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Isenberg RY, Holschbach CS, Gao J, Mandel MJ. Functional analysis of cyclic diguanylate-modulating proteins in Vibrio fischeri. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550417. [PMID: 37546929 PMCID: PMC10402110 DOI: 10.1101/2023.07.24.550417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
As bacterial symbionts transition from a motile free-living state to a sessile biofilm state, they must coordinate behavior changes suitable to each lifestyle. Cyclic diguanylate (c-di-GMP) is an intracellular signaling molecule that can regulate this transition, and it is synthesized by diguanylate cyclase (DGC) enzymes and degraded by phosphodiesterase (PDE) enzymes. Generally, c-di-GMP inhibits motility and promotes biofilm formation. While c-di-GMP and the enzymes that contribute to its metabolism have been well-studied in pathogens, considerably less focus has been placed on c-di-GMP regulation in beneficial symbionts. Vibrio fischeri is the sole beneficial symbiont of the Hawaiian bobtail squid (Euprymna scolopes) light organ, and the bacterium requires both motility and biofilm formation to efficiently colonize. C-di-GMP regulates swimming motility and cellulose exopolysaccharide production in V. fischeri. The genome encodes 50 DGCs and PDEs, and while a few of these proteins have been characterized, the majority have not undergone comprehensive characterization. In this study, we use protein overexpression to systematically characterize the functional potential of all 50 V. fischeri proteins. All 28 predicted DGCs and 14 predicted PDEs displayed at least one phenotype consistent with their predicted function, and a majority of each displayed multiple phenotypes. Finally, active site mutant analysis of proteins with the potential for both DGC and PDE activities revealed potential activities for these proteins. This work presents a systems-level functional analysis of a family of signaling proteins in a tractable animal symbiont and will inform future efforts to characterize the roles of individual proteins during lifestyle transitions.
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Affiliation(s)
- Ruth Y. Isenberg
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Chandler S. Holschbach
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
| | - Jing Gao
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mark J. Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
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2
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Pozdeev G, Beckett MC, Mogre A, Thomson NR, Dorman CJ. Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence. Microb Genom 2022; 8. [PMID: 35166652 PMCID: PMC8942017 DOI: 10.1099/mgen.0.000768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Integration Host Factor (IHF) is a heterodimeric nucleoid-associated protein that plays roles in bacterial nucleoid architecture and genome-wide gene regulation. The ihfA and ihfB genes encode the subunits and are located 350 kbp apart, in the Right replichore of the Salmonella chromosome. IHF is composed of one IhfA and one IhfB subunit. Despite this 1 : 1 stoichiometry, MS revealed that IhfB is produced in 2-fold excess over IhfA. We re-engineered Salmonella to exchange reciprocally the protein-coding regions of ihfA and ihfB, such that each relocated protein-encoding region was driven by the expression signals of the other's gene. MS showed that in this 'rewired' strain, IhfA is produced in excess over IhfB, correlating with enhanced stability of the hybrid ihfB-ihfA mRNA that was expressed from the ihfB promoter. Nevertheless, the rewired strain grew at a similar rate to the wild-type and was similar in competitive fitness. However, compared to the wild-type, it was less motile, had growth-phase-specific reductions in SPI-1 and SPI-2 gene expression, and was engulfed at a higher rate by RAW macrophage. Our data show that while exchanging the physical locations of its ihf genes and the rewiring of their regulatory circuitry are well tolerated in Salmonella, genes involved in the production of type 3 secretion systems exhibit dysregulation accompanied by altered phenotypes.
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Affiliation(s)
- German Pozdeev
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Michael C Beckett
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Aalap Mogre
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | | | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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3
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Zhao X, Yang F, Wang Y, Zhang Y. hns mRNA downregulates the expression of galU and attenuates the motility of Salmonella enterica serovar Typhi. Int J Med Microbiol 2021; 311:151525. [PMID: 34340061 DOI: 10.1016/j.ijmm.2021.151525] [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: 01/09/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 10/20/2022] Open
Abstract
Recently, multiple bifunctional RNAs have been discovered, which can both be translated into proteins and play regulatory roles. hns encodes the global gene silencing factor H-NS, which is widespread in Gram-negative bacteria. This study reported that hns mRNA of Salmonella enterica serovar Typhi (S. Typhi) was a bifunctional RNA that could act as an antisense RNA downregulating the expression of galU, the coding gene of uridine triphosphate-glucose-1-phosphate uridylyltransferase, and attenuating bacterial motility. galU, which is located at the opposite strand of hns, was identified to have a long 3'-untranslated region that overlapped with hns and could be processed to produce short RNA fragments. The overexpression of hns mRNA inhibited the expression of galU. The deletion of galU attenuated the motility of S. Typhi, while the complementation of galU nearly restored the phenotype. Overexpressing hns mRNA in the wild-type strain of S. Typhi inhibited the motility and the expression of flagellar genes, while overexpressing hns mRNA in the galU-deletion mutant did not influence bacterial motility. In conclusion, hns mRNA has been identified to be a new bifunctional RNA that attenuates the motility of S. Typhi by downregulating the expression of galU.
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Affiliation(s)
- Xin Zhao
- Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210006, China.
| | - Fanfan Yang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Yurou Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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Bouteiller M, Dupont C, Bourigault Y, Latour X, Barbey C, Konto-Ghiorghi Y, Merieau A. Pseudomonas Flagella: Generalities and Specificities. Int J Mol Sci 2021; 22:ijms22073337. [PMID: 33805191 PMCID: PMC8036289 DOI: 10.3390/ijms22073337] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
Flagella-driven motility is an important trait for bacterial colonization and virulence. Flagella rotate and propel bacteria in liquid or semi-liquid media to ensure such bacterial fitness. Bacterial flagella are composed of three parts: a membrane complex, a flexible-hook, and a flagellin filament. The most widely studied models in terms of the flagellar apparatus are E. coli and Salmonella. However, there are many differences between these enteric bacteria and the bacteria of the Pseudomonas genus. Enteric bacteria possess peritrichous flagella, in contrast to Pseudomonads, which possess polar flagella. In addition, flagellar gene expression in Pseudomonas is under a four-tiered regulatory circuit, whereas enteric bacteria express flagellar genes in a three-step manner. Here, we use knowledge of E. coli and Salmonella flagella to describe the general properties of flagella and then focus on the specificities of Pseudomonas flagella. After a description of flagellar structure, which is highly conserved among Gram-negative bacteria, we focus on the steps of flagellar assembly that differ between enteric and polar-flagellated bacteria. In addition, we summarize generalities concerning the fuel used for the production and rotation of the flagellar macromolecular complex. The last part summarizes known regulatory pathways and potential links with the type-six secretion system (T6SS).
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Affiliation(s)
- Mathilde Bouteiller
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Charly Dupont
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yvann Bourigault
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Corinne Barbey
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Annabelle Merieau
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
- Correspondence:
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5
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Khan F, Tabassum N, Pham DTN, Oloketuyi SF, Kim YM. Molecules involved in motility regulation in Escherichia coli cells: a review. BIOFOULING 2020; 36:889-908. [PMID: 33028083 DOI: 10.1080/08927014.2020.1826939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
The initial colonization of the host organism by commensal, probiotic, and pathogenic Escherichia coli strains is an important step in the development of infections and biofilms. Sensing and colonization of host cell surfaces are governed by flagellar and fimbriae/pili appendages, respectively. Biofilm formation confers great advantages on pathogenic E. coli cells such as protection against the host immune system, antimicrobial agents, and several environmental stress factors. The transition from planktonic to sessile physiological states involves several signaling cascades and factors responsible for the regulation of flagellar motility in E. coli cells. These regulatory factors have thus become important targets to control pathogenicity. Hence, attenuation of flagellar motility is considered a potential therapy against pathogenic E. coli. The present review describes signaling pathways and proteins involved in direct or indirect regulation of flagellar motility. Furthermore, application strategies for antimotility natural or synthetic compounds are discussed also.
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Affiliation(s)
- Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
| | - Nazia Tabassum
- Industrial Convergence Bionix Engineering, Pukyong National University, Busan, Republic of Korea
| | - Dung Thuy Nguyen Pham
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | | | - Young-Mog Kim
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
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6
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The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA. mBio 2020; 11:mBio.00448-20. [PMID: 32518183 PMCID: PMC7373187 DOI: 10.1128/mbio.00448-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacteria organize their genetic material in a structure called the nucleoid, which needs to be compact to fit inside the cell and, at the same time, dynamic to allow high rates of replication and transcription. Nucleoid-associated proteins (NAPs) play a pivotal role in this process, so their detailed characterization is crucial for our understanding of DNA organization into bacterial cells. Even though NAPs affect DNA-related processes differently, all of them have to oligomerize and bind DNA for their function. The significance of this study is the identification of structural elements involved in the oligomerization and DNA binding of a newly discovered NAP in C. crescentus and the demonstration that structural elements are conserved in evolutionarily distant and functionally distinct NAPs. Nucleoid-associated proteins (NAPs) are DNA binding proteins critical for the organization and function of the bacterial chromosome. A newly discovered NAP in Caulobacter crescentus, GapR, is thought to facilitate the movement of the replication and transcription machines along the chromosome by stimulating type II topoisomerases to remove positive supercoiling. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recently published DNA-bound crystal structure of GapR, we identified the structural elements involved in oligomerization and DNA binding. Moreover, we show that GapR is maintained as a tetramer upon its dissociation from DNA and that tetrameric GapR is capable of binding DNA molecules in vitro. Analysis of protein chimeras revealed that two helices of GapR are functionally conserved in H-NS, demonstrating that two evolutionarily distant NAPs with distinct mechanisms of action utilize conserved structural elements to oligomerize and bind DNA.
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7
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Ikeda T, Shinagawa T, Ito T, Ohno Y, Kubo A, Nishi J, Gotoh Y, Ogura Y, Ooka T, Hayashi T. Hypoosmotic stress induces flagellar biosynthesis and swimming motility in Escherichia albertii. Commun Biol 2020; 3:87. [PMID: 32111956 PMCID: PMC7048735 DOI: 10.1038/s42003-020-0816-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/10/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria use flagella as propellers to move to favorable environments. Escherichia albertii, a growing cause of foodborne illness and diarrhea, is reportedly non-motile and lacks flagella on its surface. Here, we report that 27 out of 59 E. albertii strains, collected mainly from humans and birds, showed swimming motility when cultured at low osmotic pressure. The biosynthesis of flagella in E. albertii cells was induced under ambient temperature and hypoosmotic pressure: conditions which resemble aquatic environments. Flagellar induction increased E. albertii survival in the intestinal epithelial cell culture containing gentamicin. Although genes involved in chemotaxis are not present in the E. albertii genome, the addition of glutamic acid, an amino acid known to regulate the internal cell osmolarity, augmented the proportion of swimming cells by 35-fold. These results suggest that flagellar biosynthesis and motility in E. albertii cells are controlled by their internal and external osmolarity. Ikeda et al. report that enteropathogen E. albertii, thought to be a non-motile microorganism, may form flagella and acquire swimming motility in a hypoosmotic environment and ambient temperatures. Further addition of glutamic acid, an amino acid known to regulate the internal cell osmolarity, augments the proportion of swimming cells.
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Affiliation(s)
- Tetsuya Ikeda
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan.
| | - Toshie Shinagawa
- Regenerative Medicine Laboratory, Nozaki Tokushukai Hospital Research Institute, 2-10-50 Tanigawa, Daito, 574-0074, Japan
| | - Takuya Ito
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan
| | - Yuta Ohno
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan
| | - Akiko Kubo
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, 060-0819, Japan
| | - Junichiro Nishi
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8544, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8544, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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8
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Gawade P, Gunjal G, Sharma A, Ghosh P. Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome-wide data analysis. Genomics 2019; 112:1264-1272. [PMID: 31356968 DOI: 10.1016/j.ygeno.2019.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/29/2022]
Abstract
Fis (Factor for inversion stimulation) and H-NS (Histone-like nucleoid-structuring protein) are two well-known nucleoid-associated proteins (NAPs) in proteobacteria, which play crucial roles in genome organization and transcriptional regulation. We performed RNA-sequencing to identify genes regulated by these NAPs. Study reveals that Fis and H-NS affect expression of 462 and 88 genes respectively in Escherichia coli at mid-exponential growth phase. By integrating available ChIP-seq data, we identified direct and indirect regulons of Fis and H-NS proteins. Functional analysis reveals that Fis controls expression of genes involved in translation, oxidative phosphorylation, sugar metabolism and transport, amino acid metabolism, bacteriocin transport, cell division, two-component system, biofilm formation, pilus organization and lipopolysaccharide biosynthesis pathways. However, H-NS represses expression of genes in cell adhesion, recombination, biofilm formation and lipopolysaccharide biosynthesis pathways under mid-exponential growth condition. The current regulatory networks thus provide a global glimpse of coordinated regulatory roles for these two important NAPs.
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Affiliation(s)
- Priyanka Gawade
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Gaurav Gunjal
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Anamika Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India.
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9
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Matteoli FP, Passarelli-Araujo H, Pedrosa-Silva F, Olivares FL, Venancio TM. Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of bla CTX-M-55, bla NDM-5 and bla IMI-1, along with sophisticated iron acquisition strategies. Genomics 2019; 112:1182-1191. [PMID: 31279858 DOI: 10.1016/j.ygeno.2019.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including blaCTX-M-55 and blaNDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of blaNDM-5 revealed the resemblance of this plasmid with other IncX plasmids from other bacteria from the same country. Three distinctive siderophore producing operons were found in E. bugandensis: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). Our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.
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Affiliation(s)
- Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil.
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10
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Shin J, Cho H, Kim S, Kim KS. Role of acid responsive genes in the susceptibility of Escherichia coli to ciclopirox. Biochem Biophys Res Commun 2018; 500:296-301. [PMID: 29654752 DOI: 10.1016/j.bbrc.2018.04.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Antibiotic resistance poses a huge threat to the effective treatment of bacterial infections. To circumvent the limitations in developing new antibiotics, researchers are attempting to repurpose pre-developed drugs that are known to be safe. Ciclopirox, an off-patent antifungal agent, inhibits the growth of Gram-negative bacteria, and genes involved in galactose metabolism and lipopolysaccharide (LPS) biosynthesis are plausible antibacterial targets for ciclopirox, since their expression levels partially increase susceptibility at restrictive concentrations. In the present study, to identify new target genes involved in the susceptibility of Escherichia coli to ciclopirox, genome-wide mRNA profiling was performed following ciclopirox addition at sublethal concentrations, and glutamate-dependent acid resistance (GDAR) genes were differentially regulated. Additional susceptibility testing, growth analyses and viability assays of GDAR regulatory genes revealed that down-regulation of evgS or hns strongly enhanced susceptibility to ciclopirox. Further microscopy and phenotypic analyses revealed that down-regulation of these genes increased cell size and decreased motility. Our findings could help to maximise the efficacy of ciclopirox against hard-to-treat Gram-negative pathogens.
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Affiliation(s)
- Jonghoon Shin
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Hyejin Cho
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Suran Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Kwang-Sun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea.
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11
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Wang Y, Zhang Y, Yin Z, Wang J, Zhu Y, Peng H, Zhou D, Qi Z, Yang W. H-NS represses transcription of the flagellin gene lafA of lateral flagella in Vibrio parahaemolyticus. Can J Microbiol 2017; 64:69-74. [PMID: 29091745 DOI: 10.1139/cjm-2017-0315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Swarming motility is ultimately mediated by the proton-powered lateral flagellar (laf) system in Vibrio parahaemolyticus. Expression of laf genes is tightly regulated by a number of environmental conditions and regulatory factors. The nucleoid-associated DNA-binding protein H-NS is a small and abundant protein that is widely distributed in bacteria, and H-NS-like protein-dependent expression of laf genes has been identified in Vibrio cholerae and V. parahaemolyticus. The data presented here show that H-NS acts as a repressor of the swarming motility in V. parahaemolyticus. A single σ28-dependent promoter was detected for lafA encoding the flagellin of the lateral flagella, and its activity was directly repressed by H-NS. Thus, H-NS represses swarming motility by directly acting on lafA. Briefly, this work revealed a novel function for H-NS as a repressor of the expression of lafA and swarming motility in V. parahaemolyticus.
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Affiliation(s)
- Yan Wang
- a Department of Biological Defence (Microbiology), Faculty of Tropical Medicine and Public Health, Second Military Medical University, Shanghai, 200433, China
| | - Yiquan Zhang
- b School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Zhe Yin
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jie Wang
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yongzhe Zhu
- a Department of Biological Defence (Microbiology), Faculty of Tropical Medicine and Public Health, Second Military Medical University, Shanghai, 200433, China
| | - Haoran Peng
- a Department of Biological Defence (Microbiology), Faculty of Tropical Medicine and Public Health, Second Military Medical University, Shanghai, 200433, China
| | - Dongsheng Zhou
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Zhongtian Qi
- a Department of Biological Defence (Microbiology), Faculty of Tropical Medicine and Public Health, Second Military Medical University, Shanghai, 200433, China
| | - Wenhui Yang
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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12
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Involvement of Two-Component Signaling on Bacterial Motility and Biofilm Development. J Bacteriol 2017; 199:JB.00259-17. [PMID: 28533218 DOI: 10.1128/jb.00259-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two-component signaling is a specialized mechanism that bacteria use to respond to changes in their environment. Nonpathogenic strains of Escherichia coli K-12 harbor 30 histidine kinases and 32 response regulators, which form a network of regulation that integrates many other global regulators that do not follow the two-component signaling mechanism, as well as signals from central metabolism. The output of this network is a multitude of phenotypic changes in response to changes in the environment. Among these phenotypic changes, many two-component systems control motility and/or the formation of biofilm, sessile communities of bacteria that form on surfaces. Motility is the first reversible attachment phase of biofilm development, followed by a so-called swim or stick switch toward surface organelles that aid in the subsequent phases. In the mature biofilm, motility heterogeneity is generated by a combination of evolutionary and gene regulatory events.
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13
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Kim EA, Panushka J, Meyer T, Ide N, Carlisle R, Baker S, Blair DF. Biogenesis of the Flagellar Switch Complex in Escherichia coli: Formation of Sub-Complexes Independently of the Basal-Body MS-Ring. J Mol Biol 2017. [PMID: 28625846 DOI: 10.1016/j.jmb.2017.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Direction switching in the flagellar motor of Escherichia coli is under the control of a complex on the rotor formed from the proteins FliG, FliM, and FliN. FliG lies at the top of the switch complex (i.e., nearest the membrane) and is arranged with its C-terminal domain (FliGC) resting on the middle domain (FliGM) of the neighboring subunit. This organization requires the protein to adopt an open conformation that exposes the surfaces engaging in intersubunit FliGC/FliGM contacts. In a recent study, Baker and coworkers [13] obtained evidence that FliG in the cytosol is monomeric and takes on a more compact conformation, with FliGC making intramolecular contact with FliGM of the same subunit. In the present work, we examine the conformational preferences and interactions of FliG through in vivo crosslinking experiments in cells that lack either all other flagellar proteins or just the MS-ring protein FliF. The results indicate that FliG has a significant tendency to form multimers independently of other flagellar components. The multimerization of FliG is promoted by FliF and also by FliM. FliM does not multimerize efficiently by itself but does so in the presence of FliG. Thus, pre-assemblies of the switch-complex proteins can form in the cytosol and might function as intermediates in assembly.
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Affiliation(s)
- Eun A Kim
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Joseph Panushka
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Trevor Meyer
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicholas Ide
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Carlisle
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Samantha Baker
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
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14
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Parker A, Cureoglu S, De Lay N, Majdalani N, Gottesman S. Alternative pathways for Escherichia coli biofilm formation revealed by sRNA overproduction. Mol Microbiol 2017; 105:309-325. [PMID: 28470798 DOI: 10.1111/mmi.13702] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2017] [Indexed: 01/06/2023]
Abstract
Small regulatory RNAs have major roles in many regulatory circuits in Escherichia coli and other bacteria, including the transition from planktonic to biofilm growth. We tested Hfq-dependent sRNAs in E. coli for their ability, when overproduced, to inhibit or stimulate biofilm formation, in two different growth media. We identify two mutually exclusive pathways for biofilm formation. In LB, PgaA, encoding an adhesion export protein, played a critical role; biofilm was independent of the general stress factor RpoS or CsgD, regulator of curli and other biofilm genes. The PgaA-dependent pathway was stimulated upon overproduction of DsrA, via negative regulation of H-NS, or of GadY, likely by titration of CsrA. In yeast extract casamino acids (YESCA) media, biofilm was dependent on RpoS and CsgD, but independent of PgaA; RpoS appears to indirectly negatively regulate the PgaA-dependent pathway in YESCA medium. Deletions of most sRNAs had very little effect on biofilm, although deletion of hfq, encoding an RNA chaperone, was defective in both LB and YESCA. Deletion of ArcZ, a small RNA activator of RpoS, decreased biofilm in YESCA; only a portion of this defect could be bypassed by overproduction of RpoS. Overall, sRNAs highlight different pathways to biofilm formation.
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Affiliation(s)
- Ashley Parker
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Suanur Cureoglu
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Nicholas De Lay
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Nadim Majdalani
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, 20892, USA
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15
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Kim EA, Panushka J, Meyer T, Carlisle R, Baker S, Ide N, Lynch M, Crane BR, Blair DF. Architecture of the Flagellar Switch Complex of Escherichia coli: Conformational Plasticity of FliG and Implications for Adaptive Remodeling. J Mol Biol 2017; 429:1305-1320. [PMID: 28259628 DOI: 10.1016/j.jmb.2017.02.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 12/29/2022]
Abstract
Structural models of the complex that regulates the direction of flagellar rotation assume either ~34 or ~25 copies of the protein FliG. Support for ~34 came from crosslinking experiments identifying an intersubunit contact most consistent with that number; support for ~25 came from the observation that flagella can assemble and rotate when FliG is genetically fused to FliF, for which the accepted number is ~25. Here, we have undertaken crosslinking and other experiments to address more fully the question of FliG number. The results indicate a copy number of ~25 for FliG. An interaction between the C-terminal and middle domains, which has been taken to support a model with ~34 copies, is also supported. To reconcile the interaction with a FliG number of ~25, we hypothesize conformational plasticity in an interdomain segment of FliG that allows some subunits to bridge gaps created by the number mismatch. This proposal is supported by mutant phenotypes and other results indicating that the normally helical segment adopts a more extended conformation in some subunits. The FliG amino-terminal domain is organized in a regular array with dimensions matching a ring in the upper part of the complex. The model predicts that FliG copy number should be tied to that of FliF, whereas FliM copy number can increase or decrease according to the number of FliG subunits that adopt the extended conformation. This has implications for the phenomenon of adaptive switch remodeling, in which the FliM copy number varies to adjust the bias of the switch.
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Affiliation(s)
- Eun A Kim
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Joseph Panushka
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Trevor Meyer
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Carlisle
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Samantha Baker
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicholas Ide
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
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16
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Transcription Factor-Mediated Gene Regulation in Archaea. RNA METABOLISM AND GENE EXPRESSION IN ARCHAEA 2017. [DOI: 10.1007/978-3-319-65795-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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17
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Fan Y, Evans CR, Ling J. Reduced Protein Synthesis Fidelity Inhibits Flagellar Biosynthesis and Motility. Sci Rep 2016; 6:30960. [PMID: 27468805 PMCID: PMC4965754 DOI: 10.1038/srep30960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/12/2016] [Indexed: 01/02/2023] Open
Abstract
Accurate translation of the genetic information from DNA to protein is maintained by multiple quality control steps from bacteria to mammals. Genetic and environmental alterations have been shown to compromise translational quality control and reduce fidelity during protein synthesis. The physiological impact of increased translational errors is not fully understood. While generally considered harmful, translational errors have recently been shown to benefit cells under certain stress conditions. In this work, we describe a novel regulatory pathway in which reduced translational fidelity downregulates expression of flagellar genes and suppresses bacterial motility. Electron microscopy imaging shows that the error-prone Escherichia coli strain lacks mature flagella. Further genetic analyses reveal that translational errors upregulate expression of a small RNA DsrA through enhancing its transcription, and deleting DsrA from the error-prone strain restores motility. DsrA regulates expression of H-NS and RpoS, both of which regulate flagellar genes. We demonstrate that an increased level of DsrA in the error-prone strain suppresses motility through the H-NS pathway. Our work suggests that bacteria are capable of switching on and off the flagellar system by altering translational fidelity, which may serve as a previously unknown mechanism to improve fitness in response to environmental cues.
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA.,Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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18
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Wan B, Zhang Q, Tao J, Zhou A, Yao YF, Ni J. Global transcriptional regulation by H-NS and its biological influence on the virulence of Enterohemorrhagic Escherichia coli. Gene 2016; 588:115-23. [PMID: 27173635 DOI: 10.1016/j.gene.2016.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
As a global transcriptional regulator, H-NS, the histone-like nucleoid-associated DNA-binding and bridging protein, plays a wide range of biological roles in bacteria. In order to determine the role of H-NS in regulating gene transcription and further find out the biological significance of this protein in Enterohemorrhagic Escherichia coli (EHEC), we conducted transcriptome analysis of hns mutant by RNA sequencing. A total of 983 genes were identified to be regulated by H-NS in EHEC. 213 and 770 genes were down-regulated and up-regulated in the deletion mutant of hns, respectively. Interestingly, 34 of 97 genes on virulence plasmid pO157 were down-regulated by H-NS. Although the deletion mutant of hns showed a decreased survival rate in macrophage compared with the wild type strain, it exhibited the higher ability to colonize mice gut and became more virulent to BALB/c mice. The BALB/c mice infected with the deletion mutant of hns showed a lower survival rate, and a higher bacterial burden in the gut, compared with those infected with wild type strain, especially when the gut microbiota was not disturbed by antibiotic administration. These findings suggest that H-NS plays an important role in virulence of EHEC by interacting with host gut microbiota.
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Affiliation(s)
- Baoshan Wan
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiufen Zhang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Tao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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