1
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Lamoureux CR, Phaneuf PV, Palsson B, Zielinski D. Escherichia coli non-coding regulatory regions are highly conserved. NAR Genom Bioinform 2024; 6:lqae041. [PMID: 38774514 PMCID: PMC11106028 DOI: 10.1093/nargab/lqae041] [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: 10/31/2023] [Revised: 04/05/2024] [Accepted: 05/15/2024] [Indexed: 05/24/2024] Open
Abstract
Microbial genome sequences are rapidly accumulating, enabling large-scale studies of sequence variation. Existing studies primarily focus on coding regions to study amino acid substitution patterns in proteins. However, non-coding regulatory regions also play a distinct role in determining physiologic responses. To investigate intergenic sequence variation on a large-scale, we identified non-coding regulatory region alleles across 2350 Escherichia coli strains. This 'alleleome' consists of 117 781 unique alleles for 1169 reference regulatory regions (transcribing 1975 genes) at single base-pair resolution. We find that 64% of nucleotide positions are invariant, and variant positions vary in a median of just 0.6% of strains. Additionally, non-coding alleles are sufficient to recover E. coli phylogroups. We find that core promoter elements and transcription factor binding sites are significantly conserved, especially those located upstream of essential or highly-expressed genes. However, variability in conservation of transcription factor binding sites is significant both within and across regulons. Finally, we contrast mutations acquired during adaptive laboratory evolution with wild-type variation, finding that the former preferentially alter positions that the latter conserves. Overall, this analysis elucidates the wealth of information found in E. coli non-coding sequence variation and expands pangenomic studies to non-coding regulatory regions at single-nucleotide resolution.
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Affiliation(s)
- Cameron R Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Patrick V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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2
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Liu J, Liu D, Sun T, Fan TP, Cai Y. Construction and characterization of a promoter library with varying strengths to enhance acetoin production from xylose in Serratia marcescens. Biotechnol Appl Biochem 2024; 71:553-564. [PMID: 38225826 DOI: 10.1002/bab.2558] [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: 08/18/2023] [Accepted: 12/30/2023] [Indexed: 01/17/2024]
Abstract
Serratia marcescens is utilized as a significant enterobacteria in the production of various high-value secondary metabolites. Acetoin serves as a crucial foundational compound of development and finds application in a broad range of fields. Furthermore, S. marcescens HBQA-7 is capable of utilizing xylose as its exclusive carbon source for acetoin production. The objective of this study was to utilize a constitutive promoter screening strategy to enhance both xylose utilization and acetoin production in S. marcescens HBQA-7. By utilizing RNA-seq, we identified the endogenous constitutive promoter P6 that is the most robust, which facilitated the overexpression of the sugar transporter protein GlfL445I, α-acetyl lactate synthase, and α-acetyl lactate decarboxylase, respectively. The resultant recombinant strains exhibited enhanced xylose utilization rates and acetoin yields. Subsequently, a recombinant plasmid, denoted as pBBR1MCS-P6-glfL445IalsSalsD, was constructed, simultaneously expressing the aforementioned three genes. The resulting recombinant strain, designated as S3, demonstrated a 1.89-fold boost in xylose consumption rate compared with the original strain during shake flask fermentation. resulting in the accumulation of 7.14 g/L acetoin in the final fermentation medium. Subsequently, in a 5 L fermenter setup, the acetoin yield reached 48.75 g/L, corresponding to a xylose-to-acetoin conversion yield of 0.375 g/g.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Di Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tingting Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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3
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uz-Zaman MH, D’Alton S, Barrick JE, Ochman H. Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli. PLoS Biol 2024; 22:e3002418. [PMID: 38713714 PMCID: PMC11101190 DOI: 10.1371/journal.pbio.3002418] [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: 10/18/2023] [Revised: 05/17/2024] [Accepted: 04/18/2024] [Indexed: 05/09/2024] Open
Abstract
The phenomenon of de novo gene birth-the emergence of genes from non-genic sequences-has received considerable attention due to the widespread occurrence of genes that are unique to particular species or genomes. Most instances of de novo gene birth have been recognized through comparative analyses of genome sequences in eukaryotes, despite the abundance of novel, lineage-specific genes in bacteria and the relative ease with which bacteria can be studied in an experimental context. Here, we explore the genetic record of the Escherichia coli long-term evolution experiment (LTEE) for changes indicative of "proto-genic" phases of new gene birth in which non-genic sequences evolve stable transcription and/or translation. Over the time span of the LTEE, non-genic regions are frequently transcribed, translated and differentially expressed, with levels of transcription across low-expressed regions increasing in later generations of the experiment. Proto-genes formed downstream of new mutations result either from insertion element activity or chromosomal translocations that fused preexisting regulatory sequences to regions that were not expressed in the LTEE ancestor. Additionally, we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter, although such cases were rare compared to those caused by recruitment of preexisting promoters. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently within evolving populations, can persist stably, and can serve as potential substrates for new gene formation.
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Affiliation(s)
- Md. Hassan uz-Zaman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Simon D’Alton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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4
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Lawaetz AC, Cowley LA, Denham EL. Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets. Microb Genom 2024; 10. [PMID: 38668652 DOI: 10.1099/mgen.0.001239] [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: 05/16/2024] Open
Abstract
Accurate annotation to single-nucleotide resolution of the transcribed regions in genomes is key to optimally analyse RNA-seq data, understand regulatory events and for the design of experiments. However, currently most genome annotations provided by GenBank generally lack information about untranslated regions. Additionally, information regarding genomic locations of non-coding RNAs, such as sRNAs, or anti-sense RNAs is frequently missing. To provide such information, diverse RNA-seq technologies, such as Rend-seq, have been developed and applied to many bacterial species. However, incorporating this vast amount of information into annotation files has been limited and is bioinformatically challenging, resulting in UTRs and other non-coding elements being overlooked or misrepresented. To overcome this problem, we present pyRAP (python Rend-seq Annotation Pipeline), a software package that analyses Rend-seq datasets to accurately resolve transcript boundaries genome-wide. We report the use of pyRAP to find novel transcripts, transcript isoforms, and RNase-dependent sRNA processing events. In Bacillus subtilis we uncovered 63 novel transcripts and provide genomic coordinates with single-nucleotide resolution for 2218 5'UTRs, 1864 3'UTRs and 161 non-coding RNAs. In Escherichia coli, we report 117 novel transcripts, 2429 5'UTRs, 1619 3'UTRs and 91 non-coding RNAs, and in Staphylococcus aureus, 16 novel transcripts, 664 5'UTRs, 696 3'UTRs, and 81 non-coding RNAs. Finally, we use pyRAP to produce updated annotation files for B. subtilis 168, E. coli K-12 MG1655, and S. aureus 8325 for use in the wider microbial genomics research community.
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Affiliation(s)
- Andreas C Lawaetz
- Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Lauren A Cowley
- Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Milner Centre for Evolution, Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Emma L Denham
- Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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5
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Handler S, Kirkpatrick CL. New layers of regulation of the general stress response sigma factor RpoS. Front Microbiol 2024; 15:1363955. [PMID: 38505546 PMCID: PMC10948607 DOI: 10.3389/fmicb.2024.1363955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
The general stress response (GSR) sigma factor RpoS from Escherichia coli has emerged as one of the key paradigms for study of how numerous signal inputs are accepted at multiple levels into a single pathway for regulation of gene expression output. While many studies have elucidated the key pathways controlling the production and activity of this sigma factor, recent discoveries have uncovered still more regulatory mechanisms which feed into the network. Moreover, while the regulon of this sigma factor comprises a large proportion of the E. coli genome, the downstream expression levels of all the RpoS target genes are not identically affected by RpoS upregulation but respond heterogeneously, both within and between cells. This minireview highlights the most recent developments in our understanding of RpoS regulation and expression, in particular those which influence the regulatory network at different levels from previously well-studied pathways.
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Elgrably-Weiss M, Hussain F, Georg J, Shraiteh B, Altuvia S. Balanced cell division is secured by two different regulatory sites in OxyS RNA. RNA (NEW YORK, N.Y.) 2024; 30:124-135. [PMID: 38071477 PMCID: PMC10798246 DOI: 10.1261/rna.079836.123] [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: 09/12/2023] [Accepted: 11/09/2023] [Indexed: 01/18/2024]
Abstract
The hydrogen peroxide-induced small RNA OxyS has been proposed to originate from the 3' UTR of a peroxide mRNA. Unexpectedly, phylogenetic OxyS targetome predictions indicate that most OxyS targets belong to the category of "cell cycle," including cell division and cell elongation. Previously, we reported that Escherichia coli OxyS inhibits cell division by repressing expression of the essential transcription termination factor nusG, thereby leading to the expression of the KilR protein, which interferes with the function of the major cell division protein, FtsZ. By interfering with cell division, OxyS brings about cell-cycle arrest, thus allowing DNA damage repair. Cell division and cell elongation are opposing functions to the extent that inhibition of cell division requires a parallel inhibition of cell elongation for the cells to survive. In this study, we report that in addition to cell division, OxyS inhibits mepS, which encodes an essential peptidoglycan endopeptidase that is responsible for cell elongation. Our study indicates that cell-cycle arrest and balancing between cell division and cell elongation are important and conserved functions of the oxidative stress-induced sRNA OxyS.
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Affiliation(s)
- Maya Elgrably-Weiss
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120 Jerusalem, Israel
| | - Fayyaz Hussain
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, 79104 Freiburg, Germany
| | - Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, 79104 Freiburg, Germany
| | - Bushra Shraiteh
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120 Jerusalem, Israel
| | - Shoshy Altuvia
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120 Jerusalem, Israel
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7
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Uz-Zaman MH, D'Alton S, Barrick JE, Ochman H. Promoter capture drives the emergence of proto-genes in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567300. [PMID: 38013999 PMCID: PMC10680751 DOI: 10.1101/2023.11.15.567300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The phenomenon of de novo gene birth-the emergence of genes from non-genic sequences-has received considerable attention due to the widespread occurrence of genes that are unique to particular species or genomes. Most instances of de novo gene birth have been recognized through comparative analyses of genome sequences in eukaryotes, despite the abundance of novel, lineage-specific genes in bacteria and the relative ease with which bacteria can be studied in an experimental context. Here, we explore the genetic record of the Escherichia coli Long-Term Evolution Experiment (LTEE) for changes indicative of "proto-genic" phases of new gene birth in which non-genic sequences evolve stable transcription and/or translation. Over the time-span of the LTEE, non-genic regions are frequently transcribed, translated and differentially expressed, thereby serving as raw material for new gene emergence. Most proto-genes result either from insertion element activity or chromosomal translocations that fused pre-existing regulatory sequences to regions that were not expressed in the LTEE ancestor. Additionally, we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently within evolving populations, persist stably, and can serve as potential substrates for new gene formation.
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8
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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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9
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Zhao L, Tabari E, Rong H, Dong X, Xue D, Su Z. Antisense transcription and its roles in adaption to environmental stress in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533988. [PMID: 36993172 PMCID: PMC10055363 DOI: 10.1101/2023.03.23.533988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
UNLABELLED It has been reported that a highly varying proportion (1% ∼ 93%) of genes in various prokaryotes have antisense RNA (asRNA) transcription. However, the extent of the pervasiveness of asRNA transcription in the well-studied E. coli K12 strain has thus far been an issue of debate. Furthermore, very little is known about the expression patterns and functions of asRNAs under various conditions. To fill these gaps, we determined the transcriptomes and proteomes of E. coli K12 at multiple time points in five culture conditions using strand-specific RNA-seq, differential RNA-seq, and quantitative mass spectrometry methods. To reduce artifacts of possible transcriptional noise, we identified asRNA using stringent criteria with biological replicate verification and transcription start sites (TSSs) information included. We identified a total of 660 asRNAs, which were generally short and largely condition-dependently transcribed. We found that the proportions of the genes which had asRNA transcription highly depended on the culture conditions and time points. We classified the transcriptional activities of the genes in six transcriptional modes according to their relative levels of asRNA to mRNA. Many genes changed their transcriptional modes at different time points of the culture conditions, and such transitions can be described in a well-defined manner. Intriguingly, the protein levels and mRNA levels of genes in the sense-only/sense-dominant mode were moderately correlated, but the same was not true for genes in the balanced/antisense-dominant mode, in which asRNAs were at a comparable or higher level to mRNAs. These observations were further validated by western blot on candidate genes, where an increase in asRNA transcription diminished gene expression in one case and enhanced it in another. These results suggest that asRNAs may directly or indirectly regulate translation by forming duplexes with cognate mRNAs. Thus, asRNAs may play an important role in the bacterium's responses to environmental changes during growth and adaption to different environments. IMPORTANCE The cis -antisense RNA (asRNA) is a type of understudied RNA molecules in prokaryotes, which is believed to be important in regulating gene expression. Our current understanding of asRNA is constrained by inconsistent reports about its identification and properties. These discrepancies are partially caused by a lack of sufficient samples, biological replicates, and culture conditions. This study aimed to overcome these disadvantages and identified 660 putative asRNAs using integrated information from strand-specific RNA-seq, differential RNA-seq, and mass spectrometry methods. In addition, we explored the relative expression between asRNAs and sense RNAs and investigated asRNA regulated transcriptional activity changes over different culture conditions and time points. Our work strongly suggests that asRNAs may play a crucial role in bacterium's responses to environmental changes during growth and adaption to different environments.
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10
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Ziemann M, Reimann V, Liang Y, Shi Y, Ma H, Xie Y, Li H, Zhu T, Lu X, Hess WR. CvkR is a MerR-type transcriptional repressor of class 2 type V-K CRISPR-associated transposase systems. Nat Commun 2023; 14:924. [PMID: 36801863 PMCID: PMC9938897 DOI: 10.1038/s41467-023-36542-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/06/2023] [Indexed: 02/20/2023] Open
Abstract
Certain CRISPR-Cas elements integrate into Tn7-like transposons, forming CRISPR-associated transposon (CAST) systems. How the activity of these systems is controlled in situ has remained largely unknown. Here we characterize the MerR-type transcriptional regulator Alr3614 that is encoded by one of the CAST (AnCAST) system genes in the genome of cyanobacterium Anabaena sp. PCC 7120. We identify a number of Alr3614 homologs across cyanobacteria and suggest naming these regulators CvkR for Cas V-K repressors. Alr3614/CvkR is translated from leaderless mRNA and represses the AnCAST core modules cas12k and tnsB directly, and indirectly the abundance of the tracr-CRISPR RNA. We identify a widely conserved CvkR binding motif 5'-AnnACATnATGTnnT-3'. Crystal structure of CvkR at 1.6 Å resolution reveals that it comprises distinct dimerization and potential effector-binding domains and that it assembles into a homodimer, representing a discrete structural subfamily of MerR regulators. CvkR repressors are at the core of a widely conserved regulatory mechanism that controls type V-K CAST systems.
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Affiliation(s)
- Marcus Ziemann
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Viktoria Reimann
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Yajing Liang
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Yue Shi
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Honglei Ma
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuman Xie
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Zhu
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China. .,Shandong Energy Institute, Qingdao, 266101, China. .,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China. .,Shandong Energy Institute, Qingdao, 266101, China. .,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany.
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11
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Xia M, Yu D, Chen H, Dai J, Gao N, Li S, Bi X, Qiu D. An RpoN-dependent PEP-CTERM gene is involved in floc formation of an Aquincola tertiaricarbonis strain. BMC Microbiol 2023; 23:20. [PMID: 36658495 PMCID: PMC9850573 DOI: 10.1186/s12866-022-02745-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The floc is a characteristic of microbial aggregate growth, displaying cloudy suspensions in water. Floc formation has been demonstrated in a series of bacteria and the floc-forming bacteria play a crucial role in activated sludge (AS) process widely used for municipal sewage and industrial wastewater treatment over a century. It has been demonstrated that some exopolysaccharide biosynthesis genes and the sigma factor (sigma54 or rpoN) were required for floc forming in some bacteria. However, the mechanism underlying the floc formation stills need to be elucidated. RESULTS In this study, we demonstrate that a TPR (Tetratricopeptide repeats) protein-encoding gene prsT is required for floc formation of Aquincola tertiaricarbonis RN12 and an upstream PEP-CTERM gene (designated pepA), regulated by RpoN1, is involved in its floc formation but not swarming motility and biofilm formation. Overexpression of PepA could rescue the floc-forming phenotype of the rpoN1 mutant by decreasing the released soluble exopolysaccharides and increasing the bound polymers. CONCLUSION Our results indicate that the wide-spread PEP-CTERM proteins play an important role in the self-flocculation of bacterial cells and may be a component of extracellular polymeric substances required for floc-formation.
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Affiliation(s)
- Ming Xia
- grid.411854.d0000 0001 0709 0000School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, 430056 China ,grid.411854.d0000 0001 0709 0000Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, 430056 China
| | - Dianzhen Yu
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.419092.70000 0004 0467 2285Institute for Nutritional Sciences, SIBS, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Han Chen
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
| | - Jingcheng Dai
- grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
| | - Na Gao
- grid.469521.d0000 0004 1756 0127Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Shuyang Li
- grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
| | - Xuezhi Bi
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, 138668 Singapore
| | - Dongru Qiu
- grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
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12
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Li Z, Gao C, Ye C, Guo L, Liu J, Chen X, Song W, Wu J, Liu L. Systems engineering of Escherichia coli for high-level shikimate production. Metab Eng 2023; 75:1-11. [PMID: 36328295 DOI: 10.1016/j.ymben.2022.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
To further increase the production efficiency of microbial shikimate, a valuable compound widely used in the pharmaceutical and chemical industries, ten key target genes contributing to shikimate production were identified by exploiting the enzyme constraint model ec_iML1515, and subsequently used for promoting metabolic flux towards shikimate biosynthesis in the tryptophan-overproducing strain Escherichia coli TRP0. The engineered E. coli SA05 produced 78.4 g/L shikimate via fed-batch fermentation. Deletion of quinate dehydrogenase and introduction of the hydroaromatic equilibration-alleviating shikimate dehydrogenase mutant AroET61W/L241I reduced the contents of byproducts quinate (7.5 g/L) and 3-dehydroshikimic acid (21.4 g/L) by 89.1% and 52.1%, respectively. Furthermore, a high concentration shikimate responsive promoter PrpoS was recruited to dynamically regulate the expression of the tolerance target ProV to enhance shikimate productivity by 23.2% (to 2 g/L/h). Finally, the shikimate titer was increased to 126.4 g/L, with a yield of 0.50 g/g glucose and productivity of 2.63 g/L/h, using a 30-L fermenter and the engineered strain E. coli SA09. This is, to the best of our knowledge, the highest reported shikimate titer and productivity in E. coli.
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Affiliation(s)
- Zhendong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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13
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El-Mansi M. Control of central metabolism’s architecture in Escherichia coli: An overview. Microbiol Res 2023; 266:127224. [DOI: 10.1016/j.micres.2022.127224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
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14
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Rasmussen RA, Wang S, Camarillo JM, Sosnowski V, Cho BK, Goo Y, Lucks J, O’Halloran T. Zur and zinc increase expression of E. coli ribosomal protein L31 through RNA-mediated repression of the repressor L31p. Nucleic Acids Res 2022; 50:12739-12753. [PMID: 36533433 PMCID: PMC9825181 DOI: 10.1093/nar/gkac1086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can adapt in response to numerous stress conditions. One such stress condition is zinc depletion. The zinc-sensing transcription factor Zur regulates the way numerous bacterial species respond to severe changes in zinc availability. Under zinc sufficient conditions, Zn-loaded Zur (Zn2-Zur) is well-known to repress transcription of genes encoding zinc uptake transporters and paralogues of a few ribosomal proteins. Here, we report the discovery and mechanistic basis for the ability of Zur to up-regulate expression of the ribosomal protein L31 in response to zinc in E. coli. Through genetic mutations and reporter gene assays, we find that Zur achieves the up-regulation of L31 through a double repression cascade by which Zur first represses the transcription of L31p, a zinc-lacking paralogue of L31, which in turn represses the translation of L31. Mutational analyses show that translational repression by L31p requires an RNA hairpin structure within the l31 mRNA and involves the N-terminus of the L31p protein. This work uncovers a new genetic network that allows bacteria to respond to host-induced nutrient limiting conditions through a sophisticated ribosomal protein switching mechanism.
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Affiliation(s)
- Rebecca A Rasmussen
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
| | - Suning Wang
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Jeannie M Camarillo
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
| | - Victoria Sosnowski
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
| | - Byoung-Kyu Cho
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
- Mass Spectrometry Technology Access Center, Washington University in St Louis, School of Medicine, USA
| | - Young Ah Goo
- Northwestern Proteomics Core, Northwestern University, Evanston, IL 60208, USA
- Mass Spectrometry Technology Access Center, Washington University in St Louis, School of Medicine, USA
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Thomas V O’Halloran
- Chemistry of Life Process Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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15
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Ogawa A, Kojima F, Miyake Y, Yoshimura M, Ishijima N, Iyoda S, Sekine Y, Yamanaka Y, Yamamoto K. Regulation of constant cell elongation and Sfm pili synthesis in Escherichia coli via two active forms of FimZ orphan response regulator. Genes Cells 2022; 27:657-674. [PMID: 36057789 DOI: 10.1111/gtc.12982] [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: 07/15/2022] [Revised: 08/21/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022]
Abstract
Escherichia coli (E. coli) has multiple copies of the chaperone-usher (CU) pili operon in five fimbria groups: CU pili, curli, type IV pili, type III secretion pili, and type IV secretion pili. Commensal E. coli K-12 contains 12 CU pili operons. Among these operons, Sfm is expressed by the sfmACDHF operon. Transcriptome analyses, reporter assays, and chromatin immunoprecipitation PCR analyses reported that FimZ directly binds to and activates the sfmA promoter, transcribing sfmACDHF. In addition, FimZ regularly induces constant cell elongation in E. coli, which is required for F-type ATPase function. The bacterial two-hybrid system showed a specific interaction between FimZ and the α subunit of the cytoplasmic F1 domain of F-type ATPase. Studies performed using mutated FimZs have revealed two active forms, I and II. Active form I is required for constant cell elongation involving amino acid residues K106 and D109. Active form II additionally required D56, a putative phosphorylation site, to activate the sfmA promoter. The chromosomal fimZ was hardly expressed in parent strain but functioned in phoB and phoP double-gene knockout strains. These insights may help to understand bacterial invasion restricted host environments by the sfm γ-type pili.
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Affiliation(s)
- Ayano Ogawa
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Fumika Kojima
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Yukari Miyake
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Miho Yoshimura
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Nozomi Ishijima
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Yuki Yamanaka
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Nippon Dental University School of Dentistry, Tokyo, Japan
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16
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The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life. PLoS One 2022; 17:e0274397. [PMID: 36129877 PMCID: PMC9491525 DOI: 10.1371/journal.pone.0274397] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022] Open
Abstract
Brucella abortus is a facultative intracellular pathogen causing a severe zoonotic disease worldwide. The two-component regulatory system (TCS) BvrR/BvrS of B. abortus is conserved in members of the Alphaproteobacteria class. It is related to the expression of genes required for host interaction and intracellular survival. Here we report that bvrR and bvrS are part of an operon composed of 16 genes encoding functions related to nitrogen metabolism, DNA repair and recombination, cell cycle arrest, and stress response. Synteny of this genomic region within close Alphaproteobacteria members suggests a conserved role in coordinating the expression of carbon and nitrogen metabolic pathways. In addition, we performed a ChIP-Seq analysis after exposure of bacteria to conditions that mimic the intracellular environment. Genes encoding enzymes at metabolic crossroads of the pentose phosphate shunt, gluconeogenesis, cell envelope homeostasis, nucleotide synthesis, cell division, and virulence are BvrR/BvrS direct targets. A 14 bp DNA BvrR binding motif was found and investigated in selected gene targets such as virB1, bvrR, pckA, omp25, and tamA. Understanding gene expression regulation is essential to elucidate how Brucella orchestrates a physiological response leading to a furtive pathogenic strategy.
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17
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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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18
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Genome-wide transcription start site mapping in the facultative intracellular pathogen Brucella melitensis by Capping-seq. Gene 2022; 844:146827. [PMID: 35995114 DOI: 10.1016/j.gene.2022.146827] [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: 04/11/2022] [Revised: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 11/20/2022]
Abstract
Brucella melitensis (B. melitensis) is an important facultative intracellular bacterium that causes global zoonotic diseases. Continuous intracellular survival and replication are the main obstruction responsible for the accessibility of prevention and treatment of brucellosis. Bacteria respond to complex environment by regulating gene expression. Many regulatory factors function at loci where RNA polymerase initiates messenger RNA synthesis. However, limited gene annotation is a current obstacle for the research on expression regulation in bacteria. To improve annotation and explore potential functional sites, we proposed a novel genome-wide method called Capping-seq for transcription start site (TSS) mapping in B. melitensis. This technique combines capture of capped primary transcripts with Single Molecule Real-Time (SMRT) sequencing technology. We identified 2,369 TSSs at single nucleotide resolution by Capping-seq. TSSs analysis of Brucella transcripts showed a preference of purine on the TSS positions. Our results revealed that -35 and -10 elements of promoter contained consensus sequences of TTGNNN and TATNNN, respectively. The 5' ends analysis showed that 57% genes are associated with more than one TSS and 47% genes contain long leader regions, suggested potential complex regulation at the 5' ends of genes in B. melitensis. Moreover, we identified 52 leaderless genes that are mainly involved in the metabolic processes. Overall, Capping-seq technology provides a unique solution for TSS determination in prokaryotes. Our findings develop a systematic insight into the primary transcriptome characterization of B. melitensis. This study represents a critical basis for investigating gene regulation and pathogenesis of Brucella.
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19
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In Silico Study of Mercury Resistance Genes Extracted from Pseudomonas spp. Involved in Bioremediation: Understanding the Promoter Regions and Regulatory Elements. Int J Genomics 2022; 2022:6185615. [PMID: 35991673 PMCID: PMC9391164 DOI: 10.1155/2022/6185615] [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: 05/30/2022] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Microbial genes and their product were diverse and beneficial for heavy metal bioremediation from the contaminated sites. Screening of genes and gene products plays a significant role in the detoxification of pollutants. Understanding of the promoter region and its regulatory elements is a vital implication of microbial genes. To the best of our knowledge, there is no in silico study reported so far on mer gene families used for heavy metal bioremediation. The motif distribution was observed densely upstream of the TSSs (transcription start sites) between +1 and -350 bp and sparsely distributed above -350 bp, according to the current study. MEME identified the best common candidate motifs of TFs (transcription factors) binding with the lowest e value (7.2
-033) and is the most statistically significant candidate motif. The EXPREG output of the 11 TFs with varying degrees of function such as activation, repression, transcription, and dual purposes was thoroughly examined. Data revealed that transcriptional gene regulation in terms of activation and repression was observed at 36.4% and 54.56%, respectively. This shows that most TFs are involved in transcription gene repression rather than activation. Likewise, EXPREG output revealed that transcriptional conformational modes, such as monomers, dimers, tetramers, and other factors, were also analyzed. The data indicated that most of the transcriptional conformation mode was dual, which accounts for 96%. CpG island analysis using online and offline tools revealed that the gene body had fewer CpG islands compared to the promoter regions. Understanding the common candidate motifs, transcriptional factors, and regulatory elements of the mer operon gene cluster using a machine learning approach could help us better understand gene expression patterns in heavy metal bioremediation.
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20
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Tierrafría VH, Rioualen C, Salgado H, Lara P, Gama-Castro S, Lally P, Gómez-Romero L, Peña-Loredo P, López-Almazo AG, Alarcón-Carranza G, Betancourt-Figueroa F, Alquicira-Hernández S, Polanco-Morelos JE, García-Sotelo J, Gaytan-Nuñez E, Méndez-Cruz CF, Muñiz LJ, Bonavides-Martínez C, Moreno-Hagelsieb G, Galagan JE, Wade JT, Collado-Vides J. RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12. Microb Genom 2022; 8. [PMID: 35584008 PMCID: PMC9465075 DOI: 10.1099/mgen.0.000833] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.
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Affiliation(s)
- Víctor H Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Claire Rioualen
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Heladia Salgado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Paloma Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, INMEGEN, Periférico Sur 4809, Arenal Tepepan, Tlalpan 14610, CDMX, Mexico
| | - Pablo Peña-Loredo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Andrés G López-Almazo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Gabriel Alarcón-Carranza
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Felipe Betancourt-Figueroa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Shirley Alquicira-Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - J Enrique Polanco-Morelos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Jair García-Sotelo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Querétaro, Mexico
| | - Estefani Gaytan-Nuñez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Carlos-Francisco Méndez-Cruz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Luis J Muñiz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - César Bonavides-Martínez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON N2L 3C5, Canada
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, USA
| | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Universitat Pompeu Fabra(UPF), Barcelona, Spain
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21
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Jain K, Stanage TH, Wood EA, Cox MM. The Escherichia coli serS gene promoter region overlaps with the rarA gene. PLoS One 2022; 17:e0260282. [PMID: 35427362 PMCID: PMC9012371 DOI: 10.1371/journal.pone.0260282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Deletion of the entire gene encoding the RarA protein of Escherichia coli results in a growth defect and additional deficiencies that were initially ascribed to a lack of RarA function. Further work revealed that most of the effects reflected the presence of sequences in the rarA gene that affect expression of the downstream gene, serS. The serS gene encodes the seryl aminoacyl-tRNA synthetase. Decreases in the expression of serS can trigger the stringent response. The sequences that affect serS expression are located in the last 15 nucleotides of the rarA gene.
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Affiliation(s)
- Kanika Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Tyler H. Stanage
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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22
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Jindal S, Iyer MS, Jyoti P, Masakapalli SK, Venkatesh KV. Mutants lacking global regulators, fis and arcA, in Escherichia coli enhanced growth fitness under acetate metabolism by pathway reprogramming. Appl Microbiol Biotechnol 2022; 106:3231-3243. [PMID: 35416487 DOI: 10.1007/s00253-022-11890-6] [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: 08/13/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022]
Abstract
Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A system-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the major substrates available in various nutrient niches such as the mammalian gut and a keto diet. A substantial amount of acetate gets secreted in aerobic metabolism. Therefore, investigating the study on acetate metabolism is highly significant. It is known that the global regulators fis and arcA regulate acetate uptake genes in E. coli under glucose conditions. This study deciphered the growth and flux distribution of E. coli transcription regulatory knockouts Δfis, ΔarcA and double deletion mutant, ΔarcAΔfis under acetate using 13C-metabolic flux analysis (MFA), which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~ 1.2-1.6-fold) with a proportionate increase in acetate uptake rates compared to the wild type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes via the TCA cycle, anaplerotic pathway and gluconeogenesis, which conferred an advantage of a faster growth rate with better carbon usage in all the mutants. This resulted in higher metabolic fluxes through the TCA cycle (~ 18-90%), lower gluconeogenesis (~ 15-35%) and higher CO2 and ATP production with the proportional increase in growth rate. The study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate, thus acting as potential candidates for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products.Key Points• Mutants exhibited a better balance between energy and precursor synthesis than WT.• Leveraged in the unravelling of regulatory control under various nutrient shifts.• Metabolic readjustment resulted in optimal biomass requirement and faster growth.
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Affiliation(s)
- Shikha Jindal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Mahesh S Iyer
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Poonam Jyoti
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, 175075, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, 175075, India.
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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Hamde F, Dinka H, Naimuddin M. In silico analysis of promoter regions to identify regulatory elements in TetR family transcriptional regulatory genes of Mycobacterium colombiense CECT 3035. J Genet Eng Biotechnol 2022; 20:53. [PMID: 35357597 PMCID: PMC8971250 DOI: 10.1186/s43141-022-00331-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/09/2022] [Indexed: 12/18/2022]
Abstract
Background Mycobacterium colombiense is an acid-fast, non-motile, rod-shaped mycobacterium confirmed to cause respiratory disease and disseminated infection in immune-compromised patients, and lymphadenopathy in immune-competent children. It has virulence mechanisms that allow them to adapt, survive, replicate, and produce diseases in the host. To tackle the diseases caused by M. colombiense, understanding of the regulation mechanisms of its genes is important. This paper, therefore, analyzes transcription start sites, promoter regions, motifs, transcription factors, and CpG islands in TetR family transcriptional regulatory (TFTR) genes of M. colombiense CECT 3035 using neural network promoter prediction, MEME, TOMTOM algorithms, and evolutionary analysis with the help of MEGA-X. Results The analysis of 22 protein coding TFTR genes of M. colombiense CECT 3035 showed that 86.36% and 13.64% of the gene sequences had one and two TSSs, respectively. Using MEME, we identified five motifs (MTF1, MTF2, MTF3, MTF4, and MTF5) and MTF1 was revealed as the common promoter motif for 100% TFTR genes of M. colombiense CECT 3035 which may serve as binding site for transcription factors that shared a minimum homology of 95.45%. MTF1 was compared to the registered prokaryotic motifs and found to match with 15 of them. MTF1 serves as the binding site mainly for AraC, LexA, and Bacterial histone-like protein families. Other protein families such as MATP, RR, σ-70 factor, TetR, LytTR, LuxR, and NAP also appear to be the binding candidates for MTF1. These families are known to have functions in virulence mechanisms, metabolism, quorum sensing, cell division, and antibiotic resistance. Furthermore, it was found that TFTR genes of M. colombiense CECT 3035 have many CpG islands with several fragments in their CpG islands. Molecular evolutionary genetic analysis showed close relationship among the genes. Conclusion We believe these findings will provide a better understanding of the regulation of TFTR genes in M. colombiense CECT 3035 involved in vital processes such as cell division, pathogenesis, and drug resistance and are likely to provide insights for drug development important to tackle the diseases caused by this mycobacterium. We believe this is the first report of in silico analyses of the transcriptional regulation of M. colombiense TFTR genes.
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Affiliation(s)
- Feyissa Hamde
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| | - Hunduma Dinka
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
| | - Mohammed Naimuddin
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
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Regulation of Leaderless mRNA Translation in Bacteria. Microorganisms 2022; 10:microorganisms10040723. [PMID: 35456773 PMCID: PMC9031893 DOI: 10.3390/microorganisms10040723] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
In bacteria, the translation of genetic information can begin through at least three different mechanisms: canonical or Shine-Dalgarno-led initiation, readthrough or 70S scanning initiation, or leaderless initiation. Here, we discuss the main features and regulation of the last, which is characterized mainly by the ability of 70S ribosomal particles to bind to AUG located at or near the 5′ end of mRNAs to initiate translation. These leaderless mRNAs (lmRNAs) are rare in enterobacteria, such as Escherichia coli, but are common in other bacteria, such as Mycobacterium tuberculosis and Deinococcus deserti, where they may represent more than 20% and even up to 60% of the genes. Given that lmRNAs are devoid of a 5′ untranslated region and the Shine-Dalgarno sequence located within it, the mechanism of translation regulation must depend on molecular strategies that are different from what has been observed in the Shine-Dalgarno-led translation. Diverse regulatory mechanisms have been proposed, including the processing of ribosomal RNA and changes in the abundance of translation factors, but all of them produce global changes in the initiation of lmRNA translation. Thus, further research will be required to understand how the initiation of the translation of particular lmRNA genes is regulated.
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25
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Khandelwal R, Jain D, Jaishankar J, Barman A, Srivastava P, Bisaria VS. Characterization of Zymomonas mobilis promoters that are functional in Escherichia coli. J Biosci Bioeng 2022; 133:301-308. [DOI: 10.1016/j.jbiosc.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 02/08/2023]
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26
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RecA gene genetic diversity and its regulatory element analysis: The case of Vibrio cholerae. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Tailoring the evolution of BL21(DE3) uncovers a key role for RNA stability in gene expression toxicity. Commun Biol 2021; 4:963. [PMID: 34385596 PMCID: PMC8361080 DOI: 10.1038/s42003-021-02493-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Gene expression toxicity is an important biological phenomenon and a major bottleneck in biotechnology. Escherichia coli BL21(DE3) is the most popular choice for recombinant protein production, and various derivatives have been evolved or engineered to facilitate improved yield and tolerance to toxic genes. However, previous efforts to evolve BL21, such as the Walker strains C41 and C43, resulted only in decreased expression strength of the T7 system. This reveals little about the mechanisms at play and constitutes only marginal progress towards a generally higher producing cell factory. Here, we restrict the solution space for BL21(DE3) to evolve tolerance and isolate a mutant strain Evo21(DE3) with a truncation in the essential RNase E. This suggests that RNA stability plays a central role in gene expression toxicity. The evolved rne truncation is similar to a mutation previously engineered into the commercially available BL21Star(DE3), which challenges the existing assumption that this strain is unsuitable for expressing toxic proteins. We isolated another dominant mutation in a presumed substrate binding site of RNase E that improves protein production further when provided as an auxiliary plasmid. This makes it easy to improve other BL21 variants and points to RNases as prime targets for cell factory optimisation.
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Abstract
Bacterial protein synthesis rates have evolved to maintain preferred stoichiometries at striking precision, from the components of protein complexes to constituents of entire pathways. Setting relative protein production rates to be well within a factor of two requires concerted tuning of transcription, RNA turnover, and translation, allowing many potential regulatory strategies to achieve the preferred output. The last decade has seen a greatly expanded capacity for precise interrogation of each step of the central dogma genome-wide. Here, we summarize how these technologies have shaped the current understanding of diverse bacterial regulatory architectures underpinning stoichiometric protein synthesis. We focus on the emerging expanded view of bacterial operons, which encode diverse primary and secondary mRNA structures for tuning protein stoichiometry. Emphasis is placed on how quantitative tuning is achieved. We discuss the challenges and open questions in the application of quantitative, genome-wide methodologies to the problem of precise protein production. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- James C Taggart
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Current affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
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29
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Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry. Nat Microbiol 2021; 6:746-756. [PMID: 33958766 PMCID: PMC7612053 DOI: 10.1038/s41564-021-00898-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023]
Abstract
Transcription initiates at promoters, DNA regions recognized by a DNA-dependent RNA polymerase. We previously identified horizontally acquired Escherichia coli promoters from which the direction of transcription was unclear. In the present study, we show that more than half of these promoters are bidirectional and drive divergent transcription. Using genome-scale approaches, we demonstrate that 19% of all transcription start sites detected in E. coli are associated with a bidirectional promoter. Bidirectional promoters are similarly common in diverse bacteria and archaea, and have inherent symmetry: specific bases required for transcription initiation are reciprocally co-located on opposite DNA strands. Bidirectional promoters enable co-regulation of divergent genes and are enriched in both intergenic and horizontally acquired regions. Divergent transcription is conserved among bacteria, archaea and eukaryotes, but the underlying mechanisms for bidirectionality are different.
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30
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Ittensohn J, Hemberger J, Griffiths H, Keller M, Albrecht S, Miethke T. Regulation of Expression of the TIR-Containing Protein C Gene of the Uropathogenic Escherichia coli Strain CFT073. Pathogens 2021; 10:pathogens10050549. [PMID: 34062817 PMCID: PMC8147327 DOI: 10.3390/pathogens10050549] [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: 11/27/2020] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/22/2022] Open
Abstract
The uropathogenic Escherichia coli strain CFT073 causes kidney abscesses in mice Toll/interleukin-1 receptor domain-containing protein C (TcpC) dependently and the corresponding gene is present in around 40% of E. coli isolates of pyelonephritis patients. It impairs the Toll-like receptor (TLR) signaling chain and the NACHT leucin-rich repeat PYD protein 3 inflammasome (NLRP3) by binding to TLR4 and myeloid differentiation factor 88 as well as to NLRP3 and caspase-1, respectively. Overexpression of the tcpC gene stopped replication of CFT073. Overexpression of several tcpC-truncation constructs revealed a transmembrane region, while its TIR domain induced filamentous bacteria. Based on these observations, we hypothesized that tcpC expression is presumably tightly controlled. We tested two putative promoters designated P1 and P2 located at 5′ of the gene c2397 and 5′ of the tcpC gene (c2398), respectively, which may form an operon. High pH and increasing glucose concentrations stimulated a P2 reporter construct that was considerably stronger than a P1 reporter construct, while increasing FeSO4 concentrations suppressed their activity. Human urine activated P2, demonstrating that tcpC might be induced in the urinary tract of infected patients. We conclude that P2, consisting of a 240 bp region 5′ of the tcpC gene, represents the major regulator of tcpC expression.
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Affiliation(s)
- Julia Ittensohn
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Jacqueline Hemberger
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Hannah Griffiths
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Maren Keller
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Simone Albrecht
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Thomas Miethke
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
- Correspondence:
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31
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Chen Y, Liu L, Yu S, Li J, Zhou J, Chen J. Identification of Gradient Promoters of Gluconobacter oxydans and Their Applications in the Biosynthesis of 2-Keto-L-Gulonic Acid. Front Bioeng Biotechnol 2021; 9:673844. [PMID: 33898410 PMCID: PMC8064726 DOI: 10.3389/fbioe.2021.673844] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 12/19/2022] Open
Abstract
The acetic acid bacterium Gluconobacter oxydans is known for its unique incomplete oxidation and therefore widely applied in the industrial production of many compounds, e.g., 2-keto-L-gulonic acid (2-KLG), the direct precursor of vitamin C. However, few molecular tools are available for metabolically engineering G. oxydans, which greatly limit the strain development. Promoters are one of vital components to control and regulate gene expression at the transcriptional level for boosting production. In this study, the low activity of SDH was found to hamper the high yield of 2-KLG, and enhancing the expression of SDH was achieved by screening the suitable promoters based on RNA sequencing data. We obtained 97 promoters from G. oxydans’s genome, including two strong shuttle promoters and six strongest promoters. Among these promoters, P3022 and P0943 revealed strong activities in both Escherichia coli and G. oxydans, and the activity of the strongest promoter (P2703) was about threefold that of the other reported strong promoters of G. oxydans. These promoters were used to overexpress SDH in G. oxydans WSH-003. The titer of 2-KLG reached 3.7 g/L when SDH was under the control of strong promoters P2057 and P2703. This study obtained a series of gradient promoters, including two strong shuttle promoters, and expanded the toolbox of available promoters for the application in metabolic engineering of G. oxydans for high-value products.
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Affiliation(s)
- Yue Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Li Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Shiqin Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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Abstract
Vitamin B6 is an ensemble of six interconvertible vitamers: pyridoxine (PN), pyridoxamine (PM), pyridoxal (PL), and their 5'-phosphate derivatives, PNP, PMP, and PLP. Pyridoxal 5'-phosphate is a coenzyme in a variety of enzyme reactions concerning transformations of amino and amino acid compounds. This review summarizes all known and putative PLP-binding proteins found in the Escherichia coli MG1655 proteome. PLP can have toxic effects since it contains a very reactive aldehyde group at its 4' position that easily forms aldimines with primary and secondary amines and reacts with thiols. Most PLP is bound either to the enzymes that use it as a cofactor or to PLP carrier proteins, protected from the cellular environment but at the same time readily transferable to PLP-dependent apoenzymes. E. coli and its relatives synthesize PLP through the seven-step deoxyxylulose-5-phosphate (DXP)-dependent pathway. Other bacteria synthesize PLP in a single step, through a so-called DXP-independent pathway. Although the DXP-dependent pathway was the first to be revealed, the discovery of the widespread DXP-independent pathway determined a decline of interest in E. coli vitamin B6 metabolism. In E. coli, as in most organisms, PLP can also be obtained from PL, PN, and PM, imported from the environment or recycled from protein turnover, via a salvage pathway. Our review deals with all aspects of vitamin B6 metabolism in E. coli, from transcriptional to posttranslational regulation. A critical interpretation of results is presented, in particular, concerning the most obscure aspects of PLP homeostasis and delivery to PLP-dependent enzymes.
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33
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Todor H, Osadnik H, Campbell EA, Myers KS, Li H, Donohue TJ, Gross CA. Rewiring the specificity of extracytoplasmic function sigma factors. Proc Natl Acad Sci U S A 2020; 117:33496-33506. [PMID: 33318184 PMCID: PMC7776599 DOI: 10.1073/pnas.2020204117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators' DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid-nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.
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Affiliation(s)
- Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Kevin S Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Hao Li
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Timothy J Donohue
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94158
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34
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Saoud J, Carrier MC, Massé É, Faucher SP. The small regulatory RNA Lpr10 regulates the expression of RpoS in Legionella pneumophila. Mol Microbiol 2020; 115:789-806. [PMID: 33191583 DOI: 10.1111/mmi.14644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022]
Abstract
Legionella pneumophila (Lp) is a waterborne bacterium able to infect human alveolar macrophages, causing Legionnaires' disease. Lp can survive for several months in water, while searching for host cells to grow in, such as ciliates and amoeba. In Lp, the sigma factor RpoS is essential for survival in water. A previous transcriptomic study showed that RpoS positively regulates the small regulatory RNA Lpr10. In the present study, deletion of lpr10 results in an increased survival of Lp in water. Microarray analysis and RT-qPCR revealed that Lpr10 negatively regulates the expression of RpoS in the postexponential phase. Electrophoretic mobility shift assay and in-line probing showed that Lpr10 binds to a region upstream of the previously identified transcription start sites (TSS) of rpoS. A third putative transcription start site was identified by primer extension analysis, upstream of the Lpr10 binding site. In addition, nlpD TSS produces a polycistronic mRNA including the downstream gene rpoS, indicating a fourth TSS for rpoS. Our results suggest that the transcripts from the third and fourth TSS are negatively regulated by the Lpr10 sRNA. Therefore, we propose that Lpr10 is involved in a negative regulatory feedback loop to maintain expression of RpoS to an optimal level.
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Affiliation(s)
- Joseph Saoud
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
| | - Marie-Claude Carrier
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, QC, Canada
| | - Éric Massé
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, QC, Canada
| | - Sébastien P Faucher
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
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The BB0345 Hypothetical Protein of Borrelia burgdorferi Is Essential for Mammalian Infection. Infect Immun 2020; 88:IAI.00472-20. [PMID: 32928963 DOI: 10.1128/iai.00472-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
During the natural enzootic life cycle of Borrelia burgdorferi (also known as Borreliella burgdorferi), the bacteria must sense conditions within the vertebrate and arthropod and appropriately regulate expression of genes necessary to persist within these distinct environments. bb0345 of B. burgdorferi encodes a hypothetical protein of unknown function that is predicted to contain an N-terminal helix-turn-helix (HTH) domain. Because HTH domains can mediate protein-DNA interactions, we hypothesized that BB0345 might represent a previously unidentified borrelial transcriptional regulator with the ability to regulate events critical for the B. burgdorferi enzootic cycle. To study the role of BB0345 within mammals, we generated a bb0345 mutant and assessed its virulence potential in immunocompetent mice. The bb0345 mutant was able to initiate localized infection and disseminate to distal tissues but was cleared from all sites by 14 days postinfection. In vitro growth curve analyses revealed that the bb0345 mutant grew similar to wild-type bacteria in standard Barbour-Stoenner-Kelley II (BSK-II) medium; however, the mutant was not able to grow in dilute BSK-II medium or dialysis membrane chambers (DMCs) implanted in rats. Proteinase K accessibility assays and whole-cell partitioning indicated that BB0345 was intracellular and partially membrane associated. Comparison of protein production profiles between the wild-type parent and the bb0345 mutant revealed no major differences, suggesting BB0345 may not be a global transcriptional regulator. Taken together, these data show that BB0345 is essential for B. burgdorferi survival in the mammalian host, potentially by aiding the spirochete with a physiological function that is required by the bacterium during infection.
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36
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Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J. Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ. RNA Biol 2020; 18:1099-1110. [PMID: 33103565 PMCID: PMC8244752 DOI: 10.1080/15476286.2020.1827785] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
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Affiliation(s)
- Laura Wicke
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lucas Coppens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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37
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Sanyal R, Vimala A, Harinarayanan R. Studies on the Regulation of (p)ppGpp Metabolism and Its Perturbation Through the Over-Expression of Nudix Hydrolases in Escherichia coli. Front Microbiol 2020; 11:562804. [PMID: 33178149 PMCID: PMC7593582 DOI: 10.3389/fmicb.2020.562804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
Abstract
Stringent response mediated by modified guanosine nucleotides is conserved across bacteria and is regulated through the Rel/Spo functions. In Escherichia coli, RelA and SpoT proteins synthesize the modified nucleotides ppGpp and pppGpp, together referred to as (p)ppGpp. SpoT is also the primary (p)ppGpp hydrolase. In this study, using hypomorphic relA alleles, we provide experimental evidence for SpoT-mediated negative regulation of the amplification of RelA-dependent stringent response. We investigated the kinetics of ppGpp degradation in cells recovering from stringent response in the complete absence of SpoT function. We found that, although greatly diminished, there was slow ppGpp degradation and growth resumption after a lag period, concomitant with decrease in ppGpp pool. We present evidence for reduction in the ppGpp degradation rate following an increase in pppGpp pool, during recovery from stringent response. From a genetic screen, the nudix hydrolases MutT and NudG were identified as over-expression suppressors of the growth defect of ΔspoT and ΔspoT ΔgppA strains. The effect of over-expression of these hydrolases on the stringent response to amino acid starvation and basal (p)ppGpp pool was studied. Over-expression of each hydrolase reduced the strength of the stringent response to amino acid starvation, and additionally, perturbed the ratio of ppGpp to pppGpp in strains with reduced SpoT hydrolase activity. In these strains that do not accumulate pppGpp during amino acid starvation, the expression of NudG or MutT supported pppGpp accumulation. This lends support to the idea that a reduction in the SpoT hydrolase activity is sufficient to cause the loss of pppGpp accumulation and therefore the phenomenon is independent of hydrolases that target pppGpp, such as GppA.
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Affiliation(s)
- Rajeshree Sanyal
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Allada Vimala
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Rajendran Harinarayanan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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38
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Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R. Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife 2020; 9:e55308. [PMID: 32955440 PMCID: PMC7567609 DOI: 10.7554/elife.55308] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/18/2020] [Indexed: 01/28/2023] Open
Abstract
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈65% of promoters we remain ignorant of their regulation. Until we crack this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method, Reg-Seq, that links massively parallel reporter assays with mass spectrometry to produce a base pair resolution dissection of more than a E. coli promoters in 12 growth conditions. We demonstrate that the method recapitulates known regulatory information. Then, we examine regulatory architectures for more than 80 promoters which previously had no known regulatory information. In many cases, we also identify which transcription factors mediate their regulation. This method clears a path for highly multiplexed investigations of the regulatory genome of model organisms, with the potential of moving to an array of microbes of ecological and medical relevance.
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Affiliation(s)
- William T Ireland
- Department of Physics, California Institute of TechnologyPasadenaUnited States
| | - Suzannah M Beeler
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Emanuel Flores-Bautista
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Nicholas S McCarty
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Tom Röschinger
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Nathan M Belliveau
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of TechnologyPasadenaUnited States
| | - Annie Moradian
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of TechnologyPasadenaUnited States
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Rob Phillips
- Department of Physics, California Institute of TechnologyPasadenaUnited States
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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39
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Walker DM, Harshey RM. Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli. Mob DNA 2020; 11:26. [PMID: 32670425 PMCID: PMC7350765 DOI: 10.1186/s13100-020-00217-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/18/2020] [Indexed: 01/12/2023] Open
Abstract
Background The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the E. coli genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (cis-immunity) as well as the entire ~ 37 kb genome of Mu (Mu genome immunity). Paradoxically, MuB is responsible for cis-immunity and is also implicated in Mu genome immunity, but via different mechanisms. This study was undertaken to dissect the role of MuB in target choice in vivo. Results We tracked Mu transposition from six different starting locations on the E. coli genome, in the presence and absence of MuB. The data reveal that Mu’s ability to sample the entire genome during a single hop in a clonal population is independent of MuB, and that MuB is responsible for cis-immunity, plays a minor role in Mu genome immunity, and facilitates insertions into transcriptionally active regions. Unexpectedly, transposition patterns in the absence of MuB have helped extend the boundaries of the insular Ter segment of the E. coli genome. Conclusions The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.
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Affiliation(s)
- David M Walker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712 USA
| | - Rasika M Harshey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712 USA
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40
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Cervantes-Rivera R, Tronnet S, Puhar A. Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination. BMC Genomics 2020; 21:285. [PMID: 32252626 PMCID: PMC7132871 DOI: 10.1186/s12864-020-6565-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
Background Shigella is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans. Shigella invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strain S. flexneri serotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches. Results We have sequenced, assembled, annotated and manually curated the full genome of S. flexneri 5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new hybrid strategy to prepare gapless, highly accurate genome sequences, which also cover AT-rich tracks or repetitive sequences that are transcribed. Furthermore, we have performed genome-wide analysis of transcriptional start sites (TSS) and determined the length of 5′ untranslated regions (5′-UTRs) at typical culture conditions for the inoculum of in vitro infection experiments. We identified 6723 primary TSS (pTSS) and 7328 secondary TSS (sTSS). The S. flexneri 5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (http://regulondb.ccg.unam.mx) and RSAT (http://embnet.ccg.unam.mx/rsat/) databases to use their analysis tools in the S. flexneri 5a M90T genome. Conclusions We provide the first complete genome for S. flexneri serotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employing S. flexneri M90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation of S. flexneri 5a M90T. Further, we present a new hybrid strategy to prepare gapless, highly accurate genome sequences. Unlike currently used hybrid strategies combining long- and short-read DNA sequencing technologies to maximize accuracy, our workflow using long-read DNA sequencing and short-read RNA sequencing provides the added value of using non-redundant technologies, which yield distinct, exploitable datasets.
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Affiliation(s)
- Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden.,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Sophie Tronnet
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden.,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden. .,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden. .,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden.
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41
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Fontana J, Dong C, Kiattisewee C, Chavali VP, Tickman BI, Carothers JM, Zalatan JG. Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements. Nat Commun 2020; 11:1618. [PMID: 32238808 PMCID: PMC7113249 DOI: 10.1038/s41467-020-15454-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 03/04/2020] [Indexed: 11/09/2022] Open
Abstract
In bacterial systems, CRISPR-Cas transcriptional activation (CRISPRa) has the potential to dramatically expand our ability to regulate gene expression, but we lack predictive rules for designing effective gRNA target sites. Here, we identify multiple features of bacterial promoters that impose stringent requirements on CRISPRa target sites. Notably, we observe narrow, 2-4 base windows of effective sites with a periodicity corresponding to one helical turn of DNA, spanning ~40 bases and centered ~80 bases upstream of the TSS. However, we also identify two features suggesting the potential for broad scope: CRISPRa is effective at a broad range of σ70-family promoters, and an expanded PAM dCas9 allows the activation of promoters that cannot be activated by S. pyogenes dCas9. These results provide a roadmap for future engineering efforts to further expand and generalize the scope of bacterial CRISPRa.
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Affiliation(s)
- Jason Fontana
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA
| | - Chen Dong
- Department of Chemistry, University of Washington, Seattle, 98195, WA, USA
| | - Cholpisit Kiattisewee
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA
| | - Venkata P Chavali
- Department of Chemical Engineering, University of Washington, Seattle, 98195, WA, USA
| | - Benjamin I Tickman
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA
| | - James M Carothers
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, 98195, WA, USA.
- Center for Synthetic Biology, University of Washington, Seattle, 98195, WA, USA.
| | - Jesse G Zalatan
- Department of Chemistry, University of Washington, Seattle, 98195, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, 98195, WA, USA.
- Center for Synthetic Biology, University of Washington, Seattle, 98195, WA, USA.
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42
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Genome engineering of E. coli for improved styrene production. Metab Eng 2020; 57:74-84. [DOI: 10.1016/j.ymben.2019.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/18/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
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43
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Häkkinen A, Oliveira SMD, Neeli-Venkata R, Ribeiro AS. Transcription closed and open complex formation coordinate expression of genes with a shared promoter region. J R Soc Interface 2019; 16:20190507. [PMID: 31822223 DOI: 10.1098/rsif.2019.0507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many genes are spaced closely, allowing coordination without explicit control through shared regulatory elements and molecular interactions. We study the dynamics of a stochastic model of a gene-pair in a head-to-head configuration, sharing promoter elements, which accounts for the rate-limiting steps in transcription initiation. We find that only in specific regions of the parameter space of the rate-limiting steps is orderly coexpression exhibited, suggesting that successful cooperation between closely spaced genes requires the coevolution of compatible rate-limiting step configuration. The model predictions are validated using in vivo single-cell, single-RNA measurements of the dynamics of pairs of genes sharing promoter elements. Our results suggest that, in E. coli, the kinetics of the rate-limiting steps in active transcription can play a central role in shaping the dynamics of gene-pairs sharing promoter elements.
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Affiliation(s)
- Antti Häkkinen
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Samuel M D Oliveira
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Ramakanth Neeli-Venkata
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Andre S Ribeiro
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
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44
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Wang L, Zhang J. Prediction of sgRNA on-target activity in bacteria by deep learning. BMC Bioinformatics 2019; 20:517. [PMID: 31651233 PMCID: PMC6814057 DOI: 10.1186/s12859-019-3151-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/04/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND One of the main challenges for the CRISPR-Cas9 system is selecting optimal single-guide RNAs (sgRNAs). Recently, deep learning has enhanced sgRNA prediction in eukaryotes. However, the prokaryotic chromatin structure is different from eukaryotes, so models trained on eukaryotes may not apply to prokaryotes. RESULTS We designed and implemented a convolutional neural network to predict sgRNA activity in Escherichia coli. The network was trained and tested on the recently-released sgRNA activity dataset. Our convolutional neural network achieved excellent performance, yielding average Spearman correlation coefficients of 0.5817, 0.7105, and 0.3602, respectively for Cas9, eSpCas9 and Cas9 with a recA coding region deletion. We confirmed that the sgRNA prediction models trained on prokaryotes do not apply to eukaryotes and vice versa. We adopted perturbation-based approaches to analyze distinct biological patterns between prokaryotic and eukaryotic editing. Then, we improved the predictive performance of the prokaryotic Cas9 system by transfer learning. Finally, we determined that potential off-target scores accumulated on a genome-wide scale affect on-target activity, which could slightly improve on-target predictive performance. CONCLUSIONS We developed convolutional neural networks to predict sgRNA activity for wild type and mutant Cas9 in prokaryotes. Our results show that the prediction accuracy of our method is improved over state-of-the-art models.
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Affiliation(s)
- Lei Wang
- School of Life Science, Beijing Institute of Technology, South Zhongguancun Street, Beijing, 100081 China
| | - Juhua Zhang
- School of Life Science, Beijing Institute of Technology, South Zhongguancun Street, Beijing, 100081 China
- Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, The Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
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45
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RNase G controls tpiA mRNA abundance in response to oxygen availability in Escherichia coli. J Microbiol 2019; 57:910-917. [DOI: 10.1007/s12275-019-9354-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 01/25/2023]
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46
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Sumi S, Suzuki Y, Matsuki T, Yamamoto T, Tsuruta Y, Mise K, Kawamura T, Ito Y, Shimada Y, Watanabe E, Watanabe S, Toriyabe M, Takano Shiratori H, Ueda K, Takano H. Light-inducible carotenoid production controlled by a MarR-type regulator in Corynebacterium glutamicum. Sci Rep 2019; 9:13136. [PMID: 31511549 PMCID: PMC6739363 DOI: 10.1038/s41598-019-49384-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/23/2019] [Indexed: 01/21/2023] Open
Abstract
Carotenoid production in some non-phototropic bacteria occurs in a light-dependent manner to protect cells from photo-oxidants. Knowledge regarding the transcriptional regulator involved in the light-dependent production of carotenoids of non-phototrophic bacteria has been mainly confined to coenzyme B12-based photo-sensitive regulator CarH/LitR family proteins belonging to a MerR family transcriptional regulator. In this study, we found that bacteria belonging to Micrococcales and Corynebacteriales exhibit light-dependent carotenoid-like pigment production including an amino acid-producer Corynebacterium glutamicum AJ1511. CrtR is a putative MarR family transcriptional regulator located in the divergent region of a carotenoid biosynthesis gene cluster in the genome of those bacteria. A null mutant for crtR of C. glutamicum AJ1511 exhibited constitutive production of carotenoids independent of light. A complemented strain of the crtR mutant produced carotenoids in a light-dependent manner. Transcriptional analysis revealed that the expression of carotenoid biosynthesis genes is regulated in a light-dependent manner in the wild type, while the transcription was upregulated in the crtR mutant irrespective of light. In vitro experiments demonstrated that a recombinant CrtR protein binds to the specific sequences within the intergenic region of crtR and crtE, which corresponds to −58 to −7 for crtE, and +26 to −28 for crtR with respect to the transcriptional start site, and serves as a repressor for crtE transcription directed by RNA polymerase containing SigA. Taken together, the results indicate that CrtR light-dependently controls the expression of the carotenoid gene cluster in C. glutamicum and probably closely related Actinobacteria.
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Affiliation(s)
- Satoru Sumi
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yuto Suzuki
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Tetsuro Matsuki
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Takahiro Yamamoto
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yudai Tsuruta
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Kou Mise
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Takuya Kawamura
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yusuke Ito
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yuka Shimada
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Erika Watanabe
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Shoko Watanabe
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Minami Toriyabe
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Hatsumi Takano Shiratori
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan.
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47
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A Novel Gene Contributing to the Initiation of Fatty Acid Biosynthesis in Escherichia coli. J Bacteriol 2019; 201:JB.00354-19. [PMID: 31331975 DOI: 10.1128/jb.00354-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 07/08/2019] [Indexed: 11/20/2022] Open
Abstract
Type II fatty acid biosynthesis in bacteria can be broadly classified into the initiation and elongation phases. The biochemical functions defining each step in the two phases have been studied in vitro Among the β-ketoacyl-acyl carrier protein (ACP) synthases, FabH catalyzes the initiation reaction, while FabB and FabF, which primarily catalyze the elongation reaction, can also drive initiation as side reactions. A role for FabB and FabF in the initiation of fatty acid biosynthesis would be supported by the viability of the ΔfabH mutant. In this study, we show that the ΔfabH and ΔyiiD mutations were synthetically lethal and that ΔfabH ΔrelA ΔspoT and ΔfabH ΔdksA synthetic lethality was rescued by the heterologous expression of yiiD In the ΔfabH mutant, the expression of yiiD was positively regulated by (p)ppGpp. The growth defect, reduced cell size, and altered fatty acid profile of the ΔfabH mutant and the growth defect of the ΔfabH ΔfabF fabB15(Ts) mutant in oleate- and palmitate-supplemented medium at 42°C were rescued by the expression of yiiD from a multicopy plasmid. Together, these results indicate that the yiiD-encoded function supported initiation of fatty acid biosynthesis in the absence of FabH. We have renamed yiiD as fabY IMPORTANCE Fatty acid biosynthesis is an essential process conserved across life forms. β-Ketoacyl-ACP synthases are essential for fatty acid biosynthesis. FabH is a β-ketoacyl-ACP synthase that contributes to the initiation of fatty acid biosynthesis in Escherichia coli In this study, we present genetic and biochemical evidence that the yiiD (renamed fabY)-encoded function contributes to the biosynthesis of fatty acid in the absence of FabH activity and that under these conditions, the expression of FabY was regulated by the stringent response factors (p)ppGpp and DksA. Combined inactivation of FabH and FabY resulted in growth arrest, possibly due to the loss of fatty acid biosynthesis. A molecule(s) that inhibits the two activities can be an effective microbicide.
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Gilman J, Singleton C, Tennant RK, James P, Howard TP, Lux T, Parker DA, Love J. Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications. ACS Synth Biol 2019; 8:1175-1186. [PMID: 30995831 DOI: 10.1021/acssynbio.9b00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space.
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Affiliation(s)
- James Gilman
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Chloe Singleton
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Richard K. Tennant
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Paul James
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Thomas P. Howard
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-upon-Tyne NE1 7RU, U.K
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich 85764, Germany
| | - David A. Parker
- Biodomain, Shell Technology Center Houston, 3333 Highway 6 South, Houston, Texas 77082-3101, United States
| | - John Love
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
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49
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Martini MC, Zhou Y, Sun H, Shell SS. Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia. Front Microbiol 2019; 10:591. [PMID: 30984135 PMCID: PMC6448022 DOI: 10.3389/fmicb.2019.00591] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
The ability of Mycobacterium tuberculosis to infect, proliferate, and survive during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome-wide analyses are key to understanding gene regulation on a global scale. Here, we combine 5′-end-directed libraries with RNAseq expression libraries to gain insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during log phase growth and under hypoxia, a physiologically relevant stress condition. Using the model organism Mycobacterium smegmatis, we identified 6,090 transcription start sites (TSSs) with high confidence during log phase growth, of which 67% were categorized as primary TSSs for annotated genes, and the remaining were classified as internal, antisense, or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and of the coding sequences that do have leaders, 53% lack a strong consensus Shine-Dalgarno site. This indicates that like M. tuberculosis, M. smegmatis can initiate translation through multiple mechanisms. Our approach also allowed us to identify over 3,000 RNA cleavage sites, which occur at a novel sequence motif. To our knowledge, this represents the first report of a transcriptome-wide RNA cleavage site map in mycobacteria. The cleavage sites show a positional bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that in low oxygen, a condition associated with the host environment during infection, mycobacteria change their transcriptomic profiles and endonucleolytic RNA cleavage is markedly reduced, suggesting a mechanistic explanation for previous reports of increased mRNA half-lives in response to stress. In addition, a number of TSSs were triggered in hypoxia, 56 of which contain the binding motif for the sigma factor SigF in their promoter regions. This suggests that SigF makes direct contributions to transcriptomic remodeling in hypoxia-challenged mycobacteria. Taken together, our data provide a foundation for further study of both transcriptional and posttranscriptional regulation in mycobacteria.
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Affiliation(s)
- M Carla Martini
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Ying Zhou
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Huaming Sun
- Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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Abstract
The increasingly complex functionality of RNA is contrasted by its simple chemical composition. RNA is generally built from only four different nucleotides (adenine, guanine, cytosine, and uracil). To date, >160 chemical modifications are known to decorate RNA molecules and thereby alter their function or stability. Many RNA modifications are conserved throughout bacteria, archaea, and eukaryotes, while some are unique to each branch of life. Most known modifications occur at internal positions, while there is limited diversity at the termini. The dynamic nature of RNA modifications and newly discovered regulatory functions of some of these RNA modifications gave birth to a new field, now often referred to as "epitranscriptomics." This review highlights the major developments in this field and summarizes detection principles for internal as well as 5'-terminal mRNA modifications in prokaryotes and archaea to investigate their biological significance.
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