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Vibrio cholerae VttR(A) and VttR(B) regulatory influences extend beyond the type 3 secretion system genomic island. J Bacteriol 2013; 195:2424-36. [PMID: 23524608 DOI: 10.1128/jb.02151-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A subset of non-O1/non-O139 serogroup strains of Vibrio cholerae cause disease using type 3 secretion system (T3SS)-mediated mechanisms. An ∼50-kb genomic island carries genes encoding the T3SS structural apparatus, effector proteins, and two transmembrane transcriptional regulators, VttR(A) and VttR(B), which are ToxR homologues. Previous experiments demonstrated that VttR(A) and VttR(B) are necessary for colonization in vivo and promote bile-dependent T3SS gene expression in vitro. To better understand the scope of genes that are potential targets of VttR(A) and VttR(B) regulation, we performed deep RNA sequencing using O39 serogroup strain AM-19226 and derivatives carrying deletions in vttR(A) and vttR(B) grown in bile. Comparison of the transcript profiles from ΔvttR(A) and ΔvttR(B) mutant strains to the isogenic parent strain confirmed that VttR(A) and VttR(B) regulate expression of some T3SS island genes and provided additional information about relative expression levels and operon organization. Interestingly, the data also suggested that additional genes, located outside the T3SS island and encoding functions involved in motility, chemotaxis, type 6 secretion, transcriptional regulation, and stress responses, may also by regulated by VttR(A) and VttR(B). We verified transcript levels for selected genes by quantitative reverse transcription (RT)-PCR and then focused additional studies on motility and biofilm formation. The results suggest that VttR(A) and VttR(B) act as part of a complex transcriptional network that coordinates virulence gene expression with multiple cellular phenotypes. VttR(A) and VttR(B) therefore represent horizontally acquired transcriptional regulators with the ability to influence global gene expression in addition to modulating gene expression within the T3SS genomic island.
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152
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Prachi P, Donati C, Masciopinto F, Rappuoli R, Bagnoli F. Deep sequencing in pre- and clinical vaccine research. Public Health Genomics 2013; 16:62-8. [PMID: 23548719 DOI: 10.1159/000345611] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Vaccine research has experienced a quantum leap after the beginning of the genomics era. High-throughput sequencing techniques, unlimited computing resources, as well as new bioinformatic algorithms are now changing the way we perform genomic studies. Whole genome sequencing will soon become the gold standard for phylogenetic and epidemiology studies and is already shedding new light on the dynamics of bacterial evolution. We believe that deep sequencing projects, together with structural studies on vaccine candidates, will allow targeting constant epitopes and avoid vaccine failure due to antigenic variability. Systems biology, which is expected to revolutionize vaccine research and clinical studies, greatly relies on high-throughput technologies such as RNA-seq. Furthermore, genomics is a key element to develop safer vaccines, and the accuracy of deep sequencing will allow monitoring vaccine coverage after their introduction on the market.
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Affiliation(s)
- P Prachi
- Novartis Vaccines, Research Center, Siena, Italy
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153
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Magoc T, Wood D, Salzberg SL. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. Evol Bioinform Online 2013; 9:127-36. [PMID: 23531787 PMCID: PMC3603529 DOI: 10.4137/ebo.s11250] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background The expression levels of bacterial genes can be measured directly using next-generation sequencing (NGS) methods, offering much greater sensitivity and accuracy than earlier, microarray-based methods. Most bioinformatics software for estimating levels of gene expression from NGS data has been designed for eukaryotic genomes, with algorithms focusing particularly on detection of splicing patterns. These methods do not perform well on bacterial genomes. Results Here we describe the first software system designed explicitly for quantifying the degree of gene expression in bacteria and other prokaryotes. EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) processes the raw data from an RNA-seq experiment on a bacterial or archaeal species and produces estimates of the expression levels for each gene in these gene-dense genomes. Software The EDGE-pro tool is implemented as a pipeline of C++ and Perl programs and is freely available as open-source code at http://www.genomics.jhu.edu/software/EDGE/index.shtml.
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Affiliation(s)
- Tanja Magoc
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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154
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Miyata ST, Bachmann V, Pukatzki S. Type VI secretion system regulation as a consequence of evolutionary pressure. J Med Microbiol 2013; 62:663-676. [PMID: 23429693 DOI: 10.1099/jmm.0.053983-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The type VI secretion system (T6SS) is a mechanism evolved by Gram-negative bacteria to negotiate interactions with eukaryotic and prokaryotic competitors. T6SSs are encoded by a diverse array of bacteria and include plant, animal, human and fish pathogens, as well as environmental isolates. As such, the regulatory mechanisms governing T6SS gene expression vary widely from species to species, and even from strain to strain within a given species. This review concentrates on the four bacterial genera that the majority of recent T6SS regulatory studies have been focused on: Vibrio, Pseudomonas, Burkholderia and Edwardsiella.
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Affiliation(s)
- Sarah T Miyata
- Department of Medical Microbiology and Immunology, 6-22 Heritage Medical Research Centre, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Verena Bachmann
- Department of Medical Microbiology and Immunology, 6-22 Heritage Medical Research Centre, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Stefan Pukatzki
- Department of Medical Microbiology and Immunology, 6-22 Heritage Medical Research Centre, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
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155
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Liao G, Liu Q, Xie J. Transcriptional analysis of the effect of exogenous decanoic acid stress on Streptomyces roseosporus. Microb Cell Fact 2013; 12:19. [PMID: 23432849 PMCID: PMC3724488 DOI: 10.1186/1475-2859-12-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 02/19/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Daptomycin is an important antibiotic against infections caused by drug-resistant pathogens. Its production critically depends on the addition of decanoic acid during fermentation. Unfortunately, decanoic acid (>2.5 mM) is toxic to daptomycin producer, Streptomyces roseosporus. RESULTS To understand the mechanism underlying decanoic tolerance or toxicity, the responses of S. roseosporus was determined by a combination of phospholipid fatty acid analysis, reactive oxygen species (ROS) measurement and RNA sequencing. Assays using fluorescent dyes indicated a sharp increase in reactive oxygen species during decanoic acid stress; fatty acid analysis revealed a marked increase in the composition of branched-chain fatty acids by approximately 10%, with a corresponding decrease in straight-chain fatty acids; functional analysis indicated decanoic acid stress has components common to other stress response, including perturbation of respiratory functions (nuo and cyd operons), oxidative stress, and heat shock. Interestingly, our transcriptomic analysis revealed that genes coding for components of proteasome and related to treholase synthesis were up-regulated in the decanoic acid -treated cells. CONCLUSION These findings represent an important first step in understanding mechanism of decanoic acid toxicity and provide a basis for engineering microbial tolerance.
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Affiliation(s)
- Guojian Liao
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of life sciences, School of Pharmaceutical Sciences Southwest University, Chongqing 400715, China
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156
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Characterizing the hexose-6-phosphate transport system of Vibrio cholerae, a utilization system for carbon and phosphate sources. J Bacteriol 2013; 195:1800-8. [PMID: 23417487 DOI: 10.1128/jb.01952-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The facultative human pathogen Vibrio cholerae transits between the gastrointestinal tract of its host and aquatic reservoirs. V. cholerae adapts to different situations by the timely coordinated expression of genes during its life cycle. We recently identified a subclass of genes that are induced at late stages of infection. Initial characterization demonstrated that some of these genes facilitate the transition of V. cholerae from host to environmental conditions. Among these genes are uptake systems lacking detailed characterization or correct annotation. In this study, we comprehensively investigated the function of the VCA0682-to-VCA0687 gene cluster, which was previously identified as in vivo induced. The results presented here demonstrate that the operon encompassing open reading frames VCA0685 to VCA0687 encodes an ABC transport system for hexose-6-phosphates with Km values ranging from 0.275 to 1.273 μM for glucose-6P and fructose-6P, respectively. Expression of the operon is induced by the presence of hexose-6P controlled by the transcriptional activator VCA0682, representing a UhpA homolog. Finally, we provide evidence that the operon is essential for the utilization of hexose-6P as a C and P source. Thereby, a physiological role can be assigned to hexose-6P uptake, which correlates with increased fitness of V. cholerae after a transition from the host into phosphate-limiting environments.
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157
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Forde BM, O'Toole PW. Next-generation sequencing technologies and their impact on microbial genomics. Brief Funct Genomics 2013; 12:440-53. [PMID: 23314033 DOI: 10.1093/bfgp/els062] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing technologies have had a dramatic impact in the field of genomic research through the provision of a low cost, high-throughput alternative to traditional capillary sequencers. These new sequencing methods have surpassed their original scope and now provide a range of utility-based applications, which allow for a more comprehensive analysis of the structure and content of microbial genomes than was previously possible. With the commercialization of a third generation of sequencing technologies imminent, we discuss the applications of current next-generation sequencing methods and explore their impact on and contribution to microbial genome research.
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Affiliation(s)
- Brian M Forde
- Department of Microbiology, University College Cork, Cork, Ireland.
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158
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Abstract
Adaptation of bacterial pathogens to a host can lead to the selection and accumulation of specific mutations in their genomes with profound effects on the overall physiology and virulence of the organisms. The opportunistic pathogen Pseudomonas aeruginosa is capable of colonizing the respiratory tract of individuals with cystic fibrosis (CF), where it undergoes evolution to optimize survival as a persistent chronic human colonizer. The transcriptome of a host-adapted, alginate-overproducing isolate from a CF patient was determined following growth of the bacteria in the presence of human respiratory mucus. This stable mucoid strain responded to a number of regulatory inputs from the mucus, resulting in an unexpected repression of alginate production. Mucus in the medium also induced the production of catalases and additional peroxide-detoxifying enzymes and caused reorganization of pathways of energy generation. A specific antibacterial type VI secretion system was also induced in mucus-grown cells. Finally, a group of small regulatory RNAs was identified and a fraction of these were mucus regulated. This report provides a snapshot of responses in a pathogen adapted to a human host through assimilation of regulatory signals from tissues, optimizing its long-term survival potential. The basis for chronic colonization of patients with cystic fibrosis (CF) by the opportunistic pathogen Pseudomonas aeruginosa continues to represent a challenging problem for basic scientists and clinicians. In this study, the host-adapted, alginate-overproducing Pseudomonas aeruginosa 2192 strain was used to assess the changes in its transcript levels following growth in respiratory CF mucus. Several significant and unexpected discoveries were made: (i) although the alginate overproduction in strain 2192 was caused by a stable mutation, a mucus-derived signal caused reduction in the transcript levels of alginate biosynthetic genes; (ii) mucus activated the expression of the type VI secretion system, a mechanism for killing of other bacteria in a mixed population; (iii) expression of a number of genes involved in respiration was altered; and (iv) several small regulatory RNAs were identified, some being mucus regulated. This work highlights the strong influence of the host environment in shaping bacterial survival strategies.
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159
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Hall JW, Ji Y. Sensing and Adapting to Anaerobic Conditions by Staphylococcus aureus. ADVANCES IN APPLIED MICROBIOLOGY 2013; 84:1-25. [PMID: 23763757 DOI: 10.1016/b978-0-12-407673-0.00001-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A highly adaptive commensal organism, Staphylococcus aureus, possesses an array of genes that allow the bacterium to survive and grow in a wide variety of niches. Several of these niches are known to be or become anaerobic during the course of an infection; additionally, biofilms that develop, commonly on implanted medical devices, become anaerobic. The metabolic capability of S. aureus provides the organism with the essential nutrients needed to continue to grow, divide, and thwart the host immune system in the presence or absence of oxygen. In order to utilize the ATP-producing pathways and maintain cellular health S. aureus has evolved a series of regulatory systems that regulate these ATP-producing pathways. In this review, we discuss the protein signaling systems that sense, indirectly and directly, anaerobic conditions, their sensory mechanisms and signals, and outline the genes that are altered due to the absence of oxygen and the subsequent response by the bacterial cell. The switch from aerobic to anaerobic growth in S. aureus is complex and highly regulated, with some metabolic pathways regulated by multiple regulatory systems to ensure maximal utilization of each pathway and substrate.
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Affiliation(s)
- Jeffrey W Hall
- Department of Veterinary and Biomedical Science, College of Veterinary Medicine, University of Minnesota, St. Paul, Minneapolis, Minnesota, USA
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160
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Jang HB, Kim YK, del Castillo CS, Nho SW, Cha IS, Park SB, Ha MA, Hikima JI, Hong SJ, Aoki T, Jung TS. RNA-seq-based metatranscriptomic and microscopic investigation reveals novel metalloproteases of Neobodo sp. as potential virulence factors for soft tunic syndrome in Halocynthia roretzi. PLoS One 2012; 7:e52379. [PMID: 23300657 PMCID: PMC3531462 DOI: 10.1371/journal.pone.0052379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/12/2012] [Indexed: 12/14/2022] Open
Abstract
Bodonids and trypanosomatids are derived from a common ancestor with the bodonids being a more primitive lineage. The Neobodonida, one of the three clades of bodonids, can be free-living, commensal or parasitic. Despite the ecological and evolutionary significance of these organisms, however, many of their biological and pathological features are currently unknown. Here, we employed metatranscriptomics using RNA-seq technology combined with field-emission microscopy to reveal the virulence factors of a recently described genus of Neobodonida that is considered to be responsible for ascidian soft tunic syndrome (AsSTS), but whose pathogenesis is unclear. Our microscopic observation of infected tunic tissues suggested putative virulence factors, enabling us to extract novel candidate transcripts; these included cysteine proteases of the families C1 and C2, serine proteases of S51 and S9 families, and metalloproteases grouped into families M1, M3, M8, M14, M16, M17, M24, M41, and M49. Protease activity/inhibition assays and the estimation of expression levels within gene clusters allowed us to identify metalloprotease-like enzymes as potential virulence attributes for AsSTS. Furthermore, a multimarker-based phylogenetic analysis using 1,184 concatenated amino acid sequences clarified the order Neobodo sp. In sum, we herein used metatranscriptomics to elucidate the in situ expression profiles of uncharacterized putative transcripts of Neobodo sp., combined these results with microscopic observation to select candidate genes relevant to pathogenesis, and used empirical screening to define important virulence factors.
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Affiliation(s)
- Ho Bin Jang
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Young Kyu Kim
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Carmelo S. del Castillo
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Seong Won Nho
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - In Seok Cha
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Seong Bin Park
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Mi Ae Ha
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Jun-ichi Hikima
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Sung Jong Hong
- Department of Medical Environmental Biology, College of Medicine, Chung-Ang University, DongJak-Gu, Seoul, South Korea
| | - Takashi Aoki
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
- Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tae Sung Jung
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
- * E-mail:
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161
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Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J. How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? BMC Genomics 2012; 13:734. [PMID: 23270466 PMCID: PMC3543199 DOI: 10.1186/1471-2164-13-734] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/15/2012] [Indexed: 12/17/2022] Open
Abstract
Background High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance. Results We have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. Our findings suggest that the number of reads typically produced in a single lane of the Illumina HiSeq sequencer far exceeds the number needed to saturate the annotated transcriptomes of diverse bacteria growing in monoculture. Moreover, as sequencing depth increases, so too does the detection of cDNAs that likely correspond to spurious transcripts or genomic DNA contamination. Finally, even when dozens of barcoded individual cDNA libraries are sequenced in a single lane, the vast majority of transcripts in each sample can be detected and numerous genes differentially expressed between samples can be identified. Conclusions Our analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species.
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Affiliation(s)
- Brian J Haas
- Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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162
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Toffano-Nioche C, Nguyen AN, Kuchly C, Ott A, Gautheret D, Bouloc P, Jacq A. Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus. RNA (NEW YORK, N.Y.) 2012; 18:2201-2219. [PMID: 23097430 PMCID: PMC3504672 DOI: 10.1261/rna.033324.112] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
Work in recent years has led to the recognition of the importance of small regulatory RNAs (sRNAs) in bacterial regulation networks. New high-throughput sequencing technologies are paving the way to the exploration of an expanding sRNA world in nonmodel bacteria. In the Vibrio genus, compared to the enterobacteriaceae, still a limited number of sRNAs have been characterized, mostly in Vibrio cholerae, where they have been shown to be important for virulence, as well as in Vibrio harveyi. In addition, genome-wide approaches in V. cholerae have led to the discovery of hundreds of potential new sRNAs. Vibrio splendidus is an oyster pathogen that has been recently associated with massive mortality episodes in the French oyster growing industry. Here, we report the first RNA-seq study in a Vibrio outside of the V. cholerae species. We have uncovered hundreds of candidate regulatory RNAs, be it cis-regulatory elements, antisense RNAs, and trans-encoded sRNAs. Conservation studies showed the majority of them to be specific to V. splendidus. However, several novel sRNAs, previously unidentified, are also present in V. cholerae. Finally, we identified 28 trans sRNAs that are conserved in all the Vibrio genus species for which a complete genome sequence is available, possibly forming a Vibrio "sRNA core."
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Affiliation(s)
- Claire Toffano-Nioche
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - An N. Nguyen
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Claire Kuchly
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Alban Ott
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Daniel Gautheret
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Philippe Bouloc
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
| | - Annick Jacq
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France
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163
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Abstract
LysR-type transcriptional regulators (LTTRs) are the largest, most diverse family of prokaryotic transcription factors, with regulatory roles spanning metabolism, cell growth and division, and pathogenesis. Using a sequence-defined transposon mutant library, we screened a panel of V. cholerae El Tor mutants to identify LTTRs required for host intestinal colonization. Surprisingly, out of 38 LTTRs, only one severely affected intestinal colonization in the suckling mouse model of cholera: the methionine metabolism regulator, MetR. Genetic analysis of genes influenced by MetR revealed that glyA1 and metJ were also required for intestinal colonization. Chromatin immunoprecipitation of MetR and quantitative reverse transcription-PCR (qRT-PCR) confirmed interaction with and regulation of glyA1, indicating that misregulation of glyA1 is likely responsible for the colonization defect observed in the metR mutant. The glyA1 mutant was auxotrophic for glycine but exhibited wild-type trimethoprim sensitivity, making folate deficiency an unlikely cause of its colonization defect. MetJ regulatory mutants are not auxotrophic but are likely altered in the regulation of amino acid-biosynthetic pathways, including those for methionine, glycine, and serine, and this misregulation likely explains its colonization defect. However, mutants defective in methionine, serine, and cysteine biosynthesis exhibited wild-type virulence, suggesting that these amino acids can be scavenged in vivo. Taken together, our results suggest that glycine biosynthesis may be required to alleviate an in vivo nutritional restriction in the mouse intestine; however, additional roles for glycine may exist. Irrespective of the precise nature of this requirement, this study illustrates the importance of pathogen metabolism, and the regulation thereof, as a virulence factor. Vibrio cholerae continues to be a severe cause of morbidity and mortality in developing countries. Identification of V. cholerae factors critical to disease progression offers the potential to develop or improve upon therapeutics and prevention strategies. To increase the efficiency of virulence factor discovery, we employed a regulator-centric approach to multiplex our in vivo screening capabilities and allow whole regulons in V. cholerae to be interrogated for pathogenic potential. We identified MetR as a new virulence regulator and serine hydroxymethyltransferase GlyA1 as a new MetR-regulated virulence factor, both required by V. cholerae to colonize the infant mouse intestine. Bacterial metabolism is a prerequisite to virulence, and current knowledge of in vivo metabolism of pathogens is limited. Here, we expand the known role of amino acid metabolism and regulation in virulence and offer new insights into the in vivo metabolic requirements of V. cholerae within the mouse intestine.
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164
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Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol 2012; 13:R23. [PMID: 22455878 PMCID: PMC3439974 DOI: 10.1186/gb-2012-13-3-r23] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 03/12/2012] [Accepted: 03/28/2012] [Indexed: 01/15/2023] Open
Abstract
We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.
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Affiliation(s)
- Georgia Giannoukos
- Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
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165
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Reddy JS, Kumar R, Watt JM, Lawrence ML, Burgess SC, Nanduri B. Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213. BMC Bioinformatics 2012; 13 Suppl 15:S4. [PMID: 23046475 PMCID: PMC3439734 DOI: 10.1186/1471-2105-13-s15-s4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background Computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. Identification of transcriptional start sites, demarcating overlapping gene boundaries, and identifying regulatory elements such as small RNA are not accurate using these approaches. In this study, we re-visit the structural annotation of Mannheimia haemolytica PHL213, a bovine respiratory disease pathogen. M. haemolytica is one of the causative agents of bovine respiratory disease that results in about $3 billion annual losses to the cattle industry. We used RNA-Seq and analyzed the data using freely-available computational methods and resources. The aim was to identify previously unannotated regions of the genome using RNA-Seq based expression profile to complement the existing annotation of this pathogen. Results Using the Illumina Genome Analyzer, we generated 9,055,826 reads (average length ~76 bp) and aligned them to the reference genome using Bowtie. The transcribed regions were analyzed using SAMTOOLS and custom Perl scripts in conjunction with BLAST searches and available gene annotation information. The single nucleotide resolution map enabled the identification of 14 novel protein coding regions as well as 44 potential novel sRNA. The basal transcription profile revealed that 2,506 of the 2,837 annotated regions were expressed in vitro, at 95.25% coverage, representing all broad functional gene categories in the genome. The expression profile also helped identify 518 potential operon structures involving 1,086 co-expressed pairs. We also identified 11 proteins with mutated/alternate start codons. Conclusions The application of RNA-Seq based transcriptome profiling to structural gene annotation helped correct existing annotation errors and identify potential novel protein coding regions and sRNA. We used computational tools to predict regulatory elements such as promoters and terminators associated with the novel expressed regions for further characterization of these novel functional elements. Our study complements the existing structural annotation of Mannheimia haemolytica PHL213 based on experimental evidence. Given the role of sRNA in virulence gene regulation and stress response, potential novel sRNA described in this study can form the framework for future studies to determine the role of sRNA, if any, in M. haemolytica pathogenesis.
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Affiliation(s)
- Joseph S Reddy
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
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167
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The NorR regulon is critical for Vibrio cholerae resistance to nitric oxide and sustained colonization of the intestines. mBio 2012; 3:e00013-12. [PMID: 22511349 PMCID: PMC3345576 DOI: 10.1128/mbio.00013-12] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Vibrio cholerae, the cause of an often fatal infectious diarrhea, remains a large global public health threat. Little is known about the challenges V. cholerae encounters during colonization of the intestines, which genes are important for overcoming these challenges, and how these genes are regulated. In this study, we examined the V. cholerae response to nitric oxide (NO), an antibacterial molecule derived during infection from various sources, including host inducible NO synthase (iNOS). We demonstrate that the regulatory protein NorR regulates the expression of NO detoxification genes hmpA and nnrS, and that all three are critical for resisting low levels of NO stress under microaerobic conditions in vitro. We also show that prxA, a gene previously thought to be important for NO detoxification, plays no role in NO resistance under microaerobic conditions and is upregulated by H2O2, not NO. Furthermore, in an adult mouse model of prolonged colonization, hmpA and norR were important for the resistance of both iNOS- and non-iNOS-derived stresses. Our data demonstrate that NO detoxification systems play a critical role in the survival of V. cholerae under microaerobic conditions resembling those of an infectious setting and during colonization of the intestines over time periods similar to that of an actual V. cholerae infection. Little is known about what environmental stresses Vibrio cholerae, the etiologic agent of cholera, encounters during infection, and even less is known about how V. cholerae senses and counters these stresses. Most prior studies of V. cholerae infection relied on the 24-h infant mouse model, which does not allow the analysis of survival over time periods comparable to that of an actual V. cholerae infection. In this study, we used a sustained mouse colonization model to identify nitric oxide resistance as a function critical for the survival of V. cholerae in the intestines and further identified the genes responsible for sensing and detoxifying this stress.
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168
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Davies BW, Bogard RW, Young TS, Mekalanos JJ. Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence. Cell 2012; 149:358-70. [PMID: 22500802 PMCID: PMC3620040 DOI: 10.1016/j.cell.2012.01.053] [Citation(s) in RCA: 327] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/08/2011] [Accepted: 01/18/2012] [Indexed: 12/23/2022]
Abstract
The function of the Vibrio 7(th) pandemic island-1 (VSP-1) in cholera pathogenesis has remained obscure. Utilizing chromatin immunoprecipitation sequencing and RNA sequencing to map the regulon of the master virulence regulator ToxT, we identify a TCP island-encoded small RNA that reduces the expression of a previously unrecognized VSP-1-encoded transcription factor termed VspR. VspR modulates the expression of several VSP-1 genes including one that encodes a novel class of di-nucleotide cyclase (DncV), which preferentially synthesizes a previously undescribed hybrid cyclic AMP-GMP molecule. We show that DncV is required for efficient intestinal colonization and downregulates V. cholerae chemotaxis, a phenotype previously associated with hyperinfectivity. This pathway couples the actions of previously disparate genomic islands, defines VSP-1 as a pathogenicity island in V. cholerae, and implicates its occurrence in 7(th) pandemic strains as a benefit for host adaptation through the production of a regulatory cyclic di-nucleotide.
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Affiliation(s)
- Bryan W. Davies
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Ryan W. Bogard
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Travis S. Young
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - John J. Mekalanos
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
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169
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Bardill JP, Hammer BK. Non-coding sRNAs regulate virulence in the bacterial pathogen Vibrio cholerae. RNA Biol 2012; 9:392-401. [PMID: 22546941 DOI: 10.4161/rna.19975] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Vibrio cholerae is the waterborne bacterium responsible for worldwide outbreaks of the acute, potentially fatal cholera diarrhea. The primary factors this human pathogen uses to cause the disease are controlled by a complex regulatory program linking extracellular signaling inputs to changes in expression of several critical virulence genes. Recently it has been uncovered that many non-coding regulatory sRNAs are important components of the V. cholerae virulence regulon. Most of these sRNAs appear to require the RNA-binding protein, Hfq, to interact with and alter the expression of target genes, while a few sRNAs appear to function by an Hfq-independent mechanism. Direct base-pairing between the sRNAs and putative target mRNAs has been shown in a few cases but the extent of each sRNAs regulon is not fully known. Genetic and biochemical methods, coupled with computational and genomics approaches, are being used to validate known sRNAs and also to identify many additional putative sRNAs that may play a role in the pathogenic lifestyle of V. cholerae.
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Affiliation(s)
- J Patrick Bardill
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
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170
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Hébrard M, Kröger C, Srikumar S, Colgan A, Händler K, Hinton JCD. sRNAs and the virulence of Salmonella enterica serovar Typhimurium. RNA Biol 2012; 9:437-45. [PMID: 22546935 PMCID: PMC3384567 DOI: 10.4161/rna.20480] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The combination of genomics and high-throughput cDNA sequencing technologies has facilitated the identification of many small RNAs (sRNAs) that play a central role in the post-transcriptional gene regulation of Salmonella enterica serovar Typhimurium. To date, most of the functionally characterized sRNAs have been involved in the regulation of processes which are not directly linked to virulence. Just five sRNAs have been found to affect the ability of Salmonella to replicate within mammalian cells, but the precise regulatory mechanisms that are used by sRNAs to control Salmonella pathogenicity at the post-transcriptional level remain to be identified. It is anticipated that an improved understanding of sRNA biology will shed new light on the virulence of Salmonella.
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Affiliation(s)
- Magali Hébrard
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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171
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RNA-Seq for Plant Pathogenic Bacteria. Genes (Basel) 2011; 2:689-705. [PMID: 24710287 PMCID: PMC3927590 DOI: 10.3390/genes2040689] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 09/30/2011] [Accepted: 09/30/2011] [Indexed: 11/18/2022] Open
Abstract
The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but it is still a technology under development with limitations and unknowns that need to be considered. Here, we review some new developments for RNA-Seq and highlight recent findings for host-associated bacteria. We also discuss the technical and statistical challenges in the practical application of RNA-Seq for studying bacterial transcriptomes and describe some of the currently available solutions.
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