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Zheng A, Panja S, Woodson SA. Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria. J Mol Biol 2016; 428:2259-2264. [PMID: 27049793 DOI: 10.1016/j.jmb.2016.03.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 12/20/2022]
Abstract
The Sm-protein Hfq facilitates interactions between small non-coding RNA (sRNA) and target mRNAs. In enteric Gram-negative bacteria, Hfq is required for sRNA regulation, and hfq deletion results in stress intolerance and reduced virulence. By contrast, the role of Hfq in Gram-positive is less established and varies among species. The RNA binding and RNA annealing activity of Hfq from Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus subtilis, and Staphylococcus aureus were compared using minimal RNAs and fluorescence spectroscopy. The results show that RNA annealing activity increases with the number of arginines in a semi-conserved patch on the rim of the Hfq hexamer and correlates with the previously reported requirement for Hfq in sRNA regulation. Thus, the amino acid sequence of the arginine patch can predict the chaperone function of Hfq in sRNA regulation in different organisms.
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Affiliation(s)
- Amy Zheng
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Subrata Panja
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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52
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Bouloc P, Repoila F. Fresh layers of RNA-mediated regulation in Gram-positive bacteria. Curr Opin Microbiol 2016; 30:30-35. [DOI: 10.1016/j.mib.2015.12.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 01/25/2023]
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53
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Feliciano JR, Grilo AM, Guerreiro SI, Sousa SA, Leitão JH. Hfq: a multifaceted RNA chaperone involved in virulence. Future Microbiol 2015; 11:137-51. [PMID: 26685037 DOI: 10.2217/fmb.15.128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hfq has emerged in recent years as a master regulator of gene expression in bacteria, mainly due to its ability to mediate the interaction of small noncoding RNAs with their mRNA targets, including those related to virulence in Gram-negative bacteria. In this work, we review current knowledge on the involvement of Hfq in the regulation of virulence traits related to secretion systems, alternative sigma factors, outer membrane proteins, polysaccharides and iron metabolism. Recent data from transcriptomics and proteomics studies performed for major pathogens are included. We also summarize and correlate current knowledge on how Hfq protein impacts pathogenicity of bacterial pathogens.
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Affiliation(s)
- Joana R Feliciano
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | | | - Soraia I Guerreiro
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sílvia A Sousa
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Jorge H Leitão
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal.,Departamento de Bioengenharia, Instituto Superior Técnico, Universidade de Lisboa. Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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54
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Arce-Rodríguez A, Calles B, Nikel PI, de Lorenzo V. The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype ofPseudomonas putida. Environ Microbiol 2015; 18:3309-3326. [DOI: 10.1111/1462-2920.13052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Alejandro Arce-Rodríguez
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Belén Calles
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Pablo I. Nikel
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
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55
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Vrentas C, Ghirlando R, Keefer A, Hu Z, Tomczak A, Gittis AG, Murthi A, Garboczi DN, Gottesman S, Leppla SH. Hfqs in Bacillus anthracis: Role of protein sequence variation in the structure and function of proteins in the Hfq family. Protein Sci 2015; 24:1808-19. [PMID: 26271475 DOI: 10.1002/pro.2773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/13/2015] [Indexed: 11/10/2022]
Abstract
Hfq proteins in Gram-negative bacteria play important roles in bacterial physiology and virulence, mediated by binding of the Hfq hexamer to small RNAs and/or mRNAs to post-transcriptionally regulate gene expression. However, the physiological role of Hfqs in Gram-positive bacteria is less clear. Bacillus anthracis, the causative agent of anthrax, uniquely expresses three distinct Hfq proteins, two from the chromosome (Hfq1, Hfq2) and one from its pXO1 virulence plasmid (Hfq3). The protein sequences of Hfq1 and 3 are evolutionarily distinct from those of Hfq2 and of Hfqs found in other Bacilli. Here, the quaternary structure of each B. anthracis Hfq protein, as produced heterologously in Escherichia coli, was characterized. While Hfq2 adopts the expected hexamer structure, Hfq1 does not form similarly stable hexamers in vitro. The impact on the monomer-hexamer equilibrium of varying Hfq C-terminal tail length and other sequence differences among the Hfqs was examined, and a sequence region of the Hfq proteins that was involved in hexamer formation was identified. It was found that, in addition to the distinct higher-order structures of the Hfq homologs, they give rise to different phenotypes. Hfq1 has a disruptive effect on the function of E. coli Hfq in vivo, while Hfq3 expression at high levels is toxic to E. coli but also partially complements Hfq function in E. coli. These results set the stage for future studies of the roles of these proteins in B. anthracis physiology and for the identification of sequence determinants of phenotypic complementation.
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Affiliation(s)
- Catherine Vrentas
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | | | - Andrea Keefer
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | - Zonglin Hu
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | | | - Apostolos G Gittis
- Structural Biology Section, Research Technologies Branch, NIAID, NIH, Twinbrook II, 12441 Parklawn Drive, Rockville, Maryland
| | - Athulaprabha Murthi
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | - David N Garboczi
- Structural Biology Section, Research Technologies Branch, NIAID, NIH, Twinbrook II, 12441 Parklawn Drive, Rockville, Maryland
| | | | - Stephen H Leppla
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
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56
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Oliva G, Sahr T, Buchrieser C. Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence. FEMS Microbiol Rev 2015; 39:331-349. [DOI: 10.1093/femsre/fuv022] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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Rochat T, Delumeau O, Figueroa-Bossi N, Noirot P, Bossi L, Dervyn E, Bouloc P. Tracking the Elusive Function of Bacillus subtilis Hfq. PLoS One 2015; 10:e0124977. [PMID: 25915524 PMCID: PMC4410918 DOI: 10.1371/journal.pone.0124977] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/20/2015] [Indexed: 11/25/2022] Open
Abstract
RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species including Escherichia coli, Salmonella enterica and Vibrio cholera. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive and somewhat controversial. In the present study, we have further addressed this point by comparing growth phenotypes and transcription profiles between wild-type and an hfq deletion mutant of the model Gram-positive bacterium, Bacillus subtilis. The absence of Hfq had no significant consequences on growth rates under nearly two thousand metabolic conditions and chemical treatments. The only phenotypic difference was a survival defect of B. subtilis hfq mutant in rich medium in stationary phase. Transcriptomic analysis correlated this phenotype with a change in the levels of nearly one hundred transcripts. Albeit a significant fraction of these RNAs (36%) encoded sporulation-related functions, analyses in a strain unable to sporulate ruled out sporulation per se as the basis of the hfq mutant’s stationary phase fitness defect. When expressed in Salmonella, B. subtilis hfq complemented the sharp loss of viability of a degP hfq double mutant, attenuating the chronic σE-activated phenotype of this strain. However, B. subtilis hfq did not complement other regulatory deficiencies resulting from loss of Hfq-dependent small RNA activity in Salmonella indicating a limited functional overlap between Salmonella and B. subtilis Hfqs. Overall, this study confirmed that, despite structural similarities with other Hfq proteins, B. subtilis Hfq does not play a central role in post-transcriptional regulation but might have a more specialized function connected with stationary phase physiology. This would account for the high degree of conservation of Hfq proteins in all 17 B. subtilis strains whose genomes have been sequenced.
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Affiliation(s)
- Tatiana Rochat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91405, Orsay, France; INRA, UR892, Virologie et Immunologie Moléculaires, F-78352, Jouy-en-Josas, France
| | - Olivier Delumeau
- INRA, UMR1319 Micalis, F-78350, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350, Jouy-en-Josas, France
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91190, Gif-sur-Yvette, France
| | - Philippe Noirot
- INRA, UMR1319 Micalis, F-78350, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350, Jouy-en-Josas, France
| | - Lionello Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91190, Gif-sur-Yvette, France
| | - Etienne Dervyn
- INRA, UMR1319 Micalis, F-78350, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350, Jouy-en-Josas, France
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, F-91405, Orsay, France
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Wilton J, Acebo P, Herranz C, Gómez A, Amblar M. Small regulatory RNAs in Streptococcus pneumoniae: discovery and biological functions. Front Genet 2015; 6:126. [PMID: 25904932 PMCID: PMC4387999 DOI: 10.3389/fgene.2015.00126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/17/2015] [Indexed: 12/23/2022] Open
Abstract
Streptococcus pneumoniae is a prominent human pathogen responsible for many severe diseases and the leading cause of childhood mortality worldwide. The pneumococcus is remarkably adept at colonizing and infecting different niches in the human body, and its adaptation to dynamic host environment is a central aspect of its pathogenesis. In the last decade, increasing findings have evidenced small RNAs (sRNAs) as vital regulators in a number of important processes in bacteria. In S. pneumoniae, a small antisense RNA was first discovered in the pMV158 plasmid as a copy number regulator. More recently, genome-wide screens revealed that the pneumococcal genome also encodes multiple sRNAs, many of which have important roles in virulence while some are implicated in competence control. The knowledge of the sRNA-mediated regulation in pneumococcus remains very limited, and future research is needed for better understanding of functions and mechanisms. Here, we provide a comprehensive summary of the current knowledge on sRNAs from S. pneumoniae, focusing mainly on the trans-encoded sRNAs.
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Affiliation(s)
- Joana Wilton
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Paloma Acebo
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Cristina Herranz
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Alicia Gómez
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Mónica Amblar
- Unidad de Patología Molecular del Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain ; CIBER Enfermedades Respiratorias Madrid, Spain
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Xu G, Zhao Y, Du L, Qian G, Liu F. Hfq regulates antibacterial antibiotic biosynthesis and extracellular lytic-enzyme production in Lysobacter enzymogenes OH11. Microb Biotechnol 2015; 8:499-509. [PMID: 25683974 PMCID: PMC4408182 DOI: 10.1111/1751-7915.12246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 12/14/2022] Open
Abstract
Lysobacter enzymogenes is an important biocontrol agent with the ability to produce a variety of lytic enzymes and novel antibiotics. Little is known about their regulatory mechanisms. Understanding these will be helpful for improving biocontrol of crop diseases and potential medical application. In the present study, we generated an hfq (encoding a putative ribonucleic acid chaperone) deletion mutant, and then utilized a new genomic marker-free method to construct an hfq-complemented strain. We showed for the first time that Hfq played a pleiotropic role in regulating the antibacterial antibiotic biosynthesis and extracellular lytic enzyme activity in L. enzymogenes. Mutation of hfq significantly increased the yield of WAP-8294A2 (an antibacterial antibiotic) as well as the transcription of its key biosynthetic gene, waps1. However, inactivation of hfq almost abolished the extracellular chitinase activity and remarkably decreased the activity of both extracellular protease and cellulase in L. enzymogenes. We further showed that the regulation of hfq in extracellular chitinase production was in part through the impairment of the secretion of chitinase A. Collectively, our results reveal the regulatory roles of hfq in antibiotic metabolite and extracellular lytic enzymes in the underexplored genus of Lysobacter.
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Affiliation(s)
- Gaoge Xu
- College of Plant Protection, Nanjing Agricultural University, China/Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, 210095, China
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60
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Saujet L, Pereira FC, Henriques AO, Martin-Verstraete I. The regulatory network controlling spore formation in Clostridium difficile. FEMS Microbiol Lett 2014; 358:1-10. [PMID: 25048412 DOI: 10.1111/1574-6968.12540] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/09/2014] [Accepted: 07/13/2014] [Indexed: 11/29/2022] Open
Abstract
Clostridium difficile, a Gram-positive, anaerobic, spore-forming bacterium, is a major cause of nosocomial infections such as antibiotic-associated diarrhea. Spores are the vector of its transmission and persistence in the environment. Despite the importance of spores in the infectious cycle of C. difficile, little was known until recently about the control of spore development in this enteropathogen. In this review, we describe recent advances in our understanding of the regulatory network controlling C. difficile sporulation. The comparison with the model organism Bacillus subtilis highlights major differences in the signaling pathways between the forespore and the mother cell and a weaker connection between morphogenesis and gene expression. Indeed, the activation of the SigE regulon in the mother cell is partially independent of SigF although the forespore protein SpoIIR, itself partially independent of SigF, is essential for pro-SigE processing. Furthermore, SigG activity is not strictly dependent on SigE. Finally, SigG is dispensable for SigK activation in agreement with the absence of a pro-SigK sequence. The excision of the C. difficile skin element is also involved in the regulation of SigK activity. The C. difficile sporulation process might be a simpler, more ancestral version of the program characterized for B. subtilis.
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Affiliation(s)
- Laure Saujet
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France; University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
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61
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Conserved oligopeptide permeases modulate sporulation initiation in Clostridium difficile. Infect Immun 2014; 82:4276-91. [PMID: 25069979 DOI: 10.1128/iai.02323-14] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The anaerobic gastrointestinal pathogen Clostridium difficile must form a metabolically dormant spore to survive in oxygenic environments and be transmitted from host to host. The regulatory factors by which C. difficile initiates and controls the early stages of sporulation in C. difficile are not highly conserved in other Clostridium or Bacillus species. Here, we investigated the role of two conserved oligopeptide permeases, Opp and App, in the regulation of sporulation in C. difficile. These permeases are known to positively affect sporulation in Bacillus species through the import of sporulation-specific quorum-sensing peptides. In contrast to other spore-forming bacteria, we discovered that inactivating these permeases in C. difficile resulted in the earlier expression of early sporulation genes and increased sporulation in vitro. Furthermore, disruption of opp and app resulted in greater virulence and increased the amounts of spores recovered from feces in the hamster model of C. difficile infection. Our data suggest that Opp and App indirectly inhibit sporulation, likely through the activities of the transcriptional regulator SinR and its inhibitor, SinI. Taken together, these results indicate that the Opp and App transporters serve a different function in controlling sporulation and virulence in C. difficile than in Bacillus subtilis and suggest that nutrient availability plays a significant role in pathogenesis and sporulation in vivo. This study suggests a link between the nutritional status of the environment and sporulation initiation in C. difficile.
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