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Li Q, Liu C, He J, Liu T, Zhang W, Xie Z, Zong J, Li Y, Sun X, Lu F. Construction and application of 3-fucosyllactose whole-cell biosensor for high-throughput screening of overproducers. BIORESOURCE TECHNOLOGY 2024; 402:130798. [PMID: 38705212 DOI: 10.1016/j.biortech.2024.130798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Biosensor-based high-throughput screening is efficient for improving industrial microorganisms. There is a severe shortage of human milk oligosaccharides (HMOs) biosensors. This study established a 3-fucosyllactose (3-FL, a kind of HMOs) whole-cell biosensor by coupling cell growth with production. To construct and optimize the biosensor, an Escherichia coli 3-FL producer was engineered by deleting the manA, yihS and manX genes, directing the mannose flux solely to 3-FL synthesis. Then, an α-L-fucosidase was introduced to hydrolyze 3-FL to fucose which was used as the only carbon source for cell growth. Using the biosensor, the 3-FL production of a screened mutant was improved by 25 % to 42.05 ± 1.28 g/L. The productivity reached 1.17 g/L/h, the highest level reported by now. The csrB mutant obtained should be a new clue for the 3-FL overproduction mechanism. In summary, this study provided a novel approach to construct HMOs biosensors for strain improvement.
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Affiliation(s)
- Qinggang Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, PR China.
| | - Chuan Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China
| | - Jinhuai He
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China
| | - Tiantian Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China
| | - Wencong Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China
| | - Zhenzhen Xie
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China
| | - Jianfei Zong
- Shandong SynBio-Vision Technology Co., Ltd, Weifang 262500, PR China
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China
| | - Xue Sun
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China
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Ji X, Yu R, Zhu M, Zhang C, Zhou L, Cai T, Li W. Diadenosine tetraphosphate modulated quorum sensing in bacteria treated with kanamycin. BMC Microbiol 2023; 23:353. [PMID: 37978430 PMCID: PMC10657157 DOI: 10.1186/s12866-023-03113-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The dinucleotide alarmone diadenosine tetraphosphate (Ap4A), which is found in cells, has been shown to affect the survival of bacteria under stress. RESULTS Here, we labeled Ap4A with biotin and incubated the labeled Ap4A with the total proteins extracted from kanamycin-treated Escherichia coli to identify the Ap4A binding protein in bacteria treated with kanamycin. Liquid chromatography‒mass spectrometry (LCMS) and bioinformatics were used to identify novel proteins that Ap4A interacts with that are involved in biofilm formation, quorum sensing, and lipopolysaccharide biosynthesis pathways. Then, we used the apaH knockout strain of E. coli K12-MG1655, which had increased intracellular Ap4A, to demonstrate that Ap4A affected the expression of genes in these three pathways. We also found that the swarming motility of the apaH mutant strain was reduced compared with that of the wild-type strain, and under kanamycin treatment, the biofilm formation of the mutant strain decreased. CONCLUSIONS These results showed that Ap4A can reduce the survival rate of bacteria treated with kanamycin by regulating quorum sensing (QS). These effects can expand the application of kanamycin combinations in the treatment of multidrug-resistant bacteria.
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Affiliation(s)
- Xia Ji
- School of Life Science, Huizhou University, Huizhou, 516007, China.
| | - Ruojing Yu
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Meilian Zhu
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Cuilin Zhang
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Libin Zhou
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Tianshu Cai
- Huizhou Health Sciences Polytechnic, Huizhou, 516025, China
| | - Weiwei Li
- Huizhou Health Sciences Polytechnic, Huizhou, 516025, China
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3
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Nava-Galeana J, Núñez C, Bustamante VH. Proteomic analysis reveals the global effect of the BarA/SirA-Csr regulatory cascade in Salmonella Typhimurium grown in conditions that favor the expression of invasion genes. J Proteomics 2023; 286:104960. [PMID: 37451358 DOI: 10.1016/j.jprot.2023.104960] [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: 03/29/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
In many bacteria, the BarA/SirA and Csr regulatory systems control expression of genes encoding a wide variety of cellular functions. The BarA/SirA two-component system induces the expression of CsrB and CsrC, two small non-coding RNAs that sequester CsrA, a protein that binds to target mRNAs and thus negatively or positively regulates their expression. BarA/SirA and CsrB/C induce expression of the Salmonella Pathogenicity Island 1 (SPI-1) genes required for Salmonella invasion of host cells. To further investigate the regulatory role of the BarA/SirA and Csr systems in Salmonella, we performed LC-MS/MS proteomic analysis using the WT S. Typhimurium strain and its derived ΔsirA and ΔcsrB ΔcsrC mutants grown in SPI-1-inducing conditions. The expression of 164 proteins with a wide diversity, or unknown, functions was significantly affected positively or negatively by the absence of SirA and/or CsrB/C. Interestingly, 19 proteins were identified as new targets for SirA-CsrB/C. Our results support that SirA and CsrB/C act in a cascade fashion to regulate gene expression in S. Typhimurium in the conditions tested. Notably, our results show that SirA-CsrB/C-CsrA controls expression of proteins required for the replication of Salmonella in the intestinal lumen, in an opposite way to its control exerted on the SPI-1 proteins. SIGNIFICANCE: The BarA/SirA and Csr global regulatory systems control a wide range of cellular processes, including the expression of virulence genes. For instance, in Salmonella, BarA/SirA and CsrB/C positively regulate expression of the SPI-1 genes, which are required for Salmonella invasion to host cells. In this study, by performing a proteomic analysis, we identified 164 proteins whose expression was positively or negatively controlled by SirA and CsrB/C in SPI-1-inducing conditions, including 19 new possible targets of these systems. Our results support the action of SirA and CsrB/C in a cascade fashion to control different cellular processes in Salmonella. Interestingly, our data indicate that SirA-CsrB/C-CsrA controls inversely the expression of proteins required for invasion of the intestinal epithelium and for replication in the intestinal lumen, which suggests a role for this regulatory cascade as a molecular switch for Salmonella virulence. Thus, our study further expands the insight into the regulatory mechanisms governing the virulence and physiology of an important pathogen.
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Affiliation(s)
- Jessica Nava-Galeana
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
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Shi M, Ye J, Fan F, Zhao F, Zhong X, Zhong Z, Wang H, Wang Z, Yang M. Precisely Controlling Csr sRNA Levels by MshH Enhances Vibrio cholerae Colonization in Adult Mice. Appl Environ Microbiol 2023; 89:e0056123. [PMID: 37404138 PMCID: PMC10370335 DOI: 10.1128/aem.00561-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/08/2023] [Indexed: 07/06/2023] Open
Abstract
Vibrio cholerae is the causative agent of cholera. Effective intestinal colonization is a key step for V. cholerae pathogenicity and transmission. In this study, we found that deleting mshH, a homolog of the Escherichia coli CsrD protein, caused a V. cholerae colonization defect in the intestine of adult mice. By analyzing the RNA levels of CsrB, CsrC, and CsrD, we found that deleting mshH increased the levels of CsrB and CsrD but decreased the level of CsrC. However, deleting CsrB and -D not only recovered the mshH deletion mutant colonization defect but also recovered CsrC to wild-type levels. These results indicated that controlling the RNA levels of CsrB, -C, and -D is crucial for V. cholerae colonization of adult mice. We further demonstrated that the RNA levels of CsrB and CsrD were mainly controlled by MshH-dependent degradation, yet the level of CsrC was mainly determined by the CsrA-dependent stabilization. Our data show that V. cholerae differentially controls CsrB, -C, and -D abundance through the MshH-CsrB/C/D-CsrA regulatory pathway to finely regulate the activity of CsrA targets such as ToxR, so as to better survive in adult mouse intestine. IMPORTANCE The ability of V. cholerae to colonize the intestine is a key factor for its fitness and transmissibility between hosts. Here, we investigated the mechanism of V. cholerae colonization of adult mammal intestine and found that precisely controlling the CsrB, -C, and -D contents by MshH and CsrA plays an essential role for V. cholerae colonization in the adult mouse intestine. These data expand our knowledge on the mechanism of V. cholerae controlling the RNA level of CsrB, -C, and -D and highlight the importance that the different strategies used by V. cholerae to regulate the RNA level of CsrB, -C, and -D confer the bacterium with a survival advantage.
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Affiliation(s)
- Mengting Shi
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jinjie Ye
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang, China
| | - Fenxia Fan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Feifei Zhao
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang, China
| | - Xiaojun Zhong
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang, China
| | - Zengtao Zhong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hui Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, China
| | - Menghua Yang
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang, China
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5
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Chang CP, Lagitnay RBJS, Li TR, Lai WT, Derilo RC, Chuang DY. Unleashing the Influence of cAMP Receptor Protein: The Master Switch of Bacteriocin Export in Pectobacterium carotovorum subsp. carotovorum. Int J Mol Sci 2023; 24:ijms24119752. [PMID: 37298703 DOI: 10.3390/ijms24119752] [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: 04/26/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Pectobacterium carotovorum subsp. carotovorum (Pcc) is a Gram-negative phytopathogenic bacterium that produces carocin, a low-molecular-weight bacteriocin that can kill related strains in response to factors in the environment such as UV exposure or nutritional deficiency. The function of the catabolite activator protein (CAP), also known as the cyclic AMP receptor protein (CRP), as a regulator of carocin synthesis was examined. The crp gene was knocked out as part of the investigation, and the outcomes were assessed both in vivo and in vitro. Analysis of the DNA sequence upstream of the translation initiation site of carocin S3 revealed two putative binding sites for CRP that were confirmed using a biotinylated probe pull-down experiment. This study revealed that the deletion of crp inhibited genes involved in extracellular bacteriocin export via the flagellar type III secretion system and impacted the production of many low-molecular-weight bacteriocins. The biotinylated probe pull-down test demonstrated that when UV induction was missing, CRP preferentially attached to one of the two CAP sites while binding to both when UV induction was present. In conclusion, our research aimed to simulate the signal transduction system that controls the expression of the carocin gene in response to UV induction.
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Affiliation(s)
- Chung-Pei Chang
- Department of Anesthesiology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
| | - Ruchi Briam James Sersenia Lagitnay
- College of Arts and Sciences, Bayombong Campus, Nueva Vizcaya State University, Bayombong 3700, Philippines
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Tzu-Rong Li
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Wei-Ting Lai
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Reymund Calanga Derilo
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
- College of Teacher Education, Bambang Campus, Nueva Vizcaya State University, Bambang 3702, Philippines
| | - Duen-Yau Chuang
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
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6
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Thompson CMA, Hall JPJ, Chandra G, Martins C, Saalbach G, Panturat S, Bird SM, Ford S, Little RH, Piazza A, Harrison E, Jackson RW, Brockhurst MA, Malone JG. Plasmids manipulate bacterial behaviour through translational regulatory crosstalk. PLoS Biol 2023; 21:e3001988. [PMID: 36787297 PMCID: PMC9928087 DOI: 10.1371/journal.pbio.3001988] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/04/2023] [Indexed: 02/15/2023] Open
Abstract
Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.
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Affiliation(s)
- Catriona M. A. Thompson
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - James P. J. Hall
- Department of Evolution, Ecology and Behaviour Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Crown Street, Liverpool, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Carlo Martins
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Gerhard Saalbach
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Supakan Panturat
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Susannah M. Bird
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Samuel Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Richard H. Little
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ainelen Piazza
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Robert W. Jackson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Michael A. Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Jacob G. Malone
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
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7
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Esteban-Torres M, Ruiz L, Rossini V, Nally K, van Sinderen D. Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait. Gut Microbes 2023; 15:2235067. [PMID: 37526383 PMCID: PMC10395257 DOI: 10.1080/19490976.2023.2235067] [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: 01/25/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.
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Affiliation(s)
- Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Benefitial Microbes (MicroHealth Group), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Valerio Rossini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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8
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Ormazábal A, Pierdominici-Sottile G, Palma J. Recognition and Binding of RsmE to an AGGAC Motif of RsmZ: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:6614-6627. [PMID: 35470666 DOI: 10.1021/acs.jcim.2c00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
CsrA/RsmE is a post-transcriptional regulator protein widely distributed in bacteria. It impedes the expression of target mRNAs by attaching their 5' untranslated region. The translation is restored by small, noncoding RNAs that sequester CsrA/RsmE acting as sponges. In both cases, the protein recognizes and attaches to specific AGGAX and AXGGAX motifs, where X refers to any nucleotide. RsmZ of Pseudomonas protegens is one of these small RNAs. The structures of some of its complexes with RsmE were disclosed a few years ago. We have used umbrella sampling simulations to force the unbinding of RsmE from the AGGAC motif located in the single-stranded region sited between stem loops 2 and 3 of RsmZ. The calculations unveiled the identity of the main residues and nucleotides involved in the process. They also showed that the region adopts a hairpin-like conformation during the initial stages of the binding. The ability to acquire this conformation requires that the region has a length of at least nine nucleotides. Besides, we performed standard molecular dynamics simulations of the isolated fragments, analyzed their typical conformations, and characterized their movements. This analysis revealed that the free molecules oscillate along specific collective coordinates that facilitate the initial stages of the binding. The results strongly suggest that the flexibility of the single-stranded region of RsmZ crucially affects the ability of its binding motif to catch RsmE.
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Affiliation(s)
- Agustín Ormazábal
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
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9
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A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria. NPJ Biofilms Microbiomes 2022; 8:54. [PMID: 35798749 PMCID: PMC9262955 DOI: 10.1038/s41522-022-00314-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 06/14/2022] [Indexed: 01/11/2023] Open
Abstract
Transcriptomic studies have revealed a large number of uncharacterized genes that are differentially expressed in biofilms, which may be important in regulating biofilm phenotypes such as resistance to antimicrobial agents. To identify biofilm genes of unknown function in P. aeruginosa, we made use of RNA-seq and selected 27 uncharacterized genes that were induced upon biofilm growth. Biofilms by respective mutants were subsequently analyzed for two biofilm characteristics, the biofilm architecture and drug susceptibility. The screen revealed 12 out of 27 genes to contribute to biofilm formation and 13 drug susceptibility, with 8 genes affecting both biofilm phenotypes. Amongst the genes affecting both biofilm phenotypes was PA2146, encoding a small hypothetical protein that exhibited some of the most substantial increases in transcript abundance during biofilm growth by P. aeruginosa PAO1 and clinical isolates. PA2146 is highly conserved in ɣ-proteobacteria. Inactivation of PA2146 affected both biofilm phenotypes in P. aeruginosa PAO1, with inactivation of homologs in Klebsiella pneumoniae and Escherichia coli having similar effects. Heterologous expression of PA2146 homologs complemented the P. aeruginosa ∆PA2146, suggesting that PA2146 homologs substitute for and play a similar role as PA2146 in P. aeruginosa.
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10
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Abstract
Despite their ubiquitous nature, few antisense RNAs have been functionally characterized, and this class of RNAs is considered by some to be transcriptional noise. Here, we report that an antisense RNA (asRNA), aMEF (antisense mazEF), functions as a dual regulator for the type II toxin-antitoxin (TA) system mazEF. Unlike type I TA systems and many other regulatory asRNAs, aMEF stimulates the synthesis and translation of mazEF rather than inhibition and degradation. Our data indicate that a double-stranded RNA intermediate and RNase III are not necessary for aMEF-dependent regulation of mazEF expression. The lack of conservation of asRNA promoters has been used to support the hypothesis that asRNAs are spurious transcriptional noise and nonfunctional. We demonstrate that the aMEF promoter is active and functional in Escherichia coli despite poor sequence conservation, indicating that the lack of promoter sequence conservation should not be correlated with functionality. IMPORTANCE Next-generation RNA sequencing of numerous organisms has revealed that transcription is widespread across the genome, termed pervasive transcription, and does not adhere to annotated gene boundaries. The function of pervasive transcription is enigmatic and has generated considerable controversy as to whether it is transcriptional noise or biologically relevant. Antisense transcription is one class of pervasive transcription that occurs from the DNA strand opposite an annotated gene. Relatively few pervasively transcribed asRNAs have been functionally characterized, and their regulatory roles or lack thereof remains unknown. It is important to study examples of these asRNAs and determine if they are functional regulators. In this study, we elucidate the function of an asRNA (aMEF) demonstrating that pervasive transcripts can be functional.
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11
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uvrY deletion and acetate reduce gut colonization of Crohn's disease-associated adherent-invasive Escherichia coli by decreasing expression of type 1 fimbriae. Infect Immun 2022; 90:e0066221. [PMID: 34978926 DOI: 10.1128/iai.00662-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) is involved in onset and/or exacerbation of Crohn's disease. AIEC adapts to the gut environment by altering gene-expression programs, leading to successful gut-lumen colonization. However, the underlying mechanism of gut colonization is still far from clarified. Here, we show the role of UvrY, a response regulator of bacterial two-component signal transduction systems, in AIEC gut colonization. An AIEC mutant lacking the uvrY gene exhibited impairment of competitive colonization in the murine intestinal tract. UvrY contributes to functional expression of type 1 fimbriae by activating expression of small RNA CsrB, which confers adherence and invasion into epithelial cells on AIEC. In contrast, acetate suppresses the UvrY-dependent expression of type 1 fimbriae, resulting in less efficient cell invasion and attenuated gut colonization. Our findings might lead to therapeutic interventions for CD, in which inhibitions of UvrY activation and acetate supplementation reduce the colonization levels of AIEC by decreasing type-1 fimbriae expression.
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12
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Jiang ZM, Zhang BH, Sun HM, Zhang T, Yu LY, Zhang YQ. Properties of Modestobacter deserti sp. nov., a Kind of Novel Phosphate-Solubilizing Actinobacteria Inhabited in the Desert Biological Soil Crusts. Front Microbiol 2021; 12:742798. [PMID: 34803963 PMCID: PMC8602919 DOI: 10.3389/fmicb.2021.742798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022] Open
Abstract
Three Gram-stain-positive, aerobic, motile actinobacterial strains designated as CPCC 205119T, CPCC 205215, and CPCC 205251 were isolated from different biological soil crust samples collected from Tengger Desert, China. The 16S rRNA gene sequence comparison of these three strains showed they had almost identical 16S rRNA genes, which were closely related to members of the family Geodermatophilaceae, with the highest similarities of 96.3–97.3% to the species of Modestobacter. In the phylogenetic tree based on 16S rRNA gene sequences, these isolates clustered into a subclade next to the branch containing the species of Modestobacter lapidis and Modestobacter multiseptatus, within the lineage of the genus Modestobacter. The comparative genomic characteristics (values of ANI, dDDH, AAI, and POCP) and the phenotypic properties (morphological, physiological, and chemotaxonomic characteristics) of these isolates readily supported to affiliate them to the genus Modestobacter as a single separate species. For which, we proposed that the isolates CPCC 205119T, CPCC 205215, and CPCC 205251 represent a novel species of the genus Modestobacter as Modestobacter deserti sp. nov. CPCC 205119T (=I12A-02624=NBRC 113528T=KCTC 49201T) is the type strain. The genome of strain CPCC 205119T consisted of one chromosome (4,843,235bp) containing 4,424 coding genes, 48 tRNA genes, five rRNA genes, three other ncRNA genes, and 101 pseudogenes, with G+C content of 74.7%. The whole-genome sequences analysis indicated that this species contained alkaline phosphatase genes (phoA/phoD), phosphate transport-related genes (phoU, phnC, phnD, phnE, phoB, phoH, phoP, phoR, pitH, ppk, pstA, pstB, pstC, and pstS), trehalose-phosphate synthase gene (otsA), trehalose 6-phosphate phosphatase gene (otsB) and other encoding genes for the properties that help the microorganisms to adapt to harsh environmental conditions prevalent in deserts. Strains of this species could solubilize tricalcium phosphate [Ca3(PO4)2] and phytin, assimilate pyrophosphate, thiophosphate, dithiophosphate, phosphoenol pyruvate, 2-deoxy-d-glucose-6-phosphate, and cysteamine-S-phosphate.
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Affiliation(s)
- Zhu-Ming Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bing-Huo Zhang
- College of Life Science, Jiujiang University, Jiujiang, China
| | - Hong-Min Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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13
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Felden B, Augagneur Y. Diversity and Versatility in Small RNA-Mediated Regulation in Bacterial Pathogens. Front Microbiol 2021; 12:719977. [PMID: 34447363 PMCID: PMC8383071 DOI: 10.3389/fmicb.2021.719977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial gene expression is under the control of a large set of molecules acting at multiple levels. In addition to the transcription factors (TFs) already known to be involved in global regulation of gene expression, small regulatory RNAs (sRNAs) are emerging as major players in gene regulatory networks, where they allow environmental adaptation and fitness. Developments in high-throughput screening have enabled their detection in the entire bacterial kingdom. These sRNAs influence a plethora of biological processes, including but not limited to outer membrane synthesis, metabolism, TF regulation, transcription termination, virulence, and antibiotic resistance and persistence. Almost always noncoding, they regulate target genes at the post-transcriptional level, usually through base-pair interactions with mRNAs, alone or with the help of dedicated chaperones. There is growing evidence that sRNA-mediated mechanisms of actions are far more diverse than initially thought, and that they go beyond the so-called cis- and trans-encoded classifications. These molecules can be derived and processed from 5' untranslated regions (UTRs), coding or non-coding sequences, and even from 3' UTRs. They usually act within the bacterial cytoplasm, but recent studies showed sRNAs in extracellular vesicles, where they influence host cell interactions. In this review, we highlight the various functions of sRNAs in bacterial pathogens, and focus on the increasing examples of widely diverse regulatory mechanisms that might compel us to reconsider what constitute the sRNA.
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Affiliation(s)
- Brice Felden
- Inserm, Bacterial Regulatory RNAs and Medicine (BRM) - UMR_S 1230, Rennes, France
| | - Yoann Augagneur
- Inserm, Bacterial Regulatory RNAs and Medicine (BRM) - UMR_S 1230, Rennes, France
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14
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Lee A, Bae E, Park J, Choi KH, Cha J. Identification of the Genes Related to the Glycogen Metabolism in Hyperthermophilic Archaeon, Sulfolobus acidocaldarius. Front Microbiol 2021; 12:661053. [PMID: 34054761 PMCID: PMC8158581 DOI: 10.3389/fmicb.2021.661053] [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: 01/30/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Glycogen is a polysaccharide that comprises α-1,4-linked glucose backbone and α-1,6-linked glucose polymers at the branching points. It is widely found in organisms ranging from bacteria to eukaryotes. The physiological role of glycogen is not confined to being an energy reservoir and carbon source but varies depending on organisms. Sulfolobus acidocaldarius, a thermoacidophilic archaeon, was observed to accumulate granular glycogen in the cell. However, the role of glycogen and genes that are responsible for glycogen metabolism in S. acidocaldarius has not been identified clearly. The objective of this study is to identify the gene cluster, which is composed of enzymes that are predicted to be involved in the glycogen metabolism, and confirm the role of each of these genes by constructing deletion mutants. This study also compares the glycogen content of mutant and wild type and elucidates the role of glycogen in this archaeon. The glycogen content of S. acidocaldarius MR31, which is used as a parent strain for constructing the deletion mutant in this study, was increased in the early and middle exponential growth phases and decreased during the late exponential and stationary growth phases. The pattern of the accumulated glycogen was independent to the type of supplemented sugar. In the comparison of the glycogen content between the gene deletion mutant and MR31, glycogen synthase (GlgA) and α-amylase (AmyA) were shown to be responsible for the synthesis of glycogen, whereas glycogen debranching enzyme (GlgX) and glucoamylase (Gaa) appeared to affect the degradation of glycogen. The expressions of glgC-gaa-glgX and amyA-glgA were detected by the promoter assay. This result suggests that the gradual decrease of glycogen content in the late exponential and stationary phases occurs due to the increase in the gene expression of glgC-gaa-glgX. When the death rate in nutrient limited condition was compared among the wild type strain, the glycogen deficient strain and the strain with increased glycogen content, the death rate of the glycogen deficient strain was found to be higher than any other strain, thereby suggesting that the glycogen in S. acidocaldarius supports cell maintenance in harsh conditions.
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Affiliation(s)
- Areum Lee
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Eunji Bae
- Research Development Institute, Cowellmedi, Busan, South Korea
| | - Jihee Park
- Department of Southern Area Crop Science, Upland Crop Breeding Research Division, National Institute of Crop Science, Rural Development Administration, Miryang, South Korea
| | - Kyoung-Hwa Choi
- Department of Microbiology, Pusan National University, Busan, South Korea
| | - Jaeho Cha
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Microbiology, Pusan National University, Busan, South Korea
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15
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Carzaniga T, Falchi FA, Forti F, Antoniani D, Landini P, Briani F. Different csrA Expression Levels in C versus K-12 E. coli Strains Affect Biofilm Formation and Impact the Regulatory Mechanism Presided by the CsrB and CsrC Small RNAs. Microorganisms 2021; 9:microorganisms9051010. [PMID: 34067197 PMCID: PMC8151843 DOI: 10.3390/microorganisms9051010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 12/03/2022] Open
Abstract
Escherichia coli C is a strong biofilm producer in comparison to E. coli K-12 laboratory strains due to higher expression of the pgaABCD operon encoding the enzymes for the biosynthesis of the extracellular polysaccharide poly-β-1,6-N-acetylglucosamine (PNAG). The pgaABCD operon is negatively regulated at the post-transcriptional level by two factors, namely CsrA, a conserved RNA-binding protein controlling multiple pathways, and the RNA exonuclease polynucleotide phosphorylase (PNPase). In this work, we investigated the molecular bases of different PNAG production in C-1a and MG1655 strains taken as representative of E. coli C and K-12 strains, respectively. We found that pgaABCD operon expression is significantly lower in MG1655 than in C-1a; consistently, CsrA protein levels were much higher in MG1655. In contrast, we show that the negative effect exerted by PNPase on pgaABCD expression is much stronger in C-1a than in MG1655. The amount of CsrA and of the small RNAs CsrB, CsrC, and McaS sRNAs regulating CsrA activity is dramatically different in the two strains, whereas PNPase level is similar. Finally, the compensatory regulation acting between CsrB and CsrC in MG1655 does not occur in E. coli C. Our results suggest that PNPase preserves CsrA-dependent regulation by indirectly modulating csrA expression.
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Affiliation(s)
- Thomas Carzaniga
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy; (T.C.); (F.A.F.); (F.F.); (D.A.); (P.L.)
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, 20054 Milan, Italy
| | - Federica A. Falchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy; (T.C.); (F.A.F.); (F.F.); (D.A.); (P.L.)
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy; (T.C.); (F.A.F.); (F.F.); (D.A.); (P.L.)
| | - Davide Antoniani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy; (T.C.); (F.A.F.); (F.F.); (D.A.); (P.L.)
| | - Paolo Landini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy; (T.C.); (F.A.F.); (F.F.); (D.A.); (P.L.)
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy; (T.C.); (F.A.F.); (F.F.); (D.A.); (P.L.)
- Correspondence:
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16
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Ormazábal A, Palma J, Pierdominici-Sottile G. Molecular Dynamics Simulations Unveil the Basis of the Sequential Binding of RsmE to the Noncoding RNA RsmZ. J Phys Chem B 2021; 125:3045-3056. [PMID: 33755488 DOI: 10.1021/acs.jpcb.0c09770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CsrA/RsmE are dimeric proteins that bind to targeted mRNAs repressing translation. This mechanism modulates several metabolic pathways and allows bacteria to efficiently adjust their responses to environmental changes. In turn, small RNAs (sRNA) such as CsrB or RsmZ, restore translation by sequestering CsrA/RsmE dimers. Thus, these molecules act in tandem as a gene-expression regulatory system. Recently, a combined NMR-EPR approach solved the structure of part of RsmZ of Pseudomonas fluorescens, attached to three RsmE dimers. The study demonstrated that RsmE assembles onto RsmZ following a specific sequential order. The reasons underlying this peculiar behavior are still unclear. Here, we present a molecular dynamics analysis that explores the conformational diversity of RsmZ and RsmZ-RsmE complexes. The results reveal a clear pattern regarding the exposure of the alternative GGA binding motifs of RsmZ. This pattern is tuned by the attachment of RsmE dimers. Altogether, the observations provide a simple and convincing explanation for the order observed in the sequestration of RsmE dimers. Typical structures for RsmZ and RsmZ-RsmE complexes have been identified. Their characteristics concerning the exposure of the GGA sequences are presented and their most significant interactions are described.
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Affiliation(s)
- Agustín Ormazábal
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
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17
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Huertas-Rosales Ó, Romero M, Chan KG, Hong KW, Cámara M, Heeb S, Barrientos-Moreno L, Molina-Henares MA, Travieso ML, Ramos-González MI, Espinosa-Urgel M. Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida. Front Mol Biosci 2021; 8:624061. [PMID: 33693029 PMCID: PMC7937890 DOI: 10.3389/fmolb.2021.624061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/21/2021] [Indexed: 12/31/2022] Open
Abstract
Post-transcriptional regulation is an important step in the control of bacterial gene expression in response to environmental and cellular signals. Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried out a global analysis to identify RNA sequences bound in vivo by each of these proteins. Affinity purification and sequencing of RNA molecules associated with Rsm proteins were used to discover direct binding targets, corresponding to 437 unique RNA molecules, 75 of them being common to the three proteins. Relevant targets include genes encoding proteins involved in signal transduction and regulation, metabolism, transport and secretion, stress responses, and the turnover of the intracellular second messenger c-di-GMP. To our knowledge, this is the first combined global analysis in a bacterium harboring three Rsm homologs. It offers a broad overview of the network of processes subjected to this type of regulation and opens the way to define what are the sequence and structure determinants that define common or differential recognition of specific RNA molecules by these proteins.
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Affiliation(s)
- Óscar Huertas-Rosales
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Manuel Romero
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Miguel Cámara
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Stephan Heeb
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Laura Barrientos-Moreno
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, Spain.,National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - María L Travieso
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | | | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, Spain
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18
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Abstract
Vibrio cholerae, a Gram-negative bacterium, is a natural inhabitant of the aqueous environment. However, once ingested, this bacterium can colonize the human host and cause the disease cholera. CsrA is a posttranscriptional global regulator in Vibrio cholerae. Although CsrA is critical for V. cholerae survival within the mammalian host, the regulatory targets of CsrA remain mostly unknown. To identify pathways controlled by CsrA, RNA-seq transcriptome analysis was carried out by comparing the wild type and the csrA mutant grown to early exponential, mid-exponential, and stationary phases of growth. This enabled us to identify the global effects of CsrA-mediated regulation throughout the V. cholerae growth cycle. We found that CsrA regulates 22% of the V. cholerae transcriptome, with significant regulation within the gene ontology (GO) processes that involve amino acid transport and metabolism, central carbon metabolism, lipid metabolism, iron uptake, and flagellum-dependent motility. Through CsrA-RNA coimmunoprecipitation experiments, we found that CsrA binds to multiple mRNAs that encode regulatory proteins. These include transcripts encoding the major sigma factors RpoS and RpoE, which may explain how CsrA regulation affects such a large proportion of the V. cholerae transcriptome. Other direct targets include flrC, encoding a central regulator in flagellar gene expression, and aphA, encoding the virulence gene transcription factor AphA. We found that CsrA binds to the aphA mRNA both in vivo and in vitro, and CsrA significantly increases AphA protein synthesis. The increase in AphA was due to increased translation, not transcription, in the presence of CsrA, consistent with CsrA binding to the aphA transcript and enhancing its translation. CsrA is required for the virulence of V. cholerae and this study illustrates the central role of CsrA in virulence gene regulation.
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19
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Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments. Microorganisms 2021; 9:microorganisms9020250. [PMID: 33530561 PMCID: PMC7911923 DOI: 10.3390/microorganisms9020250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.
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20
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Samuels DS, Lybecker MC, Yang XF, Ouyang Z, Bourret TJ, Boyle WK, Stevenson B, Drecktrah D, Caimano MJ. Gene Regulation and Transcriptomics. Curr Issues Mol Biol 2020; 42:223-266. [PMID: 33300497 DOI: 10.21775/cimb.042.223] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma factor cascade, the Hk1/Rrp1 two-component system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or fine- tuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by high-throughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each.
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Affiliation(s)
- D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Meghan C Lybecker
- Department of Biology, University of Colorado, Colorado Springs, CO 80918, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - William K Boyle
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY 40536, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
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21
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Pourciau C, Lai YJ, Gorelik M, Babitzke P, Romeo T. Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA. Front Microbiol 2020; 11:601352. [PMID: 33193284 PMCID: PMC7652899 DOI: 10.3389/fmicb.2020.601352] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
The carbon storage regulator (Csr) or repressor of stationary phase metabolites (Rsm) system of Gammaproteobacteria is among the most complex and best-studied posttranscriptional regulatory systems. Based on a small RNA-binding protein, CsrA and homologs, it controls metabolism, physiology, and bacterial lifestyle decisions by regulating gene expression on a vast scale. Binding of CsrA to sequences containing conserved GGA motifs in mRNAs can regulate translation, RNA stability, riboswitch function, and transcript elongation. CsrA governs the expression of dozens of transcription factors and other regulators, further expanding its influence on cellular physiology, and these factors can participate in feedback to the Csr system. Expression of csrA itself is subject to autoregulation via translational inhibition and indirect transcriptional activation. CsrA activity is controlled by small noncoding RNAs (sRNAs), CsrB and CsrC in Escherichia coli, which contain multiple high affinity CsrA binding sites that compete with those of mRNA targets. Transcription of CsrB/C is induced by certain nutrient limitations, cellular stresses, and metabolites, while these RNAs are targeted for degradation by the presence of a preferred carbon source. Consistent with these findings, CsrA tends to activate pathways and processes that are associated with robust growth and repress stationary phase metabolism and stress responses. Regulatory loops between Csr components affect the signaling dynamics of the Csr system. Recently, systems-based approaches have greatly expanded our understanding of the roles played by CsrA, while reinforcing the notion that much remains to be learned about the Csr system.
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Affiliation(s)
- Christine Pourciau
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Ying-Jung Lai
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Mark Gorelik
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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22
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Quintero-Yanes A, Lee CM, Monson R, Salmond G. The FloR master regulator controls flotation, virulence and antibiotic production in Serratia sp. ATCC 39006. Environ Microbiol 2020; 22:2921-2938. [PMID: 32352190 DOI: 10.1111/1462-2920.15048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 11/26/2022]
Abstract
Serratia sp. ATCC 39006 produces intracellular gas vesicles to enable upward flotation in water columns. It also uses flagellar rotation to swim through liquid and swarm across semi-solid surfaces. Flotation and motility can be co-regulated with production of a β-lactam antibiotic (carbapenem carboxylate) and a linear tripyrrole red antibiotic, prodigiosin. Production of gas vesicles, carbapenem and prodigiosin antibiotics, and motility are controlled by master transcriptional and post-transcriptional regulators, including the SmaI/SmaR-based quorum sensing system and the mRNA binding protein, RsmA. Recently, the ribose operon repressor, RbsR, was also defined as a pleiotropic regulator of flotation and virulence factor elaboration in this strain. Here, we report the discovery of a new global regulator (FloR; a DeoR family transcription factor) that modulates flotation through control of gas vesicle morphogenesis. The floR mutation is highly pleiotropic, down-regulating production of gas vesicles, carbapenem and prodigiosin antibiotics, and infection in Caenorhabditis elegans, but up-regulating flagellar motility. Detailed proteomic analysis using TMT peptide labelling and LC-MS/MS revealed that FloR is a physiological master regulator that operates through subordinate pleiotropic regulators including Rap, RpoS, RsmA, PigU, PstS and PigT.
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Affiliation(s)
- Alex Quintero-Yanes
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK.,Bacterial Cell cycle and Development (BCcD), University of Namur, 61 Rue de Bruxelles, Namur, 5000, Belgium
| | - Chin Mei Lee
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK.,Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, 26300, Malaysia
| | - Rita Monson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK
| | - George Salmond
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, UK
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23
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Goetz A, Mader A, von Bronk B, Weiss AS, Opitz M. Gene expression noise in a complex artificial toxin expression system. PLoS One 2020; 15:e0227249. [PMID: 31961890 PMCID: PMC6974158 DOI: 10.1371/journal.pone.0227249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/16/2019] [Indexed: 01/29/2023] Open
Abstract
Gene expression is an intrinsically stochastic process. Fluctuations in transcription and translation lead to cell-to-cell variations in mRNA and protein levels affecting cellular function and cell fate. Here, using fluorescence time-lapse microscopy, we quantify noise dynamics in an artificial operon in Escherichia coli, which is based on the native operon of ColicinE2, a toxin. In the natural system, toxin expression is controlled by a complex regulatory network; upon induction of the bacterial SOS response, ColicinE2 is produced (cea gene) and released (cel gene) by cell lysis. Using this ColicinE2-based operon, we demonstrate that upon induction of the SOS response noise of cells expressing the operon is significantly lower for the (mainly) transcriptionally regulated gene cea compared to the additionally post-transcriptionally regulated gene cel. Likewise, we find that mutations affecting the transcriptional regulation by the repressor LexA do not significantly alter the population noise, whereas specific mutations to post-transcriptionally regulating units, strongly influence noise levels of both genes. Furthermore, our data indicate that global factors, such as the plasmid copy number of the operon encoding plasmid, affect gene expression noise of the entire operon. Taken together, our results provide insights on how noise in a native toxin-producing operon is controlled and underline the importance of post-transcriptional regulation for noise control in this system.
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Affiliation(s)
- Alexandra Goetz
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Andreas Mader
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Benedikt von Bronk
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Anna S. Weiss
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Madeleine Opitz
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
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Modestobacter excelsi sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil. Syst Appl Microbiol 2019; 43:126051. [PMID: 31892483 DOI: 10.1016/j.syapm.2019.126051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6T, 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H4), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9 % similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6T and M. italicus BC 501T were 90.9 % and 42.3 %, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6T (=DSM 107535T =PCM 3004T) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome.
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25
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Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries. PLANTS 2019; 8:plants8090302. [PMID: 31454955 PMCID: PMC6784238 DOI: 10.3390/plants8090302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Competing endogenous RNAs (ceRNAs) are natural transcripts that can act as endogenous sponges of microRNAs (miRNAs), modulating miRNA action upon target mRNAs. Circular RNAs (circRNAs) are one among the various classes of ceRNAs. They are produced from a process called back-splicing and have been identified in many eukaryotes. In plants, their effective action as a miRNA sponge was not yet demonstrated. To address this question, public mRNAseq data from Argonaute-immunoprecipitation libraries (AGO-IP) of Arabidopsis thaliana flowers were used in association with a bioinformatics comparative multi-method to identify putative circular RNAs. A total of 27,812 circRNAs, with at least two reads at the back-splicing junction, were identified. Further analyses were used to select those circRNAs with potential miRNAs binding sites. As AGO forms a ternary complex with miRNA and target mRNA, targets count in AGO-IP and input libraries were compared, demonstrating that mRNA targets of these miRNAs are enriched in AGO-IP libraries. Through this work, five circRNAs that may function as miRNA sponges were identified and one of them were validated by PCR and sequencing. Our findings indicate that this post-transcriptional regulation can also occur in plants.
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26
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Abstract
The global regulatory protein CsrA coordinates gene expression in response to physiological cues reflecting cellular stress and nutrition. CsrA binding to the 5' segments of mRNA targets affects their translation, RNA stability, and/or transcript elongation. Recent studies identified probable mRNA targets of CsrA that are involved in iron uptake and storage in Escherichia coli, suggesting an unexplored role for CsrA in regulating iron homeostasis. Here, we assessed the impact of CsrA on iron-related gene expression, cellular iron, and growth under various iron levels. We investigated five new targets of CsrA regulation, including the genes for 4 ferritin or ferritin-like iron storage proteins (ISPs) and the stress-inducible Fe-S repair protein, SufA. CsrA bound with high affinity and specificity to ftnB, bfr, and dps mRNAs and inhibited their translation, while it modestly activated ftnA expression. Furthermore, CsrA was found to regulate cellular iron levels and support growth by repressing the expression of genes for ISPs, most importantly, ferritin B (FtnB) and bacterioferritin (Bfr). Iron starvation did not substantially affect cellular levels of CsrA or its small RNA (sRNA) antagonists, CsrB and CsrC. csrA disruption led to increased resistance to the lethal effects of H2O2 during exponential growth, consistent with a regulatory role in oxidative stress resistance. We propose that during exponential growth and under minimal stress, CsrA represses the deleterious expression of the ISPs that function under oxidative stress and stationary-phase conditions (FtnB, Bfr, and Dps), thus ensuring that cellular iron is available to processes that are required for growth.IMPORTANCE Iron is an essential micronutrient for nearly all living organisms but is toxic in excess. Consequently, the maintenance of iron homeostasis is a critical biological process, and the genes involved in this function are tightly regulated. Here, we explored a new role for the bacterial RNA binding protein CsrA in the regulation of iron homeostasis. CsrA was shown to be a key regulator of iron storage genes in Escherichia coli, with consequential effects on cellular iron levels and growth. Our findings establish a model in which robust CsrA activity during the exponential phase of growth leads to repression of genes whose products sequester iron or divert it to unnecessary stress response processes. In so doing, CsrA supports E. coli growth under iron-limiting laboratory conditions and may promote fitness in the competitive iron-limited environment of the host large intestine.
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27
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Schachterle JK, Zeng Q, Sundin GW. Three Hfq-dependent small RNAs regulate flagellar motility in the fire blight pathogen Erwinia amylovora. Mol Microbiol 2019; 111:1476-1492. [PMID: 30821016 DOI: 10.1111/mmi.14232] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/13/2022]
Abstract
Erwinia amylovora, the causative agent of fire blight disease of apple and pear trees, causes disease on flowers by invading natural openings at the base of the floral cup. To reach these openings, the bacteria use flagellar motility to swim from stigma tips to the hypanthium and through nectar. We have previously shown that the Hfq-dependent sRNAs ArcZ, OmrAB and RmaA regulate swimming motility in E. amylovora. Here, we tested these three sRNAs to determine at what regulatory level they exert their effects and to what extent they can complement each other. We found that ArcZ and OmrAB repress the flagellar master regulator flhD post-transcriptionally. We also found that ArcZ and RmaA positively regulate flhD at the transcriptional level. The role of ArcZ as an activator of flagellar motility appears to be unique to E. amylovora and may have recently evolved. Our results suggest that the Hfq-dependent sRNAs ArcZ, OmrAB and RmaA play an integral role in regulation of flagellar motility by acting primarily on the master regulator, FlhD, but also through additional factors.
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Affiliation(s)
- Jeffrey K Schachterle
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Quan Zeng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA.,Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
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28
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Nitta K, Laviña WA, Pontrelli S, Liao JC, Putri SP, Fukusaki E. Metabolome analysis revealed the knockout of glyoxylate shunt as an effective strategy for improvement of 1-butanol production in transgenic Escherichia coli. J Biosci Bioeng 2019; 127:301-308. [DOI: 10.1016/j.jbiosc.2018.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
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29
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Abstract
RNA-binding proteins (RBPs) function in all aspects of RNA processes including stability, structure, export, localization and translation, and control gene expression at the posttranscriptional level. To investigate the roles of RBPs and their direct RNA ligands in vivo, recent global approaches combining RNA immunoprecipitation and deep sequencing (RIP-seq) as well as UV-cross-linking (CLIP-seq) have become instrumental in dissecting RNA-protein interactions. However, the computational analysis of these high-throughput sequencing data is still challenging. Here, we provide a computational pipeline to analyze CLIP-seq and RIP-seq datasets. This generic analytic procedure may help accelerate the identification of direct RNA-protein interactions from high-throughput RBP profiling experiments in a variety of bacterial species.
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Roles of d-Lactate Dehydrogenases in the Anaerobic Growth of Shewanella oneidensis MR-1 on Sugars. Appl Environ Microbiol 2019; 85:AEM.02668-18. [PMID: 30504209 DOI: 10.1128/aem.02668-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/18/2018] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis MR-1 is a facultative anaerobe that respires using a variety of electron acceptors. Although this organism is incapable of fermentative growth in the absence of electron acceptors, its genome encodes LdhA (a putative fermentative NADH-dependent d-lactate dehydrogenase [d-LDH]) and Dld (a respiratory quinone-dependent d-LDH). However, the physiological roles of LdhA in MR-1 are unclear. Here, we examined the activity, transcriptional regulation, and traits of deletion mutants to gain insight into the roles of LdhA in the anaerobic growth of MR-1. Analyses of d-LDH activity in MR-1 and the ldhA deletion mutant confirmed that LdhA functions as an NADH-dependent d-LDH that catalyzes the reduction of pyruvate to d-lactate. In vivo and in vitro assays revealed that ldhA expression was positively regulated by the cyclic-AMP receptor protein, a global transcription factor that regulates anaerobic respiratory pathways in MR-1, suggesting that LdhA functions in coordination with anaerobic respiration. Notably, we found that a deletion mutant of all four NADH dehydrogenases (NDHs) in MR-1 (ΔNDH mutant) retained the ability to grow on N-acetylglucosamine under fumarate-respiring conditions, while an additional deletion of ldhA or dld deprived the ΔNDH mutant of this growth ability. These results indicate that LdhA-Dld serves as a bypass of NDH in electron transfer from NADH to quinones. Our findings suggest that the LdhA-Dld system manages intracellular redox balance by utilizing d-lactate as a temporal electron sink under electron acceptor-limited conditions.IMPORTANCE NADH-dependent LDHs are conserved among diverse organisms and contribute to NAD+ regeneration in lactic acid fermentation. However, this type of LDH is also present in nonfermentative bacteria, including members of the genus Shewanella, while their physiological roles in these bacteria remain unknown. Here, we show that LdhA (an NADH-dependent d-LDH) works in concert with Dld (a quinone-dependent d-LDH) to transfer electrons from NADH to quinones during sugar catabolism in S. oneidensis MR-1. Our results indicate that d-lactate acts as an intracellular electron mediator to transfer electrons from NADH to membrane quinones. In addition, d-lactate serves as a temporal electron sink when respiratory electron acceptors are not available. Our study suggests novel physiological roles for d-LDHs in providing nonfermentative bacteria with catabolic flexibility under electron acceptor-limited conditions.
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31
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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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32
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Chatterjee R, Shreenivas MM, Sunil R, Chakravortty D. Enteropathogens: Tuning Their Gene Expression for Hassle-Free Survival. Front Microbiol 2019; 9:3303. [PMID: 30687282 PMCID: PMC6338047 DOI: 10.3389/fmicb.2018.03303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/19/2018] [Indexed: 12/27/2022] Open
Abstract
Enteropathogenic bacteria have been the cause of the majority of foodborne illnesses. Much of the research has been focused on elucidating the mechanisms by which these pathogens evade the host immune system. One of the ways in which they achieve the successful establishment of a niche in the gut microenvironment and survive is by a chain of elegantly regulated gene expression patterns. Studies have shown that this process is very elaborate and is also regulated by several factors. Pathogens like, enteropathogenic Escherichia coli (EPEC), Salmonella Typhimurium, Shigellaflexneri, Yersinia sp. have been seen to employ various regulated gene expression strategies. These include toxin-antitoxin systems, quorum sensing systems, expression controlled by nucleoid-associated proteins (NAPs), several regulons and operons specific to these pathogens. In the following review, we have tried to discuss the common gene regulatory systems of enteropathogenic bacteria as well as pathogen-specific regulatory mechanisms.
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Affiliation(s)
- Ritika Chatterjee
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India
| | - Meghanashree M Shreenivas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Undergraduate Studies, Indian Institute of Science, Bengaluru, India
| | - Rohith Sunil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Undergraduate Studies, Indian Institute of Science, Bengaluru, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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33
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Jemielita M, Wingreen NS, Bassler BL. Quorum sensing controls Vibrio cholerae multicellular aggregate formation. eLife 2018; 7:42057. [PMID: 30582742 PMCID: PMC6351105 DOI: 10.7554/elife.42057] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/23/2018] [Indexed: 12/15/2022] Open
Abstract
Bacteria communicate and collectively regulate gene expression using a process called quorum sensing (QS). QS relies on group-wide responses to signal molecules called autoinducers. Here, we show that QS activates a new program of multicellularity in Vibrio cholerae. This program, which we term aggregation, is distinct from the canonical surface-biofilm formation program, which QS represses. Aggregation is induced by autoinducers, occurs rapidly in cell suspensions, and does not require cell division, features strikingly dissimilar from those characteristic of V. cholerae biofilm formation. Extracellular DNA limits aggregate size, but is not sufficient to drive aggregation. A mutagenesis screen identifies genes required for aggregate formation, revealing proteins involved in V. cholerae intestinal colonization, stress response, and a protein that distinguishes the current V. cholerae pandemic strain from earlier pandemic strains. We suggest that QS-controlled aggregate formation is important for V. cholerae to successfully transit between the marine niche and the human host.
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Affiliation(s)
- Matthew Jemielita
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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34
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Leistra AN, Curtis NC, Contreras LM. Regulatory non-coding sRNAs in bacterial metabolic pathway engineering. Metab Eng 2018; 52:190-214. [PMID: 30513348 DOI: 10.1016/j.ymben.2018.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/31/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) are versatile and powerful controllers of gene expression that have been increasingly linked to cellular metabolism and phenotype. In bacteria, identified and characterized ncRNAs range from trans-acting, multi-target small non-coding RNAs to dynamic, cis-encoded regulatory untranslated regions and riboswitches. These native regulators have inspired the design and construction of many synthetic RNA devices. In this work, we review the design, characterization, and impact of ncRNAs in engineering both native and exogenous metabolic pathways in bacteria. We also consider the opportunities afforded by recent high-throughput approaches for characterizing sRNA regulators and their corresponding networks to showcase their potential applications and impact in engineering bacterial metabolism.
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Affiliation(s)
- Abigail N Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Nicholas C Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
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35
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Shangguan W, Liang X, Shi W, Liu T, Wang M, Li G. Identification and characterization of circular RNAs in rapid atrial pacing dog atrial tissue. Biochem Biophys Res Commun 2018; 506:1-6. [PMID: 29772236 DOI: 10.1016/j.bbrc.2018.05.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/13/2018] [Indexed: 12/11/2022]
Abstract
Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs, and participating in the process of many diseases. However, the expression and functions of circRNAs in Rapid atrial pacing (RAP) dog atrial tissue still unknown. 12 canines were randomly assigned to control and pacing group. RAP at 500 beats per minute was maintained 14 days in the pacing group. The expression characterization of circRNAs were revealed by high-throughput sequencing. We totally predicted 15,990 circRNAs in dog atrial tissues. Moreover, we found 146 differentially expressed circRNAs between control and RAP dogs. Five circRNAs were selected for subsequent RT-PCR validation, and four circRNAs confirmed with the high throughput sequencing analysis. GO analysis showed that the differentially expressed circRNAs might involve in the process of "structural constituent of cytoskeleton, ion channel activity". We explored the circRNA-miRNA interaction network, and found extensive interaction among differentially expressed circRNAs and AF related miRNAs and mRNAs. Our work firstly identified the characterization of circRNAs in the dog atrial, and revealed the differentially expressed circRNAs in the RAP dog, this might lay a solid foundation on the function of circRNA in the mechanisms of AF.
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Affiliation(s)
- Wenfeng Shangguan
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, 300211, People's Republic of China
| | - Xue Liang
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, 300211, People's Republic of China
| | - Wen Shi
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, 300211, People's Republic of China
| | - Tong Liu
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, 300211, People's Republic of China
| | - Manman Wang
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, 300211, People's Republic of China
| | - Guangping Li
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, 300211, People's Republic of China.
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36
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Knittel V, Vollmer I, Volk M, Dersch P. Discovering RNA-Based Regulatory Systems for Yersinia Virulence. Front Cell Infect Microbiol 2018; 8:378. [PMID: 30460205 PMCID: PMC6232918 DOI: 10.3389/fcimb.2018.00378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 12/26/2022] Open
Abstract
The genus Yersinia includes three human pathogenic species, Yersinia pestis, the causative agent of the bubonic and pneumonic plague, and enteric pathogens Y. enterocolitica and Y. pseudotuberculosis that cause a number of gut-associated diseases. Over the past years a large repertoire of RNA-based regulatory systems has been discovered in these pathogens using different RNA-seq based approaches. Among them are several conserved or species-specific RNA-binding proteins, regulatory and sensory RNAs as well as various RNA-degrading enzymes. Many of them were shown to control the expression of important virulence-relevant factors and have a very strong impact on Yersinia virulence. The precise targets, the molecular mechanism and their role for Yersinia pathogenicity is only known for a small subset of identified genus- or species-specific RNA-based control elements. However, the ongoing development of new RNA-seq based methods and data analysis methods to investigate the synthesis, composition, translation, decay, and modification of RNAs in the bacterial cell will help us to generate a more comprehensive view of Yersinia RNA biology in the near future.
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Affiliation(s)
- Vanessa Knittel
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ines Vollmer
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marcel Volk
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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37
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Komori T, Shibai A, Saito H, Akeno Y, Germond A, Horinouchi T, Furusawa C, Tsuru S. Enhancement of K-strategy evolution in histidine utilization using a container with compartments. Genes Cells 2018; 23:893-903. [DOI: 10.1111/gtc.12640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/19/2018] [Accepted: 08/07/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Takahiro Komori
- Graduate School of Information Science and Technology; Osaka University; Suita Osaka Japan
| | - Atsushi Shibai
- Center for Biosystems Dynamics Research (BDR); RIKEN; Suita Osaka Japan
| | - Hiromi Saito
- Graduate School of Information Science and Technology; Osaka University; Suita Osaka Japan
| | - Yuya Akeno
- Graduate School of Information Science and Technology; Osaka University; Suita Osaka Japan
| | - Arno Germond
- Center for Biosystems Dynamics Research (BDR); RIKEN; Suita Osaka Japan
| | | | - Chikara Furusawa
- Center for Biosystems Dynamics Research (BDR); RIKEN; Suita Osaka Japan
- Universal Biology Institute; The University of Tokyo; Bunkyo-ku Tokyo Japan
| | - Saburo Tsuru
- Universal Biology Institute; The University of Tokyo; Bunkyo-ku Tokyo Japan
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38
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Arnold WK, Savage CR, Lethbridge KG, Smith TC, Brissette CA, Seshu J, Stevenson B. Transcriptomic insights on the virulence-controlling CsrA, BadR, RpoN, and RpoS regulatory networks in the Lyme disease spirochete. PLoS One 2018; 13:e0203286. [PMID: 30161198 PMCID: PMC6117026 DOI: 10.1371/journal.pone.0203286] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/19/2018] [Indexed: 01/17/2023] Open
Abstract
Borrelia burgdorferi, the causative agent of Lyme disease, survives in nature through a cycle that alternates between ticks and vertebrates. To facilitate this defined lifestyle, B. burgdorferi has evolved a gene regulatory network that ensures transmission between those hosts, along with specific adaptations to niches within each host. Several regulatory proteins are known to be essential for the bacterium to complete these critical tasks, but interactions between regulators had not previously been investigated in detail, due to experimental uses of different strain backgrounds and growth conditions. To address that deficit in knowledge, the transcriptomic impacts of four critical regulatory proteins were examined in a uniform strain background. Pairs of mutants and their wild-type parent were grown simultaneously under a single, specific culture condition, permitting direct comparisons between the mutant strains. Transcriptomic analyses were strand-specific, and assayed both coding and noncoding RNAs. Intersection analyses identified regulatory overlaps between regulons, including transcripts involved in carbohydrate and polyamine metabolism. In addition, it was found that transcriptional units such as ospC and dbpBA, which were previously observed to be affected by alternative sigma factors, are transcribed by RNA polymerase using the housekeeping sigma factor, RpoD.
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Affiliation(s)
- William K. Arnold
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Christina R. Savage
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Kathryn G. Lethbridge
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Trever C. Smith
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Catherine A. Brissette
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States of America
| | - Janakiram Seshu
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
- Department of Entomology, University of Kentucky, Lexington, KY, United States of America
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Berne C, Ellison CK, Ducret A, Brun YV. Bacterial adhesion at the single-cell level. Nat Rev Microbiol 2018; 16:616-627. [DOI: 10.1038/s41579-018-0057-5] [Citation(s) in RCA: 266] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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López-Pliego L, García-Ramírez L, Cruz-Gómez EA, Domínguez-Ojeda P, López-Pastrana A, Fuentes-Ramírez LE, Núñez C, Castañeda M. Transcriptional Study of the RsmZ-sRNAs and Their Relationship to the Biosynthesis of Alginate and Alkylresorcinols in Azotobacter vinelandii. Mol Biotechnol 2018; 60:670-680. [DOI: 10.1007/s12033-018-0102-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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41
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Cheah HL, Raabe CA, Lee LP, Rozhdestvensky TS, Citartan M, Ahmed SA, Tang TH. Bacterial regulatory RNAs: complexity, function, and putative drug targeting. Crit Rev Biochem Mol Biol 2018; 53:335-355. [PMID: 29793351 DOI: 10.1080/10409238.2018.1473330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, RNA-deep sequencing has uncovered copious non-protein coding RNAs (npcRNAs) in bacteria. Many of them are key players in the regulation of gene expression, taking part in various regulatory circuits, such as metabolic responses to different environmental stresses, virulence, antibiotic resistance, and host-pathogen interactions. This has contributed to the high adaptability of bacteria to changing or even hostile environments. Their mechanisms include the regulation of transcriptional termination, modulation of translation, and alteration of messenger RNA (mRNA) stability, as well as protein sequestration. Here, the mechanisms of gene expression by regulatory bacterial npcRNAs are comprehensively reviewed and supplemented with well-characterized examples. This class of molecules and their mechanisms of action might be useful targets for the development of novel antibiotics.
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Affiliation(s)
- Hong-Leong Cheah
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Carsten A Raabe
- b Institute of Experimental Pathology, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany.,c Brandenburg Medical School (MHB) , Neuruppin , Germany.,d Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany
| | - Li-Pin Lee
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Timofey S Rozhdestvensky
- e Medical Faculty, Transgenic Mouse and Genome Engineering Model Core Facility (TRAM) , University of Münster , Münster , Germany
| | - Marimuthu Citartan
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Siti Aminah Ahmed
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Thean-Hock Tang
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
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Abstract
Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting). The repertoire of ncRNAs present in the genome of P. salmonis and its possible role in bacterial physiology and pathogenesis are unknown. Here, we predicted and analyzed the core ncRNAs of P. salmonis base on structure and correlate this prediction to RNA sequencing data. We identified a total of 69 ncRNA classes related to tRNAs, rRNA, thermoregulators, antitoxins, ribozymes, riboswitches, miRNAs and antisense-RNAs. Among these ncRNAs, 29 classes of ncRNAs are shared between all P. salmonis genomes, constituting the core ncRNAs of P. salmonis. The ncRNA core of P. salmonis could serve to develop diagnostic tools and explore the role of ncRNA in fish pathogenesis.
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George AS, Cox CE, Desai P, Porwollik S, Chu W, de Moraes MH, McClelland M, Brandl MT, Teplitski M. Interactions of Salmonella enterica Serovar Typhimurium and Pectobacterium carotovorum within a Tomato Soft Rot. Appl Environ Microbiol 2018; 84:e01913-17. [PMID: 29247060 PMCID: PMC5812938 DOI: 10.1128/aem.01913-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Salmonella spp. are remarkably adaptable pathogens, and this adaptability allows these bacteria to thrive in a variety of environments and hosts. The mechanisms with which these pathogens establish within a niche amid the native microbiota remain poorly understood. Here, we aimed to uncover the mechanisms that enable Salmonella enterica serovar Typhimurium strain ATCC 14028 to benefit from the degradation of plant tissue by a soft rot plant pathogen, Pectobacterium carotovorum The hypothesis that in the soft rot, the liberation of starch (not utilized by P. carotovorum) makes this polymer available to Salmonella spp., thus allowing it to colonize soft rots, was tested first and proven null. To identify the functions involved in Salmonella soft rot colonization, we carried out transposon insertion sequencing coupled with the phenotypic characterization of the mutants. The data indicate that Salmonella spp. experience a metabolic shift in response to the changes in the environment brought on by Pectobacterium spp. and likely coordinated by the csrBC small regulatory RNA. While csrBC and flhD appear to be of importance in the soft rot, the global two-component system encoded by barA sirA (which controls csrBC and flhDC under laboratory conditions) does not appear to be necessary for the observed phenotype. Motility and the synthesis of nucleotides and amino acids play critical roles in the growth of Salmonella spp. in the soft rot.IMPORTANCE Outbreaks of produce-associated illness continue to be a food safety concern. Earlier studies demonstrated that the presence of phytopathogens on produce was a significant risk factor associated with increased Salmonella carriage on fruits and vegetables. Here, we genetically characterize some of the requirements for interactions between Salmonella and phytobacteria that allow Salmonella spp. to establish a niche within an alternate host (tomato). Pathways necessary for nucleotide synthesis, amino acid synthesis, and motility are identified as contributors to the persistence of Salmonella spp. in soft rots.
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Affiliation(s)
- Andrée S George
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
| | - Clayton E Cox
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
| | - Prerak Desai
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Weiping Chu
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Marcos H de Moraes
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Maria T Brandl
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Max Teplitski
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
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Dai Q, Xu L, Xiao L, Zhu K, Song Y, Li C, Zhu L, Shen X, Wang Y. RovM and CsrA Negatively Regulate Urease Expression in Yersinia pseudotuberculosis. Front Microbiol 2018; 9:348. [PMID: 29535702 PMCID: PMC5835112 DOI: 10.3389/fmicb.2018.00348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/13/2018] [Indexed: 01/07/2023] Open
Abstract
Urease acts as an important acid resistance system and virulence factor that is widespread among microorganisms. RovM is a global regulator that regulates a series of genes and pathways including acid survival systems in the enteric bacterium Yersinia pseudotuberculosis (Yptb). However, whether RovM regulates the urease activity in Yptb was still unknown. In this study, by using qualitative and quantitative urease assays, we show that the urease expression responds to nutrient conditions and the RovM protein represses urease expression by binding to its promoter. A previously reported positive regulator OmpR activates urease activity but RovM plays a dominant role in different nutrient conditions. In addition, carbon storage regulator system A (CsrA), the upstream regulator of RovM, dramatically down-regulates urease activity possibly by its binding to the Shine-Dalgarno (SD) sequence of the mRNA encoding the urease. In conclusion, this study demonstrates that urease activity is strictly controlled by nutrient conditions and is down-regulated by the CsrA-RovM pathway.
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Affiliation(s)
- Qingyun Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
| | - Lei Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Lu Xiao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
| | - Kaixiang Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yunhong Song
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Changfu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
| | - Lingfang Zhu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xihui Shen
- College of Life Sciences, Northwest A&F University, Yangling, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
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Regulation of host–pathogen interactions via the post-transcriptional Csr/Rsm system. Curr Opin Microbiol 2018; 41:58-67. [DOI: 10.1016/j.mib.2017.11.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/18/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022]
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46
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Hou S, López-Pérez M, Pfreundt U, Belkin N, Stüber K, Huettel B, Reinhardt R, Berman-Frank I, Rodriguez-Valera F, Hess WR. Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise. ISME JOURNAL 2018; 12:981-996. [PMID: 29335641 PMCID: PMC5864184 DOI: 10.1038/s41396-017-0034-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 12/21/2022]
Abstract
Interactions between co-existing microorganisms deeply affect the physiology of the involved organisms and, ultimately, the function of the ecosystem as a whole. Copiotrophic Alteromonas are marine gammaproteobacteria that thrive during the late stages of phytoplankton blooms in the marine environment and in laboratory co-cultures with cyanobacteria such as Trichodesmium. The response of this heterotroph to the sometimes rapid and transient changes in nutrient supply when the phototroph crashes is not well understood. Here, we isolated and sequenced the strain Alteromonas macleodii str. Te101 from a laboratory culture of Trichodesmium erythraeum IMS101, yielding a chromosome of 4.63 Mb and a single plasmid of 237 kb. Increasing salinities to ≥43 ppt inhibited the growth of Trichodesmium but stimulated growth of the associated Alteromonas. We characterized the transcriptomic responses of both microorganisms and identified the complement of active transcriptional start sites in Alteromonas at single-nucleotide resolution. In replicate cultures, a similar set of genes became activated in Alteromonas when growth rates of Trichodesmium declined and mortality was high. The parallel activation of fliA, rpoS and of flagellar assembly and growth-related genes indicated that Alteromonas might have increased cell motility, growth, and multiple biosynthetic activities. Genes with the highest expression in the data set were three small RNAs (Aln1a-c) that were identified as analogs of the small RNAs CsrB-C in E. coli or RsmX-Z in pathogenic bacteria. Together with the carbon storage protein A (CsrA) homolog Te101_05290, these RNAs likely control the expression of numerous genes in responding to changes in the environment.
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Affiliation(s)
- Shengwei Hou
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, 03550, Alicante, Spain
| | - Ulrike Pfreundt
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany.,ETH Zürich, Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, Stefano-Franscini-Platz 5, CH-8093, Zürich, Switzerland
| | - Natalia Belkin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Kurt Stüber
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - Bruno Huettel
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - Richard Reinhardt
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, 03550, Alicante, Spain
| | - Wolfgang R Hess
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany. .,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, D-79104, Freiburg, Germany.
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Ozturk G, LeGrand K, Zheng Y, Young GM. Yersinia enterocolitica CsrA regulates expression of the Ysa and Ysc type 3 secretion system in unique ways. FEMS Microbiol Lett 2017; 364:4222792. [PMID: 29044402 DOI: 10.1093/femsle/fnx204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
This study investigated how carbon storage regulator A (CsrA) affects expression of the Ysa and Ysc type 3 secretion (T3S) system genetic regulatory cascades that control Ysps (Yersinia secreted proteins) and Yops (Yersinia outer proteins) export, respectively. Given that most often CsrA acts as a mediator of mRNA stability, an activity that can be monitored using lacZ transcriptional fusions, we employed a collection of reporter strains to assess Ysa and Ysc gene expression. To this end, bacteria were cultivated to induce either the Ysa or the Ysc T3S system. Comparison of csrA mutants to the wild-type strain revealed that, in response to the respective inducing conditions, genes spanning the Ysa and Ysc gene cascades displayed increased expressions. Then, the possibility that CsrA affects secretion of Ysps and Yops was tested and the profiles of secreted proteins by wild-type and csrA mutant strains were compared by proteomic analysis. Ysps were over-secreted and Yops were under-secreted, for the csrA mutant. These results support the hypothesis that CsrA affects both the Ysa and Ysc T3S systems in Yersinia enterocolitica. They further support the conclusion that CsrA plays an important role in controlling adaptation of this pathogenic bacterium during its lifecycle shift between a terrestrial and parasitic existence.
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Affiliation(s)
- Gulustan Ozturk
- Department of Food Science and Technology, University of California, One Shields Avenue, Davis, CA 95616-8598, USA
| | - Karen LeGrand
- Department of Food Science and Technology, University of California, One Shields Avenue, Davis, CA 95616-8598, USA
| | - Yan Zheng
- Department of Food Science and Technology, University of California, One Shields Avenue, Davis, CA 95616-8598, USA.,College of Food Science, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, Liaoning Province, 110866, P. R. China
| | - Glenn M Young
- Department of Food Science and Technology, University of California, One Shields Avenue, Davis, CA 95616-8598, USA
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Mei L, Xu S, Lu P, Lin H, Guo Y, Wang Y. CsrB, a noncoding regulatory RNA, is required for BarA-dependent expression of biocontrol traits in Rahnella aquatilis HX2. PLoS One 2017; 12:e0187492. [PMID: 29091941 PMCID: PMC5665550 DOI: 10.1371/journal.pone.0187492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 10/21/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Rahnella aquatilis is ubiquitous and its certain strains have the applicative potent as a plant growth-promoting rhizobacteria. R. aquatilis HX2 is a biocontrol agent to produce antibacterial substance (ABS) and showed efficient biocontrol against crown gall caused by Agrobacterium vitis on sunflower and grapevine plants. The regulatory network of the ABS production and biocontrol activity is still limited known. METHODOLOGY/PRINCIPAL FINDINGS In this study, a transposon-mediated mutagenesis strategy was used to investigate the regulators that involved in the biocontrol activity of R. aquatilis HX2. A 366-nt noncoding RNA CsrB was identified in vitro and in vivo, which regulated ABS production and biocontrol activity against crown gall on sunflower plants, respectively. The predicted product of noncoding RNA CsrB contains 14 stem-loop structures and an additional ρ-independent terminator harpin, with 23 characteristic GGA motifs in the loops and other unpaired regions. CsrB is required for ABS production and biocontrol activity in the biocontrol regulation by a two-component regulatory system BarA/UvrY in R. aquatilis HX2. CONCLUSION/SIGNIFICANCE The noncoding RNA CsrB regulates BarA-dependent ABS production and biocontrol activity in R. aquatilis HX2. To the best of our knowledge, this is the first report of noncoding RNA as a regulator for biocontrol function in R. aquatilis.
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Affiliation(s)
- Li Mei
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’An, China
| | - Sanger Xu
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’An, China
| | - Peng Lu
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’An, China
| | - Haiping Lin
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’An, China
| | - Yanbin Guo
- Department of Ecological Science and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yongjun Wang
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin’An, China
- National and Provincial Joint Engineering Laboratory of Bio-pesticide Preparation, Lin’An, China
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Sharan M, Förstner KU, Eulalio A, Vogel J. APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. Nucleic Acids Res 2017; 45:e96. [PMID: 28334975 PMCID: PMC5499795 DOI: 10.1093/nar/gkx137] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 02/27/2017] [Indexed: 11/14/2022] Open
Abstract
RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches. We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using position-specific scoring matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot.
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Affiliation(s)
- Malvika Sharan
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Ana Eulalio
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
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50
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Damage to the microbial cell membrane during pyrolytic sugar utilization and strategies for increasing resistance. ACTA ACUST UNITED AC 2017; 44:1279-1292. [DOI: 10.1007/s10295-017-1958-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/20/2017] [Indexed: 11/25/2022]
Abstract
Abstract
Lignocellulosic biomass is an appealing feedstock for the production of biorenewable fuels and chemicals, and thermochemical processing is a promising method for depolymerizing it into sugars. However, trace compounds in this pyrolytic sugar syrup are inhibitory to microbial biocatalysts. This study demonstrates that hydrophobic inhibitors damage the cell membrane of ethanologenic Escherichia coli KO11+lgk. Adaptive evolution was employed to identify design strategies for improving pyrolytic sugar tolerance and utilization. Characterization of the resulting evolved strain indicates that increased resistance to the membrane-damaging effects of the pyrolytic sugars can be attributed to a glutamine to leucine mutation at position 29 of carbon storage regulator CsrA. This single amino acid change is sufficient for decreasing EPS protein production and increasing membrane integrity when exposed to pyrolytic sugars.
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