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Bell RT, Sahakyan H, Makarova KS, Wolf YI, Koonin EV. CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.31.551357. [PMID: 37790407 PMCID: PMC10542128 DOI: 10.1101/2023.07.31.551357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote CoCoNuTs (coiled-coil nuclease tandems) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with 3 distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.
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Affiliation(s)
- Ryan T. Bell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Harutyun Sahakyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Tan XY, Citartan M, Chinni SV, Ahmed SA, Tang TH. Biocomputational Identification of sRNAs in Leptospira interrogans Serovar Lai. Indian J Microbiol 2023; 63:33-41. [PMID: 37188232 PMCID: PMC10172424 DOI: 10.1007/s12088-022-01050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Regulatory small RNAs (sRNA) are RNA transcripts that are not translated into proteins but act as functional RNAs. Pathogenic Leptospira cause an epidemic spirochaetal zoonosis, Leptospirosis. It is speculated that Leptospiral sRNAs are involved in orchestrating their pathogenicity. In this study, biocomputational approach was adopted to identify Leptospiral sRNAs. In this study, two sRNA prediction programs, i.e., RNAz and nocoRNAc, were employed to screen the reference genome of Leptospira interrogans serovar Lai. Out of 126 predicted sRNAs, there are 96 cis-antisense sRNAs, 28 trans-encoded sRNAs and 2 sRNAs that partially overlap with protein-coding genes in a sense orientation. To determine whether these candidates are expressed in the pathogen, they were compared with the coverage files generated from our RNA-seq datasets. It was found out that 7 predicted sRNAs are expressed in mid-log phase, stationary phase, serum stress, temperature stress and iron stress while 2 sRNAs are expressed in mid-log phase, stationary phase, serum stress, and temperature stress. Besides, their expressions were also confirmed experimentally via RT-PCR. These experimentally validated candidates were also subjected to mRNA target prediction using TargetRNA2. Taken together, our study demonstrated that biocomputational strategy can serve as an alternative or as a complementary strategy to the laborious and expensive deep sequencing methods not only to uncover putative sRNAs but also to predict their targets in bacteria. In fact, this is the first study that integrates computational approach to predict putative sRNAs in L. interrogans serovar Lai. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-022-01050-9.
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Affiliation(s)
- Xinq Yuan Tan
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
| | - Marimuthu Citartan
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
| | - Suresh Venkata Chinni
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah Malaysia
| | - Siti Aminah Ahmed
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
| | - Thean-Hock Tang
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
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da Silva GC, Rossi CC, Rosa JN, Sanches NM, Cardoso DL, Li Y, Witney AA, Gould KA, Fontes PP, Callaghan AJ, Bossé JT, Langford PR, Bazzolli DMS. Identification of small RNAs associated with RNA chaperone Hfq reveals a new stress response regulator in Actinobacillus pleuropneumoniae. Front Microbiol 2022; 13:1017278. [PMID: 36267174 PMCID: PMC9577009 DOI: 10.3389/fmicb.2022.1017278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
The RNA chaperone Hfq promotes the association of small RNAs (sRNAs) with cognate mRNAs, controlling the expression of bacterial phenotype. Actinobacillus pleuropneumoniae hfq mutants strains are attenuated for virulence in pigs, impaired in the ability to form biofilms, and more susceptible to stress, but knowledge of the extent of sRNA involvement is limited. Here, using A. pleuropneumoniae strain MIDG2331 (serovar 8), 14 sRNAs were identified by co-immunoprecipitation with Hfq and the expression of eight, identified as trans-acting sRNAs, were confirmed by Northern blotting. We focused on one of these sRNAs, named Rna01, containing a putative promoter for RpoE (stress regulon) recognition. Knockout mutants of rna01 and a double knockout mutant of rna01 and hfq, both had decreased biofilm formation and hemolytic activity, attenuation for virulence in Galleria mellonella, altered stress susceptibility, and an altered outer membrane protein profile. Rna01 affected extracellular vesicle production, size and toxicity in G. mellonella. qRT-PCR analysis of rna01 and putative cognate mRNA targets indicated that Rna01 is associated with the extracytoplasmic stress response. This work increases our understanding of the multilayered and complex nature of the influence of Hfq-dependent sRNAs on the physiology and virulence of A. pleuropneumoniae.
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Affiliation(s)
- Giarlã Cunha da Silva
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Ciro César Rossi
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Jéssica Nogueira Rosa
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Newton Moreno Sanches
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Daniela Lopes Cardoso
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Yanwen Li
- Section of Pediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Adam A. Witney
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | - Kate A. Gould
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | | | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Janine Thérèse Bossé
- Section of Pediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul Richard Langford
- Section of Pediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Denise Mara Soares Bazzolli
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
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Ju X, Fang X, Xiao Y, Li B, Shi R, Wei C, You C. Small RNA GcvB Regulates Oxidative Stress Response of Escherichia coli. Antioxidants (Basel) 2021; 10:antiox10111774. [PMID: 34829644 PMCID: PMC8614746 DOI: 10.3390/antiox10111774] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
Small non-translated regulatory RNAs control plenty of bacterial vital activities. The small RNA GcvB has been extensively studied, indicating the multifaceted roles of GcvB beyond amino acid metabolism. However, few reported GcvB-dependent regulation in minimal medium. Here, by applying a high-resolution RNA-seq assay, we compared the transcriptomes of a wild-type Escherichia coli K-12 strain and its gcvB deletion derivative grown in minimal medium and identified putative targets responding to GcvB, including flu, a determinant gene of auto-aggregation. The following molecular studies and the enhanced auto-aggregation ability of the gcvB knockout strain further substantiated the induced expression of these genes. Intriguingly, the reduced expression of OxyR (the oxidative stress regulator) in the gcvB knockout strain was identified to account for the increased expression of flu. Additionally, GcvB was characterized to up-regulate the expression of OxyR at the translational level. Accordingly, compared to the wild type, the GcvB deletion strain was more sensitive to oxidative stress and lost some its ability to eliminate endogenous reactive oxygen species. Taken together, we reveal that GcvB regulates oxidative stress response by up-regulating OxyR expression. Our findings provide an insight into the diversity of GcvB regulation and add an additional layer to the regulation of OxyR.
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Affiliation(s)
- Xian Ju
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China; (X.J.); (X.F.); (Y.X.); (B.L.); (R.S.)
| | - Xingxing Fang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China; (X.J.); (X.F.); (Y.X.); (B.L.); (R.S.)
| | - Yunzhu Xiao
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China; (X.J.); (X.F.); (Y.X.); (B.L.); (R.S.)
| | - Bingyu Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China; (X.J.); (X.F.); (Y.X.); (B.L.); (R.S.)
- Health Science Center, Shenzhen University, Shenzhen 518055, China;
| | - Ruoping Shi
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China; (X.J.); (X.F.); (Y.X.); (B.L.); (R.S.)
| | - Chaoliang Wei
- Health Science Center, Shenzhen University, Shenzhen 518055, China;
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China; (X.J.); (X.F.); (Y.X.); (B.L.); (R.S.)
- Correspondence:
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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6
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Koul V, Srivastava D, Singh PP, Kochar M. Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions. BMC Genomics 2020; 21:821. [PMID: 33228533 PMCID: PMC7685610 DOI: 10.1186/s12864-020-07212-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date. RESULTS Expression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data. CONCLUSIONS Differential expression of 468 A. brasilense sRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.
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Affiliation(s)
- Vatsala Koul
- The Energy and Resources Institute, Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi, 110003, India
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Divya Srivastava
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Pushplata Prasad Singh
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
| | - Mandira Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
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A novel small RNA contributes to restrain cellular chain length and anti-phagocytic ability in Streptococcus suis 2. Microb Pathog 2019; 137:103730. [PMID: 31499182 DOI: 10.1016/j.micpath.2019.103730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 02/04/2023]
Abstract
Streptococcus suis serotype 2 (SS2) is an important porcine and human pathogen. Regulatory small non-coding RNAs (sRNAs) play an essential role in diverse physiological processes, although they remain poorly understood in SS2. In this study, we identified eight novel sRNAs through a combination of computational strategies and experimental identification. To explore roles of these novel sRNAs, sRNA34 was preferentially selected to assess phenotypes of the deletion strain in vitro and in vivo. The inactivation of sRNA34 significantly elongated the cellular chain, remarkably increased sensitivity to phagocytosis by RAW264.7, and attenuated virulence in a mouse infection model. Transcriptomic analysis revealed that inactivation of sRNA34 altered expression of multiple genes contributing to cellular chain formation and elongation, indicating a potential mechanism of sRNA34 in maintaining proper bacterial chain length to resist phagocytosis by the host cell. In summary, sRNA34 is a novel sRNA that contributes to cellular chain regulation and the anti-phagocytosis ability of SS2.
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Carvalho Garcia A, Dos Santos VLP, Santos Cavalcanti TC, Collaço LM, Graf H. Bacterial Small RNAs in the Genus Herbaspirillum spp. Int J Mol Sci 2018; 20:ijms20010046. [PMID: 30583511 PMCID: PMC6337395 DOI: 10.3390/ijms20010046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 12/26/2022] Open
Abstract
The genus Herbaspirillum includes several strains isolated from different grasses. The identification of non-coding RNAs (ncRNAs) in the genus Herbaspirillum is an important stage studying the interaction of these molecules and the way they modulate physiological responses of different mechanisms, through RNA⁻RNA interaction or RNA⁻protein interaction. This interaction with their target occurs through the perfect pairing of short sequences (cis-encoded ncRNAs) or by the partial pairing of short sequences (trans-encoded ncRNAs). However, the companion Hfq can stabilize interactions in the trans-acting class. In addition, there are Riboswitches, located at the 5' end of mRNA and less often at the 3' end, which respond to environmental signals, high temperatures, or small binder molecules. Recently, CRISPR (clustered regularly interspaced palindromic repeats), in prokaryotes, have been described that consist of serial repeats of base sequences (spacer DNA) resulting from a previous exposure to exogenous plasmids or bacteriophages. We identified 285 ncRNAs in Herbaspirillum seropedicae (H. seropedicae) SmR1, expressed in different experimental conditions of RNA-seq material, classified as cis-encoded ncRNAs or trans-encoded ncRNAs and detected RNA riboswitch domains and CRISPR sequences. The results provide a better understanding of the participation of this type of RNA in the regulation of the metabolism of bacteria of the genus Herbaspirillum spp.
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Affiliation(s)
- Amanda Carvalho Garcia
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
| | | | | | - Luiz Martins Collaço
- Department of Pathology, Federal University of Paraná, PR, Curitiba 80.060-240, Brazil.
| | - Hans Graf
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
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9
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Pereira MF, Rossi CC, Seide LE, Martins Filho S, Dolinski CDM, Bazzolli DMS. Antimicrobial resistance, biofilm formation and virulence reveal Actinobacillus pleuropneumoniae strains' pathogenicity complexity. Res Vet Sci 2018; 118:498-501. [DOI: 10.1016/j.rvsc.2018.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 05/02/2018] [Accepted: 05/06/2018] [Indexed: 01/11/2023]
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10
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Gulliver EL, Wright A, Lucas DD, Mégroz M, Kleifeld O, Schittenhelm RB, Powell DR, Seemann T, Bulitta JB, Harper M, Boyce JD. Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of the GcvB seed binding region. RNA (NEW YORK, N.Y.) 2018; 24:704-720. [PMID: 29440476 PMCID: PMC5900567 DOI: 10.1261/rna.063248.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/01/2018] [Indexed: 05/12/2023]
Abstract
Pasteurella multocida is a Gram-negative bacterium responsible for many important animal diseases. While a number of P. multocida virulence factors have been identified, very little is known about how gene expression and protein production is regulated in this organism. Small RNA (sRNA) molecules are critical regulators that act by binding to specific mRNA targets, often in association with the RNA chaperone protein Hfq. In this study, transcriptomic analysis of the P. multocida strain VP161 revealed a putative sRNA with high identity to GcvB from Escherichia coli and Salmonella enterica serovar Typhimurium. High-throughput quantitative liquid proteomics was used to compare the proteomes of the P. multocida VP161 wild-type strain, a gcvB mutant, and a GcvB overexpression strain. These analyses identified 46 proteins that displayed significant differential production after inactivation of gcvB, 36 of which showed increased production. Of the 36 proteins that were repressed by GcvB, 27 were predicted to be involved in amino acid biosynthesis or transport. Bioinformatic analyses of putative P. multocida GcvB target mRNAs identified a strongly conserved 10 nucleotide consensus sequence, 5'-AACACAACAT-3', with the central eight nucleotides identical to the seed binding region present within GcvB mRNA targets in E. coli and S. Typhimurium. Using a defined set of seed region mutants, together with a two-plasmid reporter system that allowed for quantification of sRNA-mRNA interactions, this sequence was confirmed to be critical for the binding of the P. multocida GcvB to the target mRNA, gltA.
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Affiliation(s)
- Emily L Gulliver
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Amy Wright
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Deanna Deveson Lucas
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Marianne Mégroz
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Oded Kleifeld
- Monash Biomedical Proteomics Facility, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B Schittenhelm
- Monash Biomedical Proteomics Facility, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800, Australia
| | - Torsten Seemann
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jürgen B Bulitta
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando, Florida 32827, USA
| | - Marina Harper
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - John D Boyce
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei. Sci Rep 2017; 7:17173. [PMID: 29215024 PMCID: PMC5719362 DOI: 10.1038/s41598-017-17356-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/22/2017] [Indexed: 12/16/2022] Open
Abstract
The Burkholderia genus includes many species that are known to survive in diverse environmental conditions including low nutrient environments. One species, Burkholderia pseudomallei is a versatile pathogen that can survive in a wide range of hosts and environmental conditions. In this study, we investigated how a nutrient depleted growth environment evokes sRNA mediated responses by B. pseudomallei. Computationally predicted B. pseudomallei D286 sRNAs were mapped to RNA-sequencing data for cultures grown under two conditions: (1) BHIB as a nutrient rich media reference environment and (2) M9 media as a nutrient depleted stress environment. The sRNAs were further selected to identify potentially cis-encoded systems by investigating their possible interactions with their flanking genes. The mappings of predicted sRNA genes and interactions analysis to their flanking genes identified 12 sRNA candidates that may possibly have cis-acting regulatory roles that are associated to a nutrient depleted growth environment. Our approach can be used for identifying novel sRNA genes and their possible role as cis-mediated regulatory systems.
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