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Mayo-Pérez S, Gama-Martínez Y, Dávila S, Rivera N, Hernández-Lucas I. LysR-type transcriptional regulators: state of the art. Crit Rev Microbiol 2023:1-33. [PMID: 37635411 DOI: 10.1080/1040841x.2023.2247477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023]
Abstract
The LysR-type transcriptional regulators (LTTRs) are DNA-binding proteins present in bacteria, archaea, and in algae. Knowledge about their distribution, abundance, evolution, structural organization, transcriptional regulation, fundamental roles in free life, pathogenesis, and bacteria-plant interaction has been generated. This review focuses on these aspects and provides a current picture of LTTR biology.
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Affiliation(s)
- S Mayo-Pérez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Y Gama-Martínez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - S Dávila
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - N Rivera
- IPN: CICATA, Unidad Morelos del Instituto Politécnico Nacional, Atlacholoaya, Mexico
| | - I Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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2
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Hespanhol JT, Nóbrega-Silva L, Bayer-Santos E. Regulation of type VI secretion systems at the transcriptional, posttranscriptional and posttranslational level. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001376. [PMID: 37552221 PMCID: PMC10482370 DOI: 10.1099/mic.0.001376] [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: 05/12/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Bacteria live in complex polymicrobial communities and are constantly competing for resources. The type VI secretion system (T6SS) is a widespread antagonistic mechanism used by Gram-negative bacteria to gain an advantage over competitors. T6SSs translocate toxic effector proteins inside target prokaryotic cells in a contact-dependent manner. In addition, some T6SS effectors can be secreted extracellularly and contribute to the scavenging scarce metal ions. Bacteria deploy their T6SSs in different situations, categorizing these systems into offensive, defensive and exploitative. The great variety of bacterial species and environments occupied by such species reflect the complexity of regulatory signals and networks that control the expression and activation of the T6SSs. Such regulation is tightly controlled at the transcriptional, posttranscriptional and posttranslational level by abiotic (e.g. pH, iron) or biotic (e.g. quorum-sensing) cues. In this review, we provide an update on the current knowledge about the regulatory networks that modulate the expression and activity of T6SSs across several species, focusing on systems used for interbacterial competition.
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Affiliation(s)
- Julia Takuno Hespanhol
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Luize Nóbrega-Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Ethel Bayer-Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
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3
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Levipan HA, Irgang R, Opazo LF, Araya-León H, Avendaño-Herrera R. Collective behavior and virulence arsenal of the fish pathogen Piscirickettsia salmonis in the biofilm realm. Front Cell Infect Microbiol 2022; 12:1067514. [PMID: 36544910 PMCID: PMC9760808 DOI: 10.3389/fcimb.2022.1067514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89T in biofilms, as determined by whole-transcriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89T were not enriched with virulence-related genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis.
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Affiliation(s)
- Héctor A. Levipan
- Laboratorio de Ecopatología y Nanobiomateriales, Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile,Centro de Espectroscopía Atómica y Molecular (ATMOS-C), Universidad de Playa Ancha, Valparaíso, Chile,*Correspondence: Héctor A. Levipan, ; ; Ruben Avendaño-Herrera, ;
| | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile,Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - L. Felipe Opazo
- Institute of Ecology and Biodiversity (IEB), Santiago, Chile,Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Henry Araya-León
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile,Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile,Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile,Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile,*Correspondence: Héctor A. Levipan, ; ; Ruben Avendaño-Herrera, ;
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4
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Nie W, Chen X, Tang Y, Xu N, Zhang H. Potential dsRNAs can be delivered to aquatic for defense pathogens. Front Bioeng Biotechnol 2022; 10:1066799. [PMID: 36466329 PMCID: PMC9712207 DOI: 10.3389/fbioe.2022.1066799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/03/2022] [Indexed: 10/29/2023] Open
Abstract
The use of antibiotics to facilitate resistance to pathogens in aquatic animals is a traditional method of pathogen control that is harmful to the environment and human health. RNAi is an emerging technology in which homologous small RNA molecules target specific genes for degradation, and it has already shown success in laboratory experiments. However, further research is needed before it can be applied in aquafarms. Many laboratories inject the dsRNA into aquatic animals for RNAi, which is obviously impractical and very time consuming in aquafarms. Therefore, to enable the use of RNAi on a large scale, the methods used to prepare dsRNA need to be continuously in order to be fast and efficient. At the same time, it is necessary to consider the issue of biological safety. This review summarizes the key harmful genes associated with aquatic pathogens (viruses, bacteria, and parasites) and provides potential targets for the preparation of dsRNA; it also lists some current examples where RNAi technology is used to control aquatic species, as well as how to deliver dsRNA to the target hydrobiont.
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Affiliation(s)
| | | | | | | | - Hao Zhang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
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5
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Du Y, Hu X, Miao L, Chen J. Current status and development prospects of aquatic vaccines. Front Immunol 2022; 13:1040336. [PMID: 36439092 PMCID: PMC9684733 DOI: 10.3389/fimmu.2022.1040336] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
Diseases are a significant impediment to aquaculture's sustainable and healthy growth. The aquaculture industry is suffering significant financial losses as a result of the worsening water quality and increasing frequency of aquatic disease outbreaks caused by the expansion of aquaculture. Drug control, immunoprophylaxis, ecologically integrated control, etc. are the principal control strategies for fish infections. For a long time, the prevention and control of aquatic diseases have mainly relied on the use of various antibiotics and chemical drugs. However, long-term use of chemical inputs not only increases pathogenic bacteria resistance but also damages the fish and aquaculture environments, resulting in drug residues in aquatic products, severely impeding the development of the aquaculture industry. The development and use of aquatic vaccines are the safest and most effective ways to prevent aquatic animal diseases and preserve the health and sustainability of aquaculture. To give references for the development and implementation of aquatic vaccines, this study reviews the development history, types, inoculation techniques, mechanisms of action, development prospects, and challenges encountered with aquatic vaccines.
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Affiliation(s)
- Yang Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoman Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Liang Miao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
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Transposon insertion sequencing analysis unveils novel genes involved in luxR expression and quorum sensing regulation in Vibrio alginolyticus. Microbiol Res 2022; 267:127243. [DOI: 10.1016/j.micres.2022.127243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022]
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7
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Chi X, Wang Y, Miao J, Wang W, Sun Y, Yu Z, Feng Z, Cheng S, Chen L, Ge Y. EppR, a new LysR-family transcription regulator, positively influences phenazine biosynthesis in the plant growth-promoting rhizobacterium Pseudomonas chlororaphis G05. Microbiol Res 2022; 260:127050. [DOI: 10.1016/j.micres.2022.127050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 10/18/2022]
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A Novel Transcription Factor VPA0041 Was Identified to Regulate the Swarming Motility in Vibrio parahaemolyticus. Pathogens 2022; 11:pathogens11040453. [PMID: 35456128 PMCID: PMC9029033 DOI: 10.3390/pathogens11040453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Vibrio parahaemolyticus can change their usual lifestyle of surviving in an aqueous environment attached to a host, wherein both swimming motility and swarming motility play important roles in lifestyle changes, respectively. VPA0041 is a novel transcription factor involved in regulating the swarming ability of V. parahaemolyticus. The deletion of the vpa0041 gene resulted in the loss of swarming motility in the brain heart infusion (BHI) agars, while the swimming motility was unaffected by VPA0041. Transmission electron microscope (TEM) assays showed that no flagellum was found around the bacterial cells. RNA-sequencing (RNA-Seq) analysis revealed that VPA0041 regulated 315 genes; 207 genes were up-regulated, and 108 genes were down-regulated. RNA-seq results indicated that the lateral flagellar genes were down-regulated by VPA0041, which was confirmed by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Electrophoretic mobility shift assays (EMSA) demonstrated that VPA0041 directly bound to the promoters of vpa0264, vpa1548, and vpa1550 to regulate the expression of the lateral flagellar genes. Our results demonstrated that the transcription factor VPA0041 could directly regulate the expression of lateral flagellar genes to mediate the swarming motility in V. parahaemolyticus.
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Ma R, Liu Y, Gan J, Qiao H, Ma J, Zhang Y, Bu Y, Shao S, Zhang Y, Wang Q. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3777-3798. [PMID: 35325196 PMCID: PMC9023278 DOI: 10.1093/nar/gkac180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | - Haoxian Qiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiabao Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yifan Bu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Qiyao Wang
- To whom correspondence should be addressed. Tel: +86 21 64253306; Fax: +86 21 64253306;
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Roles of virulence regulator ToxR in viable but non-culturable formation by controlling reactive oxygen species resistance in pathogen Vibrio alginolyticus. Microbiol Res 2021; 254:126900. [PMID: 34700184 DOI: 10.1016/j.micres.2021.126900] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/08/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023]
Abstract
Under adverse circumstances, bacteria enter the viable but non-culturable (VBNC) state, a dormancy-like state for survival. The altered gene regulation underlying the entry of the VBNC state has not yet been well elucidated. Here, we reported that a subpopulation of cells (23.8 %) in Vibrio alginolyticus cultures enters the VBNC state in response to nutrient limitation at alkaline pH. The proteolysis of pivotal virulence regulator ToxR at these conditions is associated with VBNC formation. Meantime, ToxR abrogation impaired the mobility and the expression of virulence-associated genes, resulting in attenuated virulence in V. alginolyticus. RNA-seq and ChIP-seq analyses of the cells grown in VBNC-inducing conditions revealed that ToxR directly controls the expression of ∼8 genes including ahpC and dps involved in reactive oxygen species (ROS) resistance. ToxR binds to the promoter regions of kdgR, ppiC, ahpC, and dps and further controls their respective expression under oxidative stress conditions. The cells with impaired ToxR accumulated detrimental intracellular ROS. Moreover, these genes contribute to bacterial culturability as their in-frame deletion strains exhibiting severely decreased plate counts and the complementary strain showed rescued viability. Collectively, this study revealed the role of ToxR in switching on the VBNC state by sensing unfavorable environmental signals such as endogenous ROS (hydrogen peroxide, H2O2) in V. alginolyticus and provided mechanistic insights into Vibrio lifestyle adaptation in the marine environment.
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Zhang J, Liu B, Gu D, Hao Y, Chen M, Ma Y, Zhou X, Reverter D, Zhang Y, Wang Q. Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression. Nucleic Acids Res 2021; 49:3274-3293. [PMID: 33693882 PMCID: PMC8034623 DOI: 10.1093/nar/gkab150] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/19/2022] Open
Abstract
LuxR is a TetR family master quorum sensing (QS) regulator activating or repressing expression of hundreds of genes that control collective behaviors in Vibrios with underlying mechanism unknown. To illuminate how this regulator controls expression of various target genes, we applied ChIP-seq and DNase I-seq technologies. Vibrio alginolyticus LuxR controls expression of ∼280 genes that contain either symmetric palindrome (repDNA) or asymmetric (actDNA) binding motifs with different binding profiles. The median number of LuxR binding sites for activated genes are nearly double for that of repressed genes. Crystal structures of LuxR in complex with the respective repDNA and actDNA motifs revealed a new mode of LuxR DNA binding that involves contacts of its N-terminal extension to the minor groove. The N-terminal contacts mediated by Arginine-9 and Arginine-11 differ when LuxR binds to repDNA vs actDNA, leading to higher binding affinity at repressed targets. Moreover, modification of LuxR binding sites, binding profiles, and N-terminal extension have important consequences on QS-regulated phenotypes. These results facilitate fundamental understanding of the high flexibility of mechanisms of LuxR control of gene activation and repression in Vibrio QS, which may facilitate to design QS inhibiting chemicals that interfere with LuxR regulation to effectively control pathogens.
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Affiliation(s)
| | | | | | - Yuan Hao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mo Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaohui Zhou
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT 06269, USA
| | - David Reverter
- Correspondence may also be addressed to David Reverter. Tel: +34 93 5868955;
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519000 Zhuhai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Qiyao Wang
- To whom correspondence should be addressed. Tel: +86 21 64253306;
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12
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Hierarchical Transcriptional Control of the LuxR Quorum-Sensing Regulon of Vibrio harveyi. J Bacteriol 2020; 202:JB.00047-20. [PMID: 32366592 DOI: 10.1128/jb.00047-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/30/2020] [Indexed: 11/20/2022] Open
Abstract
In vibrios, quorum sensing controls hundreds of genes that are required for cell density-specific behaviors including bioluminescence, biofilm formation, competence, secretion, and swarming motility. The central transcription factor in the quorum-sensing pathway is LuxR/HapR, which directly regulates ∼100 genes in the >400-gene regulon of Vibrio harveyi Among these directly controlled genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the LuxR regulon. We confirmed that LuxR binds to the promoters of these genes in vitro and quantified the extent of LuxR activation or repression of transcript levels. Transcriptome sequencing (RNA-seq) indicates that most of these transcriptional regulators control only a few genes, with the exception of MetJ, which is a global regulator. The genes regulated by these transcription factors are predicted to be involved in methionine and thiamine biosynthesis, membrane stability, RNA processing, c-di-GMP degradation, sugar transport, and other cellular processes. These data support a hierarchical model in which LuxR directly regulates 15 transcription factors that drive the second level of the gene expression cascade to influence cell density-dependent metabolic states and behaviors in V. harveyi IMPORTANCE Quorum sensing is important for survival of bacteria in nature and influences the actions of bacterial groups. In the relatively few studied examples of quorum-sensing-controlled genes, these genes are associated with competition or cooperation in complex microbial communities and/or virulence in a host. However, quorum sensing in vibrios controls the expression of hundreds of genes, and their functions are mostly unknown or uncharacterized. In this study, we identify the regulators of the second tier of gene expression in the quorum-sensing system of the aquaculture pathogen Vibrio harveyi Our identification of regulatory networks and metabolic pathways controlled by quorum sensing can be extended and compared to other Vibrio species to understand the physiology, ecology, and pathogenesis of these organisms.
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Ndagi U, Falaki AA, Abdullahi M, Lawal MM, Soliman ME. Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design. RSC Adv 2020; 10:18451-18468. [PMID: 35685616 PMCID: PMC9122625 DOI: 10.1039/d0ra01484b] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022] Open
Abstract
The use of antibiotics to manage infectious diseases dates back to ancient civilization, but the lack of a clear distinction between the therapeutic and toxic dose has been a major challenge. This precipitates the notion that antibiotic resistance was from time immemorial, principally because of a lack of adequate knowledge of therapeutic doses and continuous exposure of these bacteria to suboptimal plasma concentration of antibiotics. With the discovery of penicillin by Alexander Fleming in 1924, a milestone in bacterial infections' treatment was achieved. This forms the foundation for the modern era of antibiotic drugs. Antibiotics such as penicillins, cephalosporins, quinolones, tetracycline, macrolides, sulphonamides, aminoglycosides and glycopeptides are the mainstay in managing severe bacterial infections, but resistant strains of bacteria have emerged and hampered the progress of research in this field. Recently, new approaches to research involving bacteria resistance to antibiotics have appeared; these involve combining the molecular understanding of bacteria systems with the knowledge of bioinformatics. Consequently, many molecules have been developed to curb resistance associated with different bacterial infections. However, because of increased emphasis on the clinical relevance of antibiotics, the synergy between in silico study and in vivo study is well cemented and this facilitates the discovery of potent antibiotics. In this review, we seek to give an overview of earlier reviews and molecular and structural understanding of bacteria resistance to antibiotics, while focusing on the recent bioinformatics approach to antibacterial drug discovery. Understanding the evolution of antibiotic resistance at the molecular level as a functional tool for bioinformatic-based drug design.![]()
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Affiliation(s)
- Umar Ndagi
- Centre for Trans-Sahara Disease, Vaccine and Drug Research
- Ibrahim Badamasi Babangida University
- Lapai
- Nigeria
| | - Abubakar A. Falaki
- Department of Microbiology
- School of Agriculture and Applied Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Maryam Abdullahi
- Faculty of Pharmaceutical Sciences
- Ahmadu Bello University Zaria
- Nigeria
| | - Monsurat M. Lawal
- School of Laboratory Medicine and Medical Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahmoud E. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu Natal
- Durban 4001
- South Africa
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14
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Four LysR-type transcriptional regulator family proteins (LTTRs) involved in antibiotic resistance in Aeromonas hydrophila. World J Microbiol Biotechnol 2019; 35:127. [DOI: 10.1007/s11274-019-2700-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/22/2019] [Indexed: 01/21/2023]
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15
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Zhang J, Hao Y, Yin K, Mao Q, Xu R, Zhang Y, Ma Y, Wang Q. VqsA controls exotoxin production by directly binding to the promoter of asp in the pathogen Vibrio alginolyticus. FEMS Microbiol Lett 2019; 366:5379279. [PMID: 30865774 DOI: 10.1093/femsle/fnz056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
Quorum sensing (QS) system is an important bacterial cell-to-cell signaling system controlling expression of various genes in response to cell densities. In vibrios, LuxR/AphA are two established master QS regulators (MQSRs), and VqsA is recently identified to be the third putative MQSR. As a novel LysR-type regulator, the regulon and the underlying regulation mechanisms of VqsA remains to be elucidated. Here our investigation indicated that the yields of alkaline serine protease (Asp), the exotoxin in Vibrio alginolyticus was dependent on both LuxR and VqsA in growth phase dependent manner. Various in vivo and in vitro analyses including electrophoretic mobility shift assays (EMSA) along with DNase I footprinting investigations demonstrated that VqsA positively controls asp expression through directly binding to the partially palindromic 29 bp binding motif in the promoter region of asp. Moreover, RNA-seq analysis validated the regulatory roles of VqsA in various processes in the organism. Collectively, our data showed that VqsA positively regulates the expression of exotoxin and other virulence-associated genes and is essential for the QS regulation in V. alginolyticus.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuan Hao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Kaiyu Yin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiaoqiao Mao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Rongjing Xu
- Yantai Development Zone TianYuan Aquatic Products Co., Ltd., Yantai 264006, Shandong Province, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, 130 Meilong Road, Shanghai 200237, China
| | - Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, 130 Meilong Road, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Shanghai Engineering Research Center of Maricultured Animal Vaccines, 130 Meilong Road, Shanghai 200237, China
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16
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Zuo Y, Zhao L, Xu X, Zhang J, Zhang J, Yan Q, Huang L. Mechanisms underlying the virulence regulation of new Vibrio alginolyticus ncRNA Vvrr1 with a comparative proteomic analysis. Emerg Microbes Infect 2019; 8:1604-1618. [PMID: 31711375 PMCID: PMC6853220 DOI: 10.1080/22221751.2019.1687261] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
The incidence of Vibrio alginolyticus infections has increased in recent years due to the influence of climate change and rising sea temperature. Vibrio virulence regulatory RNA 1 (Vvrr1) is a newly found noncoding RNA (ncRNA) predicted to be closely related to the adhesion ability of V. alginolyticus based on the previous RNA-seq. In this study, the target genes of Vvrr1 were fully screened and verified by constructing Vvrr1-overexpressing strains and using the proteome sequencing technology. Pyruvate kinase I (pykF) gene was predicted to be a chief target gene of Vvrr1 involved in virulence regulation. The adhesion ability, biofilm formation and virulence were significantly reduced in the Vvrr1-overexpressing and the pykF-silenced strain compared with the wild strains. Similar to the overexpression of Vvrr1, the silencing of pykF also reduced the expression level of virulence genes, such as ndk, eno, sdhB, glpF, and cysH. Meanwhile, by constructing the "pykF-GFP" fusion expression plasmid and using the GFP reporter gene analysis in Escherichia coli, the fluorescence intensity of the strain containing Vvrr1 whole ncRNA sequence vector was found to be significantly weakened. These indicated that Vvrr1 participated in the virulence regulation mechanism of V. alginolyticus by interacting with the virulence gene pykF.
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Affiliation(s)
- Yanfei Zuo
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, PR People’s Republic of China
| | - Lingmin Zhao
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, PR People’s Republic of China
| | - Xiaojin Xu
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, PR People’s Republic of China
| | - Jiaonan Zhang
- Key Laboratory of Special Aquatic Feed for Fujian, Fujian Tianma Technology Company Limited, Fuzhou, People’s Republic of China
| | - Jiaolin Zhang
- Key Laboratory of Special Aquatic Feed for Fujian, Fujian Tianma Technology Company Limited, Fuzhou, People’s Republic of China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, PR People’s Republic of China
| | - Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, PR People’s Republic of China
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17
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Dong Y, Wang Y, Liu J, Ma S, Awan F, Lu C, Liu Y. Discovery of lahS as a Global Regulator of Environmental Adaptation and Virulence in Aeromonas hydrophila. Int J Mol Sci 2018; 19:E2709. [PMID: 30208624 PMCID: PMC6163582 DOI: 10.3390/ijms19092709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 01/06/2023] Open
Abstract
Aeromonas hydrophila is an important aquatic microorganism that can cause fish hemorrhagic septicemia. In this study, we identified a novel LysR family transcriptional regulator (LahS) in the A. hydrophila Chinese epidemic strain NJ-35 from a library of 947 mutant strains. The deletion of lahS caused bacteria to exhibit significantly decreased hemolytic activity, motility, biofilm formation, protease production, and anti-bacterial competition ability when compared to the wild-type strain. In addition, the determination of the fifty percent lethal dose (LD50) in zebrafish demonstrated that the lahS deletion mutant (ΔlahS) was highly attenuated in virulence, with an approximately 200-fold increase in LD50 observed as compared with that of the wild-type strain. However, the ΔlahS strain exhibited significantly increased antioxidant activity (six-fold). Label-free quantitative proteome analysis resulted in the identification of 34 differentially expressed proteins in the ΔlahS strain. The differentially expressed proteins were involved in flagellum assembly, metabolism, redox reactions, and cell density induction. The data indicated that LahS might act as a global regulator to directly or indirectly regulate various biological processes in A. hydrophila NJ-35, contributing to a greater understanding the pathogenic mechanisms of A. hydrophila.
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Affiliation(s)
- Yuhao Dong
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yao Wang
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jin Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shuiyan Ma
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Furqan Awan
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chengping Lu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yongjie Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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