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Liu Z, Liao C, Wang L. Fitness and transcriptomic analysis of pathogenic Vibrio parahaemolyticus in seawater at different shellfish harvesting temperatures. Microbiol Spectr 2023; 11:e0278323. [PMID: 37962397 PMCID: PMC10715093 DOI: 10.1128/spectrum.02783-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Given the involvement of Vibrio parahaemolyticus (Vp) in a wide range of seafood outbreaks, a systematical characterization of Vp fitness and transcriptomic changes at temperatures of critical importance for seafood production and storage is needed. In this study, one of each virulent Vp strain (tdh+ and trh+) was tested. While no difference in survival behavior of the two virulent strains was observed at 10°C, the tdh+ strain had a faster growth rate than the trh+ strain at 30°C. Transcriptomic analysis showed that a significantly higher number of genes were upregulated at 30°C than at 10°C. The majority of differentially expressed genes of Vp at 30°C were annotated to functional categories supporting cellular growth. At 10°C, the downregulation of the biofilm formation and histidine metabolism indicates that the current practice of storing seafood at low temperatures not only protects seafood quality but also ensures seafood safety.
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Affiliation(s)
- Zhuosheng Liu
- Department of Food Science and Technology, University of California, Davis, California, USA
| | - Chao Liao
- Department of Food Science and Technology, University of California, Davis, California, USA
| | - Luxin Wang
- Department of Food Science and Technology, University of California, Davis, California, USA
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2
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Hussain A, Ray MK. Functional activity of E. coli RNase R in the Antarctic Pseudomonas syringae Lz4W. J Genet Eng Biotechnol 2023; 21:101. [PMID: 37843651 PMCID: PMC10579198 DOI: 10.1186/s43141-023-00553-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND In Antarctic P. syringae RNase R play an essential role in the processing of 16S and 5S rRNA, thereby playing an important role in cold-adapted growth of the bacterium. This study is focused on deciphering the in vivo functional activity of mesophilic exoribonuclease R and its catalytic domain (RNB) in an evolutionary distant psychrophilic bacterium Pseudomonas syringae Lz4W. RESULTS Our results confirm that E. coli RNase R complemented the physiological functions of the psychrophilic bacterium P. syringae RNase R and rescued the cold-sensitive phenotype of Pseudomonas syringae ∆rnr mutant. More importantly, the catalytic domain (RNB) of the E. coli RNase R is also capable of alleviating the cold-sensitive growth defects of ∆rnr mutant as seen with the catalytic domain (RNB) of the P. syringae enzyme. The Catalytic domain of E. coli RNase R was less efficient than the Catalytic domain of P. syringae RNase R in rescuing the cold-sensitive growth of ∆rnr mutant at 4°C, as the ∆rnr expressing the RNBEc (catalytic domain of E. coli RNase R) displayed longer lag phase than the RNBPs (Catalytic domain of P. syringae RNase R) complemented ∆rnr mutant at 4°C. Altogether it appears that the E. coli RNase R and P. syringae RNase R are functionally exchangeable for the growth requirements of P. syringae at low temperature (4°C). Our results also confirm that in P. syringae the requirement of RNase R for supporting the growth at 4°C is independent of the degradosomal complex. CONCLUSION E. coli RNase R (RNase REc) rescues the cold-sensitive phenotype of the P. syringae Δrnr mutant. Similarly, the catalytic domain of E. coli RNase R (RNBEc) is also capable of supporting the growth of Δrnr mutant at low temperatures. These findings have a vast scope in the design and development of low-temperature-based expression systems.
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Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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Miyamoto K, Sujino T, Harada Y, Ashida H, Yoshimatsu Y, Yonemoto Y, Nemoto Y, Tomura M, Melhem H, Niess JH, Suzuki T, Suzuki T, Suzuki S, Koda Y, Okamoto R, Mikami Y, Teratani T, Tanaka KF, Yoshimura A, Sato T, Kanai T. The gut microbiota-induced kynurenic acid recruits GPR35-positive macrophages to promote experimental encephalitis. Cell Rep 2023; 42:113005. [PMID: 37590143 DOI: 10.1016/j.celrep.2023.113005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
The intricate interplay between gut microbes and the onset of experimental autoimmune encephalomyelitis (EAE) remains poorly understood. Here, we uncover remarkable similarities between CD4+ T cells in the spinal cord and their counterparts in the small intestine. Furthermore, we unveil a synergistic relationship between the microbiota, particularly enriched with the tryptophan metabolism gene EC:1.13.11.11, and intestinal cells. This symbiotic collaboration results in the biosynthesis of kynurenic acid (KYNA), which modulates the recruitment and aggregation of GPR35-positive macrophages. Subsequently, a robust T helper 17 (Th17) immune response is activated, ultimately triggering the onset of EAE. Conversely, modulating the KYNA-mediated GPR35 signaling in Cx3cr1+ macrophages leads to a remarkable amelioration of EAE. These findings shed light on the crucial role of microbial-derived tryptophan metabolites in regulating immune responses within extraintestinal tissues.
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Affiliation(s)
- Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; Miyarisan Pharmaceutical Co., Ltd., Research Laboratory, 1-10-3, Kaminagazato, Kita-ku, Tokyo 114-0016, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Yosuke Harada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hiroshi Ashida
- Department of Bacterial Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Cyuo-ku, Chiba city, Chiba 260-8673, Japan
| | - Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuki Yonemoto
- Department of Gastroenterology and Hepatology, Tokyo Medical Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yasuhiro Nemoto
- Department of Gastroenterology and Hepatology, Tokyo Medical Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Michio Tomura
- Laboratory of Immunology, Faculty of Pharmacy, Osaka Otani University, 3-11-1 Nshikiorikita, Tondabayshi, Osaka, 584-8584, Japan
| | - Hassan Melhem
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland; Clarunis-University Center for Gastrointestinal and Liver Diseases, University Hospital Basel, 4002 Basel, Switzerland
| | - Toshihiko Suzuki
- Department of Bacterial Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Toru Suzuki
- Division of Brain Sciences Institute for Advanced Medical Research, Keio University School of Medicne, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Shohei Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuzo Koda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Tokyo Medical Dental University (TMDU), 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kenji F. Tanaka
- Division of Brain Sciences Institute for Advanced Medical Research, Keio University School of Medicne, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1, Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.
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Umeda S, Sujino T, Miyamoto K, Yoshimatsu Y, Harada Y, Nishiyama K, Aoto Y, Adachi K, Hayashi N, Amafuji K, Moritoki N, Shibata S, Sasaki N, Mita M, Tanemoto S, Ono K, Mikami Y, Sasabe J, Takabayashi K, Hosoe N, Suzuki T, Sato T, Atarashi K, Teratani T, Ogata H, Nakamoto N, Shiomi D, Ashida H, Kanai T. D-amino Acids Ameliorate Experimental Colitis and Cholangitis by Inhibiting Growth of Proteobacteria: Potential Therapeutic Role in Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 16:1011-1031. [PMID: 37567385 PMCID: PMC10632532 DOI: 10.1016/j.jcmgh.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND & AIMS D-amino acids, the chiral counterparts of protein L-amino acids, were primarily produced and utilized by microbes, including those in the human gut. However, little was known about how orally administered or microbe-derived D-amino acids affected the gut microbial community or gut disease progression. METHODS The ratio of D- to L-amino acids was analyzed in feces and blood from patients with ulcerative colitis (UC) and healthy controls. Also, composition of microbe was analyzed from patients with UC. Mice were treated with D-amino acid in dextran sulfate sodium colitis model and liver cholangitis model. RESULTS The ratio of D- to L-amino acids was lower in the feces of patients with UC than that of healthy controls. Supplementation of D-amino acids ameliorated UC-related experimental colitis and liver cholangitis by inhibiting growth of Proteobacteria. Addition of D-alanine, a major building block for bacterial cell wall formation, to culture medium inhibited expression of the ftsZ gene required for cell fission in the Proteobacteria Escherichia coli and Klebsiella pneumoniae, thereby inhibiting growth. Overexpression of ftsZ restored growth of E. coli even when D-alanine was present. We found that D-alanine not only inhibited invasion of pathological K. pneumoniae into the host via pore formation in intestinal epithelial cells but also inhibited growth of E. coli and generation of antibiotic-resistant strains. CONCLUSIONS D-amino acids might have potential for use in novel therapeutic approaches targeting Proteobacteria-associated dysbiosis and antibiotic-resistant bacterial diseases by means of their effects on the intestinal microbiota community.
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Affiliation(s)
- Satoko Umeda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan.
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan; Miyarisan Pharmaceutical Co, Ltd., Tokyo, Japan
| | - Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yosuke Harada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keita Nishiyama
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan; JSR-Keio University Medical and Chemical Innovation Center (JKiC), Keio University School of Medicine, Tokyo, Japan
| | - Yoshimasa Aoto
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Keika Adachi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Naoki Hayashi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Kimiko Amafuji
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp, Tokyo, Japan
| | - Nobuko Moritoki
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Nobuo Sasaki
- Institute of Molecular and Cellular Regulation, Gunma University, Maebashi City, Japan
| | | | - Shun Tanemoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Ono
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Jumpei Sasabe
- Department of Pharmacology, School of Medicine, Keio University, Tokyo, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hosoe
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Ogata
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Hiroshi Ashida
- Department of Bacterial Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan; AMED-CREST, Tokyo, Japan.
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CRISPR-Cas-Guided Mutagenesis of Chromosome and Virulence Plasmid in Shigella flexneri by Cytosine Base Editing. mSystems 2023; 8:e0104522. [PMID: 36541764 PMCID: PMC9948704 DOI: 10.1128/msystems.01045-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Shigella is a Gram-negative bacterium that invades the human gut epithelium. The resulting infection, shigellosis, is the deadliest bacterial diarrheal disease. Much of the information about the genes dictating the pathophysiology of Shigella, both on the chromosome and the virulence plasmid, was obtained by classical reverse genetics. However, technical limitations of the prevalent mutagenesis techniques restrict the generation of mutants in a single reaction to a small number, preventing large-scale targeted mutagenesis of Shigella and the subsequent assessment of phenotype. We adopted a CRISPR-Cas-dependent approach, where a nickase Cas9 and cytidine deaminase fusion is guided by single guide RNA (sgRNA) to introduce targeted C→T transitions, resulting in internal stop codons and premature termination of translation. In proof-of-principle experiments using an mCherry fluorescent reporter, we were able to generate loss-of-function mutants in both Escherichia coli and Shigella flexneri with up to 100% efficacy. Using a modified fluctuation assay, we determined that under optimized conditions, the frequency of untargeted mutations introduced by the Cas9-deaminase fusion was in the same range as spontaneous mutations, making our method a safe choice for bacterial mutagenesis. Furthermore, we programmed the method to mutate well-characterized chromosomal and plasmid-borne Shigella flexneri genes and found the mutant phenotype to be similar to those of the reported gene deletion mutants, with no apparent polar effects at the phenotype level. This method can be used in a 96-well-plate format to increase the throughput and generate an array of targeted loss-of-function mutants in a few days. IMPORTANCE Loss-of-function mutagenesis is critical in understanding the physiological role of genes. Therefore, high-throughput techniques to generate such mutants are important for facilitating the assessment of gene function at a pace that matches systems biology approaches. However, to our knowledge, no such method was available for generating an array of single gene mutants in an important enteropathogen-Shigella. This pathogen causes high morbidity and mortality in children, and antibiotic-resistant strains are quickly emerging. Therefore, determination of the function of unknown Shigella genes is of the utmost importance to develop effective strategies to control infections. Our present work will bridge this gap by providing a rapid method for generating loss-of-function mutants. The highly effective and specific method has the potential to be programmed to generate multiple mutants in a single, massively parallel reaction. By virtue of plasmid compatibility, this method can be extended to other members of Enterobacteriaceae.
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Developing New Tools to Fight Human Pathogens: A Journey through the Advances in RNA Technologies. Microorganisms 2022; 10:microorganisms10112303. [DOI: 10.3390/microorganisms10112303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of the advantages of RNA in terms of its functional performance, have attracted the attention of synthetic biologists to create potent RNA-based tools for biotechnological and medical applications. In this review, we have gathered the knowledge on the connection between RNA metabolism and pathogenesis in Gram-positive and Gram-negative bacteria. We further discuss how RNA techniques have contributed to the building of this knowledge and the development of new tools in synthetic biology for the diagnosis and treatment of diseases caused by pathogenic microorganisms. Infectious diseases are still a world-leading cause of death and morbidity, and RNA-based therapeutics have arisen as an alternative way to achieve success. There are still obstacles to overcome in its application, but much progress has been made in a fast and effective manner, paving the way for the solid establishment of RNA-based therapies in the future.
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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Roy S, Mittal P, Tayi L, Bondada S, Ray MK, Patel HK, Sonti RV. Xanthomonas oryzae pv. oryzae Exoribonuclease R Is Required for Complete Virulence in Rice, Optimal Motility, and Growth Under Stress. PHYTOPATHOLOGY 2022; 112:501-510. [PMID: 34384245 DOI: 10.1094/phyto-07-21-0310-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Exoribonuclease R (RNase R) is a 3' hydrolytic exoribonuclease that can degrade structured RNA. Mutation in RNase R affects virulence of certain human pathogenic bacteria. The aim of this study was to determine whether RNase R is necessary for virulence of the phytopathogen that causes bacterial blight in rice, Xanthomonas oryzae pv. oryzae (Xoo). In silico analysis has indicated that RNase R is highly conserved among various xanthomonads. Amino acid sequence alignment of Xoo RNase R with RNase R from various taxa indicated that Xoo RNase R clustered with RNase R of order Xanthomonadales. To study its role in virulence, we generated a gene disruption mutant of Xoo RNase R. The Xoo rnr- mutant is moderately virulence deficient, and the complementing strain (rnr-/pHM1::rnr) rescued the virulence deficiency of the mutant. We investigated swimming and swarming motilities in both nutrient-deficient minimal media and nutrient-optimal media. We observed that RNase R mutation has adversely affected the swimming and swarming motilities of Xoo in optimal media. However, in nutrient-deficient media only swimming motility was noticeably affected. Growth curves in optimal media at suboptimal temperature (15°C cold stress) indicate that the Xoo rnr- mutant grows more slowly than the Xoo wild type and complementing strain (rnr-/pHM1::rnr). Given these findings, we report for the first time that RNase R function is necessary for complete virulence of Xoo in rice. It is also important for motility of Xoo in media and for growth of Xoo at suboptimal temperature.
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Affiliation(s)
- Sharmila Roy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Pragya Mittal
- MRC Human Genetics Unit, University of Edinburgh, Crewe Road South, Edinburgh, UK, EH4 2XU
| | - Lavanya Tayi
- Center for Plant Molecular Biology, Osmania University, Tarnaka, Hyderabad, Telangana State, India 500007
| | - Sahitya Bondada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Malay K Ray
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Ramesh V Sonti
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India 517507
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RNase R, a New Virulence Determinant of Streptococcus pneumoniae. Microorganisms 2022; 10:microorganisms10020317. [PMID: 35208772 PMCID: PMC8875335 DOI: 10.3390/microorganisms10020317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/30/2022] Open
Abstract
Pneumococcal infections have increasingly high mortality rates despite the availability of vaccines and antibiotics. Therefore, the identification of new virulence determinants and the understanding of the molecular mechanisms behind pathogenesis have become of paramount importance in the search of new targets for drug development. The exoribonuclease RNase R has been involved in virulence in a growing number of pathogens. In this work, we used Galleria mellonella as an infection model to demonstrate that the presence of RNase R increases the pneumococcus virulence. Larvae infected with the RNase R mutant show an increased expression level of antimicrobial peptides. Furthermore, they have a lower bacterial load in the hemolymph in the later stages of infection, leading to a higher survival rate of the larvae. Interestingly, pneumococci expressing RNase R show a sudden drop in bacterial numbers immediately after infection, resembling the eclipse phase observed after intravenous inoculation in mice. Concomitantly, we observed a lower number of mutant bacteria inside larval hemocytes and a higher susceptibility to oxidative stress when compared to the wild type. Together, our results indicate that RNase R is involved in the ability of pneumococci to evade the host immune response, probably by interfering with internalization and/or replication inside the larval hemocytes.
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Ageorges V, Monteiro R, Leroy S, Burgess CM, Pizza M, Chaucheyras-Durand F, Desvaux M. Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): from bacterial adhesion to biofilm formation. FEMS Microbiol Rev 2021; 44:314-350. [PMID: 32239203 DOI: 10.1093/femsre/fuaa008] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.
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Affiliation(s)
- Valentin Ageorges
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Ricardo Monteiro
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,GSK, Via Fiorentina 1, 53100 Siena, Italy
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Catherine M Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | | | - Frédérique Chaucheyras-Durand
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,Lallemand Animal Nutrition SAS, F-31702 Blagnac Cedex, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
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Zhu L, Shahid MA, Markham J, Browning GF, Noormohammadi AH, Marenda MS. Comparative genomic analyses of Mycoplasma synoviae vaccine strain MS-H and its wild-type parent strain 86079/7NS: implications for the identification of virulence factors and applications in diagnosis of M. synoviae. Avian Pathol 2019; 48:537-548. [PMID: 31244324 DOI: 10.1080/03079457.2019.1637514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mycoplasma synoviae is an economically important avian pathogen worldwide, causing respiratory disease, infectious synovitis, airsacculitis and eggshell apex abnormalities in commercial chickens. Despite the widespread use of MS-H as a live attenuated vaccine over the past two decades, the precise molecular basis for loss of virulence in this vaccine is not yet fully understood. To address this, the whole genome sequence of the vaccine parent strain, 86079/7NS, was obtained and compared to that of the MS-H vaccine. Except for the vlhA expressed region, both genomes were nearly identical. Thirty-two single nucleotide polymorphisms (SNPs) were identified in MS-H, including 11 non-synonymous mutations that were predicted, by bioinformatics analysis, to have changed the secondary structure of the deduced proteins. One of these mutations caused truncation of the oppF-1 gene, which encodes the ATP-binding protein of an oligopeptide permease transporter. Overall, the attenuation of MS-H strain may be caused by the cumulative and complex effects of several mutations. The SNPs identified in MS-H were further analyzed by comparing the MS-H and 86079/7NS sequences with the strains WVU-1853 and MS53. In the genomic regions conserved between all strains, 30 SNPs were found to be unique to MS-H lineage. These results have provided a foundation for developing novel biomarkers for the detection of virulence in M. synoviae and also for designing new genotyping assays for discrimination of MS-H from field strains.
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Affiliation(s)
- Ling Zhu
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Werribee , Australia
| | - Muhammad A Shahid
- Department of Pathobiology, Faculty of Veterinary Sciences, Bahauddin Zakariya University , Multan , Pakistan
| | - John Markham
- Department of Electrical and Electronic Engineering, the University of Melbourne , Parkville , Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Parkville , Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Werribee , Australia
| | - Marc S Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Werribee , Australia
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Dressaire C, Pobre V, Laguerre S, Girbal L, Arraiano CM, Cocaign-Bousquet M. PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli. BMC Genomics 2018; 19:848. [PMID: 30486791 PMCID: PMC6264599 DOI: 10.1186/s12864-018-5259-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/16/2018] [Indexed: 12/02/2022] Open
Abstract
Background Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. Results The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. Conclusions This work had identified PNPase as a central player associated with mRNA degradation in stationary phase. Electronic supplementary material The online version of this article (10.1186/s12864-018-5259-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clémentine Dressaire
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - Cecilia Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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Pobre V, Arraiano CM. Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-Seq. Methods Enzymol 2018; 612:1-24. [PMID: 30502937 DOI: 10.1016/bs.mie.2018.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Differential RNA-Seq is a next-generation technology method to determine the significant transcriptomic differences between two and more samples. With this method it is possible to analyze the total RNA content of different samples making it the best global analysis method currently available to study the roles of exoribonucleases in the cell. These enzymes are responsible for the RNA processing and degradation in the cells and therefore affect the total RNA pool in ways not yet fully understood. In Escherichia coli there are three main degradative exoribonucleases RNase II, RNase R, and PNPase that degrade the RNA from the 3' to the 5'-end. These enzymes have several roles in the cell and even though they are degradative enzymes RNase II and PNPase can also protect some RNAs from degradation and PNPase can also act as an RNA polymerase under some conditions. The multiplicity of roles of these exoribonucleases leads to a very high number of transcripts that are affected by their absence in the cell. With the differential RNA-Seq it is possible to obtain a much deeper understanding of how these enzymes work and regulate the bacterial gene expression. In this chapter we have described a differential RNA-Seq data analysis protocol applied to the study of exoribonucleases. We also included the protocol for experimental validation of the RNA-Seq data using qPCR and motility assays. Although the methods described in this chapter were applied to the study of the exoribonucleases, they can also be used for other differential RNA-Seq studies.
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Affiliation(s)
- Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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14
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Dos Santos RF, Quendera AP, Boavida S, Seixas AF, Arraiano CM, Andrade JM. Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:101-155. [PMID: 30340785 DOI: 10.1016/bs.pmbts.2018.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Boavida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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15
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Matos RG, Casinhas J, Bárria C, dos Santos RF, Silva IJ, Arraiano CM. The Role of Ribonucleases and sRNAs in the Virulence of Foodborne Pathogens. Front Microbiol 2017; 8:910. [PMID: 28579982 PMCID: PMC5437115 DOI: 10.3389/fmicb.2017.00910] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/04/2017] [Indexed: 12/02/2022] Open
Abstract
Contaminated food is the source of many severe infections in humans. Recent advances in food science have discovered new foodborne pathogens and progressed in characterizing their biology, life cycle, and infection processes. All this knowledge has been contributing to prevent food contamination, and to develop new therapeutics to treat the infections caused by these pathogens. RNA metabolism is a crucial biological process and has an enormous potential to offer new strategies to fight foodborne pathogens. In this review, we will summarize what is known about the role of bacterial ribonucleases and sRNAs in the virulence of several foodborne pathogens and how can we use that knowledge to prevent infection.
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Affiliation(s)
- Rute G. Matos
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de LisboaOeiras, Portugal
| | | | | | | | | | - Cecília M. Arraiano
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de LisboaOeiras, Portugal
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16
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Genes essential for the morphogenesis of the Shiga toxin 2-transducing phage from Escherichia coli O157:H7. Sci Rep 2016; 6:39036. [PMID: 27966628 PMCID: PMC5155283 DOI: 10.1038/srep39036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/16/2016] [Indexed: 11/28/2022] Open
Abstract
Shiga toxin 2 (Stx2), one of the most important virulence factors of enterohaemorrhagic Escherichia coli (EHEC), is encoded by phages. These phages (Stx2 phages) are often called lambda-like. However, most Stx2 phages are short-tailed, thus belonging to the family Podoviridae, and the functions of many genes, especially those in the late region, are unknown. In this study, we performed a systematic genetic and morphological analysis of genes with unknown functions in Sp5, the Stx2 phage from EHEC O157:H7 strain Sakai. We identified nine essential genes, which, together with the terminase genes, determine Sp5 morphogenesis. Four of these genes most likely encoded portal, major capsid, scaffolding and tail fiber proteins. Although exact roles/functions of the other five genes are unknown, one was involved in head formation and four were required for tail formation. One of the four tail genes encoded an unusually large protein of 2,793 amino-acid residues. Two genes that are likely required to maintain the lysogenic state were also identified. Because the late regions of Stx2 phages from various origins are highly conserved, the present study provides an important basis for better understanding the biology of this unique and medically important group of bacteriophages.
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17
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Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli. BMC Genomics 2015; 16:72. [PMID: 25757888 PMCID: PMC4335698 DOI: 10.1186/s12864-015-1237-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background The RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. Although there are many studies about these exoribonucleases not much is known about their global effect in the transcriptome. Results In order to study the effects of the exoribonucleases on the transcriptome, we sequenced the total RNA (RNA-Seq) from wild-type cells and from mutants for each of the exoribonucleases (∆rnb, ∆rnr and ∆pnp). We compared each of the mutant transcriptome with the wild-type to determine the global effects of the deletion of each exoribonucleases in exponential phase. We determined that the deletion of RNase II significantly affected 187 transcripts, while deletion of RNase R affects 202 transcripts and deletion of PNPase affected 226 transcripts. Surprisingly, many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The results obtained from the transcriptomic analysis pointed to the fact that these enzymes were changing the expression of genes related with flagellum assembly, motility and biofilm formation. The three exoribonucleases affected some stable RNAs, but PNPase was the main exoribonuclease affecting this class of RNAs. We confirmed by qPCR some fold-change values obtained from the RNA-Seq data, we also observed that all the exoribonuclease mutants were significantly less motile than the wild-type cells. Additionally, RNase II and RNase R mutants were shown to produce more biofilm than the wild-type control while the PNPase mutant did not form biofilms. Conclusions In this work we demonstrate how deep sequencing can be used to discover new and relevant functions of the exoribonucleases. We were able to obtain valuable information about the transcripts affected by each of the exoribonucleases and compare the roles of the three enzymes. Our results show that the three exoribonucleases affect cell motility and biofilm formation that are two very important factors for cell survival, especially for pathogenic cells. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1237-6) contains supplementary material, which is available to authorized users.
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18
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Haddad N, Matos RG, Pinto T, Rannou P, Cappelier JM, Prévost H, Arraiano CM. The RNase R from Campylobacter jejuni has unique features and is involved in the first steps of infection. J Biol Chem 2014; 289:27814-24. [PMID: 25100732 DOI: 10.1074/jbc.m114.561795] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacterial pathogens must adapt/respond rapidly to changing environmental conditions. Ribonucleases (RNases) can be crucial factors contributing to the fast adaptation of RNA levels to different environmental demands. It has been demonstrated that the exoribonuclease polynucleotide phosphorylase (PNPase) facilitates survival of Campylobacter jejuni in low temperatures and favors swimming, chick colonization, and cell adhesion/invasion. However, little is known about the mechanism of action of other ribonucleases in this microorganism. Members of the RNB family of enzymes have been shown to be involved in virulence of several pathogens. We have searched C. jejuni genome for homologues and found one candidate that displayed properties more similar to RNase R (Cj-RNR). We show here that Cj-RNR is important for the first steps of infection, the adhesion and invasion of C. jejuni to eukaryotic cells. Moreover, Cj-RNR proved to be active in a wide range of conditions. The results obtained lead us to conclude that Cj-RNR has an important role in the biology of this foodborne pathogen.
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Affiliation(s)
- Nabila Haddad
- From the LUNAM Université, Oniris, University of Nantes, 44200 Nantes, France, the UMR1014 Sécurité des Aliments et Microbiologie, INRA, 44322 Nantes, France, and
| | - Rute G Matos
- the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Teresa Pinto
- the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Pauline Rannou
- From the LUNAM Université, Oniris, University of Nantes, 44200 Nantes, France, the UMR1014 Sécurité des Aliments et Microbiologie, INRA, 44322 Nantes, France, and
| | - Jean-Michel Cappelier
- From the LUNAM Université, Oniris, University of Nantes, 44200 Nantes, France, the UMR1014 Sécurité des Aliments et Microbiologie, INRA, 44322 Nantes, France, and
| | - Hervé Prévost
- From the LUNAM Université, Oniris, University of Nantes, 44200 Nantes, France, the UMR1014 Sécurité des Aliments et Microbiologie, INRA, 44322 Nantes, France, and
| | - Cecília M Arraiano
- the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
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A screen of Coxiella burnetii mutants reveals important roles for Dot/Icm effectors and host autophagy in vacuole biogenesis. PLoS Pathog 2014; 10:e1004286. [PMID: 25080348 PMCID: PMC4117601 DOI: 10.1371/journal.ppat.1004286] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 06/17/2014] [Indexed: 12/18/2022] Open
Abstract
Coxiella burnetii is an intracellular pathogen that replicates in a lysosome-derived vacuole. The molecular mechanisms used by this bacterium to create a pathogen-occupied vacuole remain largely unknown. Here, we conducted a visual screen on an arrayed library of C. burnetii NMII transposon insertion mutants to identify genes required for biogenesis of a mature Coxiella-containing vacuole (CCV). Mutants defective in Dot/Icm secretion system function or the PmrAB regulatory system were incapable of intracellular replication. Several mutants with intracellular growth defects were found to have insertions in genes encoding effector proteins translocated into host cells by the Dot/Icm system. These included mutants deficient in the effector proteins Cig57, CoxCC8 and Cbu1754. Mutants that had transposon insertions in genes important in central metabolism or encoding tRNA modification enzymes were identified based on the appearance filamentous bacteria intracellularly. Lastly, mutants that displayed a multi-vacuolar phenotype were identified. All of these mutants had a transposon insertion in the gene encoding the effector protein Cig2. Whereas vacuoles containing wild type C. burnetii displayed robust accumulation of the autophagosome protein LC3, the vacuoles formed by the cig2 mutant did not contain detectible amounts of LC3. Furthermore, interfering with host autophagy during infection by wild type C. burnetii resulted in a multi-vacuolar phenotype similar to that displayed by the cig2 mutant. Thus, a functional Cig2 protein is important for interactions between the CCV and host autophagosomes and this drives a process that enhances the fusogenic properties of this pathogen-occupied organelle. Coxiella burnetii is the causative agent of the human disease Q fever. This bacterium uses the Dot/Icm type IV secretion system to deliver effectors into the cytosol of host cells. The Dot/Icm system is required for intracellular replication of C. burnetii. To determine the contribution of individual proteins to the establishment of a vacuole that supports C. burnetii replication, we conducted a visual screen on a library of C. burnetii transposon insertion mutants and identified genes required for distinct stages of intracellular replication. This approach was validated through the identification of intracellular replication mutants that included insertions in most of the dot and icm genes, and through the identification of individual effector proteins delivered into host cell by the Dot/Icm system that participate in creating a vacuole that supports intracellular replication of C. burnetii. Complementation studies showed convincingly that the effector Cig57 was critical for intracellular replication. The effector protein Cig2 was found to play a unique role in promoting homotypic fusion of C. burnetii vacuoles. Disrupting host autophagy phenocopied the defect displayed by the cig2 mutant. Thus, our visual screen has successfully identified effectors required for intracellular replication of C. burnetii and indicates that Dot/Icm-dependent subversion of host autophagy promotes homotypic fusion of CCVs.
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Matos RG, Bárria C, Moreira RN, Barahona S, Domingues S, Arraiano CM. The importance of proteins of the RNase II/RNB-family in pathogenic bacteria. Front Cell Infect Microbiol 2014; 4:68. [PMID: 24918089 PMCID: PMC4042491 DOI: 10.3389/fcimb.2014.00068] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/09/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rute G Matos
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cátia Bárria
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Ricardo N Moreira
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Susana Barahona
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Susana Domingues
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cecília M Arraiano
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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21
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Fischer M, Zilkenat S, Gerlach RG, Wagner S, Renard BY. Pre- and post-processing workflow for affinity purification mass spectrometry data. J Proteome Res 2014; 13:2239-49. [PMID: 24641689 DOI: 10.1021/pr401249b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The reliable detection of protein-protein interactions by affinity purification mass spectrometry (AP-MS) is crucial for the understanding of biological processes. Quantitative information can be used to separate truly interacting proteins from false-positives by contrasting counts of proteins binding to specific baits with counts of negative controls. Several approaches have been proposed for computing scores for potential interaction proteins, for example, the commonly used SAINT software. However, it remains a subjective decision where to set the cutoff score for candidate selection; furthermore, no precise control for the expected number of false-positives is provided. In related fields, successful data analysis strongly relies on statistical pre- and post-processing steps, which, so far, have played only a minor role in AP-MS data analysis. We introduce a complete workflow, embedding either the scoring method SAINT or alternatively a two-stage Poisson model into a pre- and post-processing framework. To this end, we investigate different normalization methods and apply a statistical filter adjusted to AP-MS data. Furthermore, we propose permutation and adjustment procedures, which allow the replacement of scores by statistical p values. The performance of the workflow is assessed on simulations as well as on a study focusing on interactions with the T3SS in Salmonella Typhimurium. Preprocessing methods significantly increase the number of detected truly interacting proteins, while a constant false-discovery rate is maintained. The software solution is freely available.
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Affiliation(s)
- Martina Fischer
- Research Group Bioinformatics (NG 4), Robert Koch-Institute , Nordufer 20, 13353 Berlin, Germany
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Rosenzweig JA, Chopra AK. The exoribonuclease Polynucleotide Phosphorylase influences the virulence and stress responses of yersiniae and many other pathogens. Front Cell Infect Microbiol 2013; 3:81. [PMID: 24312901 PMCID: PMC3832800 DOI: 10.3389/fcimb.2013.00081] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022] Open
Abstract
Microbes are incessantly challenged by both biotic and abiotic stressors threatening their existence. Therefore, bacterial pathogens must possess mechanisms to successfully subvert host immune defenses as well as overcome the stress associated with host-cell encounters. To achieve this, bacterial pathogens typically experience a genetic re-programming whereby anti-host/stress factors become expressed and eventually translated into effector proteins. In that vein, the bacterial host-cell induced stress-response is similar to any other abiotic stress to which bacteria respond by up-regulating specific stress-responsive genes. Following the stress encounter, bacteria must degrade unnecessary stress responsive transcripts through RNA decay mechanisms. The three pathogenic yersiniae (Yersinia pestis, Y. pseudo-tuberculosis, and Y. enterocolitica) are all psychrotropic bacteria capable of growth at 4°C; however, cold growth is dependent on the presence of an exoribonuclease, polynucleotide phosphorylase (PNPase). PNPase has also been implicated as a virulence factor in several notable pathogens including the salmonellae, Helicobacter pylori, and the yersiniae [where it typically influences the type three secretion system (TTSS)]. Further, PNPase has been shown to associate with ribonuclease E (endoribonuclease), RhlB (RNA helicase), and enolase (glycolytic enzyme) in several Gram-negative bacteria forming a large, multi-protein complex known as the RNA degradosome. This review will highlight studies demonstrating the influence of PNPase on the virulence potentials and stress responses of various bacterial pathogens as well as focusing on the degradosome-dependent and -independent roles played by PNPase in yersiniae stress responses.
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Affiliation(s)
- Jason A Rosenzweig
- Department of Biology, Center for Bionanotechnology and Environmental Research, Texas Southern University Houston, TX, USA ; Department of Environmental and Interdisciplinary Sciences, Texas Southern University Houston, TX, USA
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Facincani AP, Moreira LM, Soares MR, Ferreira CB, Ferreira RM, Ferro MIT, Ferro JA, Gozzo FC, de Oliveira JCF. Comparative proteomic analysis reveals that T3SS, Tfp, and xanthan gum are key factors in initial stages of Citrus sinensis infection by Xanthomonas citri subsp. citri. Funct Integr Genomics 2013; 14:205-17. [PMID: 24676796 DOI: 10.1007/s10142-013-0340-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/18/2013] [Accepted: 09/26/2013] [Indexed: 01/02/2023]
Abstract
The bacteria Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. The disease symptoms are characterized by localized host cell hyperplasia followed by tissue necrosis at the infected area. An arsenal of bacterial pathogenicity- and virulence-related proteins is expressed to ensure a successful infection process. At the post-genomic stage of Xac, we used a proteomic approach to analyze the proteins that are displayed differentially over time when the pathogen attacks the host plant. Protein extracts were prepared from infectious Xac grown in inducing medium (XAM1) for 24 h or from host citrus plants for 3 or 5 days after infection, detached times to evaluate the adaptation and virulence of the pathogen. The protein extracts were proteolyzed, and the peptides derived from tryptic digestion were investigated using liquid chromatography and tandem mass spectrometry. Changes in the protein expression profile were compared with the Xac genome and the proteome recently described under non-infectious conditions. An analysis of the proteome of Xac under infectious conditions revealed proteins directly involved in virulence such as the type III secretion system (T3SS) and effector proteins (T3SS-e), the type IV pilus (Tfp), and xanthan gum biosynthesis. Moreover, four new mutants related to proteins detected in the proteome and with different functions exhibited reduced virulence relative to the wild-type proteins. The results of the proteome analysis of infectious Xac define the processes of adaptation to the host and demonstrate the induction of the virulence factors of Xac involved in plant-pathogen interactions.
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Affiliation(s)
- Agda P Facincani
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Departamento de Tecnologia, UNESP-Universidade Estadual Paulista, São Paulo, SP, Brazil
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24
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Reis FP, Pobre V, Silva IJ, Malecki M, Arraiano CM. The RNase II/RNB family of exoribonucleases: putting the 'Dis' in disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:607-15. [PMID: 23776156 DOI: 10.1002/wrna.1180] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/03/2013] [Accepted: 05/14/2013] [Indexed: 12/21/2022]
Abstract
Important findings over the last years have shed new light onto the mechanistic details of RNA degradation by members of the RNase II/RNB family of exoribonucleases. Members of this family have been shown to be involved in growth, normal chloroplast biogenesis, mitotic control and cancer. Recently, different publications have linked human orthologs (Dis3 and Dis3L2) to important human diseases. This article describes the structural and biochemical characteristics of members of this family of enzymes, and the physiological implications that relate them with disease.
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Affiliation(s)
- Filipa P Reis
- Instituto de Tecnologia Química e Biológica-ITQB, Universidade Nova de Lisboa, Oeiras, Portugal
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Dwidar M, Leung BM, Yaguchi T, Takayama S, Mitchell RJ. Patterning bacterial communities on epithelial cells. PLoS One 2013; 8:e67165. [PMID: 23785519 PMCID: PMC3681762 DOI: 10.1371/journal.pone.0067165] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/15/2013] [Indexed: 11/23/2022] Open
Abstract
Micropatterning of bacteria using aqueous two phase system (ATPS) enables the localized culture and formation of physically separated bacterial communities on human epithelial cell sheets. This method was used to compare the effects of Escherichia coli strain MG1655 and an isogenic invasive counterpart that expresses the invasin (inv) gene from Yersinia pseudotuberculosis on the underlying epithelial cell layer. Large portions of the cell layer beneath the invasive strain were killed or detached while the non-invasive E. coli had no apparent effect on the epithelial cell layer over a 24 h observation period. In addition, simultaneous testing of the localized effects of three different bacterial species; E. coli MG1655, Shigella boydii KACC 10792 and Pseudomonas sp DSM 50906 on an epithelial cell layer is also demonstrated. The paper further shows the ability to use a bacterial predator, Bdellovibriobacteriovorus HD 100, to selectively remove the E. coli, S. boydii and P. sp communities from this bacteria-patterned epithelial cell layer. Importantly, predation and removal of the P. Sp was critical for maintaining viability of the underlying epithelial cells. Although this paper focuses on a few specific cell types, the technique should be broadly applicable to understand a variety of bacteria-epithelial cell interactions.
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Affiliation(s)
- Mohammed Dwidar
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Brendan M. Leung
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Toshiyuki Yaguchi
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Nagoya Institute of Technology, Biomechanics Laboratory, Gokiso-cho, Showa-ku, Nagoya, Japan
| | - Shuichi Takayama
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Department Biomedical Engineering and Macromolecular Science & Engineering Program, University of Michigan, Ann Arbor, United States of America
| | - Robert J. Mitchell
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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26
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Menanteau-Ledouble S, Lawrence ML. Use of bioluminescence mutant screening for identification of Edwardsiella ictaluri genes involved in channel catfish (Ictalurus punctatus) skin colonization. Vet Microbiol 2013; 162:724-730. [DOI: 10.1016/j.vetmic.2012.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/05/2012] [Accepted: 09/28/2012] [Indexed: 01/02/2023]
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Moreira RN, Domingues S, Viegas SC, Amblar M, Arraiano CM. Synergies between RNA degradation and trans-translation in Streptococcus pneumoniae: cross regulation and co-transcription of RNase R and SmpB. BMC Microbiol 2012; 12:268. [PMID: 23167513 PMCID: PMC3534368 DOI: 10.1186/1471-2180-12-268] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ribonuclease R (RNase R) is an exoribonuclease that recognizes and degrades a wide range of RNA molecules. It is a stress-induced protein shown to be important for the establishment of virulence in several pathogenic bacteria. RNase R has also been implicated in the trans-translation process. Transfer-messenger RNA (tmRNA/SsrA RNA) and SmpB are the main effectors of trans-translation, an RNA and protein quality control system that resolves challenges associated with stalled ribosomes on non-stop mRNAs. Trans-translation has also been associated with deficiencies in stress-response mechanisms and pathogenicity. RESULTS In this work we study the expression of RNase R in the human pathogen Streptococcus pneumoniae and analyse the interplay of this enzyme with the main components of the trans-translation machinery (SmpB and tmRNA/SsrA). We show that RNase R is induced after a 37°C to 15°C temperature downshift and that its levels are dependent on SmpB. On the other hand, our results revealed a strong accumulation of the smpB transcript in the absence of RNase R at 15°C. Transcriptional analysis of the S. pneumoniae rnr gene demonstrated that it is co-transcribed with the flanking genes, secG and smpB. Transcription of these genes is driven from a promoter upstream of secG and the transcript is processed to yield mature independent mRNAs. This genetic organization seems to be a common feature of Gram positive bacteria, and the biological significance of this gene cluster is further discussed. CONCLUSIONS This study unravels an additional contribution of RNase R to the trans-translation system by demonstrating that smpB is regulated by this exoribonuclease. RNase R in turn, is shown to be under the control of SmpB. These proteins are therefore mutually dependent and cross-regulated. The data presented here shed light on the interactions between RNase R, trans-translation and cold-shock response in an important human pathogen.
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Affiliation(s)
- Ricardo N Moreira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
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28
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Matos RG, Bárria C, Pobre V, Andrade JM, Arraiano CM. Exoribonucleases as modulators of virulence in pathogenic bacteria. Front Cell Infect Microbiol 2012; 2:65. [PMID: 22919656 PMCID: PMC3417396 DOI: 10.3389/fcimb.2012.00065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/23/2012] [Indexed: 11/24/2022] Open
Affiliation(s)
- Rute G Matos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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29
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Guo D, Lu Y, Zhang A, Liu J, Yuan D, Jiang Q, Lin H, Si C, Qu L. Identification of genes transcribed by Pasteurella multocida in rabbit livers through the selective capture of transcribed sequences. FEMS Microbiol Lett 2012; 331:105-12. [DOI: 10.1111/j.1574-6968.2012.02559.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/20/2012] [Accepted: 03/22/2012] [Indexed: 12/18/2022] Open
Affiliation(s)
- Dongchun Guo
- State Key Laboratory of Veterinary Biotechnology; Harbin Veterinary Research Institute; Chinese Academy of Agricultural Sciences (CAAS); Harbin; China
| | | | | | - Jiasen Liu
- State Key Laboratory of Veterinary Biotechnology; Harbin Veterinary Research Institute; Chinese Academy of Agricultural Sciences (CAAS); Harbin; China
| | - Dongwei Yuan
- State Key Laboratory of Veterinary Biotechnology; Harbin Veterinary Research Institute; Chinese Academy of Agricultural Sciences (CAAS); Harbin; China
| | - Qian Jiang
- State Key Laboratory of Veterinary Biotechnology; Harbin Veterinary Research Institute; Chinese Academy of Agricultural Sciences (CAAS); Harbin; China
| | - Huan Lin
- State Key Laboratory of Veterinary Biotechnology; Harbin Veterinary Research Institute; Chinese Academy of Agricultural Sciences (CAAS); Harbin; China
| | - Changde Si
- State Key Laboratory of Veterinary Biotechnology; Harbin Veterinary Research Institute; Chinese Academy of Agricultural Sciences (CAAS); Harbin; China
| | - Liandong Qu
- State Key Laboratory of Veterinary Biotechnology; Harbin Veterinary Research Institute; Chinese Academy of Agricultural Sciences (CAAS); Harbin; China
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30
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Eidem TM, Roux CM, Dunman PM. RNA decay: a novel therapeutic target in bacteria. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:443-54. [PMID: 22374855 DOI: 10.1002/wrna.1110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The need for novel antibiotics is greater now than perhaps any time since the pre-antibiotic era. Indeed, the recent collapse of most pharmaceutical antibacterial groups, combined with the emergence of hypervirulent and pan-antibiotic-resistant bacteria have, in effect, created a 'perfect storm' that has severely compromised infection treatment options and led to dramatic increases in the incidence and severity of bacterial infections. To put simply, it is imperative that we develop new classes of antibiotics for the therapeutic intervention of bacterial infections. In that regard, RNA degradation is an essential biological process that has not been exploited for antibiotic development. Herein we discuss the factors that govern bacterial RNA degradation, highlight members of this machinery that represent attractive antimicrobial drug development targets and describe the use of high-throughput screening as a means of developing antimicrobials that target these enzymes. Such agents would represent first-in-class antibiotics that would be less apt to inactivation by currently encountered enzymatic antibiotic-resistance determinants.
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Affiliation(s)
- Tess M Eidem
- Department of Microbiology and Pathology, University of Nebraska Medical Center, Omaha, NE, USA
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31
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Murase K, Ooka T, Iguchi A, Ogura Y, Nakayama K, Asadulghani M, Islam MR, Hiyoshi H, Kodama T, Beutin L, Hayashi T. Haemolysin E- and enterohaemolysin-derived haemolytic activity of O55/O157 strains and other Escherichia coli lineages. MICROBIOLOGY-SGM 2011; 158:746-758. [PMID: 22194351 DOI: 10.1099/mic.0.054775-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Among three haemolysins identified thus far in Escherichia coli, alpha-haemolysin (HlyA) is encoded on the pathogenicity islands of extraintestinal pathogenic strains, while enterohaemolysin (EhxA) is encoded on the virulence plasmids of enterohaemorrhagic E. coli (EHEC) strains. In contrast, the gene for haemolysin E (HlyE) is located on the E. coli chromosome backbone and is therefore widely distributed among E. coli strains. However, because hlyE gene expression is repressed by the H-NS protein and because the gene has been disrupted in many strains, its haemolytic activity cannot be detected in wild-type strains by routine screening on blood agar plates. In this study, we found that the HlyE-derived haemolytic activity of enteropathogenic E. coli (EPEC) O55 : H7 can be detected after anaerobic cultivation on a washed blood agar plate (EHX plate) that is used to detect the production of EhxA. We also found that the haemolytic activity of EHEC O157 : H7 observed on EHX plates under aerobic and anaerobic growth conditions is derived from EhxA and HlyE, respectively; this differential expression of the two haemolysins occurs at the transcriptional level. Our analysis of 60 E. coli strains of various pathotypes and phylogenies for their repertoires of haemolysin genes, haemolytic phenotypes and hlyE gene sequences revealed that HlyE activity can generally be detected on EHX plates under anaerobic growth conditions if the gene is intact. Furthermore, our results indicate that hlyE gene inactivation occurred in three of the five E. coli lineages (phylogroups A, B1 and B2), which demonstrates phylogroup-specific gene disruption patterns.
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Affiliation(s)
- Kazunori Murase
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Tadasuke Ooka
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Atsushi Iguchi
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Yoshitoshi Ogura
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan.,Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Keisuke Nakayama
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Md Asadulghani
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Md Rakibul Islam
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Hirotaka Hiyoshi
- Laboratory of Genomic Research on Pathogenic Bacteria, International Research Center for Infectious Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshio Kodama
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Lothar Beutin
- National Reference Laboratory for Escherichia coli, Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Tetsuya Hayashi
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan.,Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
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32
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Islam MR, Ogura Y, Asadulghani M, Ooka T, Murase K, Gotoh Y, Hayashi T. A sensitive and simple plaque formation method for the Stx2 phage of Escherichia coli O157:H7, which does not form plaques in the standard plating procedure. Plasmid 2011; 67:227-35. [PMID: 22186359 DOI: 10.1016/j.plasmid.2011.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/28/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
Abstract
Bacteriophages are fascinating genetic elements that play key roles in the evolution and diversification of bacterial genomes. Shiga toxin (Stx)-transducing phages are important genetic elements that disseminate the stx genes among enterohemorrhagic Escherichia coli (EHEC). They are generally regarded as lambda-like phages, but their biological and genetic properties have not been fully elucidated. This is partly due to a serious obstacle in obtaining visible plaques. Here, we describe a modified double agar overlay method that allows us to easily detect and accurately enumerate plaques of Sp5, the Stx2 phage of the EHEC O157 Sakai strain, which otherwise does not produce plaques in the standard plating procedure. In the modified method, the top agar was supplemented with mitomycin C (MMC) and Ca(2+) (or Mg(2+)). MMC appears to prevent the lysogenization of Sp5 and/or compel Sp5 to follow the lytic cycle by inducing the SOS response in the host cells. The divalent cations significantly improve phage adsorption to the host cells and thus yield a synergistic effect in combination with MMC. We further applied this method to a receptor analysis of Sp5 and obtained findings that suggest that the YaeT (BamA) protein serves as the receptor of Sp5. This method would be a very useful tool in studies of Stx2 phages and studies of other phages from various bacteria, in which researchers often encounter problems with plaque formation.
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Affiliation(s)
- Md Rakibul Islam
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
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Matos RG, Barbas A, Gómez-Puertas P, Arraiano CM. Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade ds RNA. Proteins 2011; 79:1853-67. [PMID: 21465561 DOI: 10.1002/prot.23010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 01/05/2011] [Accepted: 01/28/2011] [Indexed: 11/06/2022]
Abstract
RNase II and RNase R are the two E. coli exoribonucleases that belong to the RNase II super family of enzymes. They degrade RNA hydrolytically in the 3' to 5' direction in a processive and sequence independent manner. However, while RNase R is capable of degrading structured RNAs, the RNase II activity is impaired by dsRNAs. The final end-product of these two enzymes is also different, being 4 nt for RNase II and 2 nt for RNase R. RNase II and RNase R share structural properties, including 60% of amino acid sequence similarity and have a similar modular domain organization: two N-terminal cold shock domains (CSD1 and CSD2), one central RNB catalytic domain, and one C-terminal S1 domain. We have constructed hybrid proteins by swapping the domains between RNase II and RNase R to determine which are the responsible for the differences observed between RNase R and RNase II. The results obtained show that the S1 and RNB domains from RNase R in an RNase II context allow the degradation of double-stranded substrates and the appearance of the 2 nt long end-product. Moreover, the degradation of structured RNAs becomes tail-independent when the RNB domain from RNase R is no longer associated with the RNA binding domains (CSD and S1) of the genuine protein. Finally, we show that the RNase R C-terminal Lysine-rich region is involved in the degradation of double-stranded substrates in an RNase II context, probably by unwinding the substrate before it enters into the catalytic cavity.
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Affiliation(s)
- Rute Gonçalves Matos
- Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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Structure and Degradation Mechanisms of 3′ to 5′ Exoribonucleases. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2011. [DOI: 10.1007/978-3-642-21078-5_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Abstract
Bacterial stress responses provide them the opportunity to survive hostile environments, proliferate and potentially cause diseases in humans and animals. The way in which pathogenic bacteria interact with host immune cells triggers a complicated series of events that include rapid genetic re‐programming in response to the various host conditions encountered. Viewed in this light, the bacterial host‐cell induced stress response (HCISR) is similar to any other well‐characterized environmental stress to which bacteria must respond by upregulating a group of specific stress‐responsive genes. Post stress, bacteria must resume their pre‐stress genetic program, and, as a consequence, must degrade unnecessary stress responsive transcripts through RNA decay mechanisms. Further, there is a well‐established role for several ribonucleases in the cold shock response whereby they modulate the changing transcript landscape in response to the stress, and during acclimation and subsequent genetic re‐programming post stress. Recently, ribonucleases have been implicated as virulence‐associated factors in several notable Gram‐negative pathogens including, the yersiniae, the salmonellae, Helicobacter pylori, Shigella flexneri and Aeromonas hydrophila. This review will focus on the roles played by ribonucleases in bacterial virulence, other bacterial stress responses, and on their novel therapeutic applications.
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Affiliation(s)
- Abidat Lawal
- Department of Biology, Center for Bionanotechnology and Environmental Research, Texas Southern University, Houston, TX, USA
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36
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Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, Silva IJ, Viegas SC. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 2010; 34:883-923. [PMID: 20659169 DOI: 10.1111/j.1574-6976.2010.00242.x] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The continuous degradation and synthesis of prokaryotic mRNAs not only give rise to the metabolic changes that are required as cells grow and divide but also rapid adaptation to new environmental conditions. In bacteria, RNAs can be degraded by mechanisms that act independently, but in parallel, and that target different sites with different efficiencies. The accessibility of sites for degradation depends on several factors, including RNA higher-order structure, protection by translating ribosomes and polyadenylation status. Furthermore, RNA degradation mechanisms have shown to be determinant for the post-transcriptional control of gene expression. RNases mediate the processing, decay and quality control of RNA. RNases can be divided into endonucleases that cleave the RNA internally or exonucleases that cleave the RNA from one of the extremities. Just in Escherichia coli there are >20 different RNases. RNase E is a single-strand-specific endonuclease critical for mRNA decay in E. coli. The enzyme interacts with the exonuclease polynucleotide phosphorylase (PNPase), enolase and RNA helicase B (RhlB) to form the degradosome. However, in Bacillus subtilis, this enzyme is absent, but it has other main endonucleases such as RNase J1 and RNase III. RNase III cleaves double-stranded RNA and family members are involved in RNA interference in eukaryotes. RNase II family members are ubiquitous exonucleases, and in eukaryotes, they can act as the catalytic subunit of the exosome. RNases act in different pathways to execute the maturation of rRNAs and tRNAs, and intervene in the decay of many different mRNAs and small noncoding RNAs. In general, RNases act as a global regulatory network extremely important for the regulation of RNA levels.
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Affiliation(s)
- Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.
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Chen C, Deutscher MP. RNase R is a highly unstable protein regulated by growth phase and stress. RNA (NEW YORK, N.Y.) 2010; 16:667-672. [PMID: 20185542 PMCID: PMC2844616 DOI: 10.1261/rna.1981010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 01/12/2010] [Indexed: 05/28/2023]
Abstract
RNase R is an important exoribonuclease that participates in the degradation of structured RNAs in Escherichia coli. In earlier work, it was shown that RNase R levels increase dramatically under certain stress conditions, particularly during cold shock and stationary phase. However, the regulatory processes that lead to this elevation are not well understood. We show here that the increase in RNase R in stationary phase is unaffected by the global regulators, RpoS and (p)ppGpp, and that it occurs despite a major reduction in rnr message. Rather, we find that RNase R is a highly unstable protein in exponential phase, with a half-life of approximately 10 min, and that the protein is stabilized in stationary phase, leading to its relative increase. RNase R is also stabilized during cold shock and by growth in minimal medium, two other conditions that lead to its elevation. These data demonstrate that RNase R is subject to regulation by a novel, posttranslational mechanism that may have important implications for our complete understanding of RNA metabolism.
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Affiliation(s)
- Chenglu Chen
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA
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Domingues S, Matos RG, Reis FP, Fialho AM, Barbas A, Arraiano CM. Biochemical characterization of the RNase II family of exoribonucleases from the human pathogens Salmonella typhimurium and Streptococcus pneumoniae. Biochemistry 2010; 48:11848-57. [PMID: 19863111 DOI: 10.1021/bi901105n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Maturation, turnover, and quality control of RNA are performed by many different classes of ribonucleases. Escherichia coli RNase II is the prototype of the RNase II family of ribonucleases, a ubiquitous family of hydrolytic, processive 3' --> 5' exonucleases crucial in RNA metabolism. RNase R is a member of this family that is modulated in response to stress and has been implicated in virulence. In this work, RNase II-like proteins were characterized in the human pathogens Salmonella typhimurium and Streptococcus pneumoniae. By sequence analysis, only one member of the RNase II family was identified in S. pneumoniae, while both RNase II and RNase R were found in Sa. typhimurium. These enzymes were cloned, expressed, purified, and characterized with regard to their biochemical features and modular architecture. The specificity of substrates and the final products generated by the enzymes were clearly demonstrated. Sa. typhimurium RNase II and RNase R behaved essentially as their respective E. coli counterparts. We have shown that the only hydrolytic RNase found in S. pneumoniae was able to degrade structured RNAs as is the case with E. coli RNase R. Our results further showed that there are differences with regard to the activity and ability to bind RNA from enzymes belonging to two distinct pneumococcal strains, and this may be related to a single amino acid substitution in the catalytic domain. Since ribonucleases have not been previously characterized in S. pneumoniae or Sa. typhimurium, this work provides an important first step in the understanding of post-transcriptional control in these pathogens.
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Affiliation(s)
- Susana Domingues
- Instituto de Tecnologia Quimica e Biologica/Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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Spaceflight and modeled microgravity effects on microbial growth and virulence. Appl Microbiol Biotechnol 2009; 85:885-91. [PMID: 19847423 PMCID: PMC2804794 DOI: 10.1007/s00253-009-2237-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 08/26/2009] [Accepted: 08/27/2009] [Indexed: 12/19/2022]
Abstract
For unsuspecting bacteria, the difference between life and death depends upon efficient and specific responses to various stressors. Facing a much larger world, microbes are invariably challenged with ever-changing environments where temperature, pH, chemicals, and nutrients are in a constant state of flux. Only those that are able to rapidly reprogram themselves and express subsets of genes needed to overcome the stress will survive and outcompete neighboring microbes. Recently, low shear stress, emulating microgravity (MG) experienced in space, has been characterized in a number of microorganisms including fungi and prokaryotes ranging from harmless surrogate organisms to bona fide pathogens. Interestingly, MG appears to induce a plethora of effects ranging from enhanced pathogenicity in several Gram-negative enterics to enhanced biofilm formation. Furthermore, MG-exposed bacteria appeared better able to handle subsequent stressors including: osmolarity, pH, temperature, and antimicrobial challenge while yeast exhibited aberrant budding post-MG-exposure. This review will focus on MG-induced alterations of virulence in various microbes with the emphasis placed on bacteria.
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RNase R mutants elucidate the catalysis of structured RNA: RNA-binding domains select the RNAs targeted for degradation. Biochem J 2009; 423:291-301. [PMID: 19630750 DOI: 10.1042/bj20090839] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The RNase II superfamily is a ubiquitous family of exoribonucleases that are essential for RNA metabolism. RNase II and RNase R degrade RNA in the 3'-->5' direction in a processive and sequence-independent manner. However, although RNase R is capable of degrading highly structured RNAs, the RNase II activity is impaired by the presence of secondary structures. RNase II and RNase R share structural properties and have a similar modular domain organization. The eukaryotic RNase II homologue, Rrp44/Dis3, is the catalytic subunit of the exosome, one of the most important protein complexes involved in the maintenance of the correct levels of cellular RNAs. In the present study, we constructed truncated RNase II and RNase R proteins and point mutants and characterized them regarding their exoribonucleolytic activity and RNA-binding ability. We report that Asp280 is crucial for RNase R activity without affecting RNA binding. When Tyr324 was changed to alanine, the final product changed from 2 to 5 nt in length, showing that this residue is responsible for setting the end-product. We have shown that the RNB domain of RNase II has catalytic activity. The most striking result is that the RNase R RNB domain itself degrades double-stranded substrates even in the absence of a 3'-overhang. Moreover, we have demonstrated for the first time that the substrate recognition of RNase R depends on the RNA-binding domains that target the degradation of RNAs that are 'tagged' by a 3'-tail. These results can have important implications for the study of poly(A)-dependent RNA degradation mechanisms.
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The 3'-to-5' exoribonuclease (encoded by HP1248) of Helicobacter pylori regulates motility and apoptosis-inducing genes. J Bacteriol 2009; 191:2691-702. [PMID: 19218383 DOI: 10.1128/jb.01182-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The human gastric pathogen Helicobacter pylori has many virulence factors involved in pathogenesis, but the mechanisms regulating these virulence factors are not yet fully understood. In this study, we cloned HP1248, which is similar in sequence to Escherichia coli vacB, which was previously shown to be associated with the expression of virulence in Shigella and enteroinvasive E. coli. E. coli vacB encodes RNase R. RNase R is involved in the posttranscriptional regulation of mRNA stability. By global transcriptional microarray profiling of an H. pylori HP1248 deletion mutant, we defined six virulence-related genes which were posttranscriptionally downregulated by HP1248, including the motility-related genes HP1192 and flaB, the chemotaxis-related gene cheY, and the apoptosis-inducing genes HP0175, cagA, and gtt. In this study, recombinant HP1248 protein expressed in E. coli showed 3'-to-5' exoribonuclease activity. Motility and apoptosis induction were increased in the H. pylori HP1248 deletion mutant. We also showed that HP1192 is associated with H. pylori motility, possibly through HP1248 regulation. Further, we suggested and studied the possible mechanisms of this specific regulation of virulent genes by HP1248. In addition, the expression level of HP1248 mRNA changed dramatically in response to a variety of altered environmental conditions, including pH and temperature. Hence, HP1248 in H. pylori seems to play a role in environmental sensing and in regulation of virulent phenotypes, such as motility and host apoptosis induction.
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Andrade JM, Pobre V, Silva IJ, Domingues S, Arraiano CM. The role of 3'-5' exoribonucleases in RNA degradation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:187-229. [PMID: 19215773 DOI: 10.1016/s0079-6603(08)00805-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA degradation is a major process controlling RNA levels and plays a central role in cell metabolism. From the labile messenger RNA to the more stable noncoding RNAs (mostly rRNA and tRNA, but also the expanding class of small regulatory RNAs) all molecules are eventually degraded. Elimination of superfluous transcripts includes RNAs whose expression is no longer required, but also the removal of defective RNAs. Consequently, RNA degradation is an inherent step in RNA quality control mechanisms. Furthermore, it contributes to the recycling of the nucleotide pool in the cell. Escherichia coli has eight 3'-5' exoribonucleases, which are involved in multiple RNA metabolic pathways. However, only four exoribonucleases appear to accomplish all RNA degradative activities: polynucleotide phosphorylase (PNPase), ribonuclease II (RNase II), RNase R, and oligoribonuclease. Here, we summarize the available information on the role of bacterial 3'-5' exoribonucleases in the degradation of different substrates, highlighting the most recent data that have contributed to the understanding of the diverse modes of operation of these degradative enzymes.
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Affiliation(s)
- José M Andrade
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Qeiras, Portugal
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Genomic analysis of the role of RNase R in the turnover of Pseudomonas putida mRNAs. J Bacteriol 2008; 190:6258-63. [PMID: 18641145 DOI: 10.1128/jb.00630-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNase R is a 3'-5' highly processive exoribonuclease that can digest RNAs with extensive secondary structure. We analyzed the global effect of eliminating RNase R on the Pseudomonas putida transcriptome and the expression of the rnr gene under diverse conditions. The absence of RNase R led to increased levels of many mRNAs, indicating that it plays an important role in mRNA turnover.
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Meinersmann RJ, Romero-Gallo J, Blaser MJ. Rate heterogeneity in the evolution of Helicobacter pylori and the behavior of homoplastic sites. INFECTION GENETICS AND EVOLUTION 2008; 8:593-602. [PMID: 18571992 DOI: 10.1016/j.meegid.2008.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 04/09/2008] [Accepted: 04/11/2008] [Indexed: 10/22/2022]
Abstract
Helicobacter pylori are bacteria with substantial inter-strain variability and phylogenetic reconstructions of sequence data from the organism have common homoplastic sites. Although frequent recombination events have been proposed to contribute to the variation, the effects of nucleotide substitution rate heterogeneities on the reconstruction of H. pylori genealogies have not been studied. We analyzed the substitution pattern of a housekeeping gene, a homologue of the ribonuclease reductase gene (rnr), to characterize rate heterogeneities between 11 H. pylori isolates. Evidence of limited recombination was demonstrated by the Sawyer's runs test, but the homoplasy test and site-by-site compatibility tests indicated frequent recombination events. Within the 1935 nucleotide gene, 292 sites were polymorphic with an average pair-wise difference of 5.01%. Xia's distances for amino acids at non-synonymous codon substitution sites were smaller at homoplastic sites than at sites that were not homoplastic. Transitions were significantly more common among homoplastic than among non-homoplastic nucleotide substitutions. Simulations of evolution with or without recombination indicated the transition/transversion ratio is expected to be higher in homoplastic sites with no recombination. Despite evidence of recombination, analyses of the rnr genealogy does not show a random tree but rather base substitution behaviors characteristic of both recombination and substitution saturation at some sites. Analyses of sequences in the H. pylori multilocus sequence-typing database provided similar evidence for substitution saturation in multiple housekeeping genes.
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Cold shock exoribonuclease R (VacB) is involved in Aeromonas hydrophila pathogenesis. J Bacteriol 2008; 190:3467-74. [PMID: 18344363 DOI: 10.1128/jb.00075-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we cloned and sequenced a virulence-associated gene (vacB) from a clinical isolate SSU of Aeromonas hydrophila. We identified this gene based on our recently annotated genome sequence of the environmental isolate ATCC 7966(T) of A. hydrophila and the vacB gene of Shigella flexneri. The A. hydrophila VacB protein contained 798 amino acid residues, had a molecular mass of 90.5 kDa, and exhibited an exoribonuclease (RNase R) activity. The RNase R of A. hydrophila was a cold-shock protein and was required for bacterial growth at low temperature. The vacB isogenic mutant, which we developed by homologous recombination using marker exchange mutagenesis, was unable to grow at 4 degrees C. In contrast, the wild-type (WT) A. hydrophila exhibited significant growth at this low temperature. Importantly, the vacB mutant was not defective in growth at 37 degrees C. The vacB mutant also exhibited reduced motility, and these growth and motility phenotype defects were restored after complementation of the vacB mutant. The A. hydrophila RNase R-lacking strain was found to be less virulent in a mouse lethality model (70% survival) when given by the intraperitoneal route at as two 50% lethal doses (LD(50)). On the other hand, the WT and complemented strains of A. hydrophila caused 80 to 90% of the mice to succumb to infection at the same LD(50) dose. Overall, this is the first report demonstrating the role of RNase R in modulating the expression of A. hydrophila virulence.
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Gilberthorpe NJ, Lee ME, Stevanin TM, Read RC, Poole RK. NsrR: a key regulator circumventing Salmonella enterica serovar Typhimurium oxidative and nitrosative stress in vitro and in IFN-gamma-stimulated J774.2 macrophages. MICROBIOLOGY-SGM 2007; 153:1756-1771. [PMID: 17526833 PMCID: PMC2884951 DOI: 10.1099/mic.0.2006/003731-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, the flavohaemoglobin Hmp has emerged as the most significant nitric oxide (NO)-detoxifying protein in many diverse micro-organisms, particularly pathogenic bacteria. Its expression in enterobacteria is dramatically increased on exposure to NO and other agents of nitrosative stress as a result of transcriptional regulation of hmp gene expression, mediated by (at least) four regulators. One such regulator, NsrR, has recently been shown to be responsible for repression of hmp transcription in the absence of NO in Escherichia coli and Salmonella, but the roles of other members of this regulon in Salmonella, particularly in surviving nitrosative stresses in vitro and in vivo, have not been elucidated. This paper demonstrates that an nsrR mutant of Salmonella enterica Serovar Typhimurium expresses high levels of Hmp both aerobically and anaerobically, exceeding those that can be elicited in vitro by supplementing media with S-nitrosoglutathione (GSNO). Elevated transcription of ytfE, ygbA, hcp and hcp is also observed, but no evidence was obtained for tehAB upregulation. The hyper-resistance to GSNO of an nsrR mutant is attributable solely to Hmp, since an nsrR hmp double mutant has a wild-type phenotype. However, overexpression of NsrR-regulated genes other than hmp confers some resistance of respiratory oxygen consumption to NO. The ability to enhance, by mutating NsrR, Hmp levels without recourse to exposure to nitrosative stress was used to test the hypothesis that control of Hmp levels is required to avoid oxidative stress, Hmp being a potent generator of superoxide. Within IFN-gamma-stimulated J774.2 macrophages, in which high levels of nitrite accumulated (indicative of NO production) an hmp mutant was severely compromised in survival. Surprisingly, under these conditions, an nsrR mutant (as well as an nsrR hmp double mutant) was also disadvantaged relative to the wild-type bacteria, attributable to the combined oxidative effect of the macrophage oxidative burst and Hmp-generated superoxide. This explanation is supported by the sensitivity in vitro of an nsrR mutant to superoxide and peroxide. Fur has recently been confirmed as a weak repressor of hmp transcription, and a fur mutant was also compromised for survival within macrophages even in the absence of elevated NO levels in non-stimulated macrophages. The results indicate the critical role of Hmp in protection of Salmonella from nitrosative stress within and outside macrophages, but also the key role of transcriptional regulation in tuning Hmp levels to prevent exacerbation of the oxidative stress encountered in macrophages.
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Affiliation(s)
- Nicola J. Gilberthorpe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Margaret E. Lee
- Academic Unit of Infection and Immunity, University of Sheffield Medical School, Royal Hallamshire Hospital, Sheffield S10 2RX, UK
| | - Tania M. Stevanin
- Academic Unit of Infection and Immunity, University of Sheffield Medical School, Royal Hallamshire Hospital, Sheffield S10 2RX, UK
| | - Robert C. Read
- Academic Unit of Infection and Immunity, University of Sheffield Medical School, Royal Hallamshire Hospital, Sheffield S10 2RX, UK
| | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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Karpathy SE, Qin X, Gioia J, Jiang H, Liu Y, Petrosino JF, Yerrapragada S, Fox GE, Haake SK, Weinstock GM, Highlander SK. Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium. PLoS One 2007; 2:e659. [PMID: 17668047 PMCID: PMC1924603 DOI: 10.1371/journal.pone.0000659] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 06/26/2007] [Indexed: 11/19/2022] Open
Abstract
Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common.
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Affiliation(s)
- Sandor E. Karpathy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jason Gioia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shailaja Yerrapragada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Susan Kinder Haake
- Associated Clinical Specialties, University of California at Los Angeles School of Dentistry, Los Angeles, California, United States of America
| | - George M. Weinstock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sarah K. Highlander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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Hsu YM, Shieh HK, Chen WH, Sun TY, Shiang JH. Antimicrobial susceptibility, plasmid profiles and haemocin activities of Avibacterium paragallinarum strains. Vet Microbiol 2007; 124:209-18. [PMID: 17485180 DOI: 10.1016/j.vetmic.2007.04.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 03/30/2007] [Accepted: 04/04/2007] [Indexed: 11/26/2022]
Abstract
In this study, 18 Avibacterium paragallinarum isolates collected in Taiwan from 1990 to 2003 were serotyped and tested for resistance to antimicrobial agents. Serotyping revealed that 13 isolates were Page serovar A and 5 isolates were Page serovar C. More than 75% of the isolates were resistant to neomycin, streptomycin and erythromycin. The most common resistance pattern (15 isolates, 83.3%) was neomycin-streptomycin. Furthermore, 88.9% of the isolates were resistant to two or more antibiotics. About 72% of isolates contained plasmids (pYMH5 and/or pA14). Plasmid pYMH5 encoded functional streptomycin, sulfonamide, kanamycin and neomycin resistance genes and revealed significant homology to a broad host-range plasmid, pLS88. Plasmid pA14 encoded a putative MglA protein and RNase II, both of which might be associated with virulence. Furthermore, seven isolates showed haemocin activity. Plasmid pYMH5 is the first multidrug-resistance plasmid reported in A. paragallinarum and it may facilitate the spread of antibiotic-resistance genes between bacteria. The putative virulence plasmid pA14 and haemocin-like activity in A. paragallinarum indicate two possible mechanisms which might be responsible for the pathogenesis.
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Affiliation(s)
- Yuan-Man Hsu
- Department of Biological Science and Technology, China Medical University, 91, Hsueh-Shih Road, Taichung 404, Taiwan.
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Abstract
This chapter discusses several topics relating to the mechanisms of mRNA decay. These topics include the following: important physical properties of mRNA molecules that can alter their stability; methods for determining mRNA half-lives; the genetics and biochemistry of proteins and enzymes involved in mRNA decay; posttranscriptional modification of mRNAs; the cellular location of the mRNA decay apparatus; regulation of mRNA decay; the relationships among mRNA decay, tRNA maturation, and ribosomal RNA processing; and biochemical models for mRNA decay. Escherichia coli has multiple pathways for ensuring the effective decay of mRNAs and mRNA decay is closely linked to the cell's overall RNA metabolism. Finally, the chapter highlights important unanswered questions regarding both the mechanism and importance of mRNA decay.
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Miyoshi A, Rosinha GMS, Camargo ILBC, Trant CMC, Cardoso FC, Azevedo V, Oliveira SC. The role of the vacB gene in the pathogenesis of Brucella abortus. Microbes Infect 2007; 9:375-81. [PMID: 17306588 DOI: 10.1016/j.micinf.2006.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2006] [Revised: 12/08/2006] [Accepted: 12/16/2006] [Indexed: 10/23/2022]
Abstract
Brucella species are important zoonotic pathogens affecting a wide variety of mammals. Therefore, the identification of new Brucella virulence factors is of great interest in understanding bacterial pathogenesis and immune evasion. In this study, we have identified Brucella abortus vacB gene that presents 2343 nucleotides and 781 amino acids and it shows 39% identity with Shigella flexneri vacB gene that encodes an exoribonuclease RNase R involved in bacterial virulence. Further, we have inactivated Brucella vacB by gene replacement strategy generating a deletion mutant strain. In order to test the role of Brucella vacB in pathogenesis, BALB/c and interferon regulatory factor-1 (IRF-1) knockout (KO) mice received Brucella vacB mutant, the virulent parental strain 2308 or the vaccine strain RB51 and the bacterial CFU numbers in spleens and mous survival were monitored. Our results demonstrated that the B. abortus DeltavacB mutant and the wild type strain 2308 showed similar CFU numbers in BALB/c mice. Additionally, IRF-1 KO mice that received either the vacB mutant or S2308 strain died in 12-14 days postinfection; in contrast, all animals that received the RB51 vaccine strain survived for 30 days postinoculation. In summary, this study reports that the vacB gene in B. abortus has no impact on bacterial pathogenesis.
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Affiliation(s)
- Anderson Miyoshi
- Department of General Biology, Federal University of Minas Gerais, Minas Gerais, Pampulha, Belo Horizonte, MG, Brazil
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