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Wei G, Li S, Ye S, Wang Z, Zarringhalam K, He J, Wang W, Shao Z. High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5. Int J Mol Sci 2022; 23:ijms232415995. [PMID: 36555635 PMCID: PMC9788540 DOI: 10.3390/ijms232415995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Alkanes are widespread in the ocean, and Alcanivorax is one of the most ubiquitous alkane-degrading bacteria in the marine ecosystem. Small RNAs (sRNAs) are usually at the heart of regulatory pathways, but sRNA-mediated alkane metabolic adaptability still remains largely unknown due to the difficulties of identification. Here, differential RNA sequencing (dRNA-seq) modified with a size selection (~50-nt to 500-nt) strategy was used to generate high-resolution sRNAs profiling in the model species Alcanivorax dieselolei B-5 under alkane (n-hexadecane) and non-alkane (acetate) conditions. As a result, we identified 549 sRNA candidates at single-nucleotide resolution of 5'-ends, 63.4% of which are with transcription start sites (TSSs), and 36.6% of which are with processing sites (PSSs) at the 5'-ends. These sRNAs originate from almost any location in the genome, regardless of intragenic (65.8%), antisense (20.6%) and intergenic (6.2%) regions, and RNase E may function in the maturation of sRNAs. Most sRNAs locally distribute across the 15 reference genomes of Alcanivorax, and only 7.5% of sRNAs are broadly conserved in this genus. Expression responses to the alkane of several core conserved sRNAs, including 6S RNA, M1 RNA and tmRNA, indicate that they may participate in alkane metabolisms and result in more actively global transcription, RNA processing and stresses mitigation. Two novel CsrA-related sRNAs are identified, which may be involved in the translational activation of alkane metabolism-related genes by sequestering the global repressor CsrA. The relationships of sRNAs with the characterized genes of alkane sensing (ompS), chemotaxis (mcp, cheR, cheW2), transporting (ompT1, ompT2, ompT3) and hydroxylation (alkB1, alkB2, almA) were created based on the genome-wide predicted sRNA-mRNA interactions. Overall, the sRNA landscape lays the ground for uncovering cryptic regulations in critical marine bacterium, among which both the core and species-specific sRNAs are implicated in the alkane adaptive metabolisms.
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Affiliation(s)
- Guangshan Wei
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Sujie Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Sida Ye
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Zining Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jianguo He
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Correspondence: (W.W.); (Z.S.)
| | - Zongze Shao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: (W.W.); (Z.S.)
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Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin. Arch Microbiol 2022; 204:461. [DOI: 10.1007/s00203-022-03085-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/08/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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徐 丽, 刘 姗, 王 敏, 刘 芳, 张 容, 张 凯. [Regulatory role of small RNA srn821978 in mutacin IV expression in Streptococcus mutans]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1725-1732. [PMID: 34916201 PMCID: PMC8685694 DOI: 10.12122/j.issn.1673-4254.2021.11.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To analyze the role of small RNA srn821798 in posttranscriptional regulation of mutacin IV expression in Streptococcus mutans. METHODS The potential target genes of srn821978 were predicted using RNAhybrid, RNAPredator and IntaRNA. We collected 10 Streptococcus mutans (S.muans) strains with high expression of mutacin IV and another 10 S.muans strains that did not express mutacin IV screened by inhibition zone test, and the expression levels of srn821798 and the candidate target genes in these strains were detected by qPCR. Using synthesized mimics and inhibitors of srn821798, we constructed S.muans strains with high or low srn821798 expression via electroporation based on the standard strain of S.muans UA159, and analyzed the expression levels of srn821798 and its candidate target genes in these strains. We also examined the binding ability of srn821798 to its target gene sepM using electrophoresis and a dual- luciferase reporter system. RESULTS The expression levels of the candidate target genes of srn821798 including sepM, comD, comE, nlmA and nlmB were significantly higher while the expression level of srn821798 was significantly lower in clinical S.muans strains with high expression of mutacin IV than in those without mutacin IV expression (P < 0.05). Although the expression levels of the candidate target genes in strains with up- regulated or down- regulated srn821798 expression did not differ significantly from those in the standard strain, the expression level of sepM showed a trend of differential distribution, and srn821798 was predicted to have a strong binding ability to sepM action site. CONCLUSION srn821798 may play a regulatory role in the expression of mutacin IV in S.muans, but the underlying mechanism remains to be explored.
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Affiliation(s)
- 丽 徐
- 蚌埠医学院第一附属医院口腔科,安徽 蚌埠 233004Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu233004, China
| | - 姗姗 刘
- 蚌埠医学院第一附属医院口腔科,安徽 蚌埠 233004Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu233004, China
| | - 敏 王
- 蚌埠医学院第二附属医院口腔科,安徽 蚌埠 233040Department of Stomatology, Second Affiliated Hospital of Bengbu Medical College, Bengbu233040, China
| | - 芳 刘
- 蚌埠医学院第一附属医院口腔科,安徽 蚌埠 233004Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu233004, China
| | - 容秀 张
- 蚌埠医学院第一附属医院口腔科,安徽 蚌埠 233004Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu233004, China
| | - 凯 张
- 蚌埠医学院第一附属医院口腔科,安徽 蚌埠 233004Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu233004, China
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Sonnenberg CB, Haugen P. The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid. G3-GENES GENOMES GENETICS 2021; 11:6325023. [PMID: 34544144 PMCID: PMC8496264 DOI: 10.1093/g3journal/jkab256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/06/2021] [Indexed: 12/02/2022]
Abstract
Bacterial genomes typically consist of one large chromosome, but can also include secondary replicons. These so-called multipartite genomes are scattered on the bacterial tree of life with the majority of cases belonging to Proteobacteria. Within the class gamma-proteobacteria, multipartite genomes are restricted to the two families Vibrionaceae and Pseudoalteromonadaceae. Whereas the genome of vibrios is well studied, information on the Pseudoalteromonadaceae genome is much scarcer. We have studied Pseudoalteromonadaceae with respect to the origin of the chromid, how pangene categories are distributed, how genes are expressed relative to their genomic location, and identified chromid hallmark genes. We calculated the Pseudoalteromonadaceae pangenome based on 25 complete genomes and found that core/softcore are significantly overrepresented in late replicating sectors of the chromid, regardless of how the chromid is replicated. On the chromosome, core/softcore and shell/cloud genes are only weakly overrepresented at the chromosomal replication origin and termination sequences, respectively. Gene expression is trending downwards with increasing distance from the chromosomal oriC, whereas the chromidal expression pattern is more complex. Moreover, we identified 78 chromid hallmark genes, and BLASTp searches suggest that the majority of them were acquired from the ancestral gene pool of Alteromonadales. Finally, our data strongly suggest that the chromid originates from a plasmid that was acquired in a relatively recent event. In summary, this study extends our knowledge on multipartite genomes, and helps us understand how and why secondary replicons are acquired, why they are maintained, and how they are shaped by evolution.
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Affiliation(s)
- Cecilie Bækkedal Sonnenberg
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø N-9037, Norway
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø N-9037, Norway
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Luo X, Esberard M, Bouloc P, Jacq A. A Small Regulatory RNA Generated from the malK 5' Untranslated Region Targets Gluconeogenesis in Vibrio Species. mSphere 2021; 6:e0013421. [PMID: 34190585 PMCID: PMC8265627 DOI: 10.1128/msphere.00134-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
Vsr217 is a small RNA from Vibrio tasmaniensis LGP32, a pathogen associated with mortality events affecting juvenile oysters. The vsr217 gene is located within the 5' untranslated region (UTR) of malK, encoding the ATPase component of the maltose importer, and is conserved within the genus Vibrio. In the presence of maltose, vsr217 is regulated by MalT, the positive regulator of the maltose regulon. vsr217 is required in cis for the full expression of malK. In addition, Vsr217 acts in trans to downregulate the expression of fbp encoding fructose-1,6-bisphosphatase, an enzyme involved in gluconeogenesis. Thus, in the presence of maltose, the induction of Vsr217 is expected to promote glycolysis by negatively regulating the expression of a key enzyme of gluconeogenesis. IMPORTANCE Juvenile pacific oysters have been subject in recent years to summer mortality episodes with deep economic consequences. The pathogen Vibrio tasmaniensis has been associated with such mortality events. For bacterial pathogens, survival within the host requires profound metabolic adaptations according to available resources. All kinds of regulatory elements, including noncoding RNAs, orchestrate this response. Oysters are rich in glycogen, a precursor of maltose, and we previously reported that V. tasmaniensis maltose-regulated genes are strongly induced during oyster infection. Here, we report the dual mechanism by which a small regulatory RNA, generated from the 5' untranslated region of a gene belonging to the maltose regulon, acts both in cis and trans. In cis, it stimulates growth on maltose, and in trans, it downregulates the expression of a gene associated with gluconeogenesis, thus coordinating maltose utilization with central carbon metabolism.
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Affiliation(s)
- Xing Luo
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Marick Esberard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Annick Jacq
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Audrézet F, Zaiko A, Lear G, Wood SA, Tremblay LA, Pochon X. Biosecurity implications of drifting marine plastic debris: Current knowledge and future research. MARINE POLLUTION BULLETIN 2021; 162:111835. [PMID: 33220912 DOI: 10.1016/j.marpolbul.2020.111835] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
The introduction and spread of marine non-indigenous species (NIS) and pathogens into new habitats are a major threat to biodiversity, ecosystem services, human health, and can have substantial economic consequences. Shipping is considered the main vector for marine biological invasions; less well understood is the increased spread of marine NIS and pathogens rafting on marine plastic debris (MPD). Despite an increasing research interest and recent progress in characterizing the plastisphere, this manuscript highlights critical knowledge gaps and research priorities towards a better understanding of the biosecurity implications of MPD. We advocate for future research to (i) investigate plastisphere community succession and the factors influencing NIS propagules and pathogens recruitment through robust experimental investigations; (ii) combine microscopy and molecular approaches to effectively assess the presence of specific taxa; (iii) include additional genetic markers to thoroughly characterize the biodiversity associated with MPD and explore the presence of specific marine pests.
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Affiliation(s)
- François Audrézet
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand.
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Louis A Tremblay
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; School of Biological Sciences, University of Auckland, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Sonnenberg CB, Kahlke T, Haugen P. Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement. BMC Genomics 2020; 21:695. [PMID: 33023476 PMCID: PMC7542380 DOI: 10.1186/s12864-020-07117-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/29/2020] [Indexed: 11/12/2022] Open
Abstract
Background The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories. Results We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression. Conclusion The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.
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Affiliation(s)
- Cecilie Bækkedal Sonnenberg
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037, Tromsø, Norway.
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The ilvGMEDA Operon Is Regulated by Transcription Attenuation in Vibrio alginolyticus ZJ-T. Appl Environ Microbiol 2019; 85:AEM.00880-19. [PMID: 31324637 DOI: 10.1128/aem.00880-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/16/2019] [Indexed: 11/20/2022] Open
Abstract
Bacteria synthesize amino acids according to their availability in the environment or, in the case of pathogens, within the host. We explored the regulation of the biosynthesis of branched-chain amino acids (BCAAs) (l-leucine, l-valine, and l-isoleucine) in Vibrio alginolyticus, a marine fish and shellfish pathogen and an emerging opportunistic human pathogen. In this species, the ilvGMEDA operon encodes the main pathway for biosynthesis of BCAAs. Its upstream regulatory region shows no sequence similarity to the corresponding region in Escherichia coli or other Enterobacteriaceae, and yet we show that this operon is regulated by transcription attenuation. The translation of a BCAA-rich peptide encoded upstream of the structural genes provides an adaptive response similar to the E. coli canonical model. This study of a nonmodel Gram-negative organism highlights the mechanistic conservation of transcription attenuation despite the absence of primary sequence conservation.IMPORTANCE This study analyzes the regulation of the biosynthesis of branched-chain amino acids (leucine, valine, and isoleucine) in Vibrio alginolyticus, a marine bacterium that is pathogenic to fish and humans. The results highlight the conservation of the main regulatory mechanism with that of the enterobacterium Escherichia coli, suggesting that such a mechanism appeared early during the evolution of Gram-negative bacteria, allowing adaptation to a wide range of environments.
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csrB Gene Duplication Drives the Evolution of Redundant Regulatory Pathways Controlling Expression of the Major Toxic Secreted Metalloproteases in Vibrio tasmaniensis LGP32. mSphere 2018; 3:3/6/e00582-18. [PMID: 30487156 PMCID: PMC6262261 DOI: 10.1128/msphere.00582-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The conserved CsrB sRNAs are an example of sibling sRNAs, i.e., sRNAs which are present in multiple copies in genomes. This report illustrates how new copies arise through gene duplication events and highlights two evolutionary advantages of having such multiple copies: differential regulation of the multiple copies allows integration of different input signals into the regulatory network of which they are parts, and the high redundancy that they provide confers a strong robustness to the system. CsrBs are bacterial highly conserved and multiple-copy noncoding small RNAs (sRNAs) that play major roles in cell physiology and virulence. In the Vibrio genus, they are known to be regulated by the two-component system VarS/VarA. They modulate the well-characterized quorum sensing pathway controlling virulence and luminescence in Vibrio cholerae and Vibrio harveyi, respectively. Remarkably, Vibrio tasmaniensis LGP32, an oyster pathogen that belongs to the Splendidus clade, was found to have four copies of csrB, named csrB1-4, compared to two to three copies in other Vibrio species. Here, we show that the extra csrB4 copy results from a csrB3 gene duplication, a characteristic of the Splendidus clade. Interestingly, csrB genes are regulated in different ways in V. tasmaniensis, with csrB1 expression being independent of the VarS/VarA system. We found that a complex regulatory network involving CsrBs, quorum sensing, and the stationary-phase sigma factor σS redundantly but differentially controls the production of two secreted metalloproteases, Vsm and PrtV, the former being a major determinant of the V. tasmaniensis extracellular product toxicity. In particular, we identified a novel VarS/VarA-dependent but CsrB-independent pathway that controls positively both Vsm production and PrtV production as well as rpoS expression. Altogether, our data show that a csrB gene duplication event in V. tasmaniensis supported the evolution of the regulatory network controlling the expression of major toxic secreted metalloproteases, thereby increasing redundancy and enabling the integration of additional input signals. IMPORTANCE The conserved CsrB sRNAs are an example of sibling sRNAs, i.e., sRNAs which are present in multiple copies in genomes. This report illustrates how new copies arise through gene duplication events and highlights two evolutionary advantages of having such multiple copies: differential regulation of the multiple copies allows integration of different input signals into the regulatory network of which they are parts, and the high redundancy that they provide confers a strong robustness to the system.
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Plágaro AH, Pearman PB, Kaberdin VR. Defining the transcription landscape of the Gram-negative marine bacterium Vibrio harveyi. Genomics 2018; 111:1547-1556. [PMID: 30423347 DOI: 10.1016/j.ygeno.2018.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/13/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022]
Abstract
Vibrio harveyi is a Gram-negative pathogenic bacterium ubiquitously present in natural aquatic systems. Although environmental adaptability in V. harveyi may be enabled by profound reprogramming of gene expression previously observed during responses to starvation, suboptimal temperatures and other stress factors, the key characteristics of V. harveyi transcripts and operons, such as their boundaries and size as well as location of small RNA genes, remain largely unknown. To reveal the main features of the V. harveyi transcriptome, total RNA of this organism was analyzed by differential RNA sequencing (dRNA-seq). Analysis of the dRNA-seq data made it possible to define the primary transcriptome of V. harveyi along with cis-acting regulatory elements (riboswitches and leader sequences) and new genes. The latter encode a number of putative polypeptides and new phylogenetically conserved antisense RNAs potentially involved in the post-transcriptional control of gene expression.
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Affiliation(s)
- Ander Hernández Plágaro
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain.
| | - Peter B Pearman
- Department of Plant Biology and Ecology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620 Plentzia, Spain.
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Deng Y, Su Y, Liu S, Guo Z, Cheng C, Ma H, Wu J, Feng J, Chen C. Identification of a Novel Small RNA srvg23535 in Vibrio alginolyticus ZJ-T and Its Characterization With Phenotype MicroArray Technology. Front Microbiol 2018; 9:2394. [PMID: 30349521 PMCID: PMC6186989 DOI: 10.3389/fmicb.2018.02394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 09/18/2018] [Indexed: 01/28/2023] Open
Abstract
Small non-coding RNAs (sRNAs) are important modulators of gene expression and are involved in the pathogenesis and survival of prokaryotes. However, few studies have been conducted with Vibrio alginolyticus, which limits our ability to probe the regulation of virulence and environmental adaptation by sRNAs in this opportunistic pathogen. In this study, the sRNA candidate srvg23535 was identified in V. alginolyticus ZJ-T. The precise transcript end, secondary structure, and sequence conservation were determined. A srvg23535 null mutant was constructed and characterized by using Phenotype MicroArray (PM) technology. In silico target prediction was conducted by IntaRNA and TargetRNA2. Subsequently, a 107 nt transcript was validated with a sigma70 promoter at the 5' end and a Rho-independent terminator at the 3' end. The sRNA srvg23535 had four stem-loop structures and was conserved among Vibrio harveyi, Vibrio parahaemolyticus, and Vibrio splendidus. Deletion of srvg23535 in V. alginolyticus ZJ-T led to a weaker utilization of D-mannose, D-melibiose, lactulose, and inosine as carbon sources but stronger utilization of L-cysteine as nitrogen source. Moreover, the srvg2353 mutant showed stronger resistance to osmotic stress but weaker resistance to pH stress. Additionally, a total of 22 common targets were identified and several were related to the observed phenotype of the mutant. This study indicated that the novel sRNA, srvg23535, is conserved and restricted to Vibrio spp., affecting the utilization of several carbon and nitrogen sources and the response to osmotic and pH stress. These results extend our understanding of sRNA regulation in V. alginolyticus and provide a significant resource for the further study of the precise target mRNAs of srvg23535, which may provide targets for antibacterial therapeutic or attenuated vaccines against Vibrio spp.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Changhong Cheng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongling Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jinjun Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chang Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Xisha/Nansha Ocean Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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12
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Rochat T, Bohn C, Morvan C, Le Lam T, Razvi F, Pain A, Toffano-Nioche C, Ponien P, Jacq A, Jacquet E, Fey PD, Gautheret D, Bouloc P. The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus. Nucleic Acids Res 2018; 46:8803-8816. [PMID: 29986060 PMCID: PMC6158497 DOI: 10.1093/nar/gky584] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 05/28/2018] [Accepted: 06/29/2018] [Indexed: 01/31/2023] Open
Abstract
RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of ΔrsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.
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Affiliation(s)
- Tatiana Rochat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Chantal Bohn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Claire Morvan
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Thao Nguyen Le Lam
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Fareha Razvi
- University of Nebraska Medical Center, Department of Pathology and Microbiology, Omaha, NE, USA
| | - Adrien Pain
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Claire Toffano-Nioche
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Annick Jacq
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Paul D Fey
- University of Nebraska Medical Center, Department of Pathology and Microbiology, Omaha, NE, USA
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
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13
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Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation. BMC Genomics 2018; 19:373. [PMID: 29783948 PMCID: PMC5963079 DOI: 10.1186/s12864-018-4716-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/23/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.
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Affiliation(s)
- Evelyne Krin
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Sebastian Aguilar Pierlé
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Odile Sismeiro
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Bernd Jagla
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Biomarker Discovery Platform, UtechS CB and Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Marie-Agnès Dillies
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Oihane Irazoki
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Susana Campoy
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Zoé Rouy
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Stéphane Cruveiller
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Claudine Médigue
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Jean-Yves Coppée
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Didier Mazel
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
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14
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Fitzgerald DM, Smith C, Lapierre P, Wade JT. The evolutionary impact of intragenic FliA promoters in proteobacteria. Mol Microbiol 2018; 108:361-378. [PMID: 29476659 PMCID: PMC5943157 DOI: 10.1111/mmi.13941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
In Escherichia coli, one sigma factor recognizes the majority of promoters, and six 'alternative' sigma factors recognize specific subsets of promoters. The alternative sigma factor FliA (σ28 ) recognizes promoters upstream of many flagellar genes. We previously showed that most E. coli FliA binding sites are located inside genes. However, it was unclear whether these intragenic binding sites represent active promoters. Here, we construct and assay transcriptional promoter-lacZ fusions for all 52 putative FliA promoters previously identified by ChIP-seq. These experiments, coupled with integrative analysis of published genome-scale transcriptional datasets, strongly suggest that most intragenic FliA binding sites are active promoters that transcribe highly unstable RNAs. Additionally, we show that widespread intragenic FliA-dependent transcription may be a conserved phenomenon, but that specific promoters are not themselves conserved. We conclude that intragenic FliA-dependent promoters and the resulting RNAs are unlikely to have important regulatory functions. Nonetheless, one intragenic FliA promoter is broadly conserved and constrains evolution of the overlapping protein-coding gene. Thus, our data indicate that intragenic regulatory elements can influence bacterial protein evolution and suggest that the impact of intragenic regulatory sequences on genome evolution should be considered more broadly.
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Affiliation(s)
- Devon M. Fitzgerald
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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15
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Liu W, Rochat T, Toffano-Nioche C, Le Lam TN, Bouloc P, Morvan C. Assessment of Bona Fide sRNAs in Staphylococcus aureus. Front Microbiol 2018. [PMID: 29515534 PMCID: PMC5826253 DOI: 10.3389/fmicb.2018.00228] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches.
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Affiliation(s)
- Wenfeng Liu
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tatiana Rochat
- VIM, Institut National de la Recherche Agronomique, Université Paris-Saclay, Institut National de la Recherche Agronomique Centre Jouy-en-Josas, Jouy-en-Josas, France
| | - Claire Toffano-Nioche
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thao Nguyen Le Lam
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Claire Morvan
- Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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16
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Ficko-Blean E, Préchoux A, Thomas F, Rochat T, Larocque R, Zhu Y, Stam M, Génicot S, Jam M, Calteau A, Viart B, Ropartz D, Pérez-Pascual D, Correc G, Matard-Mann M, Stubbs KA, Rogniaux H, Jeudy A, Barbeyron T, Médigue C, Czjzek M, Vallenet D, McBride MJ, Duchaud E, Michel G. Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. Nat Commun 2017; 8:1685. [PMID: 29162826 PMCID: PMC5698469 DOI: 10.1038/s41467-017-01832-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/17/2017] [Indexed: 12/01/2022] Open
Abstract
Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria using largely uncharacterized mechanisms. Here we describe the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, in the marine heterotrophic bacterium Zobellia galactanivorans. Carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and genes distal to the PUL, including a susCD-like pair. The carrageenan utilization system is well conserved in marine Bacteroidetes but modified in other phyla of marine heterotrophic bacteria. The core system is completed by additional functions that might be assumed by non-orthologous genes in different species. This complex genetic structure may be the result of multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion. Carrageenans, major cell wall polysaccharides of red macroalgae, are metabolised by marine heterotrophic bacteria through unclear mechanisms. Here, the authors identify an unusual polysaccharide-utilization locus encoding carrageenan catabolism in a marine bacterium, and characterise the complete pathway.
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Affiliation(s)
- Elizabeth Ficko-Blean
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Aurélie Préchoux
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - François Thomas
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Tatiana Rochat
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert Larocque
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Yongtao Zhu
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53201, Milwaukee, WI, USA
| | - Mark Stam
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Sabine Génicot
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Murielle Jam
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Alexandra Calteau
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Benjamin Viart
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - David Ropartz
- INRA, UR1268 Biopolymers Interactions Assemblies, F-44316, Nantes, France
| | | | - Gaëlle Correc
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Maria Matard-Mann
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymers Interactions Assemblies, F-44316, Nantes, France
| | - Alexandra Jeudy
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Claudine Médigue
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - David Vallenet
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Mark J McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53201, Milwaukee, WI, USA
| | - Eric Duchaud
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France.
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17
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Cerutti F, Mallet L, Painset A, Hoede C, Moisan A, Bécavin C, Duval M, Dussurget O, Cossart P, Gaspin C, Chiapello H. Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria. BMC Genomics 2017; 18:882. [PMID: 29145803 PMCID: PMC5689173 DOI: 10.1186/s12864-017-4242-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/29/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes. We applied this approach on 79 complete genomes of the Listeria genus and identified fifty-two accessory sRNAs, of which most were present in the Listeria common ancestor and lost during Listeria evolution. We detected significant coevolution between 23 sRNA and 52 coding genes and inferred the Listeria sRNA-coding genes coevolution network. We characterized a main hub of 12 sRNAs that coevolved with genes encoding cell wall proteins and virulence factors. Among them, an sRNA specific to L. monocytogenes species, rli133, coevolved with genes involved either in pathogenicity or in interaction with host cells, possibly acting as a direct negative post-transcriptional regulation. CONCLUSIONS Our approach allowed the identification of candidate sRNAs potentially involved in pathogenicity and host interaction, consistent with recent findings on known pathogenicity actors. We highlight four sRNAs coevolving with seven internalin genes, some of which being important virulence factors in Listeria.
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Affiliation(s)
- Franck Cerutti
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Ludovic Mallet
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Anaïs Painset
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France.,Present address: Public Health England, 61 Colindale Avenue, London, NW9 5EQ, England
| | - Claire Hoede
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Annick Moisan
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Christophe Bécavin
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | - Mélodie Duval
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France
| | - Olivier Dussurget
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, F-75013, Paris, France
| | - Pascale Cossart
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015, Paris, France.,INSERM, U604,F-75015, Paris, France.,INRA, USC2020, F-75015, Paris, France
| | - Christine Gaspin
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France
| | - Hélène Chiapello
- Université de Toulouse, INRA, UR 875 Unité Mathématiques et Informatique Appliquées de Toulouse, Auzeville, 31326, Castanet-Tolosan, France.
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Impact of bacterial sRNAs in stress responses. Biochem Soc Trans 2017; 45:1203-1212. [PMID: 29101308 PMCID: PMC5730939 DOI: 10.1042/bst20160363] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
Bacterial life is harsh and involves numerous environmental and internal challenges that are perceived as stresses. Consequently, adequate responses to survive, cope with, and counteract stress conditions have evolved. In the last few decades, a class of small, non-coding RNAs (sRNAs) has been shown to be involved as key players in stress responses. This review will discuss — primarily from an enterobacterial perspective — selected stress response pathways that involve antisense-type sRNAs. These include themes of how bacteria deal with severe envelope stress, threats of DNA damage, problems with poisoning due to toxic sugar intermediates, issues of iron homeostasis, and nutrient limitation/starvation. The examples discussed highlight how stress relief can be achieved, and how sRNAs act mechanistically in regulatory circuits. For some cases, we will propose scenarios that may suggest why contributions from post-transcriptional control by sRNAs, rather than transcriptional control alone, appear to be a beneficial and universally selected feature.
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Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M, Youguo L. A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R. Front Microbiol 2017; 8:1730. [PMID: 28943874 PMCID: PMC5596092 DOI: 10.3389/fmicb.2017.01730] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/24/2017] [Indexed: 01/23/2023] Open
Abstract
In bacteria, small non-coding RNAs (sRNAs) are critical regulators of cellular adaptation to changes in metabolism, physiology, or the external environment. In the last decade, more than 2000 of sRNA families have been reported in the Rfam database and have been shown to exert various regulatory functions in bacterial transcription and translation. However, little is known about sRNAs and their functions in Mesorhizobium. Here, we predicted putative sRNAs in the intergenic regions (IGRs) of M. huakuii 7653R by genome-wide comparisons with four related Mesorhizobial strains. The expression and transcribed regions of candidate sRNAs were analyzed using a set of high-throughput RNA deep sequencing data. In all, 39 candidate sRNAs were found, with 5 located in the symbiotic megaplasmids and 34 in the chromosome of M. huakuii 7653R. Of these, 24 were annotated as functional sRNAs in the Rfam database and 15 were recognized as putative novel sRNAs. The expression of nine selected sRNAs was confirmed by Northern blotting, and most of the nine selected sRNAs were highly expressed in 28 dpi nodules and under symbiosis-mimicking conditions. For those putative novel sRNAs, functional categorizations of their target genes were performed by analyzing the enriched GO terms. In addition, MH_s15 was shown to be an abundant and conserved sRNA.
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Affiliation(s)
- Xie Fuli
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Zhao Wenlong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Wang Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Zhang Jing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Hao Baohai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Zou Zhengzheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Ma Bin-Guang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Li Youguo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
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Chen ICK, Velicer GJ, Yu YTN. Divergence of functional effects among bacterial sRNA paralogs. BMC Evol Biol 2017; 17:199. [PMID: 28830343 PMCID: PMC5568312 DOI: 10.1186/s12862-017-1037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus. Specifically, Pxr prevents the initiation of fruiting body development when nutrients are abundant. Previous work has shown that Pxr appears to have a recent origin within a sub-clade of the myxobacteria, which allowed us to infer the most recent common ancestor of pxr and examine the divergence of Pxr since its origin. RESULTS To test for inter-specific divergence in functional effects, extant pxr homologs from several species and their inferred ancestor were introduced into an M. xanthus deletion mutant lacking pxr. Both the inferred ancestral pxr and all extant alleles from species containing only one copy of pxr were found to control development in M. xanthus in a qualitatively similar manner to the native M. xanthus allele. However, multiple paralogs present in Cystobacter species exhibited divergent effects, with two paralogs controlling M. xanthus development but two others failing to do so. These differences may have occurred through changes in gene expression caused by apparent structural differences in the sRNA variants encoded by these paralogs. CONCLUSIONS Taken together, our results suggest that Pxr plays a common fundamental role in developmental gene regulation across diverse species of myxobacteria but also that the functional effects of some Pxr variants may be evolving in some lineages.
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Affiliation(s)
- I-Chen Kimberly Chen
- Department of Biology, Indiana University, Bloomington, IN47405, USA. .,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland. .,Present address: School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332, USA.
| | - Gregory J Velicer
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
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Thode SK, Bækkedal C, Söderberg JJ, Hjerde E, Hansen H, Haugen P. Construction of a fur null mutant and RNA-sequencing provide deeper global understanding of the Aliivibrio salmonicida Fur regulon. PeerJ 2017; 5:e3461. [PMID: 28717590 PMCID: PMC5511505 DOI: 10.7717/peerj.3461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its target genes. Due to its importance in virulence, the Fur regulon is well studied for several model bacteria. In our previous work, we used computational predictions and microarray to gain insights into Fur-regulation in Aliivibrio salmonicida, and have identified a number of genes and operons that appear to be under direct control of Fur. To provide a more accurate and deeper global understanding of the biological role of Fur we have now generated an A. salmonicida fur knock-out strain and used RNA-sequencing to compare gene expression between the wild-type and fur null mutant strains. RESULTS An A. salmonicida fur null mutant strain was constructed. Biological assays demonstrate that deletion of fur results in loss of fitness, with reduced growth rates, and reduced abilities to withstand low-iron conditions, and oxidative stress. When comparing expression levels in the wild-type and the fur null mutant we retrieved 296 differentially expressed genes distributed among 18 of 21 functional classes of genes. A gene cluster encoding biosynthesis of the siderophore bisucaberin represented the highest up-regulated genes in the fur null mutant. Other highly up-regulated genes all encode proteins important for iron acquisition. Potential targets for the RyhB sRNA was predicted from the list of down-regulated genes, and significant complementarities were found between RyhB and mRNAs of the fur, sodB, cysN and VSAL_I0422 genes. Other sRNAs with potential functions in iron homeostasis were identified. CONCLUSION The present work provides by far the most comprehensive and deepest understanding of the Fur regulon in A. salmonicida to date. Our data also contribute to a better understanding of how Fur plays a key role in iron homeostasis in bacteria in general, and help to show how Fur orchestrates iron uptake when iron levels are extremely low.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Cecilie Bækkedal
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Jenny Johansson Söderberg
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Hilde Hansen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
| | - Peik Haugen
- Department of Chemistry and The Norwegian Structural Biology Centre, Faculty of Science and Technology, UiTThe Arctic University of Norway, Tromsø, Norway
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Zhang Y, Yan D, Xia L, Zhao X, Osei-Adjei G, Xu S, Sheng X, Huang X. The malS-5′UTR regulates hisG, a key gene in the histidine biosynthetic pathway in Salmonella enterica serovar Typhi. Can J Microbiol 2017; 63:287-295. [DOI: 10.1139/cjm-2016-0490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial noncoding RNAs (ncRNA) regulate diverse cellular processes, including virulence and environmental fitness. The malS 5′ untranslated region (named malS-5′UTR) was identified as a regulatory ncRNA that increases the invasive capacity of Salmonella enterica serovar Typhi. An IntaRNA search suggested base pairing between malS-5′UTR and hisG mRNA, a key gene in the histidine biosynthetic pathway. Overexpression of malS-5′UTR markedly reduced bacterial growth in minimal medium without histidine. Overexpression of malS-5′UTR increased mRNA from his operon genes, independently of the bax gene, and decreased HisG protein in Salmonella Typhi. RNA structure analysis showed base pairing of the malS-5′UTR RNA with the hisG mRNA across the ribosome binding site. Thus, we propose that malS-5′UTR inhibited hisG translation, probably by base pairing to the Shine–Dalgarno sequence.
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Affiliation(s)
- Ying Zhang
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu 212013, People’s Republic of China
| | - Dongmei Yan
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu 212013, People’s Republic of China
| | - Lin Xia
- Department of Clinical Laboratory, Affiliated hospital, Jiangsu University, Zhenjiang, Jiangsu 212001, People’s Republic of China
| | - Xin Zhao
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu 212013, People’s Republic of China
| | - George Osei-Adjei
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu 212013, People’s Republic of China
| | - Shungao Xu
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu 212013, People’s Republic of China
| | - Xiumei Sheng
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu 212013, People’s Republic of China
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu 212013, People’s Republic of China
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Barquist L, Vogel J. Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies. Annu Rev Genet 2015; 49:367-94. [PMID: 26473381 DOI: 10.1146/annurev-genet-112414-054804] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
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24
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Le Roux F, Wegner KM, Baker-Austin C, Vezzulli L, Osorio CR, Amaro C, Ritchie JM, Defoirdt T, Destoumieux-Garzón D, Blokesch M, Mazel D, Jacq A, Cava F, Gram L, Wendling CC, Strauch E, Kirschner A, Huehn S. The emergence of Vibrio pathogens in Europe: ecology, evolution, and pathogenesis (Paris, 11-12th March 2015). Front Microbiol 2015; 6:830. [PMID: 26322036 PMCID: PMC4534830 DOI: 10.3389/fmicb.2015.00830] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/28/2015] [Indexed: 02/02/2023] Open
Abstract
Global change has caused a worldwide increase in reports of Vibrio-associated diseases with ecosystem-wide impacts on humans and marine animals. In Europe, higher prevalence of human infections followed regional climatic trends with outbreaks occurring during episodes of unusually warm weather. Similar patterns were also observed in Vibrio-associated diseases affecting marine organisms such as fish, bivalves and corals. Basic knowledge is still lacking on the ecology and evolutionary biology of these bacteria as well as on their virulence mechanisms. Current limitations in experimental systems to study infection and the lack of diagnostic tools still prevent a better understanding of Vibrio emergence. A major challenge is to foster cooperation between fundamental and applied research in order to investigate the consequences of pathogen emergence in natural Vibrio populations and answer federative questions that meet societal needs. Here we report the proceedings of the first European workshop dedicated to these specific goals of the Vibrio research community by connecting current knowledge to societal issues related to ocean health and food security.
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Affiliation(s)
- Frédérique Le Roux
- Unié Physiologie Fonctionnelle des Organismes Marins, Ifremer , Plouzané, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Paris 06 , Roscoff cedex, France
| | - K Mathias Wegner
- Coastal Ecology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research , List, Germany
| | | | - Luigi Vezzulli
- Department of Earth, Environmental and Life Sciences, University of Genoa , Genoa, Italy
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela , Santiago de Compostela, Spain
| | - Carmen Amaro
- Estructura de Investigación Interdisciplinar en Biotecnología y Biomedicina, Department of Microbiology and Ecology, University of Valencia , Valencia, Spain
| | - Jennifer M Ritchie
- Faculty of Health and Medical Sciences, University of Surrey , Guildford, UK
| | - Tom Defoirdt
- UGent Aquaculture R&D Consortium, Ghent University , Ghent, Belgium
| | - Delphine Destoumieux-Garzón
- Interactions Hôtes-Pathogènes-Environnements, UMR 5244, CNRS, Ifremer, Université de Perpignan Via Domita, Université de Montpellier , Montpellier, France
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne , Lausanne, Switzerland
| | - Didier Mazel
- Département Génomes et Génétique, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Institut Pasteur , Paris, France
| | - Annick Jacq
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud , Orsay, France
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University , Umeå, Sweden
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark , Kongens Lyngby, Denmark
| | | | - Eckhard Strauch
- Federal Institute for Risk Assessment, National Reference Laboratory for Monitoring Bacteriological Contamination of Bivalve Molluscs , Berlin, Germany
| | - Alexander Kirschner
- Institute for Hygiene and Applied Immunology, Medical University of Vienna , Vienna, Austria
| | - Stephan Huehn
- Institute of Food Hygiene, Free University Berlin , Berlin, Germany
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25
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Gong M, Xu S, Jin Y, Zhang Y, Dadzie I, Zhang X, Wang Z, Zhu Y, Ni B, Sheng X, Huang X. 5′-UTR of malS increases the invasive capacity of Salmonella enterica serovar Typhi by influencing the expression of bax. Future Microbiol 2015; 10:941-54. [DOI: 10.2217/fmb.15.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
ABSTRACT Aim: An RNA-seq analysis recently identified a 236-nucleotide transcript upstream from malS in Salmonella enterica serovar Typhi. Here, we investigated its molecular characteristics and function. Materials & methods: RACE and northern blotting were used to determine the molecular characteristics of the sequence, and mutagenesis, microarray, immunoblotting and an invasion assay were used to investigate the functions of the transcript. Results: The transcript was identified as the malS 5′-untranslated region (UTR), which could influence the expression of the flagellar and SPI-1 genes and the invasion of HeLa cells by S. Typhi. Deletion of bax increased the expression of the invasion genes and the invasive capacity of S. Typhi, whereas the expression of the malS 5′-UTR reduced the expression of bax. Conclusion: The malS 5′-UTR reduces the expression of bax and increases the invasive capacity of S. Typhi.
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Affiliation(s)
- Mingyu Gong
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Department of Biochemistry, Chengde Medical College, Chengde, Hebei 067000, China
| | - Shungao Xu
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yue Jin
- Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical College, Huai'an, 223002, China
| | - Ying Zhang
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Isaac Dadzie
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaolei Zhang
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Zhexin Wang
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yunxia Zhu
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Bin Ni
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiumei Sheng
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xinxiang Huang
- Department of Biochemistry & Molecular Biology, School of Medical Science & Laboratory Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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26
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Updegrove TB, Shabalina SA, Storz G. How do base-pairing small RNAs evolve? FEMS Microbiol Rev 2015; 39:379-91. [PMID: 25934120 DOI: 10.1093/femsre/fuv014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 01/12/2023] Open
Abstract
The increasing numbers of characterized base-pairing small RNAs (sRNAs) and the identification of these regulators in a broad range of bacteria are allowing comparisons between species and explorations of sRNA evolution. In this review, we describe some examples of trans-encoded base-pairing sRNAs that are species-specific and others that are more broadly distributed. We also describe examples of sRNA orthologs where different features are conserved. These examples provide the background for a discussion of mechanisms of sRNA evolution and selective pressures on the sRNAs and their mRNA target(s).
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Affiliation(s)
- Taylor B Updegrove
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institutes of Health, Bethesda, MD 20892, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institutes of Health, Bethesda, MD 20892, USA
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27
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Rey J, Deschavanne P, Tuffery P. BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau106. [PMID: 25377257 PMCID: PMC4221844 DOI: 10.1093/database/bau106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the recent progress in complete genome sequencing, mining the increasing amount of genomic information available should in theory provide the means to discover new classes of peptides. However, annotation pipelines often do not consider small reading frames likely to be expressed. BactPepDB, available online at http://bactpepdb.rpbs.univ-paris-diderot.fr, is a database that aims at providing an exhaustive re-annotation of all complete prokaryotic genomes—chromosomal and plasmid DNA—available in RefSeq for coding sequences ranging between 10 and 80 amino acids. The identified peptides are classified as (i) previously identified in RefSeq, (ii) entity-overlapping (intragenic) or intergenic, and (iii) potential pseudogenes—intergenic sequences corresponding to a portion of a previously annotated larger gene. Additional information is related to homologs within order, predicted signal sequence, transmembrane segments, disulfide bonds, secondary structure, and the existence of a related 3D structure in the Protein Databank. As a result, BactPepDB provides insights about candidate peptides, and provides information about their conservation, together with some of their expected biological/structural features. The BactPepDB interface allows to search for candidate peptides in the database, or to search for peptides similar to a query, according to the multiple properties predicted or related to genomic localization. Database URL:http://www.yeastgenome.org/
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Affiliation(s)
- Julien Rey
- INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France
| | - Patrick Deschavanne
- INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France
| | - Pierre Tuffery
- INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France INSERM, U973, MTi, F-75205 Paris, France, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France and RPBS, F-75205 Paris, France
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28
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Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis. BMC Genomics 2014; 15:684. [PMID: 25127548 PMCID: PMC4247193 DOI: 10.1186/1471-2164-15-684] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/30/2014] [Indexed: 01/02/2023] Open
Abstract
Background Prokaryotes have relatively small genomes, densely-packed with protein-encoding sequences. RNA sequencing has, however, revealed surprisingly complex transcriptomes and here we report the transcripts present in the model hyperthermophilic Archaeon, Thermococcus kodakarensis, under different physiological conditions. Results Sequencing cDNA libraries, generated from RNA isolated from cells under different growth and metabolic conditions has identified >2,700 sites of transcription initiation, established a genome-wide map of transcripts, and consensus sequences for transcription initiation and post-transcription regulatory elements. The primary transcription start sites (TSS) upstream of 1,254 annotated genes, plus 644 primary TSS and their promoters within genes, are identified. Most mRNAs have a 5'-untranslated region (5'-UTR) 10 to 50 nt long (median = 16 nt), but ~20% have 5'-UTRs from 50 to 300 nt long and ~14% are leaderless. Approximately 50% of mRNAs contain a consensus ribosome binding sequence. The results identify TSS for 1,018 antisense transcripts, most with sequences complementary to either the 5'- or 3'-region of a sense mRNA, and confirm the presence of transcripts from all three CRISPR loci, the RNase P and 7S RNAs, all tRNAs and rRNAs and 69 predicted snoRNAs. Two putative riboswitch RNAs were present in growing but not in stationary phase cells. The procedure used is designed to identify TSS but, assuming that the number of cDNA reads correlates with transcript abundance, the results also provide a semi-quantitative documentation of the differences in T. kodakarensis genome expression under different growth conditions and confirm previous observations of substrate-dependent specific gene expression. Many previously unanticipated small RNAs have been identified, some with relative low GC contents (≤50%) and sequences that do not fold readily into base-paired secondary structures, contrary to the classical expectations for non-coding RNAs in a hyperthermophile. Conclusion The results identify >2,700 TSS, including almost all of the primary sites of transcription initiation upstream of annotated genes, plus many secondary sites, sites within genes and sites resulting in antisense transcripts. The T. kodakarensis genome is small (~2.1 Mbp) and tightly packed with protein-encoding genes, but the transcriptomes established also contain many non-coding RNAs and predict extensive RNA-based regulation in this model Archaeon. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-684) contains supplementary material, which is available to authorized users.
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29
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Peer A, Margalit H. Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions. RNA (NEW YORK, N.Y.) 2014; 20:994-1003. [PMID: 24865611 PMCID: PMC4114697 DOI: 10.1261/rna.043133.113] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/23/2014] [Indexed: 06/03/2023]
Abstract
Most bacterial small RNAs (sRNAs) are post-transcriptional regulators of gene expression, exerting their regulatory function by base-pairing with their target mRNAs. While it has become evident that sRNAs play central regulatory roles in the cell, little is known about their evolution and the evolution of their regulatory interactions. Here we used the prokaryotic phylogenetic tree to reconstruct the evolutionary history of Escherichia coli sRNAs and their binding sites on target mRNAs. We discovered that sRNAs currently present in E. coli mainly accumulated inside the Enterobacteriales order, succeeding the appearance of other types of noncoding RNAs and concurrently with the evolution of a variant of the Hfq protein exhibiting a longer C-terminal region. Our analysis of the evolutionary ages of sRNA-mRNA interactions revealed that while all sRNAs were evolutionarily older than most of their known binding sites on mRNA targets, for quite a few sRNAs there was at least one binding site that coappeared with or preceded them. It is conceivable that the establishment of these first interactions forced selective pressure on the sRNAs, after which additional targets were acquired by fitting a binding site to the active region of the sRNA. This conjecture is supported by the appearance of many binding sites on target mRNAs only after the sRNA gain, despite the prior presence of the target gene in ancestral genomes. Our results suggest a selective mechanism that maintained the sRNAs across the phylogenetic tree, and shed light on the evolution of E. coli post-transcriptional regulatory network.
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Vercruysse M, Köhrer C, Davies BW, Arnold MFF, Mekalanos JJ, RajBhandary UL, Walker GC. The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing. PLoS Pathog 2014; 10:e1004175. [PMID: 24901994 PMCID: PMC4047096 DOI: 10.1371/journal.ppat.1004175] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
YbeY, a highly conserved protein, is an RNase in E. coli and plays key roles in both processing of the critical 3′ end of 16 S rRNA and in 70 S ribosome quality control under stress. These central roles account for YbeY's inclusion in the postulated minimal bacterial genome. However, YbeY is not essential in E. coli although loss of ybeY severely sensitizes it to multiple physiological stresses. Here, we show that YbeY is an essential endoribonuclease in Vibrio cholerae and is crucial for virulence, stress regulation, RNA processing and ribosome quality control, and is part of a core set of RNases essential in most representative pathogens. To understand its function, we analyzed the rRNA and ribosome profiles of a V. cholerae strain partially depleted for YbeY and other RNase mutants associated with 16 S rRNA processing; our results demonstrate that YbeY is also crucial for 16 S rRNA 3′ end maturation in V. cholerae and that its depletion impedes subunit assembly into 70 S ribosomes. YbeY's importance to V. cholerae pathogenesis was demonstrated by the complete loss of mice colonization and biofilm formation, reduced cholera toxin production, and altered expression levels of virulence-associated small RNAs of a V. cholerae strain partially depleted for YbeY. Notably, the ybeY genes of several distantly related pathogens can fully complement an E. coli ΔybeY strain under various stress conditions, demonstrating the high conservation of YbeY's activity in stress regulation. Taken together, this work provides the first comprehensive exploration of YbeY's physiological role in a human pathogen, showing its conserved function across species in essential cellular processes. Bacteria adapt and survive unfavorable environments by quickly changing their gene expression and physiology, for example as pathogens do during infection of host cells. Gene expression is often determined by RNA turnover, a balance between transcription and RNA decay carried out by multiple RNases. The recently identified RNase YbeY was shown in E. coli to participate in rRNA maturation and 70 S ribosome quality control, however YbeY's roles in other organisms and the extent of functional conservation is unknown. Here, we show that YbeY is an essential RNase in the pathogen Vibrio cholerae, critical for cell fitness and general stress tolerance. We demonstrate that YbeY is crucial for 16 S rRNA 3′ end maturation, assembly of functional 70 S ribosomes and ribosome quality control. Moreover, YbeY regulates virulence-associated small RNAs and its depletion leads to an overall reduction in pathogenesis, exemplified by significantly decreased biofilm formation, mouse colonization and cholera toxin production. We also show that YbeY belongs to a minimal core set of RNases essential in most representative pathogens. The multifaceted roles of YbeY in several essential cellular processes and its highly conserved function across bacterial species, suggest that YbeY could be an attractive new antimicrobial target.
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Affiliation(s)
- Maarten Vercruysse
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bryan W. Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Markus F. F. Arnold
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John J. Mekalanos
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachussets, United States of America
| | - Uttam L. RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Nguyen AN, Jacq A. Small RNAs in the Vibrionaceae: an ocean still to be explored. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:381-92. [PMID: 24458378 DOI: 10.1002/wrna.1218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 12/13/2013] [Accepted: 12/16/2013] [Indexed: 11/09/2022]
Abstract
In bacteria, the discovery of noncoding small RNAs (sRNAs) as modulators of gene expression in response to environmental signals has brought new insights into bacterial gene regulation, including control of pathogenicity. The Vibrionaceae constitute a family of marine bacteria of which many are responsible for infections affecting not only humans, such as Vibrio cholerae but also fish and marine invertebrates, representing the major cause of mortality in farmed marine species. They are able to colonize many habitats, existing as planktonic forms, in biofilms or associated with various hosts. This high adaptability is linked to their capacity to generate genetic diversity, in part through lateral gene transfer, but also by varying gene expression control. In the recent years, several major studies have illustrated the importance of small regulatory sRNAs in the Vibrionaceae for the control of pathogenicity and adaptation to environment and nutrient sources such as chitin, especially in V. cholerae and Vibrio harveyi. The existence of a complex regulatory network controlled by quorum sensing has been demonstrated in which sRNAs play central roles. This review covers major advances made in the discovery and elucidation of functions of Vibrionaceae sRNAs within the last 10 years.
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Affiliation(s)
- An Ngoc Nguyen
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, 91405 Orsay Cedex, France
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Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J. Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics 2013; 14:714. [PMID: 24138339 PMCID: PMC4046766 DOI: 10.1186/1471-2164-14-714] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/25/2013] [Indexed: 12/11/2022] Open
Abstract
Background Recent discoveries on bacterial transcriptomes gave evidence that small RNAs (sRNAs) have important regulatory roles in prokaryotic cells. Modern high-throughput sequencing approaches (RNA-Seq) enable the most detailed view on transcriptomes offering an unmatched comprehensiveness and single-base resolution. Whole transcriptome data obtained by RNA-Seq can be used to detect and characterize all transcript species, including small RNAs. Here, we describe an RNA-Seq approach for comprehensive detection and characterization of small RNAs from Corynebacterium glutamicum, an actinobacterium of high industrial relevance and model organism for medically important Corynebacterianeae, such as C. diphtheriae and Mycobacterium tuberculosis. Results In our RNA-Seq approach, total RNA from C. glutamicum ATCC 13032 was prepared from cultures grown in minimal medium at exponential growth or challenged by physical (heat shock, cold shock) or by chemical stresses (diamide, H2O2, NaCl) at this time point. Total RNA samples were pooled and sequencing libraries were prepared from the isolated small RNA fraction. High throughput short read sequencing and mapping yielded over 800 sRNA genes. By determining their 5′- and 3′-ends and inspection of their locations, these potential sRNA genes were classified into UTRs of mRNAs (316), cis-antisense sRNAs (543), and trans-encoded sRNAs (262). For 77 of trans-encoded sRNAs significant sequence and secondary structure conservation was found by a computational approach using a whole genome alignment with the closely related species C. efficiens YS-314 and C. diphtheriae NCTC 13129. Three selected trans-encoded sRNAs were characterized by Northern blot analysis and stress-specific transcript patterns were found. Conclusions The study showed comparable numbers of sRNAs known from genome-wide surveys in other bacteria. In detail, our results give deep insight into the comprehensive equipment of sRNAs in C. glutamicum and provide a sound basis for further studies concerning the functions of these sRNAs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-714) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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Moody MJ, Young RA, Jones SE, Elliot MA. Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria. BMC Genomics 2013; 14:558. [PMID: 23947565 PMCID: PMC3765725 DOI: 10.1186/1471-2164-14-558] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/13/2013] [Indexed: 12/11/2022] Open
Abstract
Background Non-coding RNAs (ncRNAs) are key regulatory elements that control a wide range of cellular processes in all bacteria in which they have been studied. Taking advantage of recent technological innovations, we set out to fully explore the ncRNA potential of the multicellular, antibiotic-producing Streptomyces bacteria. Results Using a comparative RNA sequencing analysis of three divergent model streptomycetes (S. coelicolor, S. avermitilis and S. venezuelae), we discovered hundreds of novel cis-antisense RNAs and intergenic small RNAs (sRNAs). We identified a ubiquitous antisense RNA species that arose from the overlapping transcription of convergently-oriented genes; we termed these RNA species ‘cutoRNAs’, for convergent untranslated overlapping RNAs. Conservation between different classes of ncRNAs varied greatly, with sRNAs being more conserved than antisense RNAs. Many species-specific ncRNAs, including many distinct cutoRNA pairs, were located within antibiotic biosynthetic clusters, including the actinorhodin, undecylprodigiosin, and coelimycin clusters of S. coelicolor, the chloramphenicol cluster of S. venezuelae, and the avermectin cluster of S. avermitilis. Conclusions These findings indicate that ncRNAs, including a novel class of antisense RNA, may exert a previously unrecognized level of regulatory control over antibiotic production in these bacteria. Collectively, this work has dramatically expanded the ncRNA repertoire of three Streptomyces species and has established a critical foundation from which to investigate ncRNA function in this medically and industrially important bacterial genus.
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Affiliation(s)
- Matthew J Moody
- Department of Biology and Michael G, DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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Toffano-Nioche C, Ott A, Crozat E, Nguyen AN, Zytnicki M, Leclerc F, Forterre P, Bouloc P, Gautheret D. RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi. RNA Biol 2013; 10:1211-20. [PMID: 23884177 PMCID: PMC3849170 DOI: 10.4161/rna.25567] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that appear to evolve more rapidly than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5′ UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5′ UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure.
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Affiliation(s)
- Claire Toffano-Nioche
- Univ. Paris-Sud 11; CNRS; UMR8621; Institut de Génétique et Microbiologie; Bâtiment 400; F-91405 Orsay Cedex; France
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Toffano-Nioche C, Luo Y, Kuchly C, Wallon C, Steinbach D, Zytnicki M, Jacq A, Gautheret D. Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline. Methods 2013; 63:60-5. [PMID: 23806640 DOI: 10.1016/j.ymeth.2013.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/21/2013] [Accepted: 06/09/2013] [Indexed: 11/29/2022] Open
Abstract
RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR'PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli.
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Affiliation(s)
- Claire Toffano-Nioche
- Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, Orsay F-91405, France
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