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Raustad N, Dai Y, Iinishi A, Mohapatra A, Soo MW, Hay E, Hernandez GM, Geisinger E. A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.599214. [PMID: 38948834 PMCID: PMC11212878 DOI: 10.1101/2024.06.16.599214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control.
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Yao T, Liu X, Li D, Huang Y, Yang W, Liu R, Wang Q, Li X, Zhou J, Jin C, Liu Y, Yang B, Pang Y. Two-component system RstAB promotes the pathogenicity of adherent-invasive Escherichia coli in response to acidic conditions within macrophages. Gut Microbes 2024; 16:2356642. [PMID: 38769708 PMCID: PMC11135836 DOI: 10.1080/19490976.2024.2356642] [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: 01/25/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strain LF82, isolated from patients with Crohn's disease, invades gut epithelial cells, and replicates in macrophages contributing to chronic inflammation. In this study, we found that RstAB contributing to the colonization of LF82 in a mouse model of chronic colitis by promoting bacterial replication in macrophages. By comparing the transcriptomes of rstAB mutant- and wild-type when infected macrophages, 83 significant differentially expressed genes in LF82 were identified. And we identified two possible RstA target genes (csgD and asr) among the differentially expressed genes. The electrophoretic mobility shift assay and quantitative real-time PCR confirmed that RstA binds to the promoters of csgD and asr and activates their expression. csgD deletion attenuated LF82 intracellular biofilm formation, and asr deletion reduced acid tolerance compared with the wild-type. Acidic pH was shown by quantitative real-time PCR to be the signal sensed by RstAB to activate the expression of csgD and asr. We uncovered a signal transduction pathway whereby LF82, in response to the acidic environment within macrophages, activates transcription of the csgD to promote biofilm formation, and activates transcription of the asr to promote acid tolerance, promoting its replication within macrophages and colonization of the intestine. This finding deepens our understanding of the LF82 replication regulation mechanism in macrophages and offers new perspectives for further studies on AIEC virulence mechanisms.
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Affiliation(s)
- Ting Yao
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Xingmei Liu
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Dan Li
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Yu Huang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Wen Yang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Ruiying Liu
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Qian Wang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Xueping Li
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Jiarui Zhou
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Chen Jin
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Yutao Liu
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Bin Yang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
| | - Yu Pang
- TEDA (Tianjin Economic-Technological Development Area) Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Ministry of Education, Nankai University, Tianjin, China
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Vinchhi R, Yelpure C, Balachandran M, Matange N. Pervasive gene deregulation underlies adaptation and maladaptation in trimethoprim-resistant E. coli. mBio 2023; 14:e0211923. [PMID: 38032208 PMCID: PMC10746255 DOI: 10.1128/mbio.02119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Bacteria employ a number of mechanisms to adapt to antibiotics. Mutations in transcriptional regulators alter the expression levels of genes that can change the susceptibility of bacteria to antibiotics. Two-component signaling proteins are a major class of signaling molecule used by bacteria to regulate transcription. In previous work, we found that mutations in MgrB, a feedback regulator of the PhoQP two-component system, conferred trimethoprim tolerance to Escherichia coli. Here, we elucidate how mutations in MgrB have a domino-like effect on the gene regulatory network of E. coli. As a result, pervasive perturbation of gene regulation ensues. Depending on the environmental context, this pervasive deregulation is either adaptive or maladaptive. Our study sheds light on how deregulation of gene expression can be beneficial for bacteria when challenged with antibiotics, and why regulators like MgrB may have evolved in the first place.
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Affiliation(s)
- Rhea Vinchhi
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Chetna Yelpure
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Manasvi Balachandran
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Nishad Matange
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
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Li L, Ma J, Cheng P, Li M, Yu Z, Song X, Yu Z, Sun H, Zhang W, Wang Z. Roles of two-component regulatory systems in Klebsiella pneumoniae: Regulation of virulence, antibiotic resistance, and stress responses. Microbiol Res 2023; 272:127374. [PMID: 37031567 DOI: 10.1016/j.micres.2023.127374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Klebsiella pneumoniae is an opportunistic pathogen belonging to the Enterobacteriaceae family, which is the leading cause of nosocomial infections. The emergence of hypervirulent and multi-drug resistant K. pneumoniae is a serious health threat. In the process of infection, K. pneumoniae needs to adapt to different environmental conditions, and the two-component regulatory system (TCS) composed of a sensor histidine kinase and response regulator is an important bacterial regulatory system in response to external stimuli. Understanding how K. pneumoniae perceives and responds to complex environmental stimuli provides insights into TCS regulation mechanisms and new targets for drug design. In this review, we analyzed the TCS composition and summarized the regulation mechanisms of TCSs, focusing on the regulation of genes involved in virulence, antibiotic resistance, and stress response. Collectively, these studies demonstrated that several TCSs play important roles in the regulation of virulence, antibiotic resistance and stress responses of K. pneumoniae. A single two-component regulatory system can participate in the regulation of several stress responses, and one stress response process may include several TCSs, forming a complex regulatory network. However, the function and regulation mechanism of some TCSs require further study. Hence, future research endeavors are required to enhance the understanding of TCS regulatory mechanisms and networks in K. pneumoniae, which is essential for the design of novel drugs targeting TCSs.
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Ghose DA, Przydzial KE, Mahoney EM, Keating AE, Laub MT. Marginal specificity in protein interactions constrains evolution of a paralogous family. Proc Natl Acad Sci U S A 2023; 120:e2221163120. [PMID: 37098061 PMCID: PMC10160972 DOI: 10.1073/pnas.2221163120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
The evolution of novel functions in biology relies heavily on gene duplication and divergence, creating large paralogous protein families. Selective pressure to avoid detrimental cross-talk often results in paralogs that exhibit exquisite specificity for their interaction partners. But how robust or sensitive is this specificity to mutation? Here, using deep mutational scanning, we demonstrate that a paralogous family of bacterial signaling proteins exhibits marginal specificity, such that many individual substitutions give rise to substantial cross-talk between normally insulated pathways. Our results indicate that sequence space is locally crowded despite overall sparseness, and we provide evidence that this crowding has constrained the evolution of bacterial signaling proteins. These findings underscore how evolution selects for "good enough" rather than optimized phenotypes, leading to restrictions on the subsequent evolution of paralogs.
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Affiliation(s)
- Dia A. Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Kaitlyn E. Przydzial
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Emily M. Mahoney
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Massachusetts Institute of Technology, Cambridge, MA02139
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Sano K, Kobayashi H, Chuta H, Matsuyoshi N, Kato Y, Ogasawara H. CsgI (YccT) Is a Novel Inhibitor of Curli Fimbriae Formation in Escherichia coli Preventing CsgA Polymerization and Curli Gene Expression. Int J Mol Sci 2023; 24:ijms24054357. [PMID: 36901788 PMCID: PMC10002515 DOI: 10.3390/ijms24054357] [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: 12/31/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Curli fimbriae are amyloids-found in bacteria (Escherichia coli)-that are involved in solid-surface adhesion and bacterial aggregation during biofilm formation. The curli protein CsgA is coded by a csgBAC operon gene, and the transcription factor CsgD is essential to induce its curli protein expression. However, the complete mechanism underlying curli fimbriae formation requires elucidation. Herein, we noted that curli fimbriae formation was inhibited by yccT-i.e., a gene that encodes a periplasmic protein of unknown function regulated by CsgD. Furthermore, curli fimbriae formation was strongly repressed by CsgD overexpression caused by a multicopy plasmid in BW25113-the non-cellulose-producing strain. YccT deficiency prevented these CsgD effects. YccT overexpression led to intracellular YccT accumulation and reduced CsgA expression. These effects were addressed by deleting the N-terminal signal peptide of YccT. Localization, gene expression, and phenotypic analyses revealed that YccT-dependent inhibition of curli fimbriae formation and curli protein expression was mediated by the two-component regulatory system EnvZ/OmpR. Purified YccT inhibited CsgA polymerization; however, no intracytoplasmic interaction between YccT and CsgA was detected. Thus, YccT-renamed CsgI (curli synthesis inhibitor)-is a novel inhibitor of curli fimbriae formation and has a dual role as an OmpR phosphorylation modulator and CsgA polymerization inhibitor.
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Affiliation(s)
- Kotaro Sano
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hiroaki Kobayashi
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hirotaka Chuta
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Nozomi Matsuyoshi
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Yuki Kato
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Graduated School of Science and Technology, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
| | - Hiroshi Ogasawara
- Research Center for Advanced Science and Technology, Division of Gene Research, Shinshu University, 3-15-1 Ueda, Nagano 386-8567, Japan
- Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Matsumoto 390-8621, Japan
- Institute for Fiber Engineering (IFES), Interdisciplinary Cluster for Cutting Edge Research (ICCER), Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
- Renaissance Center for Applied Microbiology, Shinshu University, Nagano-shi, Nagano 380-8553, Japan
- Correspondence: ; Tel.: +81-268-21-5803
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Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
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Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
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Liu Y, Xu T, Wang Q, Huang J, Zhu Y, Liu X, Liu R, Yang B, Zhou K. Vibrio cholerae senses human enteric α-defensin 5 through a CarSR two-component system to promote bacterial pathogenicity. Commun Biol 2022; 5:559. [PMID: 35676416 PMCID: PMC9178039 DOI: 10.1038/s42003-022-03525-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/23/2022] [Indexed: 11/09/2022] Open
Abstract
Vibrio cholerae (V. cholerae) is an aquatic bacterium responsible for acute and fatal cholera outbreaks worldwide. When V. cholerae is ingested, the bacteria colonize the epithelium of the small intestine and stimulate the Paneth cells to produce large amounts of cationic antimicrobial peptides (CAMPs). Human defensin 5 (HD-5) is the most abundant CAMPs in the small intestine. However, the role of the V. cholerae response to HD-5 remains unclear. Here we show that HD-5 significantly upregulates virulence gene expression. Moreover, a two-component system, CarSR (or RstAB), is essential for V. cholerae virulence gene expression in the presence of HD-5. Finally, phosphorylated CarR can directly bind to the promoter region of TcpP, activating transcription of tcpP, which in turn activates downstream virulence genes to promote V. cholerae colonization. In conclusion, this study reveals a virulence-regulating pathway, in which the CarSR two-component regulatory system senses HD-5 to activate virulence genes expression in V. cholerae.
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Affiliation(s)
- Yutao Liu
- TEDA Institute of Biological Sciences and Biotechnology, TEDA, Nankai University, Tianjin, PR China
| | - Tingting Xu
- The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, Guangdong, PR China
| | - Qian Wang
- TEDA Institute of Biological Sciences and Biotechnology, TEDA, Nankai University, Tianjin, PR China
| | - Junxi Huang
- The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, Guangdong, PR China
| | - Yangfei Zhu
- The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Laboratory Department, Shenzhen People's Hospital, Shenzhen, Guangdong, PR China
| | - Xingmei Liu
- TEDA Institute of Biological Sciences and Biotechnology, TEDA, Nankai University, Tianjin, PR China
| | - Ruiying Liu
- TEDA Institute of Biological Sciences and Biotechnology, TEDA, Nankai University, Tianjin, PR China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, TEDA, Nankai University, Tianjin, PR China.
| | - Kai Zhou
- The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, Guangdong, PR China.
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Liu R, Zhang F, Sang Y, Katouzian I, Jafari SM, Wang X, Li W, Wang J, Mohammadi Z. Screening, identification, and application of nucleic acid aptamers applied in food safety biosensing. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Yao X, Liu P, Chen B, Wang X, Tao F, Lin Z, Yang X. Synthetic acid stress-tolerance modules improve growth robustness and lysine productivity of industrial Escherichia coli in fermentation at low pH. Microb Cell Fact 2022; 21:68. [PMID: 35459210 PMCID: PMC9026648 DOI: 10.1186/s12934-022-01795-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
Background During fermentation, industrial microorganisms encounter multiple stresses that inhibit cell growth and decrease fermentation yields, in particular acid stress, which is due to the accumulation of acidic metabolites in the fermentation medium. Although the addition of a base to the medium can counteract the effect of acid accumulation, the engineering of acid-tolerant strains is considered a more intelligent and cost-effective solution. While synthetic biology theoretically provides a novel approach for devising such tolerance modules, in practice it is difficult to assemble stress-tolerance modules from hundreds of stress-related genes. Results In this study, we designed a set of synthetic acid-tolerance modules for fine-tuning the expression of multi-component gene blocks comprising a member of the proton-consuming acid resistance system (gadE), a periplasmic chaperone (hdeB), and reactive oxygen species (ROS) scavengers (sodB and katE). Directed evolution was used to construct an acid-responsive asr promoter library, from which four variants were selected and used in the synthetic modules. The module variants were screened in a stepwise manner under mild acidic conditions (pH 5–6), first by cell growth using the laboratory Escherichia coli strain MG1655 cultured in microplates, and then by lysine production performance using the industrial lysine-producing E. coli strain MG1655 SCEcL3 cultured first in multiple 10-mL micro-bioreactors, and then in 1.3-L parallel bioreactors. The procedure resulted in the identification of a best strain with lysine titer and yield at pH 6.0 comparable to the parent strain at pH 6.8. Conclusion Our results demonstrate a promising synthetic-biology strategy to enhance the growth robustness and productivity of E. coli upon the mildly acidic conditions, in both a general lab strain MG1655 and an industrial lysine-producing strain SCEcL3, by using the stress-responsive synthetic acid-tolerance modules comprising a limited number of genes. This study provides a reliable and efficient method for achieving synthetic modules of interest, particularly in improving the robustness and productivity of industrial strains. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01795-4.
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Affiliation(s)
- Xurong Yao
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China
| | - Peng Liu
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China
| | - Bo Chen
- COFCO Nutrition & Health Research Institute, Beijing, 102209, China
| | - Xiaoyan Wang
- COFCO Nutrition & Health Research Institute, Beijing, 102209, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China.
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, Guangdong, China.
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Ren C, Zheng Y, Liu C, Mencius J, Wu Z, Quan S. Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action. J Mol Biol 2021; 434:167405. [PMID: 34914967 DOI: 10.1016/j.jmb.2021.167405] [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: 08/13/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/18/2022]
Abstract
Molecular chaperones are diverse biomacromolecules involved in the maintenance of cellular protein homeostasis (proteostasis). Here we demonstrate that in contrast to most chaperones with defined three-dimensional structures, the acid-inducible protein Asr in Escherichia coli is intrinsically disordered and exhibits varied aggregation-preventing or aggregation-promoting activities, acting as a "conditionally active chaperone". Bioinformatics and experimental analyses of Asr showed that it is devoid of hydrophobic patches but rich in positive charges and local polyproline II backbone structures. Asr contributes to the integrity of the bacterial outer membrane under mildly acidic conditions in vivo and possesses chaperone activities toward model clients in vitro. Notably, its chaperone activity is dependent on the net charges of clients: on the one hand, it inhibits the aggregation of clients with similar net charges; on the other hand, it stimulates the aggregation of clients with opposite net charges. Mutational analysis confirmed that positively charged residues in Asr are essential for the varied effects on protein aggregation, suggesting that electrostatic interactions are the major driving forces underlying Asr's proteostasis-related activity. These findings present a unique example of an intrinsically disordered molecular chaperone with distinctive dual functions-as an aggregase or as a chaperone-depending on the net charges of clients.
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Affiliation(s)
- Chang Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Yongxin Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Chunlan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Zhili Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai 200237, China.
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12
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The Two-Component System RstA/RstB Regulates Expression of Multiple Efflux Pumps and Influences Anaerobic Nitrate Respiration in Pseudomonas fluorescens. mSystems 2021; 6:e0091121. [PMID: 34726491 PMCID: PMC8562477 DOI: 10.1128/msystems.00911-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Multidrug resistance (MDR) efflux pumps are involved in bacterial intrinsic resistance to multiple antimicrobials. Expression of MDR efflux pumps can be either constitutive or transiently induced by various environmental signals, which are typically perceived by bacterial two-component systems (TCSs) and relayed to the bacterial nucleoid, where gene expression is modulated for niche adaptation. Here, we demonstrate that RstA/RstB, a TCS previously shown to control acid-induced and biofilm-related genes in Escherichiacoli, confers resistance to multiple antibiotics in Pseudomonas fluorescens by directly regulating the MDR efflux pumps EmhABC and MexCD-OprJ. Moreover, we show that phosphorylation of the conserved Asp52 residue in RstA greatly enhances RstA-DNA interaction, and regulation of the multidrug resistance by RstA/RstB is dependent on the phosphorylation of the RstA Asp52 residue by RstB. Proteome analysis reveals RstA/RstB also positively regulates the efflux pump MexEF-OprN and enzymes involved in anaerobic nitrate respiration and pyoverdine biosynthesis. Our results suggest that, by coupling the expression of multiple efflux pumps and anaerobic nitrate respiration, RstA/RstB could play a role in defense against nitrosative stress caused by anaerobic nitrate respiration. IMPORTANCE Microenvironmental hypoxia typically increases bacterial multidrug resistance by elevating expression of multidrug efflux pumps, but the precise mechanism is currently not well understood. Here, we showed that the two-component system RstA/RstB not only positively regulated expression of several efflux pumps involved in multidrug resistance, but also promoted expression of enzymes involved in anaerobic nitrate respiration and pyoverdine biosynthesis. These results suggested that, by upregulating expression of efflux pumps and pyoverdine biosynthesis-related enzymes, RstA/RstB could play a role in promoting bacterial tolerance to hypoxia by providing protection against nitrosative stress.
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13
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Matanza XM, López-Suárez L, do Vale A, Osorio CR. The two-component system RstAB regulates production of a polysaccharide capsule with a role in virulence in the marine pathogen Photobacterium damselae subsp. damselae. Environ Microbiol 2021; 23:4859-4880. [PMID: 34423883 DOI: 10.1111/1462-2920.15731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 06/23/2021] [Accepted: 07/21/2021] [Indexed: 12/29/2022]
Abstract
The marine bacterium Photobacterium damselae subsp. damselae (Pdd) causes disease in marine animals and humans. Previous studies demonstrated that mutation of the two-component system RstAB strongly impacts virulence of this pathogen, but the RstAB regulon has not been thoroughly elucidated. We here compared the transcriptomes of Pdd RM-71 and ΔrstA and ΔrstB derivatives using RNA-seq. In accordance with previous studies, RstAB positively regulated cytotoxins Dly, PhlyP and PhlyC. This analysis also demonstrated a positive regulation of outer membrane proteins, resistance against antimicrobials and potential virulence factors by this system. Remarkably, RstAB positively regulated two hitherto uncharacterised gene clusters involved in the synthesis of a polysaccharide capsule. Presence of a capsular layer in wild-type cells was confirmed by transmission electron microscopy, whereas rstA and rstB mutants were non-capsulated. Mutants for capsule synthesis genes, wza and wzc exhibited acapsular phenotypes, were impaired in resistance against the bactericidal action of fish serum and mucus, and were strongly impaired in virulence for fish, indicating a major role of capsule in virulence. Collectively, this study demonstrates that RstAB is a major positive regulator of key virulence factors including a polysaccharide capsule essential for full virulence in a pathogenic Photobacterium.
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Affiliation(s)
- Xosé M Matanza
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura López-Suárez
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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14
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Georgieva M, Heinonen T, Vitale A, Hargraves S, Causevic S, Pillonel T, Eberl L, Widmann C, Jacquier N. Bacterial surface properties influence the activity of the TAT-RasGAP 317-326 antimicrobial peptide. iScience 2021; 24:102923. [PMID: 34430812 PMCID: PMC8365389 DOI: 10.1016/j.isci.2021.102923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an increasing threat for public health, underscoring the need for new antibacterial agents. Antimicrobial peptides (AMPs) represent an alternative to classical antibiotics. TAT-RasGAP317-326 is a recently described AMP effective against a broad range of bacteria, but little is known about the conditions that may influence its activity. Using RNA-sequencing and screening of mutant libraries, we show that Escherichia coli and Pseudomonas aeruginosa respond to TAT-RasGAP317-326 by regulating metabolic and stress response pathways, possibly implicating two-component systems. Our results also indicate that bacterial surface properties, in particular integrity of the lipopolysaccharide layer, influence peptide binding and entry. Finally, we found differences between bacterial species with respect to their rate of resistance emergence against this peptide. Our findings provide the basis for future investigation on the mode of action of TAT-RasGAP317-326, which may help developing antimicrobial treatments based on this peptide.
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Affiliation(s)
- Maria Georgieva
- Department of Biomedical Sciences, University of Lausanne, Lausanne 1005, Switzerland
| | - Tytti Heinonen
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Alessandra Vitale
- Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
| | - Simone Hargraves
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Senka Causevic
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
| | - Christian Widmann
- Department of Biomedical Sciences, University of Lausanne, Lausanne 1005, Switzerland
- Corresponding author
| | - Nicolas Jacquier
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
- Corresponding author
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15
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Groisman EA, Duprey A, Choi J. How the PhoP/PhoQ System Controls Virulence and Mg 2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution. Microbiol Mol Biol Rev 2021; 85:e0017620. [PMID: 34191587 PMCID: PMC8483708 DOI: 10.1128/mmbr.00176-20] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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16
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Gao X, Xu K, Ahmad N, Qin L, Li C. Recent advances in engineering of microbial cell factories for intelligent pH regulation and tolerance. Biotechnol J 2021; 16:e2100151. [PMID: 34164941 DOI: 10.1002/biot.202100151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/12/2022]
Abstract
pH regulation is a serious concern in the industrial fermentation process as pH adjustment heavily utilizes acid/base and pollutes the environment. Under pH-stress conditions, microbial growth and production of valuable target products may be severely affected. Furthermore, some strains generating acidic or alkaline products require self pH regulation and increased tolerance against pH-stress. For pH control, synthetic biology has provided advanced engineering approaches to construct robust and more intelligent microbial strains, exhibiting tolerance to pH-stress to cope with limitations of pH regulation. This study reviewed the current progress of advanced strain evolution strategies to engineer pH-stress tolerant strains via synthetic biology. In addition, a large number of pH-responsive elements, including promoters, riboswitches, and some proteins have been investigated and applied for construction of pH-responsive genetic circuits and intelligent pH-responsive microbial strains.
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Affiliation(s)
- Xiaopeng Gao
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China.,School of Life Science, Yan'an University, Shanxi, PR China
| | - Ke Xu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China.,Tangshan Key Laboratory of Agricultural Pathogenic Fungi and Toxins, Department of Life Science, Tangshan Normal University, Tangshan, PR China
| | - Nadeem Ahmad
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Lei Qin
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China.,School of Life Science, Yan'an University, Shanxi, PR China.,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
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17
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Structural basis for promoter DNA recognition by the response regulator OmpR. J Struct Biol 2020; 213:107638. [PMID: 33152421 DOI: 10.1016/j.jsb.2020.107638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 11/21/2022]
Abstract
OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp residue in the N-terminal receiver domain (OmpRn) and recognizes the promoter DNA from its C-terminal DNA-binding domain (OmpRc) to elicit an adaptive response. Apart from that, OmpR regulates many genes in Escherichia coli and is important for virulence in several pathogens. However, the molecular mechanism of the regulation and the structural basis of OmpR-DNA binding is still not fully clear. In this study, we presented the crystal structure of OmpRc in complex with the F1 region of the ompF promoter DNA from E. coli. Our structural analysis suggested that OmpRc binds to its cognate DNA as a homodimer, only in a head-to-tail orientation. Also, the OmpRc apo-form showed a unique domain-swapped crystal structure under different crystallization conditions. Biophysical experimental data, such as NMR, fluorescent polarization and thermal stability, showed that inactive OmpR-FL (unphosphorylated) could bind to promoter DNA with a weaker binding affinity as compared with active OmpR-FL (phosphorylated) or OmpRc, and also confirmed that phosphorylation may only enhance DNA binding. Furthermore, the dimerization interfaces in the OmpRc-DNA complex structure identified in this study provide an opportunity to understand the regulatory role of OmpR and explore the potential for this "druggable" target.
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18
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Li C, Gao X, Peng X, Li J, Bai W, Zhong J, He M, Xu K, Wang Y, Li C. Intelligent microbial cell factory with genetic pH shooting (GPS) for cell self-responsive base/acid regulation. Microb Cell Fact 2020; 19:202. [PMID: 33138821 PMCID: PMC7607686 DOI: 10.1186/s12934-020-01457-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/17/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In industrial fermentation, pH fluctuation resulted from microbial metabolism influences the strain performance and the final production. The common way to control pH is adding acid or alkali after probe detection, which is not a fine-tuned method and often leads to increased costs and complex downstream processing. Here, we constructed an intelligent pH-sensing and controlling genetic circuits called "Genetic pH Shooting (GPS)" to realize microbial self-regulation of pH. RESULTS In order to achieve the self-regulation of pH, GPS circuits consisting of pH-sensing promoters and acid-/alkali-producing genes were designed and constructed. Designed pH-sensing promoters in the GPS can respond to high or low pHs and generate acidic or alkaline substances, achieving endogenously self-responsive pH adjustments. Base shooting circuit (BSC) and acid shooting circuit (ASC) were constructed and enabled better cell growth under alkaline or acidic conditions, respectively. Furthermore, the genetic circuits including GPS, BSC and ASC were applied to lycopene production with a higher yield without an artificial pH regulation compared with the control under pH values ranging from 5.0 to 9.0. In scale-up fermentations, the lycopene titer in the engineered strain harboring GPS was increased by 137.3% and ammonia usage decreased by 35.6%. CONCLUSIONS The pH self-regulation achieved through the GPS circuits is helpful to construct intelligent microbial cell factories and reduce the production costs, which would be much useful in industrial applications.
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Affiliation(s)
- Chenyi Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Xiaopeng Gao
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.,School of Life Science, Yan'an University, Shanxi, 716000, People's Republic of China
| | - Xiao Peng
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Jinlin Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Wenxin Bai
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Jiadong Zhong
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Mengchao He
- School of Life Science, Yan'an University, Shanxi, 716000, People's Republic of China
| | - Ke Xu
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Ying Wang
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.
| | - Chun Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China. .,School of Life Science, Yan'an University, Shanxi, 716000, People's Republic of China. .,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China.
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19
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Puja H, Comment G, Chassagne S, Plésiat P, Jeannot K. Coordinate overexpression of two
RND
efflux systems,
ParXY
and
TtgABC
, is responsible for multidrug resistance in
Pseudomonas putida. Environ Microbiol 2020; 22:5222-5231. [DOI: 10.1111/1462-2920.15200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Hélène Puja
- UMR 6249 Chrono‐environnement UFR Santé, Université de Bourgogne‐Franche Comté Besançon France
| | - Gwendoline Comment
- UMR 6249 Chrono‐environnement UFR Santé, Université de Bourgogne‐Franche Comté Besançon France
| | - Sophie Chassagne
- UMR 6249 Chrono‐environnement UFR Santé, Université de Bourgogne‐Franche Comté Besançon France
| | - Patrick Plésiat
- UMR 6249 Chrono‐environnement UFR Santé, Université de Bourgogne‐Franche Comté Besançon France
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon Besançon France
| | - Katy Jeannot
- UMR 6249 Chrono‐environnement UFR Santé, Université de Bourgogne‐Franche Comté Besançon France
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon Besançon France
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20
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Ogasawara H, Ishizuka T, Hotta S, Aoki M, Shimada T, Ishihama A. Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12. Microbiology (Reading) 2020; 166:880-890. [DOI: 10.1099/mic.0.000947] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Under stressful conditions,
Escherichia coli
forms biofilm for survival by sensing a variety of environmental conditions. CsgD, the master regulator of biofilm formation, controls cell aggregation by directly regulating the synthesis of Curli fimbriae. In agreement of its regulatory role, as many as 14 transcription factors (TFs) have so far been identified to participate in regulation of the csgD promoter, each monitoring a specific environmental condition or factor. In order to identify the whole set of TFs involved in this typical multi-factor promoter, we performed in this study ‘promoter-specific transcription-factor’ (PS-TF) screening in vitro using a set of 198 purified TFs (145 TFs with known functions and 53 hitherto uncharacterized TFs). A total of 48 TFs with strong binding to the csgD promoter probe were identified, including 35 known TFs and 13 uncharacterized TFs, referred to as Y-TFs. As an attempt to search for novel regulators, in this study we first analysed a total of seven Y-TFs, including YbiH, YdcI, YhjC, YiaJ, YiaU, YjgJ and YjiR. After analysis of curli fimbriae formation, LacZ-reporter assay, Northern-blot analysis and biofilm formation assay, we identified at least two novel regulators, repressor YiaJ (renamed PlaR) and activator YhjC (renamed RcdB), of the csgD promoter.
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Affiliation(s)
- Hiroshi Ogasawara
- Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Asahi 3-1-1, Matsumoto, 390–8621, Japan
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Toshiyuki Ishizuka
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Shuhei Hotta
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Michiko Aoki
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, 1-1-1 Higashi Mita, Tama-ku, Kawasaki, Kanagawa 214–8571, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
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21
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Liu R, Liang L, Freed EF, Choudhury A, Eckert CA, Gill RT. Engineering regulatory networks for complex phenotypes in E. coli. Nat Commun 2020; 11:4050. [PMID: 32792485 PMCID: PMC7426931 DOI: 10.1038/s41467-020-17721-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli, with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.
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Affiliation(s)
- Rongming Liu
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, USA
| | - Liya Liang
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, USA
| | - Emily F Freed
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, USA
| | - Alaksh Choudhury
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, USA
| | - Carrie A Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, USA.,National Renewable Energy Laboratory (NREL), Golden, Colorado, USA
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, USA. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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22
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Gerken H, Vuong P, Soparkar K, Misra R. Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli. mBio 2020; 11:e01192-20. [PMID: 32576675 PMCID: PMC7315122 DOI: 10.1128/mbio.01192-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 12/31/2022] Open
Abstract
Escherichia coli secretes high-affinity Fe3+ chelators to solubilize and transport chelated Fe3+ via specific outer membrane receptors. In microaerobic and anaerobic growth environments, where the reduced Fe2+ form is predominant, ferrous transport systems fulfill the bacterial need for iron. Expression of genes coding for iron metabolism is controlled by Fur, which when bound to Fe2+ acts as a repressor. Work carried out here shows that the constitutively activated EnvZ/OmpR two-component system, which normally controls expression of the ompC and ompF porin genes, dramatically increases the intracellular pool of accessible iron, as determined by whole-cell electron paramagnetic resonance spectroscopy, by inducing the OmpC/FeoB-mediated ferrous transport pathway. Elevated levels of intracellular iron in turn activated Fur, which inhibited the ferric transport pathway but not the ferrous transport pathway. The data show that the positive effect of constitutively activated EnvZ/OmpR on feoB expression is sufficient to overcome the negative effect of activated Fur on feoB In a tonB mutant, which lacks functional ferric transport systems, deletion of ompR severely impairs growth on rich medium not supplemented with iron, while the simultaneous deletion of ompC and ompF is not viable. These data, together with the observation of derepression of the Fur regulon in an OmpC mutant, show that the porins play an important role in iron homeostasis. The work presented here also resolves a long-standing paradoxical observation of the effect of certain mutant envZ alleles on iron regulon.IMPORTANCE The work presented here solved a long-standing paradox of the negative effects of certain missense alleles of envZ, which codes for kinase of the EnvZ/OmpR two-component system, on the expression of ferric uptake genes. The data revealed that the constitutive envZ alleles activate the Feo- and OmpC-mediated ferrous uptake pathway to flood the cytoplasm with accessible ferrous iron. This activates the ferric uptake regulator, Fur, which inhibits ferric uptake system but cannot inhibit the feo operon due to the positive effect of activated EnvZ/OmpR. The data also revealed the importance of porins in iron homeostasis.
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Affiliation(s)
- Henri Gerken
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Phu Vuong
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Ketaki Soparkar
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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23
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Rajeev L, Garber ME, Mukhopadhyay A. Tools to map target genes of bacterial two-component system response regulators. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:267-276. [PMID: 32212247 PMCID: PMC7318608 DOI: 10.1111/1758-2229.12838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 05/05/2023]
Abstract
Studies on bacterial physiology are incomplete without knowledge of the signalling and regulatory systems that a bacterium uses to sense and respond to its environment. Two-component systems (TCSs) are among the most prevalent bacterial signalling systems, and they control essential and secondary physiological processes; however, even in model organisms, we lack a complete understanding of the signals sensed, the phosphotransfer partners and the functions regulated by these systems. In this review, we discuss several tools to map the genes targeted by transcriptionally acting TCSs. Many of these tools have been used for studying individual TCSs across diverse species, but systematic approaches to delineate entire signalling networks have been very few. Since genome sequences and high-throughput technologies are now readily available, the methods presented here can be applied to characterize the entire DNA-binding TCS signalling network in any bacterial species and are especially useful for non-model environmental bacteria.
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Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Megan E. Garber
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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24
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Stirling F, Naydich A, Bramante J, Barocio R, Certo M, Wellington H, Redfield E, O’Keefe S, Gao S, Cusolito A, Way J, Silver P. Synthetic Cassettes for pH-Mediated Sensing, Counting, and Containment. Cell Rep 2020; 30:3139-3148.e4. [DOI: 10.1016/j.celrep.2020.02.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/15/2019] [Accepted: 02/07/2020] [Indexed: 12/18/2022] Open
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25
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Rottinghaus AG, Amrofell MB, Moon TS. Biosensing in Smart Engineered Probiotics. Biotechnol J 2020; 15:e1900319. [PMID: 31860168 DOI: 10.1002/biot.201900319] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/05/2019] [Indexed: 01/01/2023]
Abstract
Engineered microbes are exciting alternatives to current diagnostics and therapeutics. Researchers have developed a wide range of genetic tools and parts to engineer probiotic and commensal microbes. Among these tools and parts, biosensors allow the microbes to sense and record or to sense and respond to chemical and environmental signals in the body, enabling them to report on health conditions of the animal host and/or deliver therapeutics in a controlled manner. This review focuses on how biosensing is applied to engineer "smart" microbes for in vivo diagnostic, therapeutic, and biocontainment goals. Hurdles that need to be overcome when transitioning from high-throughput in vitro systems to low-throughput in vivo animal models, new technologies that can be implemented to alleviate this experimental gap, and areas where future advancements can be made to maximize the utility of biosensing for medical applications are also discussed. As technologies for engineering microbes continue to be developed, these engineered organisms will be used to address many medical challenges.
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Affiliation(s)
- Austin G Rottinghaus
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Matthew B Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
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26
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Gao Q, Su S, Li X, Wang H, Liu J, Gao S. Transcriptional analysis of RstA/RstB in avian pathogenic Escherichia coli identifies its role in the regulation of hdeD-mediated virulence and survival in chicken macrophages. Vet Microbiol 2019; 241:108555. [PMID: 31928702 DOI: 10.1016/j.vetmic.2019.108555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 10/25/2022]
Abstract
Avian pathogenic Escherichia coli (APEC) causes avian colibacillosis in poultry, which is characterized by systemic infections such as septicemia, air sacculitis, and pericarditis. APEC uses two-component regulatory systems (TCSs) to handle the stressful environments present in infected hosts. While many TCSs in E. coli have been well characterized, the RstA/RstB system in APEC has not been thoroughly investigated. The involvement of the RstA regulator in APEC pathogenesis was demonstrated during previous studies investigating its role in APEC persistence in chicken macrophages and respiratory infections. However, the mechanism underlying this phenomenon has not been clarified. Transcriptional analysis of the effect of rstAB deletion was therefore performed to improve the understanding of the RstA/RstB regulatory mechanism, and particularly its role in virulence. The transcriptomes of the rstAB mutant and the wild-type strain E058 were compared during their growth in the bloodstreams of challenged chickens. Overall, 198 differentially expressed (DE) genes were identified, and these indicated that RstA/RstB mainly regulates systems involved in nitrogen metabolism, iron acquisition, and acid resistance. Phenotypic assays indicated that the rstAB mutant responded more to an acidic pH than the wild-type strain did, possibly because of the repression of the acid-resistance operons hdeABD and gadABE by the deletion of rstAB. Based on the reported RstA box motif TACATNTNGTTACA, we identified four possible RstA target genes (hdeD, fadE, narG, and metE) among the DE genes. An electrophoretic mobility shift assay confirmed that RstA binds directly to the promoter of hdeD, and β-galactosidase assays showed that hdeD expression was reduced by rstAB deletion, indicating that RstA directly regulates hdeD expression. The hdeD mutation resulted in virulence attenuation in both cultured chicken macrophages and experimentally infected chickens. In conclusion, our data suggest that RstA affects APEC E058 virulence partly by directly regulating the acidic resistance gene hdeD.
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Affiliation(s)
- Qingqing Gao
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China
| | - Senyan Su
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China
| | - Xi Li
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China
| | - Hang Wang
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China
| | - Jinbiao Liu
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China
| | - Song Gao
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
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27
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Ogasawara H, Ishizuka T, Yamaji K, Kato Y, Shimada T, Ishihama A. Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12. FEMS Microbiol Lett 2019; 366:5675631. [PMID: 31834370 DOI: 10.1093/femsle/fnz251] [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: 07/29/2019] [Accepted: 12/12/2019] [Indexed: 12/29/2022] Open
Abstract
Pyruvate, the key regulator in connection of a variety of metabolic pathways, influences transcription of the Escherichia coli genome through controlling the activity of two pyruvate-sensing two-component systems (TCSs), BtsSR and PyrSR. Previously, we identified the whole set of regulatory targets of PyrSR with low-affinity to pyruvate. Using gSELEX screening system, we found here that BtsSR with high-affinity to pyruvate regulates more than 100 genes including as many as 13 transcription factors genes including the csgD gene encoding the master regulator of biofilm formation. CsgD regulates more than 20 target genes including the csg operons encoding the Curli fimbriae. In addition, we identified the csgBAC as one of the regulatory targets of BtsR, thus indicating the involvement of two pyruvate-dependent regulatory pathways of the curli formation: indirect regulation by CsgD; and direct regulation by BtsR. Based on the findings of the whole set of regulatory targets by two pyruvate-sensing BtsR and PyrR, we further propose an innovative concept that the pyruvate level-dependent regulation of different gene sets takes place through two pyruvate-sensing TCS systems, high-affinity BtsSR and low-affinity PyrSR to pyruvate.
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Affiliation(s)
- Hiroshi Ogasawara
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan.,Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa 8304, Kamiina, Nagano 399-4598, Japan.,Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Asahi 3-1-1, Matsumoto, 390-8621, Japan
| | - Toshiyuki Ishizuka
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
| | - Kotaro Yamaji
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
| | - Yuki Kato
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Tokida 3-15-1, Ueda, Nagano 386-8567, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, 1-1-1 Higashi Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
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28
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Liu Y, Li S, Li W, Wang P, Ding P, Li L, Wang J, Yang P, Wang Q, Xu T, Xiong Y, Yang B. RstA, a two-component response regulator, plays important roles in multiple virulence-associated processes in enterohemorrhagic Escherichia coli O157:H7. Gut Pathog 2019; 11:53. [PMID: 31695752 PMCID: PMC6824119 DOI: 10.1186/s13099-019-0335-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/24/2019] [Indexed: 01/09/2023] Open
Abstract
Background Enterohemorrhagic Escherichia coli O157:H7 (EHEC O157) causes bloody diarrhea and hemolytic-uremic syndrome. EHEC O157 encounters varied microenvironments during infection, and can efficiently adapt to these using the two-component system (TCS). Recently, a functional TCS, RstAB, has been implicated in the regulation of virulence of several bacterial pathogens. However, the regulatory function of RstAB in EHEC O157 is poorly understood. This study aimed at providing insights into the global effects of RstA on gene expression in EHEC O157. Results In the present study, we analyzed gene expression differences between the EHEC O157 wild-type strain and a ΔrstA mutant using RNA-seq technology. Genes with differential expression in the ΔrstA mutant compared to that in the wild-type strain were identified and grouped into clusters of orthologous categories. RstA promoted EHEC O157 LEE gene expression, adhesion in vitro, and colonization in vivo by indirect regulation. We also found that RstA could bind directly to the promoter region of hdeA and yeaI to enhance acid tolerance and decrease biofilm formation by modulating the concentration of c-di-GMP. Conclusions In summary, the RstAB TCS in EHEC O157 plays a major role in the regulation of virulence, acid tolerance, and biofilm formation. We clarified the regulatory function of RstA, providing an insight into mechanisms that may be potential drug targets for treatment of EHEC O157-related infections.
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Affiliation(s)
- Yutao Liu
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Shujie Li
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Wendi Li
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Peisheng Wang
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Peng Ding
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Lingyu Li
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Junyue Wang
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Pan Yang
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Qian Wang
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Tingting Xu
- 3Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020 People's Republic of China
| | - Yingying Xiong
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
| | - Bin Yang
- 1The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071 People's Republic of China.,TEDA, Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457 People's Republic of China
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29
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Andreassen PR, Pettersen JS, Szczerba M, Valentin-Hansen P, Møller-Jensen J, Jørgensen MG. sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA. Nucleic Acids Res 2019; 46:6746-6760. [PMID: 29905843 PMCID: PMC6061853 DOI: 10.1093/nar/gky479] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022] Open
Abstract
Production of curli, extracellular protein structures important for Escherichia coli biofilm formation, is governed by a highly complex regulatory mechanism that integrates multiple environmental signals through the involvement of numerous proteins and small non-coding RNAs (sRNAs). No less than seven sRNAs (McaS, RprA, GcvB, RydC, RybB, OmrA and OmrB) are known to repress the expression of the curli activator CsgD. Many of the sRNAs repress CsgD production by binding to the csgD mRNA at sites far upstream of the ribosomal binding site. The precise mechanism behind sRNA-mediated regulation of CsgD synthesis is largely unknown. In this study, we identify a conserved A/U-rich region in the csgD mRNA 5′ untranslated region, which is cleaved upon binding of the small RNAs, McaS, RprA or GcvB, to sites located more than 30 nucleotides downstream. Mutational analysis shows that the A/U-rich region as well as an adjacent stem–loop structure are required for McaS-stimulated degradation, also serving as a binding platform for the RNA chaperone Hfq. Prevention of McaS-activated cleavage completely relieves repression, suggesting that endoribonucleolytic cleavage of csgD mRNA is the primary regulatory effect exerted by McaS. Moreover, we find that McaS-mediated degradation of the csgD 5′ untranslated region requires RNase E.
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Affiliation(s)
- Patrick Rosendahl Andreassen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
| | - Jens Sivkær Pettersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
| | - Mateusz Szczerba
- Ira A. Fulton Schools of Engineering and School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Biodesign Center for Immunotherapy, Vaccines, and Virotherapy (B-CIVV), Biodesign Institute, Arizona State University. 727 East Tyler Street, Tempe, AZ 85287-5001, USA
| | - Poul Valentin-Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
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30
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Duprey A, Taib N, Leonard S, Garin T, Flandrois JP, Nasser W, Brochier-Armanet C, Reverchon S. The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity. Environ Microbiol 2019; 21:2809-2835. [PMID: 30969462 DOI: 10.1111/1462-2920.14627] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.
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Affiliation(s)
- Alexandre Duprey
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Najwa Taib
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Simon Leonard
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Tiffany Garin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Jean-Pierre Flandrois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - William Nasser
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Sylvie Reverchon
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
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31
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Terceti MS, Vences A, Matanza XM, Barca AV, Noia M, Lisboa J, dos Santos NMS, do Vale A, Osorio CR. The RstAB System Impacts Virulence, Motility, Cell Morphology, Penicillin Tolerance and Production of Type II Secretion System-Dependent Factors in the Fish and Human Pathogen Photobacterium damselae subsp. damselae. Front Microbiol 2019; 10:897. [PMID: 31105680 PMCID: PMC6491958 DOI: 10.3389/fmicb.2019.00897] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/08/2019] [Indexed: 01/04/2023] Open
Abstract
The RstB histidine kinase of the two component system RstAB positively regulates the expression of damselysin (Dly), phobalysin P (PhlyP) and phobalysin C (PhlyC) cytotoxins in the fish and human pathogen Photobacterium damselae subsp. damselae, a marine bacterium of the family Vibrionaceae. However, the function of the predicted cognate response regulator RstA has not been studied so far, and the role of the RstAB system in other cell functions and phenotypes remain uninvestigated. Here, we analyzed the effect of rstA and rstB mutations in cell fitness and in diverse virulence-related features. Both rstA and rstB mutants were severely impaired in virulence for sea bream and sea bass fish. Mutants in rstA and rstB genes were impaired in hemolysis and in Dly-dependent phospholipase activity but had intact PlpV-dependent phospholipase and ColP-dependent gelatinase activities. rstA and rstB mutants grown at 0.5% NaCl exhibited impaired swimming motility, enlarged cell size and impaired ability to separate after cell division, whereas at 1% NaCl the mutants exhibited normal phenotypes. Mutation of any of the two genes also impacted tolerance to benzylpenicillin. Notably, rstA and rstB mutants showed impaired secretion of a number of type II secretion system (T2SS)-dependent proteins, which included the three major cytotoxins Dly, PhlyP and PhlyC, as well as a putative delta-endotoxin and three additional uncharacterized proteins which might constitute novel virulence factors of this pathogenic bacterium. The analysis of the T2SS-dependent secretome of P. damselae subsp. damselae also led to the identification of RstAB-independent potential virulence factors as lipoproteins, sialidases and proteases. The RstAB regulon included plasmid, chromosome I and chromosome II-encoded genes that showed a differential distribution among isolates of this subspecies. This study establishes RstAB as a major regulator of virulence and diverse cellular functions in P. damselae subsp. damselae.
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Affiliation(s)
- Mateus S. Terceti
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Ana Vences
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Xosé M. Matanza
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Alba V. Barca
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Manuel Noia
- Departamento de Bioloxía Funcional, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Johnny Lisboa
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Nuno M. S. dos Santos
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carlos R. Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
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32
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Cross-talk between the RcsCDB and RstAB systems to control STM1485 gene expression in Salmonella Typhimurium during acid-resistance response. Biochimie 2019; 160:46-54. [PMID: 30763640 DOI: 10.1016/j.biochi.2019.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/08/2019] [Indexed: 01/13/2023]
Abstract
Bacterial survive and respond to adverse changes in the environment by regulating gene transcription through two-component regulatory systems. In Salmonella Typhimurium the STM1485 gene expression is induced under low pH (4.5) during replication inside the epithelial host cell, but it is not involved in sensing or resisting to this condition. Since the RcsCDB system is activated under acidic conditions, we investigated whether this system is able to modulate STM1485 expression. We demonstrated that acid-induced activation of the RcsB represses STM1485 transcription by directly binding to the promoter. Under the same condition, the RstA regulator activates the expression of this gene. Physiologically, we observed that RcsB-dependent repression is required for the survival of bacteria when they are exposed to pancreatic fluids. We hypothesized that STM1485 plays an important role in Salmonella adaptation to pH changes, during transition in the gastrointestinal tract. We suggest that bacteria surviving the gastrointestinal environment invade the epithelial cells, where they can remain in vacuoles. In this new environment, acidity and magnesium starvation activate the expression of the RstA regulator in a PhoPQ-dependent manner, which in turn induces STM1485 expression. These levels of STM1485 allow increased bacterial replication within vacuoles to continue the course of infection.
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33
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Zupok A, Iobbi-Nivol C, Méjean V, Leimkühler S. The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria. Metallomics 2019; 11:1602-1624. [DOI: 10.1039/c9mt00186g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.
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Affiliation(s)
- Arkadiusz Zupok
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Vincent Méjean
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Silke Leimkühler
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
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Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO, Galagan JE, Collado-Vides J. A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. BMC Biol 2018; 16:91. [PMID: 30115066 PMCID: PMC6094552 DOI: 10.1186/s12915-018-0555-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/25/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription factors and gene expression profiles. In the case of widely used model organisms, such as Escherichia coli K-12, the new knowledge gained from these approaches needs to be integrated with the legacy of accumulated knowledge from genetic and molecular biology experiments conducted in the pre-genomic era in order to attain the deepest level of understanding possible based on the available data. RESULTS In this paper, we describe an expansion of RegulonDB, the database containing the rich legacy of decades of classic molecular biology experiments supporting what we know about gene regulation and operon organization in E. coli K-12, to include the genome-wide dataset collections from 32 ChIP and 19 gSELEX publications, in addition to around 60 genome-wide expression profiles relevant to the functional significance of these datasets and used in their curation. Three essential features for the integration of this information coming from different methodological approaches are: first, a controlled vocabulary within an ontology for precisely defining growth conditions; second, the criteria to separate elements with enough evidence to consider them involved in gene regulation from isolated transcription factor binding sites without such support; and third, an expanded computational model supporting this knowledge. Altogether, this constitutes the basis for adequately gathering and enabling the comparisons and integration needed to manage and access such wealth of knowledge. CONCLUSIONS This version 10.0 of RegulonDB is a first step toward what should become the unifying access point for current and future knowledge on gene regulation in E. coli K-12. Furthermore, this model platform and associated methodologies and criteria can be emulated for gathering knowledge on other microbial organisms.
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Affiliation(s)
- Alberto Santos-Zavaleta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos México
| | - Mishael Sánchez-Pérez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos México
| | - Heladia Salgado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos México
| | | | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos México
| | - Víctor H. Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos México
| | | | - Patricia Aquino
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts USA
| | - Xin Fang
- Department of Bioengineering, University of California San Diego, La Jolla, California USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California USA
- Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - James E. Galagan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts USA
| | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos México
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts USA
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35
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Joyce AP, Havranek JJ. Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors. QUANTITATIVE BIOLOGY 2018; 6:68-84. [PMID: 37990674 PMCID: PMC10662834 DOI: 10.1007/s40484-018-0130-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 10/18/2022]
Abstract
Background Sequence-specific binding by transcription factors (TFs) plays a significant role in the selection and regulation of target genes. At the protein:DNA interface, amino acid side-chains construct a diverse physicochemical network of specific and non-specific interactions, and seemingly subtle changes in amino acid identity at certain positions may dramatically impact TF:DNA binding. Variation of these specificity-determining residues (SDRs) is a major mechanism of functional divergence between TFs with strong structural or sequence homology. Methods In this study, we employed a combination of high-throughput specificity profiling by SELEX and Spec-seq, structural modeling, and evolutionary analysis to probe the binding preferences of winged helix-turn-helix TFs belonging to the OmpR sub-family in Escherichia coli. Results We found that E. coli OmpR paralogs recognize tandem, variably spaced repeats composed of "GT-A" or "GCT"-containing half-sites. Some divergent sequence preferences observed within the "GT-A" mode correlate with amino acid similarity; conversely, "GCT"-based motifs were observed for a subset of paralogs with low sequence homology. Direct specificity profiling of a subset of OmpR homologues (CpxR, RstA, and OmpR) as well as predicted "SDR-swap" variants revealed that individual SDRs may impact sequence preferences locally through direct contact with DNA bases or distally via the DNA backbone. Conclusions Overall, our work provides evidence for a common structural code for sequence-specific wHTH:DNA interactions, and demonstrates that surprisingly modest residue changes can enable recognition of highly divergent sequence motifs. Further examination of SDR predictions will likely reveal additional mechanisms controlling the evolutionary divergence of this important class of transcriptional regulators.
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Affiliation(s)
- Adam P. Joyce
- Program in Developmental, Regenerative, and Stem Cell Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - James J. Havranek
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA
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Shimada T, Momiyama E, Yamanaka Y, Watanabe H, Yamamoto K, Ishihama A. Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12. FEMS Microbiol Lett 2018; 364:4566516. [PMID: 29087459 DOI: 10.1093/femsle/fnx220] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/24/2017] [Indexed: 01/02/2023] Open
Abstract
The genome of Escherichia coli K-12 contains ten cryptic phages, altogether constituting about 3.6% of the genome in sequence. Among more than 200 predicted genes in these cryptic phages, 14 putative transcription factor (TF) genes exist, but their regulatory functions remain unidentified. As an initial attempt to make a breakthrough for understanding the regulatory roles of cryptic phage-encoded TFs, we tried to identify the regulatory function of CP4-6 cryptic prophage-encoded YagI with unknown function. After SELEX screening, YagI was found to bind mainly at a single site within the spacer of bidirectional transcription units, yagA (encoding another uncharacterized TF) and yagEF (encoding 2-keto-3-deoxy gluconate aldolase, and dehydratase, respectively) within this prophage region. YagEF enzymes are involved in the catabolism of xylose downstream from xylonate. We then designated YagI as XynR (regulator of xylonate catabolism), one of the rare single-target TFs. In agreement with this predicted regulatory function, the activity of XynR was suggested to be controlled by xylonate. Even though low-affinity binding sites of XynR were identified in the E. coli K-12 genome, they all were inside open reading frames, implying that the regulation network of XynR is still fixed within the CR4-6 prophage without significant influence over the host E. coli K-12.
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Affiliation(s)
- Tomohiro Shimada
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Eri Momiyama
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Yuki Yamanaka
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Hiroki Watanabe
- Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Kaneyoshi Yamamoto
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan.,Department of Frontier Bioscience, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo 184-0003, Japan
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37
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Vorobyeva MA, Davydova AS, Vorobjev PE, Pyshnyi DV, Venyaminova AG. Key Aspects of Nucleic Acid Library Design for in Vitro Selection. Int J Mol Sci 2018; 19:E470. [PMID: 29401748 PMCID: PMC5855692 DOI: 10.3390/ijms19020470] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.
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Affiliation(s)
- Maria A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Pavel E. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
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Utsumi R. Bacterial signal transduction networks via connectors and development of the inhibitors as alternative antibiotics. Biosci Biotechnol Biochem 2017; 81:1663-1669. [PMID: 28743208 DOI: 10.1080/09168451.2017.1350565] [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] [Indexed: 01/03/2023]
Abstract
Bacterial cells possess a signal transduction system that differs from those described in higher organisms, including human cells. These so-called two-component signal transduction systems (TCSs) consist of a sensor (histidine kinase, HK) and a response regulator, and are involved in cellular functions, such as virulence, drug resistance, biofilm formation, cell wall synthesis, cell division. They are conserved in bacteria across all species. Although TCSs are often studied and characterized individually, they are assumed to interact with each other and form signal transduction networks within the cell. In this review, I focus on the formation of TCS networks via connectors. I also explore the possibility of using TCS inhibitors, especially HK inhibitors, as alternative antimicrobial agents.
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Affiliation(s)
- Ryutaro Utsumi
- a Department of Bioscience, Graduate School of Agriculture , Kindai University , Nara , Japan
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39
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Kay KL, Breidt F, Fratamico PM, Baranzoni GM, Kim GH, Grunden AM, Oh DH. Escherichia coli O157:H7 Acid Sensitivity Correlates with Flocculation Phenotype during Nutrient Limitation. Front Microbiol 2017; 8:1404. [PMID: 28798736 PMCID: PMC5526969 DOI: 10.3389/fmicb.2017.01404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 07/11/2017] [Indexed: 01/16/2023] Open
Abstract
Shiga toxin producing Escherichia coli (STEC) strains vary in acid resistance; however, little is known about the underlying mechanisms that result in strain specific differences. Among 25 STEC O157:H7 strains tested, 7 strains flocculated when grown statically for 18 h in minimal salts medium at 37°C, while 18 strains did not. Interestingly, the flocculation phenotype (cells came out of suspension) was found to correlate with degree of acid sensitivity in an assay with 400 mM acetic acid solution at pH 3.3 targeting acidified foods. Strains exhibiting flocculation were more acid sensitive and were designated FAS, for flocculation acid sensitive, while the acid resistant strain designated PAR for planktonic acid resistant. Flocculation was not observed for any strains during growth in complex medium (Luria Bertani broth). STEC strains B201 and B241 were chosen as representative FAS (2.4 log reduction) and PAR (0.15 log reduction) strains, respectively, due to differences in acid resistance and flocculation phenotype. Results from electron microscopy showed evidence of fimbriae production in B201, whereas fimbriae were not observed in B241.Curli fimbriae production was identified through plating on Congo red differential medium, and all FAS strains showed curli fimbriae production. Surprisingly, 5 PAR strains also had evidence of curli production. Transcriptomic and targeted gene expression data for B201 and B241indicated that csg and hde (curli and acid induced chaperone genes, respectively) expression positively correlated with the phenotypic differences observed for these strains. These data suggest that FAS strains grown in minimal medium express curli, resulting in a flocculation phenotype. This may be regulated by GcvB, which positively regulates curli fimbriae production and represses acid chaperone proteins. RpoS and other regulatory mechanisms may impact curli fimbriae production, as well. These findings may help elucidate mechanisms underlying differences among STEC strains in relating acid resistance and biofilm formation.
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Affiliation(s)
- Kathryn L. Kay
- Department of Plant and Microbial Biology, North Carolina State UniversityRaleigh, NC, United States
- Food Science Research Unit, United States Department of Agriculture-Agriculture Research ServiceRaleigh, NC, United States
| | - Frederick Breidt
- Department of Plant and Microbial Biology, North Carolina State UniversityRaleigh, NC, United States
- Food Science Research Unit, United States Department of Agriculture-Agriculture Research ServiceRaleigh, NC, United States
| | - Pina M. Fratamico
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research CenterWyndmoor, PA, United States
| | - Gian M. Baranzoni
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research CenterWyndmoor, PA, United States
| | - Gwang-Hee Kim
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research CenterWyndmoor, PA, United States
- Department of Food Science and Biotechnology, College of Bioscience and Biotechnology, Kangwon National UniversityChuncheon, South Korea
| | - Amy M. Grunden
- Department of Plant and Microbial Biology, North Carolina State UniversityRaleigh, NC, United States
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Bioscience and Biotechnology, Kangwon National UniversityChuncheon, South Korea
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40
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Sugino H, Usui T, Shimada T, Nakano M, Ogasawara H, Ishihama A, Hirata A. A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation. FEBS Lett 2017; 591:2019-2031. [PMID: 28608551 DOI: 10.1002/1873-3468.12713] [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: 02/17/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 12/23/2022]
Abstract
RcdA is a regulator of curlin subunit gene D, the master regulator of biofilm formation in Escherichia coli. Here, we determined the X-ray structure of RcdA at 2.55 Å resolution. RcdA consists of an N-terminal DNA-binding domain (DBD) containing a helix-turn-helix (HTH) motif and a C-terminal dimerization domain, and forms a homodimer in crystals. A computational docking model of the RcdA-DNA complex allowed prediction of the candidate residues responsible for DNA binding. Our structure-guided mutagenesis, in combination with gel shift assay, atomic force microscopic observation, and reporter assay, indicate that R32 in α2 of the HTH motif plays an essential role in the recognition and binding of target DNA while T46 in α3 influences the mode of oligomerization. These results provide insights into the DNA-binding mode of RcdA.
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Affiliation(s)
- Hirotaka Sugino
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Takanori Usui
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Tama-ku, Kawasaki-shi, Kanagawa, Japan
| | - Masahiro Nakano
- Department of Virus Research, Institute for Frontier Life and Medical Science, Kyoto University, Japan
| | - Hiroshi Ogasawara
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano, Japan.,Research Center for Fungal and Microbial Dynamism, Shinshu University, Nagano, Japan
| | - Akira Ishihama
- Micro-Nano Technology Research Center and Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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41
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Terceti MS, Rivas AJ, Alvarez L, Noia M, Cava F, Osorio CR. rstB Regulates Expression of the Photobacterium damselae subsp. damselae Major Virulence Factors Damselysin, Phobalysin P and Phobalysin C. Front Microbiol 2017; 8:582. [PMID: 28443076 PMCID: PMC5385354 DOI: 10.3389/fmicb.2017.00582] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/21/2017] [Indexed: 01/24/2023] Open
Abstract
The marine pathogenic bacterium Photobacterium damselae subsp. damselae causes septicemia in marine animals and in humans. The pPHDD1 plasmid-encoded hemolysins damselysin (Dly) and phobalysin P (PhlyP), and the chromosome-encoded hemolysin phobalysin C (PhlyC) constitute its main virulence factors. However, the mechanisms by which expression of these three hemolysins is regulated remain unknown. Here we report the isolation of a mini-Tn10 transposon mutant which showed a strong impairment in its hemolytic activity. The transposon disrupted a putative sensor histidine kinase gene vda_000600 (rstB), which together with vda_000601 (rstA) is predicted to encode a putative two-component regulatory system. This system showed to be homologous to the Vibrio cholerae CarSR/VprAB and Escherichia coli RstAB systems. Reconstruction of the mutant by allelic exchange of rstB showed equal impairment in hemolysis, and complementation with a plasmid expressing rstAB restored hemolysis to wild-type levels. Remarkably, we demonstrated by promoter expression analyses that the reduced hemolysis in the rstB mutant was accompanied by a strong decrease in transcription activities of the three hemolysin genes dly (damselysin), hlyApl (phobalysin P) and hlyAch (phobalysin C). Thus, RstB, encoded in the small chromosome, regulates plasmid and chromosomal virulence genes. We also found that reduced expression of the three virulence genes correlated with a strong decrease in virulence in a sea bass model, demonstrating that RstB constitutes a master regulator of the three P. damselae subsp. damselae hemolysins and plays critical roles in the pathogenicity of this bacterium. This study represents the first evidence of a direct role of a RstAB-like system in the regulation of bacterial toxins.
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Affiliation(s)
- Mateus S Terceti
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - Amable J Rivas
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Manuel Noia
- Departamento de Bioloxía Funcional, Facultade de Bioloxía - CIBUS, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
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Hoynes-O'Connor A, Shopera T, Hinman K, Creamer JP, Moon TS. Enabling complex genetic circuits to respond to extrinsic environmental signals. Biotechnol Bioeng 2017; 114:1626-1631. [PMID: 28262949 DOI: 10.1002/bit.26279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/02/2017] [Accepted: 03/01/2017] [Indexed: 02/06/2023]
Abstract
Genetic circuits have the potential to improve a broad range of metabolic engineering processes and address a variety of medical and environmental challenges. However, in order to engineer genetic circuits that can meet the needs of these real-world applications, genetic sensors that respond to relevant extrinsic and intrinsic signals must be implemented in complex genetic circuits. In this work, we construct the first AND and NAND gates that respond to temperature and pH, two signals that have relevance in a variety of real-world applications. A previously identified pH-responsive promoter and a temperature-responsive promoter were extracted from the E. coli genome, characterized, and modified to suit the needs of the genetic circuits. These promoters were combined with components of the type III secretion system in Salmonella typhimurium and used to construct a set of AND gates with up to 23-fold change. Next, an antisense RNA was integrated into the circuit architecture to invert the logic of the AND gate and generate a set of NAND gates with up to 1168-fold change. These circuits provide the first demonstration of complex pH- and temperature-responsive genetic circuits, and lay the groundwork for the use of similar circuits in real-world applications. Biotechnol. Bioeng. 2017;114: 1626-1631. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Allison Hoynes-O'Connor
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis 63130, One Brookings Dr., Box 1180, Missouri
| | - Tatenda Shopera
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis 63130, One Brookings Dr., Box 1180, Missouri
| | - Kristina Hinman
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis 63130, One Brookings Dr., Box 1180, Missouri
| | - John Philip Creamer
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis 63130, One Brookings Dr., Box 1180, Missouri.,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri
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Urano H, Yoshida M, Ogawa A, Yamamoto K, Ishihama A, Ogasawara H. Cross-regulation between two common ancestral response regulators, HprR and CusR, in Escherichia coli. MICROBIOLOGY-SGM 2017; 163:243-252. [PMID: 27983483 DOI: 10.1099/mic.0.000410] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The uncharacterized two-component system YedVW of Escherichia coli is involved in stress response to hydrogen peroxide. To identify the H2O2-sensing role of YedV, a set of single Cys-to-Ala substitution mutants were constructed. One particular mutant with C165A substitution in the membrane domain rendered YedV inactive in H2O2-dependent transcription of its regulatory target hiuH. We then proposed to rename YedVW to HprSR (hydrogen peroxide response sensor/regulator). One unique characteristic of HprR is the overlapping of its recognition sequence with that of the Cu(II)-response two-component system regulator CusR. Towards understanding this unique regulation system, in this study we analysed the interplay between HprR and CusR with respect to transcription of hiuH, a regulatory target of HprR, and cusC, a target of CusR. Under low protein concentrations in vitro and in vivo, two regulators recognize and transcribe both hiuH and cusC promoters, albeit at different efficiency, apparently in a collaborative fashion. This is a new type of transcription regulation of the common target genes in response to different external signals. Upon increase in protein concentrations, however, HprR and CusR compete with each other in transcription of the common targets, thereby exhibiting a competitive interplay.
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Affiliation(s)
- Hiroyuki Urano
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Myu Yoshida
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Ayano Ogawa
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Hiroshi Ogasawara
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan.,Research Center for Fungal and Microbial Dynamism, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan
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44
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Takada H, Shimada T, Dey D, Quyyum MZ, Nakano M, Ishiguro A, Yoshida H, Yamamoto K, Sen R, Ishihama A. Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli. PLoS One 2016; 11:e0163057. [PMID: 28005933 PMCID: PMC5179076 DOI: 10.1371/journal.pone.0163057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/01/2016] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order) and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3’ proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP) holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon), within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons are expressed independent of rRNA synthesis under specific conditions where further synthesis of ribosomes is not needed.
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Affiliation(s)
- Hiraku Takada
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
| | - Tomohiro Shimada
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
| | - Debashish Dey
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Masahiro Nakano
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Akira Ishiguro
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
| | - Hideji Yoshida
- Department of Physics, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Kaneyoshi Yamamoto
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Ranjan Sen
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
- * E-mail:
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Gao Q, Xia L, Liu J, Wang X, Gao S, Liu X. DNA microarray-mediated transcriptional profiling of avian pathogenic Escherichia coli O2 strain E058 during its infection of chicken. Microb Pathog 2016; 100:1-9. [PMID: 27569534 DOI: 10.1016/j.micpath.2016.08.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/24/2016] [Accepted: 08/24/2016] [Indexed: 01/15/2023]
Abstract
Avian pathogenic Escherichia coli (APEC) cause typical extraintestinal infections in poultry, including acute fatal septicemia, subacute pericarditis, and airsacculitis. These bacteria most often infect chickens, turkeys, ducks, and other avian species, and therefore pose a significant economic burden on the poultry industry worldwide. Few studies have analyzed the genome-wide transcriptional profile of APEC during infection in vivo. In this study, we examined the genome-wide transcriptional response of APEC O2 strain E058 in an in vivo chicken infection model to better understand the factors necessary for APEC colonization, growth, and survival in vivo. An Affymetrix multigenome DNA microarray, which contains most of the genomic open reading frames of E. coli K-12 strain MG1655, uropathogenic E. coli strain CFT073, and E. coli O157:H7 strain EDL 933, was used to profile the gene expression in APEC E058. We identified the in vivo transcriptional response of APEC E058 bacteria collected directly from the blood of infected chickens. Significant differences in expression levels were detected between the in vivo expression profile and the in vitro expression profile in LB medium. The genes highly expressed during infection were involved in metabolism, iron acquisition or transport, virulence, response to stress, and biological regulation. The reliability of the microarray data was confirmed by performing quantitative real-time PCR on 12 representative genes. Moreover, several significantly upregulated genes, including yjiY, sodA, phoB and spy, were selected to study their role in APEC pathogenesis. The data will help to better understand the mechanisms of APEC pathogenesis.
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Affiliation(s)
- Qingqing Gao
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China.
| | - Le Xia
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China.
| | - Juanhua Liu
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China.
| | - Xiaobo Wang
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China.
| | - Song Gao
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China.
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, Ministry of Agriculture, Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China.
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Maeda M, Shimada T, Ishihama A. Strength and Regulation of Seven rRNA Promoters in Escherichia coli. PLoS One 2015; 10:e0144697. [PMID: 26717514 PMCID: PMC4696680 DOI: 10.1371/journal.pone.0144697] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 11/23/2015] [Indexed: 11/18/2022] Open
Abstract
The model prokaryote Escherichia coli contains seven copies of the rRNA operon in the genome. The presence of multiple rRNA operons is an advantage for increasing the level of ribosome, the key apparatus of translation, in response to environmental conditions. The complete sequence of E. coli genome, however, indicated the micro heterogeneity between seven rRNA operons, raising the possibility in functional heterogeneity and/or differential mode of expression. The aim of this research is to determine the strength and regulation of the promoter of each rRNA operon in E. coli. For this purpose, we used the double-fluorescent protein reporter pBRP system that was developed for accurate and precise determination of the promoter strength of protein-coding genes. For application of this promoter assay vector for measurement of the rRNA operon promoters devoid of the signal for translation, a synthetic SD sequence was added at the initiation codon of the reporter GFP gene, and then approximately 500 bp-sequence upstream each 16S rRNA was inserted in front of this SD sequence. Using this modified pGRS system, the promoter activity of each rrn operon was determined by measuring the rrn promoter-directed GFP and the reference promoter-directed RFP fluorescence, both encoded by a single and the same vector. Results indicated that: the promoter activity was the highest for the rrnE promoter under all growth conditions analyzed, including different growth phases of wild-type E. coli grown in various media; but the promoter strength of other six rrn promoters was various depending on the culture conditions. These findings altogether indicate that seven rRNA operons are different with respect to the regulation mode of expression, conferring an advantage to E. coli through a more fine-tuned control of ribosome formation in a wide range of environmental situations. Possible difference in the functional role of each rRNA operon is also discussed.
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Affiliation(s)
- Michihisa Maeda
- Meiji University, Faculty of Agriculture Chemistry, Kawasaki, Kanagawa 214–8571, Japan
| | - Tomohiro Shimada
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama 226–8503, Japan
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184–8584, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184–8584, Japan
- * E-mail:
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Abstract
This review provides a brief review of the current understanding of the structure-function relationship of the Escherichia coli nucleoid developed after the overview by Pettijohn focusing on the physical properties of nucleoids. Isolation of nucleoids requires suppression of DNA expansion by various procedures. The ability to control the expansion of nucleoids in vitro has led to purification of nucleoids for chemical and physical analyses and for high-resolution imaging. Isolated E. coli genomes display a number of individually intertwined supercoiled loops emanating from a central core. Metabolic processes of the DNA double helix lead to three types of topological constraints that all cells must resolve to survive: linking number, catenates, and knots. The major species of nucleoid core protein share functional properties with eukaryotic histones forming chromatin; even the structures are different from histones. Eukaryotic histones play dynamic roles in the remodeling of eukaryotic chromatin, thereby controlling the access of RNA polymerase and transcription factors to promoters. The E. coli genome is tightly packed into the nucleoid, but, at each cell division, the genome must be faithfully replicated, divided, and segregated. Nucleoid activities such as transcription, replication, recombination, and repair are all affected by the structural properties and the special conformations of nucleoid. While it is apparent that much has been learned about the nucleoid, it is also evident that the fundamental interactions organizing the structure of DNA in the nucleoid still need to be clearly defined.
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Simm R, Ahmad I, Rhen M, Le Guyon S, Römling U. Regulation of biofilm formation in Salmonella enterica serovar Typhimurium. Future Microbiol 2015; 9:1261-82. [PMID: 25437188 DOI: 10.2217/fmb.14.88] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In animals, plants and the environment, Salmonella enterica serovar Typhimurium forms the red dry and rough (rdar) biofilm characterized by extracellular matrix components curli and cellulose. With complex expression control by at least ten transcription factors, the bistably expressed orphan response regulator CsgD directs rdar morphotype development. CsgD expression is an integral part of the Hfq regulon and the complex cyclic diguanosine monophosphate signaling network partially controlled by the global RNA-binding protein CsrA. Cell wall turnover and the periplasmic redox status regulate csgD expression on a post-transcriptional level by unknown mechanisms. Furthermore, phosphorylation of CsgD is a potential inactivation and degradation signal in biofilm dissolution. Including complex incoherent feed-forward loops, regulation of biofilm formation versus motility and virulence is of recognized complexity.
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Affiliation(s)
- Roger Simm
- Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, Oslo, Norway
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The functional landscape bound to the transcription factors of Escherichia coli K-12. Comput Biol Chem 2015; 58:93-103. [PMID: 26094112 DOI: 10.1016/j.compbiolchem.2015.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 05/31/2015] [Accepted: 06/03/2015] [Indexed: 01/05/2023]
Abstract
Motivated by the experimental evidences accumulated in the last ten years and based on information deposited in RegulonDB, literature look up, and sequence analysis, we analyze the repertoire of 304 DNA-binding Transcription factors (TFs) in Escherichia coli K-12. These regulators were grouped in 78 evolutionary families and are regulating almost half of the total genes in this bacterium. In structural terms, 60% of TFs are composed by two-domains, 30% are monodomain, and 10% three- and four-structural domains. As previously noticed, the most abundant DNA-binding domain corresponds to the winged helix-turn-helix, with few alternative DNA-binding structures, resembling the hypothesis of successful protein structures with the emergence of new ones at low scales. In summary, we identified and described the characteristics associated to the DNA-binding TF in E. coli K-12. We also identified twelve functional modules based on a co-regulated gene matrix. Finally, diverse regulons were predicted based on direct associations between the TFs and potential regulated genes. This analysis should increase our knowledge about the gene regulation in the bacterium E. coli K-12, and provide more additional clues for comprehensive modelling of transcriptional regulatory networks in other bacteria.
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Ogasawara H, Ohe S, Ishihama A. Role of transcription factor NimR (YeaM) in sensitivity control of Escherichia coli to 2-nitroimidazole. FEMS Microbiol Lett 2015; 362:1-8. [DOI: 10.1093/femsle/fnu013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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