRNAs, mRNAs, and pre-miRNAs. We also analyzed the quantitative aspects of RAMPAGE to produce a promoter activity atlas, reaching highly reproducible results comparable to traditional RNA-seq. Coexpression networks revealed considerable use of tissue-specific promoters, especially between brain and testicle, which expressed several genes in common from alternate loci. Furthermore, regions surrounding coexpressed modules were enriched in binding factor motifs representative of each tissue. The comprehensive annotation of promoters in such a large collection of tissues will substantially contribute to our understanding of gene expression in cattle and other mammalian species, shortening the gap between genotypes and phenotypes.
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Affiliation(s)
- Daniel E Goszczynski
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Michelle M Halstead
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Alma D Islas-Trejo
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, California 95616, USA
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