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Anand D, Jakkala K, Nair RR, Sharan D, Pradhan A, Mukkayyan N, Ajitkumar P. Complete identity and expression of StfZ, the cis-antisense RNA to the mRNA of the cell division gene ftsZ, in Escherichia coli. Front Microbiol 2022; 13:920117. [PMID: 36338044 PMCID: PMC9628754 DOI: 10.3389/fmicb.2022.920117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria regulate FtsZ protein levels through transcriptional and translational mechanisms for proper cell division. A cis-antisense RNA, StfZ, produced from the ftsA-ftsZ intergenic region, was proposed to regulate FtsZ level in Escherichia coli. However, its structural identity remained unknown. In this study, we determined the complete sequence of StfZ and identified the isoforms and its promoters. We find that under native physiological conditions, StfZ is expressed at a 1:6 ratio of StfZ:ftsZ mRNA at all growth phases from three promoters as three isoforms of 366, 474, and 552 nt RNAs. Overexpression of StfZ reduces FtsZ protein level, increases cell length, and blocks cell division without affecting the ftsZ mRNA stability. We did not find differential expression of StfZ under the stress conditions of heat shock, cold shock, or oxidative stress, or at any growth phase. These data indicated that the cis-encoded StfZ antisense RNA to ftsZ mRNA may be involved in the fine tuning of ftsZ mRNA levels available for translation as per the growth-phase-specific requirement at all phases of growth and cell division.
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Affiliation(s)
- Deepak Anand
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Biology, Lund University, Lund, Sweden
- *Correspondence: Deepak Anand,
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbiology, The University of Chicago, Chicago, IL, United States
| | - Atul Pradhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, United States
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Li X, Xue C, Chen H, Zhang H, Wang Q. Small antisense RNA ThfR positively regulates Thf1 in Synechocystis sp. PCC 6803. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153642. [PMID: 35193088 DOI: 10.1016/j.jplph.2022.153642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Thylakoid formation1 (Thf1), encoded by sll1414 (thf1), is a multifunctional protein conserved in all photosynthetic organisms. thf1 expression is highly induced by high light in Synechocystis during photosynthesis-related stress. In this study, differential RNA sequencing analysis of the Synechocystis sp. PCC 6803 revealed a small antisense RNA (asRNA) gene located on the reverse-complementary strand of the thf1 gene. The full length of this asRNA (designated ThfR) was determined by 5' and 3' RACE analysis. The accumulation of thf1 mRNA was up-regulated synchronously with the ThfR level during survival after high-light stress or nitrogen starvation. Under nitrogen starvation or high-light stress, compared with the wild type, a ThfR overexpression mutant demonstrated relatively more Thf1 protein content, while a ThfR reduced-expression mutant accumulated less Thf1 protein. Furthermore, the overexpression of ThfR enhanced the electron transport rate and the proliferation of cyanobacteria under high-light stress. These results, which we confirmed further using an Escherichia coli sRNA expression platform, suggest that the thf1 gene is positively regulated by ThfR, possibly through protection of the RAUUW element at the RNase E cleavage site. This study represents the first report, to our knowledge, of a cis-transcript antisense RNA that targets thf1 in Synechocystis sp. PCC 6803 and provides evidence that ThfR regulates photosynthesis by positively modulating thf1 under high-light conditions.
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Affiliation(s)
- Xiang Li
- Hefei National Laboratory for Physical Sciences at Microscale, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Chunling Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Huafeng Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, China.
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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3
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Yang H, Huang X, Zhang X, Zhang X, Xu X, She F, Wen Y. AI-2 Induces Urease Expression Through Downregulation of Orphan Response Regulator HP1021 in Helicobacter pylori. Front Med (Lausanne) 2022; 9:790994. [PMID: 35433748 PMCID: PMC9010608 DOI: 10.3389/fmed.2022.790994] [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: 11/13/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Helicobacter pylori causes gastric infections in more than half of the world's population. The bacterium's survival in the stomach is mediated by the abundant production of urease to enable acid acclimation. In this study, our transcriptomic analysis demonstrated that the expression of urease structural proteins, UreA and UreB, is induced by the autoinducer AI-2 in H. pylori. We also found that the orphan response regulator HP1021 is downregulated by AI-2, resulting in the induction of urease expression. HP1021 represses the expression of urease by directly binding to the promoter region of ureAB, ranging from −47 to +3 with respect to the transcriptional start site. The study findings suggest that quorum sensing via AI-2 enhances acid acclimation when bacterial density increases, and might enable bacterial dispersal to other sites when entering gastric acid.
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Affiliation(s)
- Huang Yang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Xiaoxing Huang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Xiaochuan Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Xiaoyan Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Xiaohong Xu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- Fujian Medical University Union Hospital, Fuzhou, China
| | - Feifei She
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- *Correspondence: Feifei She
| | - Yancheng Wen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- Yancheng Wen
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4
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Charbonnier M, González-Espinoza G, Kehl-Fie TE, Lalaouna D. Battle for Metals: Regulatory RNAs at the Front Line. Front Cell Infect Microbiol 2022; 12:952948. [PMID: 35865816 PMCID: PMC9294342 DOI: 10.3389/fcimb.2022.952948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, respiration, and oxidative stress responses. While essential, in excess these nutrients can also be toxic. The immune system leverages both of these facets, to limit bacterial proliferation and combat invaders. Metal binding immune proteins reduce the bioavailability of metals at the infection sites starving intruders, while immune cells intoxicate pathogens by providing metals in excess leading to enzyme mismetallation and/or reactive oxygen species generation. In this dynamic metal environment, maintaining metal homeostasis is a critical process that must be precisely coordinated. To achieve this, bacteria utilize diverse metal uptake and efflux systems controlled by metalloregulatory proteins. Recently, small regulatory RNAs (sRNAs) have been revealed to be critical post-transcriptional regulators, working in conjunction with transcription factors to promote rapid adaptation and to fine-tune bacterial adaptation to metal abundance. In this mini review, we discuss the expanding role for sRNAs in iron homeostasis, but also in orchestrating adaptation to the availability of other metals like manganese and nickel. Furthermore, we describe the sRNA-mediated interdependency between metal homeostasis and oxidative stress responses, and how regulatory networks controlled by sRNAs contribute to survival and virulence.
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Affiliation(s)
- Mathilde Charbonnier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | | | - Thomas E Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana IL, United States.,Carl R. Woese Institute for Genomic Biology University of Illinois Urbana-Champaign, Urbana IL, United States
| | - David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
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5
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MicroRNAs Encoded by Virus and Small RNAs Encoded by Bacteria Associated with Oncogenic Processes. Processes (Basel) 2021. [DOI: 10.3390/pr9122234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cancer is a deadly disease and, globally, represents the second leading cause of death in the world. Although it is a disease where several factors can help its development, virus induced infections have been associated with different types of neoplasms. However, in bacterial infections, their participation is not known for certain. Among the proposed approaches to oncogenesis risks in different infections are microRNAs (miRNAs). These are small molecules composed of RNA with a length of 22 nucleotides capable of regulating gene expression by directing protein complexes that suppress the untranslated region of mRNA. These miRNAs and other recently described, such as small RNAs (sRNAs), are deregulated in the development of cancer, becoming promising biomarkers. Thus, resulting in a study possibility, searching for new tools with diagnostic and therapeutic approaches to multiple oncological diseases, as miRNAs and sRNAs are main players of gene expression and host–infectious agent interaction. Moreover, sRNAs with limited complementarity are similar to eukaryotic miRNAs in their ability to modulate the activity and stability of multiple mRNAs. Here, we will describe the regulatory RNAs from viruses that have been associated with cancer and how sRNAs in bacteria can be related to this disease.
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6
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Valdez-Salazar HA, Ares MA, Fernández FJ, Ibarra JA, Torres J, Bustamante VH, De la Cruz MA. Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes. PeerJ 2021; 9:e12270. [PMID: 34760355 PMCID: PMC8567857 DOI: 10.7717/peerj.12270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
Infection with Helicobacter pylori is one of the most important risk factors for developing gastric cancer (GC). The type IV secretion system (T4SS) encoded in the cag pathogenicity island is the main virulence factor of H. pylori associated with GC. Additionally, other virulence factors have been shown to play a role in the H. pylori virulence, such as vacuolizing cytotoxin (VacA), urease, flagella, and adhesins. Long-chain fatty acids (LCFAs) are signaling molecules that affect the transcription of virulence genes in several pathogenic bacteria such as Salmonella enterica, Vibrio cholerae, Pseudomonas aeruginosa and Mycobacterium tuberculosis. However, the effect of LCFAs on the transcription of H. pylori virulence and regulatory genes remains unknown. Here we analyzed whether the transcription of virulence genes that encode T4SS and cellular envelope components, flagellins, adhesins, toxins, urease, as well as the transcription of different regulatory genes of the H. pylori strain 26695, are altered by the presence of five distinct LCFAs: palmitic, stearic, oleic, linoleic, and linolenic acids. Palmitic and oleic acids up-regulated the transcription of most of the virulence genes tested, including cagL, cagM, flaB, sabA, mraY and vacA, as well as that of the genes encoding the transcriptional regulators NikR, Fur, CheY, ArsR, FlgR, HspR, HsrA, Hup, and CrdR. In contrast, the other LCFAs differentially affected the transcription of the virulence and regulatory genes assessed. Our data show that LCFAs can act as signaling molecules that control the transcription of the H. pylori virulome.
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Affiliation(s)
- Hilda A Valdez-Salazar
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Posgrado en Biología Experimental, DCBS., Universidad Autónoma Metropolitana (UAM) Iztapalapa, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco J Fernández
- Laboratorio de Ingeniería Genética y Metabolismo Secundario, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - J Antonio Ibarra
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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7
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Tejada-Arranz A, De Reuse H. Riboregulation in the Major Gastric Pathogen Helicobacter pylori. Front Microbiol 2021; 12:712804. [PMID: 34335549 PMCID: PMC8322730 DOI: 10.3389/fmicb.2021.712804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/23/2021] [Indexed: 02/05/2023] Open
Abstract
Helicobacter pylori is a Gram-negative bacterial pathogen that colonizes the stomach of about half of the human population worldwide. Infection by H. pylori is generally acquired during childhood and this bacterium rapidly establishes a persistent colonization. H. pylori causes chronic gastritis that, in some cases, progresses into peptic ulcer disease or adenocarcinoma that is responsible for about 800,000 deaths in the world every year. H. pylori has evolved efficient adaptive strategies to colonize the stomach, a particularly hostile acidic environment. Few transcriptional regulators are encoded by the small H. pylori genome and post-transcriptional regulation has been proposed as a major level of control of gene expression in this pathogen. The transcriptome and transcription start sites (TSSs) of H. pylori strain 26695 have been defined at the genome level. This revealed the existence of a total of 1,907 TSSs among which more than 900 TSSs for non-coding RNAs (ncRNAs) including 60 validated small RNAs (sRNAs) and abundant anti-sense RNAs, few of which have been experimentally validated. An RNA degradosome was shown to play a central role in the control of mRNA and antisense RNA decay in H. pylori. Riboregulation, genetic regulation by RNA, has also been revealed and depends both on antisense RNAs and small RNAs. Known examples will be presented in this review. Antisense RNA regulation was reported for some virulence factors and for several type I toxin antitoxin systems, one of which controls the morphological transition of H. pylori spiral shape to round coccoids. Interestingly, the few documented cases of small RNA-based regulation suggest that their mechanisms do not follow the same rules that were well established in the model organism Escherichia coli. First, the genome of H. pylori encodes none of the two well-described RNA chaperones, Hfq and ProQ that are important for riboregulation in several organisms. Second, some of the reported small RNAs target, through "rheostat"-like mechanisms, repeat-rich stretches in the 5'-untranslated region of genes encoding important virulence factors. In conclusion, there are still many unanswered questions about the extent and underlying mechanisms of riboregulation in H. pylori but recent publications highlighted original mechanisms making this important pathogen an interesting study model.
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Affiliation(s)
- Alejandro Tejada-Arranz
- Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Département de Microbiologie, Institut Pasteur, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Hilde De Reuse
- Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Département de Microbiologie, Institut Pasteur, Paris, France
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8
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Wang C, Hu Y, Yang H, Wang S, Zhou B, Bao Y, Huang Y, Luo Q, Yang C, Xie X, Yang S. Function of Non-coding RNA in Helicobacter pylori-Infected Gastric Cancer. Front Mol Biosci 2021; 8:649105. [PMID: 34046430 PMCID: PMC8144459 DOI: 10.3389/fmolb.2021.649105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer is a common malignant tumor of the digestive system. Its occurrence and development are the result of a combination of genetic, environmental, and microbial factors. Helicobacter pylori infection is a chronic infection that is closely related to the occurrence of gastric tumorigenesis. Non-coding RNA has been demonstrated to play a very important role in the organism, exerting a prominent role in the carcinogenesis, proliferation, apoptosis, invasion, metastasis, and chemoresistance of tumor progression. H. pylori infection affects the expression of non-coding RNA at multiple levels such as genetic polymorphisms and signaling pathways, thereby promoting or inhibiting tumor progression or chemoresistance. This paper mainly introduces the relationship between H. pylori-infected gastric cancer and non-coding RNA, providing a new perspective for gastric cancer treatment.
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Affiliation(s)
- Chao Wang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Yiyang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Huan Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Sumin Wang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Bo Zhou
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Yulu Bao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Yu Huang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Qiang Luo
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Chuan Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xia Xie
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
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9
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Du J, Zhang W, Li XH, Li YJ. Bioinformatics analysis of small RNAs in Helicobacter pylori and the role of NAT‑67 under tinidazole treatment. Mol Med Rep 2020; 22:1227-1234. [PMID: 32626984 PMCID: PMC7339756 DOI: 10.3892/mmr.2020.11232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/30/2020] [Indexed: 11/27/2022] Open
Abstract
Helicobacter pylori (Hp) infection is a major cause of gastrointestinal disease. However, the pathogenesis of gastric mucosa injury by Hp has remained elusive. Small non-coding RNA (sRNA) is a type of widespread RNA in prokaryotic organisms and regulates bacterial growth, reproduction and virulence. In the present study, Hp sRNA profiles were generated to reveal the sequences and possible functions of sRNA by bioinformatics analysis. The role of sRNA in tinidazole (TNZ) treatment was also explored. Total sRNAs of HP26695 were sequenced using an Illumina HiSeq2000. Detected Tags were then compared with a known sRNA database to build an sRNA profile. Reverse transcription-quantitative (RT-q)PCR products were sequenced directly and agarose gel electrophoresis was used to identify NAT-67 and 5′ureB-sRNA in HP. Furthermore, HP was treated with TNZ for 6, 12 and 24 h. The bacterial concentration was measured, the expression of NAT-67, 5′ureB-sRNA and ceuE was determined by RT-qPCR and superoxide dismutase (SOD) activity and reactive oxygen species (ROS) production were detected. A total of 163 sRNA tags were predicted in Hp through bioinformatics analysis. Among them, 35 tags were evolutionarily aconserved in different Hp strains. By target prediction, it was indicated that certain candidate sRNAs were associated with bacterial oxidative stress, virulence and chemotaxis. It was also observed that NAT-67 and 5′ureB-sRNA were downregulated in TNZ-treated HP. TNZ treatment inhibited the growth of Hp, which was accompanied by downregulation of ceuE and SOD activity, as well as upregulation of ROS. RNA sequencing and bioinformatics are valuable in predicting the expression profile and function of sRNA in HP. sRNA-targeted genes may be associated with virulence, oxidative stress and chemokines. Downregulation of NAT-67 by TNZ may be involved in Hp oxidative stress regulation, which may comprise one of the mechanisms of the antibacterial effects of TNZ.
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Affiliation(s)
- Jie Du
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Wang Zhang
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Xiao-Hui Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yuan-Jian Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, P.R. China
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10
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Lejars M, Hajnsdorf E. The world of asRNAs in Gram-negative and Gram-positive bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194489. [PMID: 31935527 DOI: 10.1016/j.bbagrm.2020.194489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022]
Abstract
Bacteria exhibit an amazing diversity of mechanisms controlling gene expression to both maintain essential functions and modulate accessory functions in response to environmental cues. Over the years, it has become clear that bacterial regulation of gene expression is still far from fully understood. This review focuses on antisense RNAs (asRNAs), a class of RNA regulators defined by their location in cis and their perfect complementarity with their targets, as opposed to small RNAs (sRNAs) which act in trans with only short regions of complementarity. For a long time, only few functional asRNAs in bacteria were known and were almost exclusively found on mobile genetic elements (MGEs), thus, their importance among the other regulators was underestimated. However, the extensive application of transcriptomic approaches has revealed the ubiquity of asRNAs in bacteria. This review aims to present the landscape of studied asRNAs in bacteria by comparing 67 characterized asRNAs from both Gram-positive and Gram-negative bacteria. First we describe the inherent ambiguity in the existence of asRNAs in bacteria, second, we highlight their diversity and their involvement in all aspects of bacterial life. Finally we compare their location and potential mode of action toward their target between Gram-negative and Gram-positive bacteria and present tendencies and exceptions that could lead to a better understanding of asRNA functions.
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Affiliation(s)
- Maxence Lejars
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005 Paris, France.
| | - Eliane Hajnsdorf
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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11
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Yang JY, Lee P, Kim JB. Effect of Evodiae fructus Methanol Extract on Virulence-Related Genes' Expression of Helicobacter pylori. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2019. [DOI: 10.15324/kjcls.2019.51.3.316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Ji Yeong Yang
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Pyeongjae Lee
- School of Industrial Bio-pharmaceutical Science, Semyung University, Jecheon, Korea
| | - Jong-Bae Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
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12
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Abstract
Bacterial regulatory RNAs are key players in adaptation to changing environmental conditions and response to diverse cellular stresses. However, while regulatory RNAs of bacterial pathogens have been intensely studied under defined conditions in vitro, characterization of their role during the infection of eukaryotic host organisms is lagging behind. This review summarizes our current understanding of the contribution of the different classes of regulatory RNAs and RNA-binding proteins to bacterial virulence and illustrates their role in infection by reviewing the mechanisms of some prominent representatives of each class. Emerging technologies are described that bear great potential for global, unbiased studies of virulence-related RNAs in bacterial model and nonmodel pathogens in the future. The review concludes by deducing common principles of RNA-mediated gene expression control of virulence programs in different pathogens, and by defining important open questions for upcoming research in the field.
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Lei L, Stipp RN, Chen T, Wu SZ, Hu T, Duncan MJ. Activity of Streptococcus mutans VicR Is Modulated by Antisense RNA. J Dent Res 2018; 97:1477-1484. [PMID: 29969955 DOI: 10.1177/0022034518781765] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The VicRK 2-component system of Streptococcus mutans regulates genes associated with cell wall biogenesis and biofilm formation. A putative RNase III-encoding gene ( rnc) is located downstream from the vicRKX operon. The goals of this study were to investigate the potential role of VicR in the regulation of adjacent downstream genes and evaluate transcription levels of vicR during planktonic and biofilm growth. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to investigate whether vicRKX and adjacent downstream genes were cotranscribed. Binding of purified recombinant VicR protein to promoter regions of vicR, rnc, and syfA genes was confirmed by electrophoretic mobility shift assay and by chromatin immunoprecipitation analyses. VicR antisense (AS vicR) RNA was detected by Northern blotting and qRT-PCR assays. AS vicR overexpression mutants were constructed, and the biofilm biomass was determined by crystal violet microtiter assay. Adjacent downstream genes rnc, smc, syfA, smu.1511, and syfB were cotranscribed with vicRKX. The predicted promoter regions of vicR, rnc, and syfA genes were directly regulated by VicR. An AS vicR RNA transcript was detected upstream of the rnc gene. Expression of the AS vicR RNA transcript was elevated in planktonic cultures and repressed during biofilm growth. In addition, Western blot data showed that expression of the VicR protein decreased by 35% in planktonic as compared with biofilm cultures. Furthermore, we show that overexpression of AS vicR led to a reduction in biofilm formation. The downstream genes rnc, smc, syfA, smu.1511, and syfB are cotranscribed with vicRKX. VicR is autophosphorylated, and rnc and syfA are directly regulated by VicR. Expression of VicR protein correlated inversely with different levels of AS vicR RNA transcript and growth conditions. The biofilm biomass decreased in the AS vicR overexpression mutant. These data suggest a role for the AS vicR RNA transcript in posttranscriptional regulation of VicR protein production in S. mutans.
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Affiliation(s)
- L Lei
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,2 The Forsyth Institute, Cambridge, MA, USA
| | - R N Stipp
- 2 The Forsyth Institute, Cambridge, MA, USA.,3 Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Campinas, Brazil
| | - T Chen
- 2 The Forsyth Institute, Cambridge, MA, USA
| | - S Z Wu
- 4 West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - T Hu
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - M J Duncan
- 2 The Forsyth Institute, Cambridge, MA, USA
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14
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Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
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15
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Hu J, Li T, Xu W, Zhan J, Chen H, He C, Wang Q. Small Antisense RNA RblR Positively Regulates RuBisCo in Synechocystis sp. PCC 6803. Front Microbiol 2017; 8:231. [PMID: 28261186 PMCID: PMC5306279 DOI: 10.3389/fmicb.2017.00231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/01/2017] [Indexed: 11/21/2022] Open
Abstract
Small regulatory RNAs (sRNAs) function as transcriptional and post-transcriptional regulators of gene expression in organisms from all domains of life. Cyanobacteria are thought to have developed a complex RNA-based regulatory mechanism. In the current study, by genome-wide analysis of differentially expressed small RNAs in Synechocystis sp. PCC 6803 under high light conditions, we discovered an asRNA (RblR) that is 113nt in length and completely complementary to its target gene rbcL, which encodes the large chain of RuBisCO, the enzyme that catalyzes carbon fixation. Further analysis of the RblR(+)/(−) mutants revealed that RblR acts as a positive regulator of rbcL under various stress conditions; Suppressing RblR adversely affects carbon assimilation and thus the yield, and those phenotypes of both the wild type and the overexpressor could be downgraded to the suppressor level by carbonate depletion, indicated a regulatory role of RblR in CO2 assimilation. In addition, a real-time expression platform in Escherichia coli was setup and which confirmed that RblR promoted the translation of the rbcL mRNA into the RbcL protein. The present study is the first report of a regulatory RNA that targets RbcL in Synechocystis sp. PCC 6803, and provides strong evidence that RblR regulates photosynthesis by positively modulating rbcL expression in Synechocystis.
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Affiliation(s)
- Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University Xi'an, China
| | - Tianpei Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of SciencesWuhan, China; University of the Chinese Academy of SciencesBeijing, China
| | - Wen Xu
- Crop Designing Centre, Henan Academy of Agricultural Sciences Zhengzhou, China
| | - Jiao Zhan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
| | - Hui Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
| | - Chenliu He
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
| | - Qiang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
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16
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Vannini A, Roncarati D, Danielli A. The cag-pathogenicity island encoded CncR1 sRNA oppositely modulates Helicobacter pylori motility and adhesion to host cells. Cell Mol Life Sci 2016; 73:3151-68. [PMID: 26863876 PMCID: PMC11108448 DOI: 10.1007/s00018-016-2151-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 01/13/2016] [Accepted: 01/28/2016] [Indexed: 02/08/2023]
Abstract
Small regulatory RNAs (sRNAs) are emerging as key post-transcriptional regulators in many bacteria. In the human pathobiont Helicobacter pylori a plethora of trans- and cis-encoded sRNAs have been pinpointed by a global transcriptome study. However, only two have been studied in depth at the functional level. Here we report the characterization of CncR1, an abundant and conserved sRNA encoded by the virulence-associated cag pathogenicity island (cag-PAI) of H. pylori. Growth-phase dependent transcription of CncR1 is directed by the PcagP promoter, which resulted to be a target of the essential transcriptional regulator HsrA (HP1043). We demonstrate that the 213 nt transcript arising from this promoter ends at an intrinsic terminator, few bases upstream of the annotated cagP open reading frame, establishing CncR1 as the predominant gene product encoded by the cagP (cag15) locus. Interestingly, the deletion of the locus resulted in the deregulation en masse of σ(54)-dependent genes, linking CncR1 to flagellar functions. Accordingly, the enhanced motility recorded for cncR1 deletion mutants was complemented by ectopic reintroduction of the allele in trans. In silico prediction identified fliK, encoding a flagellar checkpoint protein, as likely regulatory target of CncR1. The interaction of CncR1 with the fliK mRNA was thus further investigated in vitro, demonstrating the formation of strand-specific interactions between the two RNA molecules. Accordingly, the full-length translational fusions of fliK with a lux reporter gene were induced in a cncR1 deletion mutant in vivo. These data suggest the involvement of CncR1 in the post-transcriptional modulation of H. pylori motility functions through down-regulation of a critical flagellar checkpoint factor. Concurrently, the cncR1 mutant revealed a decrease of transcript levels for several H. pylori adhesins, resulting in a phenotypically significant impairment of bacterial adhesion to a host gastric cell line. The data presented support a model in which the cag-PAI encoded CncR1 sRNA is able to oppositely modulate bacterial motility and adhesion to host cells.
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Affiliation(s)
- Andrea Vannini
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Alberto Danielli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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17
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Marcus EA, Sachs G, Wen Y, Scott DR. Phosphorylation-dependent and Phosphorylation-independent Regulation of Helicobacter pylori Acid Acclimation by the ArsRS Two-component System. Helicobacter 2016; 21:69-81. [PMID: 25997502 PMCID: PMC4655181 DOI: 10.1111/hel.12235] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The pH-sensitive Helicobacter pylori ArsRS two-component system (TCS) aids survival of this neutralophile in the gastric environment by directly sensing and responding to environmental acidity. ArsS is required for acid-induced trafficking of urease and its accessory proteins to the inner membrane, allowing rapid, urea-dependent cytoplasmic and periplasmic buffering. Expression of ArsR, but not its phosphorylation, is essential for bacterial viability. The aim of this study was to characterize the roles of ArsS and ArsR in the response of H. pylori to acid. MATERIALS AND METHODS Wild-type H. pylori and an arsR(D52N) phosphorylation-deficient strain were incubated at acidic or neutral pH. Gene and protein expression, survival, membrane trafficking of urease proteins, urease activity, and internal pH were studied. RESULTS Phosphorylation of ArsR is not required for acid survival. ArsS-driven trafficking of urease proteins to the membrane in acid, required for recovery of internal pH, is independent of ArsR phosphorylation. ArsR phosphorylation increases expression of the urease gene cluster, and the loss of negative feedback in a phosphorylation-deficient mutant leads to an increase in total urease activity. CONCLUSIONS ArsRS has a dual function in acid acclimation: regulation of urease trafficking to UreI at the cytoplasmic membrane, driven by ArsS, and regulation of urease gene cluster expression, driven by phosphorylation of ArsR. ArsS and ArsR work through phosphorylation-dependent and phosphorylation-independent regulatory mechanisms to impact acid acclimation and allow gastric colonization. Furthering understanding of the intricacies of acid acclimation will impact the future development of targeted, nonantibiotic treatment regimens.
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Affiliation(s)
- Elizabeth A. Marcus
- Department of Pediatrics, DGSOM at UCLA, Los Angeles, CA
- VA GLAHS, Los Angeles, CA
| | - George Sachs
- Department of Physiology, DGSOM at UCLA, Los Angeles, CA
- Department of Medicine, DGSOM at UCLA, Los Angeles, CA
- VA GLAHS, Los Angeles, CA
| | - Yi Wen
- Department of Physiology, DGSOM at UCLA, Los Angeles, CA
- VA GLAHS, Los Angeles, CA
| | - David R. Scott
- Department of Physiology, DGSOM at UCLA, Los Angeles, CA
- VA GLAHS, Los Angeles, CA
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18
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Haley KP, Gaddy JA. Metalloregulation of Helicobacter pylori physiology and pathogenesis. Front Microbiol 2015; 6:911. [PMID: 26388855 PMCID: PMC4557348 DOI: 10.3389/fmicb.2015.00911] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/19/2015] [Indexed: 12/23/2022] Open
Abstract
Helicobacter pylori is a Gram-negative spiral-shaped bacterium that colonizes over half of the world's population. Chronic H. pylori infection is associated with increased risk for numerous disease outcomes including gastritis, dysplasia, neoplasia, B-cell lymphoma of mucosal-associated lymphoid tissue (MALT lymphoma), and invasive adenocarcinoma. The complex interactions that occur between pathogen and host are dynamic and exquisitely regulated, and the relationship between H. pylori and its human host are no exception. To successfully colonize, and subsequently persist, within the human stomach H. pylori must temporally regulate numerous genes to ensure localization to the gastric lumen and coordinated expression of virulence factors to subvert the host's innate and adaptive immune response. H. pylori achieves this precise gene regulation by sensing subtle environmental changes including host-mediated alterations in nutrient availability and responding with dramatic global changes in gene expression. Recent studies revealed that the presence or absence of numerous metal ions encountered in the lumen of the stomach, or within host tissues, including nickel, iron, copper and zinc, can influence regulatory networks to alter gene expression in H. pylori. These expression changes modulate the deployment of bacterial virulence factors that can ultimately influence disease outcome. In this review we will discuss the environmental stimuli that are detected by H. pylori as well as the trans regulatory elements, specifically the transcription regulators and transcription factors, that allow for these significant transcriptional shifts.
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Affiliation(s)
- Kathryn P Haley
- Tennessee Valley Healthcare Services, Department of Veterans Affairs Nashville, TN, USA
| | - Jennifer A Gaddy
- Department of Medicine, Vanderbilt University School of Medicine Nashville, TN, USA ; Tennessee Valley Healthcare Services, Department of Veterans Affairs Nashville, TN, USA
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19
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Hung CL, Cheng HH, Hsieh WC, Tsai ZTY, Tsai HK, Chu CH, Hsieh WP, Chen YF, Tsou Y, Lai CH, Wang WC. The CrdRS two-component system in Helicobacter pylori responds to nitrosative stress. Mol Microbiol 2015; 97:1128-41. [PMID: 26082024 DOI: 10.1111/mmi.13089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 11/28/2022]
Abstract
Helicobacter pylori inhabits the gastric mucosa where it senses and responds to various stresses via a two-component systems (TCSs) that enable its persistent colonization. The aim of this study was to investigate whether any of the three paired TCSs (ArsRS, FleRS and CrdRS) in H. pylori respond to nitrosative stress. The results showed that the expression of crdS was significantly increased upon exposure to nitric oxide (NO). crdS-knockout (ΔcrdS) and crdR/crdS-knockout (ΔcrdRS) H. pylori, but not arsS-knockout (ΔarsS) or fleS-knockout (ΔfleS) H. pylori, showed a significant loss of viability upon exposure to NO compared with wild-type strain. Knockin crdS (ΔcrdS-in) significantly restored viability in the presence of NO. Global transcriptional profiling analysis of wild-type and ΔcrdS H. pylori in the presence or absence of NO showed that 101 genes were differentially expressed, including copper resistance determinant A (crdA), transport, binding and envelope proteins. The CrdR binding motifs were investigated by competitive electrophoretic mobility shift assay, which revealed that the two AC-rich regions in the crdA promoter region are required for binding. These results demonstrate that CrdR-crdA interaction enables H. pylori to survive under nitrosative stress.
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Affiliation(s)
- Chiu-Lien Hung
- Department of Biochemistry and Molecular Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California, USA.,Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsin-Hung Cheng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Wan-Chen Hsieh
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Zing Tsung-Yeh Tsai
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Huai-Kuang Tsai
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Chia-Han Chu
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Ping Hsieh
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Fan Chen
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu Tsou
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Ho Lai
- Department of Nursing, Asia University, Taichung, Taiwan.,Graduate Institute of Basic Medical Science, School of Medicine, China Medical University, Taichung, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
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20
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Dunne C, Dolan B, Clyne M. Factors that mediate colonization of the human stomach by Helicobacter pylori. World J Gastroenterol 2014; 20:5610-24. [PMID: 24914320 PMCID: PMC4024769 DOI: 10.3748/wjg.v20.i19.5610] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/04/2013] [Accepted: 01/19/2014] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) colonizes the stomach of humans and causes chronic infection. The majority of bacteria live in the mucus layer overlying the gastric epithelial cells and only a small proportion of bacteria are found interacting with the epithelial cells. The bacteria living in the gastric mucus may act as a reservoir of infection for the underlying cells which is essential for the development of disease. Colonization of gastric mucus is likely to be key to the establishment of chronic infection. How H. pylori manages to colonise and survive in the hostile environment of the human stomach and avoid removal by mucus flow and killing by gastric acid is the subject of this review. We also discuss how bacterial and host factors may together go some way to explaining the susceptibility to colonization and the outcome of infection in different individuals. H. pylori infection of the gastric mucosa has become a paradigm for chronic infection. Understanding of why H. pylori is such a successful pathogen may help us understand how other bacterial species colonise mucosal surfaces and cause disease.
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21
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Pandey GS, Hang'ombe BM, Mushabati F, Kataba A. Prevalence of tuberculosis among southern Zambian cattle and isolation of Mycobacterium bovis in raw milk obtained from tuberculin positive cows. Vet World 2013. [DOI: 10.14202/vetworld.2013.986-991] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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22
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Han Y, Liu L, Fang N, Yang R, Zhou D. Regulation of pathogenicity by noncoding RNAs in bacteria. Future Microbiol 2013; 8:579-91. [PMID: 23642114 DOI: 10.2217/fmb.13.20] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulatory noncoding RNAs (ncRNAs) play important roles in bacterial gene regulation, primarily at the post-transcriptional level. There are four broad categories of regulatory ncRNAs including trans-encoded ncRNAs, cis-encoded ncRNAs, RNA thermometers and riboswitches, and they can influence the translation and/or stability of mRNAs by binding to the base-pairing sites in their target transcripts. In pathogenic bacteria, numerous ncRNAs are involved in the coordinated expression of virulence determinants to facilitate the pathogenicity in a concerted manner. This review discusses the modes of action of different regulatory ncRNAs and, furthermore, exemplifies their roles in regulating bacterial pathogenicity.
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Affiliation(s)
- Yanping Han
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
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23
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Taveirne ME, Theriot CM, Livny J, DiRita VJ. The complete Campylobacter jejuni transcriptome during colonization of a natural host determined by RNAseq. PLoS One 2013; 8:e73586. [PMID: 23991199 PMCID: PMC3749233 DOI: 10.1371/journal.pone.0073586] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/22/2013] [Indexed: 11/19/2022] Open
Abstract
Campylobacter jejuni is a major human pathogen and a leading cause of bacterial derived gastroenteritis worldwide. C. jejuni regulates gene expression under various environmental conditions and stresses, indicative of its ability to survive in diverse niches. Despite this ability to highly regulate gene transcription, C. jejuni encodes few transcription factors and its genome lacks many canonical transcriptional regulators. High throughput deep sequencing of mRNA transcripts (termed RNAseq) has been used to study the transcriptome of many different organisms, including C. jejuni; however, this technology has yet to be applied to defining the transcriptome of C. jejuni during in vivo colonization of its natural host, the chicken. In addition to its use in profiling the abundance of annotated genes, RNAseq is a powerful tool for identifying and quantifying, as-of-yet, unknown transcripts including non-coding regulatory RNAs, 5’ untranslated regulatory elements, and anti-sense transcripts. Here we report the complete transcriptome of C. jejuni during colonization of the chicken cecum and in two different in vitro growth phases using strand-specific RNAseq. Through this study, we identified over 250 genes differentially expressed in vivo in addition to numerous putative regulatory RNAs, including trans-acting non-coding RNAs and anti-sense transcripts. These latter potential regulatory elements were not identified in two prior studies using ORF-based microarrays, highlighting the power and value of the RNAseq approach. Our results provide new insights into how C. jejuni responds and adapts to the cecal environment and reveals new functions involved in colonization of its natural host.
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Affiliation(s)
- Michael E. Taveirne
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Casey M. Theriot
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, Division of Pulmonary and Critical Care, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jonathan Livny
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail: (VJD); (JL)
| | - Victor J. DiRita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (VJD); (JL)
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24
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Helicobacter pylori 5'ureB-sRNA, a cis-encoded antisense small RNA, negatively regulates ureAB expression by transcription termination. J Bacteriol 2012; 195:444-52. [PMID: 23104809 DOI: 10.1128/jb.01022-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Urease is an essential component of gastric acid acclimation by Helicobacter pylori. The increased level of urease in gastric acidity is due, in part, to acid activation of the two-component system consisting of the membrane sensor HP0165 (ArsS) and its response regulator HP0166 (ArsR), which regulates transcription of the seven genes in two separate operons (ureAB and ureIEFGH) of the urease gene cluster. Recently, we identified a novel cis-encoded antisense small RNA, 5'ureB-sRNA, targeted at the 5' end of ureB, which downregulates ureAB expression by truncation of the ureAB transcript at neutral pH. It is not known whether the truncated transcript is due to transcription termination or processing of the full-length mRNA by codegradation of a ureAB mRNA-sRNA hybrid complex. S1 nuclease mapping assays show that the truncated transcript is due to transcription termination. Further studies using an in vitro transcription assay found that 5'ureB-sRNA promotes premature termination of transcription of ureAB mRNA. These results suggest that the antisense small RNA 5'ureB-sRNA downregulates ureAB expression by enhancing transcription termination 5' of ureB. With this mechanism, a limited amount of 5'ureB-sRNA is sufficient to regulate the relatively high level of ureAB transcript.
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25
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Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RAT, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 2012; 335:1103-6. [PMID: 22383849 DOI: 10.1126/science.1206848] [Citation(s) in RCA: 660] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.
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Affiliation(s)
- Pierre Nicolas
- INRA, UR1077, Mathématique Informatique et Génome, Jouy-en-Josas, France
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26
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Pernitzsch SR, Sharma CM. Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori. Front Cell Infect Microbiol 2012; 2:14. [PMID: 22919606 PMCID: PMC3417511 DOI: 10.3389/fcimb.2012.00014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 02/02/2012] [Indexed: 12/21/2022] Open
Abstract
The Gram-negative Epsilonproteobacterium Helicobacter pylori is considered as one of the major human pathogens and many studies have focused on its virulence mechanisms as well as genomic diversity. In contrast, only very little is known about post-transcriptional regulation and small regulatory RNAs (sRNAs) in this spiral-shaped microaerophilic bacterium. Considering the absence of the common RNA chaperone Hfq, which is a key-player in post-transcriptional regulation in enterobacteria, H. pylori was even regarded as an organism without riboregulation. However, analysis of the H. pylori primary transcriptome using RNA-seq revealed a very complex transcriptional output from its small genome. Furthermore, the identification of a wealth of sRNAs as well as massive antisense transcription indicates that H. pylori uses riboregulation for its gene expression control. The ongoing functional characterization of sRNAs along with the identification of associated RNA binding proteins will help to understand their potential roles in Helicobacter virulence and stress response. Moreover, research on riboregulation in H. pylori will provide new insights into its virulence mechanisms and will also help to shed light on post-transcriptional regulation in other Epsilonproteobacteria, including widespread and emerging pathogens such as Campylobacter.
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Affiliation(s)
- Sandy R Pernitzsch
- Research Center for Infectious Diseases, University of Würzburg Würzburg, Germany
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Göpel Y, Görke B. Rewiring two-component signal transduction with small RNAs. Curr Opin Microbiol 2011; 15:132-9. [PMID: 22197250 DOI: 10.1016/j.mib.2011.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/24/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
Abstract
Bacterial two-component systems (TCSs) and small regulatory RNAs (sRNAs) form densely interconnected networks that integrate and transduce information from the environment into fine-tuned changes of gene expression. Many TCSs control target genes indirectly through regulation of sRNAs, which in turn regulate gene expression by base-pairing with mRNAs or targeting a protein. Conversely, sRNAs may control TCS synthesis, thereby recruiting the TCS regulon to other regulatory networks. Several TCSs control expression of multiple homologous sRNAs providing the regulatory networks with further flexibility. These sRNAs act redundantly, additively or hierarchically on targets. The regulatory speed of sRNAs and their unique features in gene regulation make them ideal players extending the flexibility, dynamic range or timing of TCS signaling.
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Affiliation(s)
- Yvonne Göpel
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstrasse 8, 37077 Göttingen, Germany
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28
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Abstract
A substantial amount of antisense transcription is a hallmark of gene expression in eukaryotes. However, antisense transcription was first demonstrated in bacteria almost 50 years ago. The transcriptomes of bacteria as different as Helicobacter pylori, Bacillus subtilis, Escherichia coli, Synechocystis sp. strain PCC6803, Mycoplasma pneumoniae, Sinorhizobium meliloti, Geobacter sulfurreducens, Vibrio cholerae, Chlamydia trachomatis, Pseudomonas syringae, and Staphylococcus aureus have now been reported to contain antisense RNA (asRNA) transcripts for a high percentage of genes. Bacterial asRNAs share functional similarities with trans-acting regulatory RNAs, but in addition, they use their own distinct mechanisms. Among their confirmed functional roles are transcription termination, codegradation, control of translation, transcriptional interference, and enhanced stability of their respective target transcripts. Here, we review recent publications indicating that asRNAs occur as frequently in simple unicellular bacteria as they do in higher organisms, and we provide a comprehensive overview of the experimentally confirmed characteristics of asRNA actions and intimately linked quantitative aspects. Emerging functional data suggest that asRNAs in bacteria mediate a plethora of effects and are involved in far more processes than were previously anticipated. Thus, the functional impact of asRNAs should be considered when developing new strategies against pathogenic bacteria and when optimizing bacterial strains for biotechnology.
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29
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Abstract
Diverse mechanisms for pH sensing and cytoplasmic pH homeostasis enable most bacteria to tolerate or grow at external pH values that are outside the cytoplasmic pH range they must maintain for growth. The most extreme cases are exemplified by the extremophiles that inhabit environments with a pH of below 3 or above 11. Here, we describe how recent insights into the structure and function of key molecules and their regulators reveal novel strategies of bacterial pH homeostasis. These insights may help us to target certain pathogens more accurately and to harness the capacities of environmental bacteria more efficiently.
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Affiliation(s)
- Terry A. Krulwich
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, Box 1603, 1 Gustave L. Levy Place, New York, NY 10029, USA; Tel. 212-241-7280; Fax. 212-996-7214
| | - George Sachs
- Departments of Physiology and Medicine, David Geffen School of Medicine at UCLA, 405 Hilgard Ave., Los Angeles, California 90024, USA Tel. 310-268-3923, Fax 310-312-9478
| | - Etana Padan
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel, Tel. 972 2 6585094, Fax 972 2 658947
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30
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Abstract
A novel mechanism aimed at controlling urease expression in Helicobacter pylori in the presence of ample nickel is described. Higher urease activities were observed in an hp0868 mutant (than in the wild type) in cells supplemented with nickel, suggesting that the HP0868 protein (herein named Mua for modulator of urease activity) represses urease activity when nickel concentrations are ample. The increase in urease activity in the Δmua mutant was linked to an increase in urease transcription and synthesis, as shown by quantitative real-time PCR, SDS-PAGE, and immunoblotting against UreAB. Increased urease synthesis was also detected in a Δmua ΔnikR double mutant strain. The Δmua mutant was more sensitive to nickel toxicity but more resistant to acid challenge than was the wild-type strain. Pure Mua protein binds 2 moles of Ni2+ per mole of dimer. Electrophoretic mobility shift assays did not reveal any binding of Mua to the ureA promoter or other selected promoters (nikR, arsRS, 5′ ureB-sRNAp). Previous yeast two-hybrid studies indicated that Mua and RpoD may interact; however, only a weak interaction was detected via cross-linking with pure components and this could not be verified by another approach. There was no significant difference in the intracellular nickel level between wild-type and mua mutant cells. Taken together, our results suggest the HP0868 gene product represses urease transcription when nickel levels are high through an as-yet-uncharacterized mechanism, thus counterbalancing the well-described NikR-mediated activation. Urease is a nickel-containing enzyme that buffers both the cytoplasm and the periplasm of Helicobacter pylori by converting urea into ammonia and carbon dioxide. The enzyme is the most abundant protein in H. pylori, accounting for an estimated 10% of the total protein content of the cell, and it is essential for early colonization and virulence. Numerous studies have focused on the transcription of the structural ureAB genes and its control by the regulatory proteins NikR and ArsR. Here we propose that urease transcription is under the control of another Ni-binding protein besides NikR, the Mua (HP0868) protein. Our results suggest that the Mua protein represses urease transcription when nickel levels are high. This mechanism would counterbalance the NikR-mediated activation of urease and ensure that, in the presence of a high nickel concentration, urease activation is limited and does not lead to massive production of detrimental ammonia.
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