1
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Abril AG, Calo-Mata P, Böhme K, Villa TG, Barros-Velázquez J, Sánchez-Pérez Á, Pazos M, Carrera M. Shotgun proteomic analyses of Pseudomonas species isolated from fish products. Food Chem 2024; 450:139342. [PMID: 38631198 DOI: 10.1016/j.foodchem.2024.139342] [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: 11/08/2023] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Numerous Pseudomonas species can infect aquatic animals, such as farmed rainbow trout, sea trout, sea bass, and sea bream, by causing disease or stress reactions. In aquaculture facilities, a number of Pseudomonas species have been isolated and identified as the main pathogens. The present study describes the characterization of 18 Pseudomonas strains, isolated from fish products using shotgun proteomics. The bacterial proteomes obtained were further analyzed to identify the main functional pathway proteins involved. In addition, this study revealed the presence of 1015 non-redundant peptides related to virulence factors. An additional 25 species-specific peptides were identified as putative Pseudomonas spp. biomarkers. The results constitute the largest dataset, described thus far for the rapid identification and characterization of Pseudomonas species present in edible fish; furthermore, these data can provide the basis for further research into the development of new therapies against these harmful pathogens.
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Affiliation(s)
- Ana G Abril
- Department of Food Technology, Marine Research Institute (IIM-CSIC), Spanish National Research Council (CSIC), 36208 Vigo, Spain; Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain.
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain.
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain.
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW 2006, Australia
| | - Manuel Pazos
- Department of Food Technology, Marine Research Institute (IIM-CSIC), Spanish National Research Council (CSIC), 36208 Vigo, Spain.
| | - Mónica Carrera
- Department of Food Technology, Marine Research Institute (IIM-CSIC), Spanish National Research Council (CSIC), 36208 Vigo, Spain.
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2
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Baglivo I, Malgieri G, Roop RM, Barton IS, Wang X, Russo V, Pirone L, Pedone EM, Pedone PV. MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein. Mol Microbiol 2024. [PMID: 38619026 DOI: 10.1111/mmi.15261] [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: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α-proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone-like Nucleoid Structuring (H-NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H-NS-like protein, which binds AT-rich regions of genomic DNA and regulates gene expression.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roy Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ian S Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Emilia M Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
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3
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Erkelens AM, van Erp B, Meijer WJJ, Dame RT. Rok from B. subtilis: Bridging genome structure and transcription regulation. Mol Microbiol 2024. [PMID: 38511404 DOI: 10.1111/mmi.15250] [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: 01/08/2024] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid-associated proteins and liquid-liquid phase separation, and has to be compatible with replication and transcription. Possibly, genome organization plays an intrinsic role in transcription regulation, in addition to classical transcription factors. In this review, we provide arguments supporting this view using the Gram-positive bacterium Bacillus subtilis as a model. Proteins BsSMC, HBsu and Rok all impact the structure of the B. subtilis chromosome. Particularly for Rok, there is compelling evidence that it combines its structural function with a role as global gene regulator. Many studies describe either function of Rok, but rarely both are addressed at the same time. Here, we review both sides of the coin and integrate them into one model. Rok forms unusually stable DNA-DNA bridges and this ability likely underlies its repressive effect on transcription by either preventing RNA polymerase from binding to DNA or trapping it inside DNA loops. Partner proteins are needed to change or relieve Rok-mediated gene repression. Lastly, we investigate which features characterize H-NS-like proteins, a family that, at present, lacks a clear definition.
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Affiliation(s)
- Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, the Netherlands
| | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, the Netherlands
| | - Wilfried J J Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Madrid, Spain
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, the Netherlands
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4
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Liu Y, Zhou M, Bu Y, Qin L, Zhang Y, Shao S, Wang Q. Lysine acetylation regulates the AT-rich DNA possession ability of H-NS. Nucleic Acids Res 2024; 52:1645-1660. [PMID: 38059366 PMCID: PMC10899749 DOI: 10.1093/nar/gkad1172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023] Open
Abstract
H-NS, the histone-like nucleoid-structuring protein in bacteria, regulates the stability of the bacterial genome by inhibiting the transcription of horizontally transferred genes, such as the type III and type VI secretion systems (T3/T6SS). While eukaryotic histone posttranslational modifications (PTMs) have been extensively studied, little is known about prokaryotic H-NS PTMs. Here, we report that the acetylation of H-NS attenuates its ability to silence horizontally transferred genes in response to amino acid nutrition and immune metabolites. Moreover, LC-MS/MS profiling showed that the acetyllysine sites of H-NS and K120 are indispensable for its DNA-binding ability. Acetylation of K120 leads to a low binding affinity for DNA and enhances T3/T6SS expression. Furthermore, acetylation of K120 impairs the AT-rich DNA recognition ability of H-NS. In addition, lysine acetylation in H-NS modulates in vivo bacterial virulence. These findings reveal the mechanism underlying H-NS PTMs and propose a novel mechanism by which bacteria counteract the xenogeneic silencing of H-NS.
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Affiliation(s)
- Yabo Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mengqing Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yifan Bu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Liang Qin
- New Product R&D, GenScript Biotech Corporation, Nanjing 211100, China
| | - Yuanxing Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
- Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
- Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
- Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China
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5
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Moreno-Blanco A, Pluta R, Espinosa M, Ruiz-Cruz S, Bravo A. Promoter DNA recognition by the Enterococcus faecalis global regulator MafR. Front Mol Biosci 2023; 10:1294974. [PMID: 38192335 PMCID: PMC10773906 DOI: 10.3389/fmolb.2023.1294974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
When Enterococcus faecalis is exposed to changing environmental conditions, the expression of many genes is regulated at the transcriptional level. We reported previously that the enterococcal MafR protein causes genome-wide changes in the transcriptome. Here we show that MafR activates directly the transcription of the OG1RF_10478 gene, which encodes a hypothetical protein of 111 amino acid residues. We have identified the P10478 promoter and demonstrated that MafR enhances the efficiency of this promoter by binding to a DNA site that contains the -35 element. Moreover, our analysis of the OG1RF_10478 protein AlphaFold model indicates high similarity to 1) structures of EIIB components of the bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system, and 2) structures of receiver domains that are found in response regulators of two-component signal transduction systems. However, unlike typical EIIB components, OG1RF_10478 lacks a Cys or His residue at the conserved phosphorylation site, and, unlike typical receiver domains, OG1RF_10478 lacks a conserved Asp residue at the position usually required for phosphorylation. Different from EIIB components and receiver domains, OG1RF_10478 contains an insertion between residues 10 and 30 that, according to ColabFold prediction, may serve as a dimerization interface. We propose that OG1RF_10478 could participate in regulatory functions by protein-protein interactions.
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Affiliation(s)
- Ana Moreno-Blanco
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Radoslaw Pluta
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Sofía Ruiz-Cruz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Alicia Bravo
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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6
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Barton IS, Ren Z, Cribb CB, Pitzer JE, Baglivo I, Martin DW, Wang X, Roop RM. Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid. mBio 2023; 14:e0220123. [PMID: 37847580 PMCID: PMC10746212 DOI: 10.1128/mbio.02201-23] [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: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 10/19/2023] Open
Abstract
Histone-like nucleoid structuring (H-NS) and H-NS-like proteins serve as global gene silencers and work with antagonistic transcriptional activators (counter-silencers) to properly coordinate the expression of virulence genes in pathogenic bacteria. In Brucella, MucR has been proposed as a novel H-NS-like gene silencer, but direct experimental evidence is lacking. Here, we show that MucR serves as an H-NS-like silencer of the Brucella abortus genes encoding the polar autotransporter adhesins BtaE and BmaC, the c-di-GMP-specific phosphodiesterase BpdB, and the quorum-sensing regulator BabR. We also demonstrate that the MarR-type transcriptional activator MdrA can displace MucR from the btaE promoter, supporting the existence of MucR counter-silencers in Brucella. Moreover, our chromatin immunoprecipitation (ChIP)-seq analysis identified 546 MucR enrichment peaks along the genome, including in the promoters of the genes encoding the Type IV secretion machinery and effectors and the quorum-sensing regulator VjbR. Importantly, MucR ChIP-seq peaks overlap with the previously described binding sites for the transcriptional activators VjbR, BvrR, and CtrA suggesting that these regulators serve as MucR counter-silencers and work in concert with MucR to coordinate virulence gene expression in Brucella. In addition, using chromosome conformation capture (Hi-C), we show that like H-NS in Escherichia coli, MucR alters the global structure of the Brucella nucleoid. Finally, a copy of the E. coli hns rescues the distinctive growth defect and elevated btaE expression of a B. abortus mucR mutant. Together, these findings solidify the role of MucR as a novel type of H-NS-like protein and suggest that MucR's gene-silencing properties play a key role in virulence in Brucella. IMPORTANCE Histone-like nucleoid structuring (H-NS) and H-NS-like proteins coordinate host-associated behaviors in many pathogenic bacteria, often through forming silencer/counter-silencer pairs with signal-responsive transcriptional activators to tightly control gene expression. Brucella and related bacteria do not encode H-NS or homologs of known H-NS-like proteins, and it is unclear if they have other proteins that perform analogous functions during pathogenesis. In this work, we provide compelling evidence for the role of MucR as a novel H-NS-like protein in Brucella. We show that MucR possesses many of the known functions attributed to H-NS and H-NS-like proteins, including the formation of silencer/counter-silencer pairs to control virulence gene expression and global structuring of the nucleoid. These results uncover a new role for MucR as a nucleoid structuring protein and support the importance of temporal control of gene expression in Brucella and related bacteria.
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Affiliation(s)
- Ian S. Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Connor B. Cribb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Joshua E. Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Daniel W. Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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7
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Beard S, Moya-Beltrán A, Silva-García D, Valenzuela C, Pérez-Acle T, Loyola A, Quatrini R. Pangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology. Front Microbiol 2023; 14:1271138. [PMID: 37817747 PMCID: PMC10561277 DOI: 10.3389/fmicb.2023.1271138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are aerobic, chemolithoautotrophic, acidophilic sulfur-oxidizers, encompassing substantial genotypic diversity attributable to MGEs. Our search for NAP protein families (PFs) in more than 90 genomes of the different species that conform the class, revealed the presence of 1,197 proteins pertaining to 12 different NAP families, with differential occurrence and conservation across species. Pangenome-level analysis revealed 6 core NAP PFs that were highly conserved across the class, some of which also existed as variant forms of scattered occurrence, in addition to NAPs of taxa-restricted distribution. Core NAPs identified are reckoned as essential based on the conservation of genomic context and phylogenetic signals. In turn, various highly diversified NAPs pertaining to the flexible gene complement of the class, were found to be encoded in known plasmids or, larger integrated MGEs or, present in genomic loci associated with MGE-hallmark genes, pointing to their role in the stabilization/maintenance of these elements in strains and species with larger genomes. Both core and flexible NAPs identified proved valuable as markers, the former accurately recapitulating the phylogeny of the class, and the later, as seed in the bioinformatic identification of novel episomal and integrated mobile elements.
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Affiliation(s)
- Simón Beard
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ana Moya-Beltrán
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Danitza Silva-García
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Cesar Valenzuela
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Tomás Pérez-Acle
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Alejandra Loyola
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
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8
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Rashid FZM, Dame RT. Three-dimensional chromosome re-modelling: The integral mechanism of transcription regulation in bacteria. Mol Microbiol 2023; 120:60-70. [PMID: 37433047 DOI: 10.1111/mmi.15062] [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: 02/01/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 07/13/2023]
Abstract
Nucleoid-associated proteins (NAPs) are architectural proteins of the bacterial chromosome and transcription factors that dynamically organise the chromosome and regulate gene expression in response to physicochemical environmental signals. While the architectural and regulatory functions of NAPs have been verified independently, the coupling between these functions in vivo has not been conclusively proven. Here we describe a model NAP - histone-like nucleoid structuring protein (H-NS) - as a coupled sensor-effector that directly regulates gene expression by chromatin re-modelling in response to physicochemical environmental signals. We outline how H-NS-binding partners and post-translational modifications modulate the role of H-NS as a transcription factor by influencing its DNA structuring properties. We consolidate our ideas in models of how H-NS may regulate the expression of the proVWX and hlyCABD operons by chromatin re-modelling. The interplay between chromosome structure and gene expression may be a common - but, at present, under-appreciated - concept of transcription regulation in bacteria.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
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9
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The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions. Int J Mol Sci 2022; 23:ijms232415536. [PMID: 36555178 PMCID: PMC9779718 DOI: 10.3390/ijms232415536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.
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10
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Ożga K, Berlicki Ł. Miniprotein-Based Artificial Retroaldolase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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11
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Erkelens AM, Qin L, van Erp B, Miguel-Arribas A, Abia D, Keek HGJ, Markus D, Cajili MKM, Schwab S, Meijer WJJ, Dame R. The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues. Nucleic Acids Res 2022; 50:12166-12185. [PMID: 36408910 PMCID: PMC9757077 DOI: 10.1093/nar/gkac1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family.
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Affiliation(s)
| | | | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Helena G J Keek
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Dorijn Markus
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Marc K M Cajili
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Wilfried J J Meijer
- Correspondence may also be addressed to Wilfried J.J. Meijer. Tel: +34 91 196 4539;
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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12
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Shi WT, Zhang B, Li ML, Liu KH, Jiao J, Tian CF. The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes. Nucleic Acids Res 2022; 50:8580-8598. [PMID: 36007892 PMCID: PMC9410896 DOI: 10.1093/nar/gkac664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial adaptation is largely shaped by horizontal gene transfer, xenogeneic silencing mediated by lineage-specific DNA bridgers (H-NS, Lsr2, MvaT and Rok), and various anti-silencing mechanisms. No xenogeneic silencing DNA bridger is known for α-proteobacteria, from which mitochondria evolved. By investigating α-proteobacterium Sinorhizobium fredii, a facultative legume microsymbiont, here we report the conserved zinc-finger bearing MucR as a novel xenogeneic silencing DNA bridger. Self-association mediated by its N-terminal domain (NTD) is required for DNA–MucR–DNA bridging complex formation, maximizing MucR stability, transcriptional silencing, and efficient symbiosis in legume nodules. Essential roles of NTD, CTD (C-terminal DNA-binding domain), or full-length MucR in symbiosis can be replaced by non-homologous NTD, CTD, or full-length protein of H-NS from γ-proteobacterium Escherichia coli, while NTD rather than CTD of Lsr2 from Gram-positive Mycobacterium tuberculosis can replace the corresponding domain of MucR in symbiosis. Chromatin immunoprecipitation sequencing reveals similar recruitment profiles of H-NS, MucR and various functional chimeric xenogeneic silencers across the multipartite genome of S. fredii, i.e. preferring AT-rich genomic islands and symbiosis plasmid with key symbiosis genes as shared targets. Collectively, the convergently evolved DNA bridger MucR predisposed α-proteobacteria to integrate AT-rich foreign DNA including symbiosis genes, horizontal transfer of which is strongly selected in nature.
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Affiliation(s)
- Wen-Tao Shi
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Biliang Zhang
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Meng-Lin Li
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Ke-Han Liu
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
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13
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Wang Z, Reid AMA, Wilson PW, Dunn IC. Identification of the Core Promoter and Variants Regulating Chicken CCKAR Expression. Genes (Basel) 2022; 13:1083. [PMID: 35741846 PMCID: PMC9222909 DOI: 10.3390/genes13061083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023] Open
Abstract
Decreased expression of chicken cholecystokinin A receptor (CCKAR) attenuates satiety, which contributes to increased food intake and growth for modern broilers. The study aims to define the core promoter of CCKAR, and to identify variants associated with expression activity. A 21 kb region around the CCKAR was re-sequenced to detect sequence variants. A series of 5'-deleted promoter plasmids were constructed to define the core promoter of CCKAR. The effects of sequence variants located in promoter (PSNP) and conserved (CSNP) regions on promoter activity were analyzed by comparing luciferase activity between haplotypes. A total of 182 variants were found in the 21 kb region. There were no large structural variants around CCKAR. pNL-328/+183, the one with the shortest insertion, showed the highest activity among the six promoter constructs, implying that the key cis elements regulating CCKAR expression are mainly distributed 328 bp upstream. We detected significant activity differences between high- and low-growth associated haplotypes in four of the six promoter constructs. The high-growth haplotypes of constructs pNL-1646/+183, pNL-799/+183 and pNL-528/+183 showed lower activities than the low-growth haplotypes, which is consistent with decreased expression of CCKAR in high-growth chickens. Lower expression of the high-growth allele was also detected for the CSNP5-containing construct. The data suggest that the core promoter of CCKAR is located the 328 bp region upstream from the transcription start site. Lower expression activities shown by the high-growth haplotypes in the reporter assay suggest that CSNP5 and variants located between 328 bp and 1646 bp upstream form a promising molecular basis for decreased expression of CCKAR and increased growth in chickens.
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Affiliation(s)
- Zhepeng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Royal (Dick) School of Veterinary Studies, Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK; (A.M.A.R.); (P.W.W.); (I.C.D.)
| | - Angus M. A. Reid
- Royal (Dick) School of Veterinary Studies, Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK; (A.M.A.R.); (P.W.W.); (I.C.D.)
| | - Peter W. Wilson
- Royal (Dick) School of Veterinary Studies, Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK; (A.M.A.R.); (P.W.W.); (I.C.D.)
| | - Ian C. Dunn
- Royal (Dick) School of Veterinary Studies, Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK; (A.M.A.R.); (P.W.W.); (I.C.D.)
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14
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Forrest D, Warman EA, Erkelens AM, Dame RT, Grainger DC. Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity. Nat Commun 2022; 13:1149. [PMID: 35241653 PMCID: PMC8894471 DOI: 10.1038/s41467-022-28747-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms: Escherichia coli and Bacillus subtilis. In E. coli, silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the B. subtilis Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in E. coli and B. subtilis, largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of B. subtilis, transcriptional promiscuity must be overcome to silence horizontally acquired DNA in E. coli. Bacteria use specific silencing proteins to prevent spurious transcription of horizontally acquired DNA. Here, Forrest et al. describe differences in silencing strategies between E. coli and Bacillus subtilis, driven by the respective specificities of the silencing protein and the RNA polymerase in each organism.
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Affiliation(s)
- David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Emily A Warman
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK.
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15
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The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity. THE ISME JOURNAL 2022; 16:738-749. [PMID: 34584215 PMCID: PMC8857273 DOI: 10.1038/s41396-021-01118-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 02/08/2023]
Abstract
Foreign AT-rich genes drive bacterial adaptation to new niches while challenging the existing regulation network. Here we report that MucR, a conserved regulator in α-proteobacteria, balances adaptation and regulatory integrity in Sinorhizobium fredii, a facultative microsymbiont of legumes. Chromatin immunoprecipitation sequencing coupled with transcriptomic data reveal that average transcription levels of both target and non-target genes, under free-living and symbiotic conditions, increase with their conservation levels. Targets involved in environmental adaptation and symbiosis belong to genus or species core and can be repressed or activated by MucR in a condition-dependent manner, implying regulatory integrations. However, most targets are enriched in strain-specific genes of lower expression levels and higher AT%. Within each conservation levels, targets have higher AT% and average transcription levels than non-target genes and can be further up-regulated in the mucR mutant. This is consistent with higher AT% of spacers between -35 and -10 elements of promoters for target genes, which enhances transcription. The MucR recruitment level linearly increases with AT% and the number of a flexible pattern (with periodic repeats of Ts) of target sequences. Collectively, MucR directly represses AT-rich foreign genes with predisposed high transcription potential while progressive erosions of its target sites facilitate regulatory integrations of foreign genes.
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16
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Abstract
AtxA, the master virulence regulator of Bacillus anthracis, regulates the expression of three toxins and genes for capsule formation that are required for the pathogenicity of B. anthracis. Recent transcriptome analyses showed that AtxA affects a large number of genes on the chromosome and plasmids, suggesting a role as a global regulator. However, information on genes directly regulated by AtxA is scarce. In this work, we conducted genome-wide analyses and cataloged the binding sites of AtxA in vivo and transcription start sites on the B. anthracis genome. By integrating these results, we detected eight genes as direct regulons of AtxA. These consisted of five protein-coding genes, including two of the three toxin genes, and three genes encoding the small RNAs XrrA and XrrB and a newly discovered 95-nucleotide small RNA, XrrC. Transcriptomes from single-knockout mutants of these small RNAs revealed changes in the transcription levels of genes related to the aerobic electron transport chain, heme biosynthesis, and amino acid metabolism, suggesting their function for the control of cell physiology. These results reveal the first layer of the gene regulatory network for the pathogenicity of B. anthracis and provide a data set for the further study of the genomics and genetics of B. anthracis. IMPORTANCEBacillus anthracis is the Gram-positive bacterial species that causes anthrax. Anthrax is still prevalent in countries mainly in Asia and Africa, where it causes economic damage and remains a public health issue. The mechanism of pathogenicity is mainly explained by the three toxin proteins expressed from the pXO1 plasmid and by proteins involved in capsule formation expressed from the pXO2 plasmid. AtxA is a protein expressed from the pXO1 plasmid that is known to upregulate genes involved in toxin production and capsule formation and is thus considered the master virulence regulator of B. anthracis. Therefore, understanding the detailed mechanism of gene regulation is important for the control of anthrax. The significance of this work lies in the identification of genes that are directly regulated by AtxA via genome-wide analyses. The results reveal the first layer of the gene regulatory network for the pathogenicity of B. anthracis and provide useful resources for a further understanding of B. anthracis.
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17
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Serrano E, Torres R, Alonso JC. Nucleoid-associated Rok differentially affects chromosomal transformation on Bacillus subtilis recombination-deficient cells. Environ Microbiol 2021; 23:3318-3331. [PMID: 33973337 DOI: 10.1111/1462-2920.15562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022]
Abstract
Rok, a Bacillus subtilis nucleoid-associated protein (NAP), negatively regulates competence development and silences xenogeneic genes. We show that rok inactivation increases rpoB482 natural intraspecies chromosomal transformation (CT) and plasmid transformation to a different extent. In ΔaddAB, ΔrecO, recF15, ΔrecU, ΔruvAB or rec+ cells intraspecies CT significantly increases, but the ΔrecD2 mutation reduces, and the ΔrecX, ΔradA or ΔdprA mutation further decreases CT in the Δrok context when compared to rok+ cells. These observations support the idea that rok inactivation, by altering the topology of the recipient DNA, differentially affects the integration of homologous DNA in rec-deficient strains, and in minor extent the competent subpopulation size. The impairment of other NAP (Hbsu or LrpC) also increased intra- and interspecies CT (nonself-DNA, ~8% nucleotide sequence divergence) in rec+ cells, but differentially reduced both types of CTs in certain rec-deficient strains. We describe that rok inactivation significantly stimulates intra and interspecies CT but differentially reduces them in transformation-deficient cells, perhaps by altering the nucleoid architecture. We extend the observation to other NAPs (Hbsu, LrpC).
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Affiliation(s)
- Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, 28049, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, 28049, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, 28049, Spain
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18
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Duan B, Ding P, Navarre WW, Liu J, Xia B. Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol 2021; 38:4135-4148. [PMID: 34003286 PMCID: PMC8476142 DOI: 10.1093/molbev/msab136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
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19
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Lippa AM, Gebhardt MJ, Dove SL. H-NS-like proteins in Pseudomonas aeruginosa coordinately silence intragenic transcription. Mol Microbiol 2020; 115:1138-1151. [PMID: 33245158 DOI: 10.1111/mmi.14656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 01/22/2023]
Abstract
The H-NS-like proteins MvaT and MvaU act coordinately as global repressors in Pseudomonas aeruginosa by binding to AT-rich regions of the chromosome. Although cells can tolerate loss of either protein, identifying their combined regulatory effects has been challenging because the loss of both proteins is lethal due to induction of prophage Pf4 and subsequent superinfection of the cell. In other bacteria, H-NS promotes the cellular fitness by inhibiting intragenic transcription from AT-rich target regions, preventing them from sequestering RNA polymerase; however, it is not known whether MvaT and MvaU function similarly. Here, we utilize a parental strain that cannot be infected by Pf4 phage to define the collective MvaT and MvaU regulon and demonstrate that the combined loss of both MvaT and MvaU leads to increased intragenic transcription from loci directly controlled by these proteins. We further show that the loss of MvaT and MvaU leads to a striking redistribution of RNA polymerase containing σ70 to genomic regions vacated by these proteins. Our findings suggest that the ability of H-NS-like proteins to repress intragenic transcription is a universal function of these proteins and point to a second mechanism by which MvaT and MvaU may contribute to the growth of P. aeruginosa.
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Affiliation(s)
- Andrew M Lippa
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J Gebhardt
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Simon L Dove
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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20
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Jiao J, Tian CF. Ancestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer? Comput Struct Biotechnol J 2020; 18:3623-3631. [PMID: 33304460 PMCID: PMC7710501 DOI: 10.1016/j.csbj.2020.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.
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Affiliation(s)
- Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
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21
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Qin L, Bdira FB, Sterckx YGJ, Volkov AN, Vreede J, Giachin G, van Schaik P, Ubbink M, Dame RT. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Res 2020; 48:2156-2172. [PMID: 31925429 PMCID: PMC7039000 DOI: 10.1093/nar/gkz1226] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/29/2019] [Accepted: 12/19/2019] [Indexed: 01/07/2023] Open
Abstract
H-NS proteins act as osmotic sensors translating changes in osmolarity into altered DNA binding properties, thus, regulating enterobacterial genome organization and genes transcription. The molecular mechanism underlying the switching process and its conservation among H-NS family members remains elusive. Here, we focus on the H-NS family protein MvaT from Pseudomonas aeruginosa and demonstrate experimentally that its protomer exists in two different conformations, corresponding to two different functional states. In the half-opened state (dominant at low salt) the protein forms filaments along DNA, in the fully opened state (dominant at high salt) the protein bridges DNA. This switching is a direct effect of ionic strength on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of MvaT. The asymmetric charge distribution and intramolecular interactions are conserved among the H-NS family of proteins. Therefore, our study establishes a general paradigm for the molecular mechanistic basis of the osmosensitivity of H-NS proteins.
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Affiliation(s)
- Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Yann G J Sterckx
- Laboratory of Medical Biochemistry, University of Antwerp, Campus Drie Eiken, University Square 1, 2610 Wilrijk, Belgium
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium.,Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jocelyne Vreede
- Department of Computational Chemistry, Van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - Peter van Schaik
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
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22
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Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of Corynebacterium glutamicum as a Model. mBio 2020; 11:mBio.02273-19. [PMID: 32019787 PMCID: PMC7002338 DOI: 10.1128/mbio.02273-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lsr2-like nucleoid-associated proteins play an important role as xenogeneic silencers (XS) of horizontally acquired genomic regions in actinobacteria. In this study, we systematically analyzed the in vivo constraints underlying silencing and counter-silencing of the Lsr2-like protein CgpS in Corynebacterium glutamicum Genome-wide analysis revealed binding of CgpS to regions featuring a distinct drop in GC profile close to the transcription start site (TSS) but also identified an overrepresented motif with multiple A/T steps at the nucleation site of the nucleoprotein complex. Binding of specific transcription factors (TFs) may oppose XS activity, leading to counter-silencing. Following a synthetic counter-silencing approach, target gene activation was realized by inserting operator sites of an effector-responsive TF within various CgpS target promoters, resulting in increased promoter activity upon TF binding. Analysis of reporter constructs revealed maximal counter-silencing when the TF operator site was inserted at the position of maximal CgpS coverage. This principle was implemented in a synthetic toggle switch, which features a robust and reversible response to effector availability, highlighting the potential for biotechnological applications. Together, our results provide comprehensive insights into how Lsr2 silencing and counter-silencing shape evolutionary network expansion in this medically and biotechnologically relevant bacterial phylum.IMPORTANCE In actinobacteria, Lsr2-like nucleoid-associated proteins function as xenogeneic silencers (XS) of horizontally acquired genomic regions, including viral elements, virulence gene clusters in Mycobacterium tuberculosis, and genes involved in cryptic specialized metabolism in Streptomyces species. Consequently, a detailed mechanistic understanding of Lsr2 binding in vivo is relevant as a potential drug target and for the identification of novel bioactive compounds. Here, we followed an in vivo approach to investigate the rules underlying xenogeneic silencing and counter-silencing of the Lsr2-like XS CgpS from Corynebacterium glutamicum Our results demonstrated that CgpS distinguishes between self and foreign by recognizing a distinct drop in GC profile in combination with a short, sequence-specific motif at the nucleation site. Following a synthetic counter-silencer approach, we studied the potential and constraints of transcription factors to counteract CgpS silencing, thereby facilitating the integration of new genetic traits into host regulatory networks.
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23
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Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands. Genes (Basel) 2020; 11:genes11020142. [PMID: 32013150 PMCID: PMC7074111 DOI: 10.3390/genes11020142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.
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24
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Qin L, Erkelens AM, Ben Bdira F, Dame RT. The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins. Open Biol 2019; 9:190223. [PMID: 31795918 PMCID: PMC6936261 DOI: 10.1098/rsob.190223] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/08/2019] [Indexed: 12/15/2022] Open
Abstract
Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns- phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.
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Affiliation(s)
- L. Qin
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - A. M. Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - F. Ben Bdira
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - R. T. Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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25
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McCall RM, Sievers ME, Fattah R, Ghirlando R, Pomerantsev AP, Leppla SH. Bacillus anthracis Virulence Regulator AtxA Binds Specifically to the pagA Promoter Region. J Bacteriol 2019; 201:e00569-19. [PMID: 31570528 PMCID: PMC6832065 DOI: 10.1128/jb.00569-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 01/12/2023] Open
Abstract
Anthrax toxin activator (AtxA) is the master virulence gene regulator of Bacillus anthracis It regulates genes on the chromosome as well as the pXO1 and pXO2 plasmids. It is not clear how AtxA regulates these genes, and direct binding of AtxA to its targets has not been shown. It has been previously suggested that AtxA and other proteins in the Mga/AtxA global transcriptional regulators family bind to the curvature of their DNA targets, although this has never been experimentally proven. Using electrophoretic mobility shift assays, we demonstrate that AtxA binds directly to the promoter region of pagA upstream of the RNA polymerase binding site. We also demonstrate that in vitro, CO2 appears to have no role in AtxA binding. However, phosphomimetic and phosphoablative substitutions in the phosphotransferase system (PTS) regulation domains (PRDs) do appear to influence AtxA binding and pagA regulation. In silico, in vitro, and in vivo analyses demonstrate that one of two hypothesized stem-loops located upstream of the RNA polymerase binding site in the pagA promoter region is important for AtxA binding in vitro and pagA regulation in vivo Our study clarifies the mechanism by which AtxA interacts with one of its targets.IMPORTANCE Anthrax toxin activator (AtxA) regulates the major virulence genes in Bacillus anthracis The bacterium produces the anthrax toxins, and understanding the mechanism of toxin production may facilitate the development of therapeutics for B. anthracis infection. Since the discovery of AtxA 25 years ago, the mechanism by which it regulates its targets has largely remained a mystery. Here, we provide evidence that AtxA binds to the promoter region of the pagA gene encoding the main central protective antigen (PA) component of the anthrax toxin. These data suggest that AtxA binding plays a direct role in gene regulation. Our work also assists in clarifying the role of CO2 in AtxA's gene regulation and provides more evidence for the role of AtxA phosphorylation in virulence gene regulation.
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Affiliation(s)
- Rita M McCall
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Mary E Sievers
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rasem Fattah
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrei P Pomerantsev
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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26
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Chromosome organization in bacteria: mechanistic insights into genome structure and function. Nat Rev Genet 2019; 21:227-242. [DOI: 10.1038/s41576-019-0185-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/28/2022]
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27
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Pfeifer E, Hünnefeld M, Popa O, Frunzke J. Impact of Xenogeneic Silencing on Phage-Host Interactions. J Mol Biol 2019; 431:4670-4683. [PMID: 30796986 PMCID: PMC6925973 DOI: 10.1016/j.jmb.2019.02.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
Phages, viruses that prey on bacteria, are the most abundant and diverse inhabitants of the Earth. Temperate bacteriophages can integrate into the host genome and, as so-called prophages, maintain a long-term association with their host. The close relationship between host and virus has significantly shaped microbial evolution and phage elements may benefit their host by providing new functions. Nevertheless, the strong activity of phage promoters and potentially toxic gene products may impose a severe fitness burden and must be tightly controlled. In this context, xenogeneic silencing (XS) proteins, which can recognize foreign DNA elements, play an important role in the acquisition of novel genetic information and facilitate the evolution of regulatory networks. Currently known XS proteins fall into four classes (H-NS, MvaT, Rok and Lsr2) and have been shown to follow a similar mode of action by binding to AT-rich DNA and forming an oligomeric nucleoprotein complex that silences gene expression. In this review, we focus on the role of XS proteins in phage-host interactions by highlighting the important function of XS proteins in maintaining the lysogenic state and by providing examples of how phages fight back by encoding inhibitory proteins that disrupt XS functions in the host. Sequence analysis of available phage genomes revealed the presence of genes encoding Lsr2-type proteins in the genomes of phages infecting Actinobacteria. These data provide an interesting perspective for future studies to elucidate the impact of phage-encoded XS homologs on the phage life cycle and phage-host interactions.
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Affiliation(s)
- Eugen Pfeifer
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
| | - Max Hünnefeld
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Ovidiu Popa
- Heinrich Heine Universität Düsseldorf, Institute for Quantitative and Theoretical Biology, 40223 Düsseldorf, Germany
| | - Julia Frunzke
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
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28
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Gulvady R, Gao Y, Kenney LJ, Yan J. A single molecule analysis of H-NS uncouples DNA binding affinity from DNA specificity. Nucleic Acids Res 2019; 46:10216-10224. [PMID: 30239908 PMCID: PMC6212787 DOI: 10.1093/nar/gky826] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/06/2018] [Indexed: 12/29/2022] Open
Abstract
Heat-stable nucleoid structuring protein (H-NS) plays a crucial role in gene silencing within prokaryotic cells and is important in pathogenesis. It was reported that H-NS silences nearly 5% of the genome, yet the molecular mechanism of silencing is not well understood. Here, we employed a highly-sensitive single-molecule counting approach, and measured the dissociation constant (KD) of H-NS binding to single DNA binding sites. Charged residues in the linker domain of H-NS provided the most significant contribution to DNA binding affinity. Although H-NS was reported to prefer A/T-rich DNA (a feature of pathogenicity islands) over G/C-rich DNA, the dissociation constants obtained from such sites were nearly identical. Using a hairpin unzipping assay, we were able to uncouple non-specific DNA binding steps from nucleation site binding and subsequent polymerization. We propose a model in which H-NS initially engages with non-specific DNA via reasonably high affinity (∼60 nM KD) electrostatic interactions with basic residues in the linker domain. This initial contact enables H-NS to search along the DNA for specific nucleation sites that drive subsequent polymerization and gene silencing.
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Affiliation(s)
- Ranjit Gulvady
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yunfeng Gao
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.,Jesse Brown Veterans Administration Medical Center, Chicago, IL 6061, USA.,Department of Microbiology and Immunology, University of Illinois-Chicago, Chicago, IL 60612, USA.,Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.,Department of Physics, National University of Singapore, Singapore 117542, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore
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H-NS Family Members MvaT and MvaU Regulate the Pseudomonas aeruginosa Type III Secretion System. J Bacteriol 2019; 201:JB.00054-19. [PMID: 30782629 DOI: 10.1128/jb.00054-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/07/2019] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen capable of causing severe disease in immunocompromised individuals. A major P. aeruginosa virulence factor is the type III secretion system (T3SS). The T3SS is used to translocate effector proteins into host cells, causing cytotoxicity. The T3SS is under the transcriptional control of the master regulator ExsA. ExsA is encoded in the exsCEBA operon and autoregulates transcription via the P exsC promoter. There is also a Vfr-dependent promoter (P exsA ) located in the intergenic region between exsB and exsA A previous chromatin immunoprecipitation (ChIP)-on-chip experiment identified strong binding signatures for MvaT and MvaU in the intergenic region containing the P exsA promoter. MvaT and MvaU are DNA-binding histone-like nucleoid-structuring proteins that can repress gene expression. As predicted from the previous ChIP data, purified MvaT specifically bound to the P exsA promoter region in electrophoretic mobility shift assays. Whereas disruption of mvaT or mvaU by either transposon insertion or clustered regularly interspaced short palindromic repeat interference (CRISPRi) derepressed P exsA promoter activity and T3SS gene expression, overexpression of MvaT or MvaU inhibited P exsA promoter activity. Disruption of mvaT, however, did not suppress the Vfr requirement for P exsA promoter activity. Mutated MvaT/MvaU defective in transcriptional silencing exhibited dominant negative activity, resulting in a significant increase in P exsA promoter activity. Because no effect of MvaT or MvaU on Vfr expression was detected, we propose a model in which the primary effect of MvaT/MvaU on T3SS gene expression is through direct silencing of the P exsA promoter.IMPORTANCE Global regulatory systems play a prominent role in controlling the P. aeruginosa T3SS and include the Gac/RsmA, c-di-GMP, and Vfr-cAMP signaling pathways. Many of these pathways appear to directly or indirectly influence exsA transcription or translation. In this study, the histone-like proteins MvaT and MvaU are added to the growing list of global regulators that control the T3SS. MvaT and MvaU bind AT-rich regions in the genome and silence xenogeneic genes, including pathogenicity islands. The T3SS gene cluster has been horizontally transmitted among many Gram-negative pathogens. Control by MvaT/MvaU may reflect a residual effect that has persisted since the initial acquisition of the gene cluster, subsequently imposing a requirement for active regulatory mechanisms to override MvaT/MvaU-mediated silencing.
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30
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Flores-Ríos R, Quatrini R, Loyola A. Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology. Comput Struct Biotechnol J 2019; 17:746-756. [PMID: 31303979 PMCID: PMC6606824 DOI: 10.1016/j.csbj.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 02/08/2023] Open
Abstract
Mobile Genetic Elements (MGEs) are mosaics of functional gene modules of diverse evolutionary origin and are generally divergent from the hosts´ genetic background. Existing biases in base composition and codon usage of these elements` genes impose transcription and translation limitations that may affect the physical and regulatory integration of MGEs in new hosts. Stable appropriation of the foreign DNA depends on a number of host factors among which are the Nucleoid-Associated Proteins (NAPs). These small, basic, highly abundant proteins bind and bend DNA, altering its topology and folding, thereby affecting all known essential DNA metabolism related processes. Both chromosomally- (endogenous) and MGE- (foreign) encoded NAPs have been shown to exist in bacteria. While the role of host-encoded NAPs in xenogeneic silencing of both episomal (plasmids) and integrative MGEs (pathogenicity islands and prophages) is well acknowledged, less is known about the role of MGE-encoded NAPs in the foreign elements biology or their influence on the host's chromosome expression dynamics. Here we review existing literature on the topic, present examples on the positive and negative effects that endogenous and foreign NAPs exert on global transcriptional gene expression, MGE integrative and excisive recombination dynamics, persistence and transfer to suitable hosts and discuss the nature and relevance of synergistic and antagonizing higher order interactions between diverse types of NAPs.
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Affiliation(s)
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Alejandra Loyola
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile
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31
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Identifying the region responsible for Brucella abortus MucR higher-order oligomer formation and examining its role in gene regulation. Sci Rep 2018; 8:17238. [PMID: 30467359 PMCID: PMC6250670 DOI: 10.1038/s41598-018-35432-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022] Open
Abstract
MucR is a member of the Ros/MucR family of prokaryotic zinc-finger proteins found in the α-proteobacteria which regulate the expression of genes required for the successful pathogenic and symbiotic interactions of these bacteria with the eukaryotic hosts. The structure and function of their distinctive zinc-finger domain has been well-studied, but only recently the quaternary structure of the full length proteins was investigated demonstrating their ability to form higher-order oligomers. The aim of this study was to identify the region of MucR involved in higher-order oligomer formation by analysing deletion and point mutants of this protein by Light Scattering, and to determine the role that MucR oligomerization plays in the regulatory function of this protein. Here we demonstrate that a conserved hydrophobic region at the N-terminus of MucR is responsible for higher-order oligomer formation and that MucR oligomerization is essential for its regulatory function in Brucella. All these features of MucR are shared by the histone-like nucleoid structuring protein, (H-NS), leading us to propose that the prokaryotic zinc-finger proteins in the MucR/Ros family control gene expression employing a mechanism similar to that used by the H-NS proteins, rather than working as classical transcriptional regulators.
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32
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Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B. How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome. Nucleic Acids Res 2018; 46:10514-10529. [PMID: 30252102 PMCID: PMC6212790 DOI: 10.1093/nar/gky836] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/28/2018] [Accepted: 09/18/2018] [Indexed: 12/11/2022] Open
Abstract
Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. Here, the detailed DNA binding properties of Rok, a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and the solution structure of its C-terminal DNA binding domain was determined in complex with DNA. The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156 at the N-terminal of α3 helix and R174 of wing W1, assisted by four lysine residues interacting electrostatically with DNA backbone phosphate groups. These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A-tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are rich in A-tracts and show a dramatic underrepresentation of AACTA and TACTA, which are significantly enriched in Rok binding regions. These observations suggest that the xenogeneic silencing protein and its resident genome may have evolved cooperatively.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
| | - Timothy R Hughes
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - William Wiley Navarre
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jun Liu
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
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33
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Tarasava K, Oh EJ, Eckert CA, Gill RT. CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes. Biotechnol J 2018; 13:e1700586. [DOI: 10.1002/biot.201700586] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 05/09/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Katia Tarasava
- Chemical and Biological Engineering, University of Colorado; Boulder CO USA
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
| | - Eun Joong Oh
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
- Biosciences Center, National Renewable Energy Laboratory; Golden CO USA
| | - Ryan T. Gill
- Chemical and Biological Engineering, University of Colorado; Boulder CO USA
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
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34
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Baglivo I, Pirone L, Malgieri G, Fattorusso R, Roop II RM, Pedone EM, Pedone PV. MucR binds multiple target sites in the promoter of its own gene and is a heat-stable protein: Is MucR a H-NS-like protein? FEBS Open Bio 2018; 8:711-718. [PMID: 29632823 PMCID: PMC5881533 DOI: 10.1002/2211-5463.12411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/17/2018] [Accepted: 02/21/2018] [Indexed: 01/08/2023] Open
Abstract
The protein MucR from Brucella spp. is involved in the expression regulation of genes necessary for host interaction and infection. MucR is a member of the Ros/MucR family, which comprises prokaryotic zinc-finger proteins and includes Ros from Agrobacterium tumefaciens and the Ml proteins from Mesorhizobium loti. MucR from Brucella spp. can regulate the expression of virulence genes and repress its own gene expression. Despite the well-known role played by MucR in the repression of its own gene, no target sequence has yet been identified in the mucR promoter gene. In this study, we provide the first evidence that MucR from Brucella abortus binds more than one target site in the promoter region of its own gene, suggesting a molecular mechanism by which this protein represses its own expression. Furthermore, a circular dichroism analysis reveals that MucR is a heat-stable protein. Overall, the results of this study suggest that MucR might resemble a H-NS protein.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Luciano Pirone
- Institute of Biostructures and BioimagingC.N.R.NaplesItaly
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Roy Martin Roop II
- Department of Microbiology and ImmunologyBrody School of MedicineEast Carolina UniversityGreenvilleNCUSA
| | | | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
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35
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Ruiz-Cruz S, Moreno-Blanco A, Espinosa M, Bravo A. DNA-binding properties of MafR, a global regulator of Enterococcus faecalis. FEBS Lett 2018. [PMID: 29537484 PMCID: PMC5947639 DOI: 10.1002/1873-3468.13032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Global transcriptional regulators play key roles during bacterial adaptation to environmental fluctuations. Protein MafR from Enterococcus faecalis was shown to activate the transcription of many genes on a genome-wide scale. We proposed that MafR is a global regulator of the Mga/AtxA family. Here, we purified an untagged form of the MafR protein and found that it binds to linear double-stranded DNAs in a nonsequence-specific manner. Moreover, multiple MafR units (likely dimers) bind sequentially to the DNA molecule generating multimeric complexes. On DNAs that contain the promoter of the mafR gene, MafR recognizes a potentially curved DNA region. We discuss that a characteristic of the Mga/AtxA regulators might be their ability to recognize particular DNA shapes across the bacterial genomes.
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Affiliation(s)
- Sofía Ruiz-Cruz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Moreno-Blanco
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alicia Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Baglivo I, Pirone L, Pedone EM, Pitzer JE, Muscariello L, Marino MM, Malgieri G, Freschi A, Chambery A, Roop Ii RM, Pedone PV. Ml proteins from Mesorhizobium loti and MucR from Brucella abortus: an AT-rich core DNA-target site and oligomerization ability. Sci Rep 2017; 7:15805. [PMID: 29150637 PMCID: PMC5693944 DOI: 10.1038/s41598-017-16127-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/07/2017] [Indexed: 11/09/2022] Open
Abstract
Mesorhizobium loti contains ten genes coding for proteins sharing high amino acid sequence identity with members of the Ros/MucR transcription factor family. Five of these Ros/MucR family members from Mesorhizobium loti (Ml proteins) have been recently structurally and functionally characterized demonstrating that Ml proteins are DNA-binding proteins. However, the DNA-binding studies were performed using the Ros DNA-binding site with the Ml proteins. Currently, there is no evidence as to when the Ml proteins are expressed during the Mesorhizobium lo ti life cycle as well as no information concerning their natural DNA-binding site. In this study, we examine the ml genes expression profile in Mesorhizobium loti and show that ml1, ml2, ml3 and ml5 are expressed during planktonic growth and in biofilms. DNA-binding experiments show that the Ml proteins studied bind a conserved AT-rich site in the promoter region of the exoY gene from Mesorhizobium loti and that the proteins make important contacts with the minor groove of DNA. Moreover, we demonstrate that the Ml proteins studied form higher-order oligomers through their N-terminal region and that the same AT-rich site is recognized by MucR from Brucella abortus using a similar mechanism involving contacts with the minor groove of DNA and oligomerization.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, C.N.R., Naples, 80134, Italy
| | | | - Joshua Edison Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Lidia Muscariello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Maria Michela Marino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Andrea Freschi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Roy-Martin Roop Ii
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.
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Sun Z, Vasileva D, Suzuki-Minakuchi C, Okada K, Luo F, Igarashi Y, Nojiri H. Growth phase-dependent expression profiles of three vital H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440 and on the pCAR1 plasmid. BMC Microbiol 2017; 17:188. [PMID: 28851281 PMCID: PMC5576294 DOI: 10.1186/s12866-017-1091-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/11/2017] [Indexed: 01/09/2023] Open
Abstract
Background H-NS family proteins are nucleoid-associated proteins that form oligomers on DNA and function as global regulators. They are found in both bacterial chromosomes and plasmids, and were suggested to be candidate effectors of the interaction between them. TurA and TurB are the predominantly expressed H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440, while Pmr is encoded on the carbazole-degradative incompatibility group P-7 plasmid pCAR1. Previous transcriptome analyses suggested that they function cooperatively, but play different roles in the global transcriptional network. In addition to differences in protein interaction and DNA-binding functions, cell expression levels are important in clarifying the detailed underlying mechanisms. Here, we determined the precise protein amounts of TurA, TurB, and Pmr in KT2440 in the presence and absence of pCAR1. Results The intracellular amounts of TurA and TurB in KT2440 and KT2440(pCAR1) were determined by quantitative western blot analysis using specific antibodies. The amount of TurA decreased from the log phase (~80,000 monomers per cell) to the stationary phase (~20,000 monomers per cell), while TurB was only detectable upon entry into the stationary phase (maximum 6000 monomers per cell). Protein amounts were not affected by pCAR1 carriage. KT2440(pCAR1pmrHis), where histidine-tagged Pmr is expressed under its original promotor, was used to determine the intracellular amount of Pmr, which was constant (~30,000 monomers per cell) during cell growth. Quantitative reverse transcription PCR demonstrated that the transcriptional levels of turA and turB were consistent with protein expression, though the transcriptional and translational profiles of Pmr differed. Conclusion The amount of TurB increases as TurA decreases, and the amount of Pmr does not affect the amounts of TurA and TurB. This is consistent with our previous observation that TurA and TurB play complementary roles, whereas Pmr works relatively independently. This study provides insight into the molecular mechanisms underlying reconstitution of the transcriptional network in KT2440 by pCAR1 carriage. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1091-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zongping Sun
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China.,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Delyana Vasileva
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Feng Luo
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China
| | - Yasuo Igarashi
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China
| | - Hideaki Nojiri
- Research Center of Bioenergy & Bioremediation, College of Resources and Environment, Southwest University, No.2 Tiansheng Road, BeiBei District, Chongqing, 400715, China. .,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Suzuki-Minakuchi C, Kawazuma K, Matsuzawa J, Vasileva D, Fujimoto Z, Terada T, Okada K, Nojiri H. Structural similarities and differences in H-NS family proteins revealed by the N-terminal structure of TurB in Pseudomonas putida KT2440. FEBS Lett 2016; 590:3583-3594. [PMID: 27709616 DOI: 10.1002/1873-3468.12425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 11/08/2022]
Abstract
H-NS family proteins play key roles in bacterial nucleoid compaction and global transcription. MvaT homologues in Pseudomonas have almost negligible amino acid sequence identity with H-NS, but can complement an hns-related phenotype of Escherichia coli. Here, we report the crystal structure of the N-terminal dimerization/oligomerization domain of TurB, an MvaT homologue in Pseudomonas putida KT2440. Our data identify two dimerization sites; the structure of the central dimerization site is almost the same as the corresponding region of H-NS, whereas the terminal dimerization sites are different. Our results reveal similarities and differences in dimerization and oligomerization mechanisms between H-NS and TurB.
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Affiliation(s)
| | - Kohei Kawazuma
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Jun Matsuzawa
- Biotechnology Research Center, The University of Tokyo, Japan
| | | | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.,Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Japan. .,Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
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39
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Ricci DP, Melfi MD, Lasker K, Dill DL, McAdams HH, Shapiro L. Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition. Proc Natl Acad Sci U S A 2016; 113:E5952-E5961. [PMID: 27647925 PMCID: PMC5056096 DOI: 10.1073/pnas.1612579113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Faithful cell cycle progression in the dimorphic bacterium Caulobacter crescentus requires spatiotemporal regulation of gene expression and cell pole differentiation. We discovered an essential DNA-associated protein, GapR, that is required for Caulobacter growth and asymmetric division. GapR interacts with adenine and thymine (AT)-rich chromosomal loci, associates with the promoter regions of cell cycle-regulated genes, and shares hundreds of recognition sites in common with known master regulators of cell cycle-dependent gene expression. GapR target loci are especially enriched in binding sites for the transcription factors GcrA and CtrA and overlap with nearly all of the binding sites for MucR1, a regulator that controls the establishment of swarmer cell fate. Despite constitutive synthesis, GapR accumulates preferentially in the swarmer compartment of the predivisional cell. Homologs of GapR, which are ubiquitous among the α-proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed in Caulobacter The Escherichia coli nucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously in Caulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. Further, GapR does not silence the expression of H-NS target genes when expressed in E. coli, suggesting that GapR and H-NS have distinct functions. We propose that Caulobacter has co-opted a nucleoid-associated protein with high AT recognition to serve as a mediator of cell cycle progression.
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Affiliation(s)
- Dante P Ricci
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Michael D Melfi
- Department of Developmental Biology, Stanford University, Stanford, CA 94305; Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Keren Lasker
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - David L Dill
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Harley H McAdams
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, Stanford, CA 94305;
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40
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Abstract
The H-NS family of DNA-binding proteins is the subject of intense study due to its important roles in the regulation of horizontally acquired genes critical for virulence, antibiotic resistance, and metabolism. Xenogeneic silencing proteins, typified by the H-NS protein of Escherichia coli, specifically target and downregulate expression from AT-rich genes by selectively recognizing specific structural features unique to the AT-rich minor groove. In doing so, these proteins facilitate bacterial evolution; enabling these cells to engage in horizontal gene transfer while buffering potential any detrimental fitness consequences that may result from it. Xenogeneic silencing and counter-silencing explain how bacterial cells can evolve effective gene regulatory strategies in the face of rampant gene gain and loss and it has extended our understanding of bacterial gene regulation beyond the classic operon model. Here we review the structures and mechanisms of xenogeneic silencers as well as their impact on bacterial evolution. Several H-NS-like proteins appear to play a role in facilitating gene transfer by other mechanisms including by regulating transposition, conjugation, and participating in the activation of virulence loci like the locus of enterocyte effacement pathogenicity island of pathogenic strains of E. coli. Evidence suggests that the critical determinants that dictate whether an H-NS-like protein will be a silencer or will perform a different function do not lie in the DNA-binding domain but, rather, in the domains that control oligomerization. This suggests that H-NS-like proteins are transcription factors that both recognize and alter the shape of DNA to exert specific effects that include but are not limited to gene silencing.
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41
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Pfeifer E, Hünnefeld M, Popa O, Polen T, Kohlheyer D, Baumgart M, Frunzke J. Silencing of cryptic prophages in Corynebacterium glutamicum. Nucleic Acids Res 2016; 44:10117-10131. [PMID: 27492287 PMCID: PMC5137423 DOI: 10.1093/nar/gkw692] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 12/14/2022] Open
Abstract
DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum. CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction.
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Affiliation(s)
- Eugen Pfeifer
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Max Hünnefeld
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ovidiu Popa
- Quantitative and Theoretical Biology, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Tino Polen
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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42
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Abstract
The H-NS (heat-stable nucleoid structuring) protein affects both nucleoid compaction and global gene regulation. H-NS appears to act primarily as a silencer of AT-rich genetic material acquired by horizontal gene transfer. As such, it is key in the regulation of most genes involved in virulence and in adaptation to new environmental niches. Here we review recent progress in understanding the biochemistry of H-NS and how xenogeneic silencing affects bacterial evolution. We highlight the strengths and weaknesses of some of the models proposed in H-NS-mediated nucleoprotein complex formation. Based on recent single-molecule studies, we also propose a novel mode of DNA compaction by H-NS termed intrabridging to explain over two decades of observations of the H-NS molecule.
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Affiliation(s)
- Kamna Singh
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada;
| | - Joshua N Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Ontario L5L 1C6, Canada.,Department of Physics, University of Toronto, Ontario M5S 1A7, Canada
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43
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Harika NK, Paul A, Stroeva E, Chai Y, Boykin DW, Germann MW, Wilson WD. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition. Nucleic Acids Res 2016; 44:4519-27. [PMID: 27131382 PMCID: PMC4889958 DOI: 10.1093/nar/gkw353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/17/2016] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ekaterina Stroeva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Yun Chai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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44
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Al-Zyoud WA, Hynson RMG, Ganuelas LA, Coster ACF, Duff AP, Baker MAB, Stewart AG, Giannoulatou E, Ho JWK, Gaus K, Liu D, Lee LK, Böcking T. Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site. Nucleic Acids Res 2016; 44:1411-20. [PMID: 26681693 PMCID: PMC4756830 DOI: 10.1093/nar/gkv1466] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022] Open
Abstract
Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR-DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR-DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites/genetics
- Chromatography, Gel
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon/genetics
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Multimerization
- Protein Structure, Tertiary
- Scattering, Small Angle
- Sequence Homology, Nucleic Acid
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
- X-Ray Diffraction
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Affiliation(s)
- Walid A Al-Zyoud
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Robert M G Hynson
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Lorraine A Ganuelas
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Adelle C F Coster
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Matthew A B Baker
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Alastair G Stewart
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Eleni Giannoulatou
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Joshua W K Ho
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Katharina Gaus
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Lawrence K Lee
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
| | - Till Böcking
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
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45
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MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently. Appl Environ Microbiol 2015; 82:832-42. [PMID: 26590283 DOI: 10.1128/aem.03071-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 11/14/2015] [Indexed: 11/20/2022] Open
Abstract
MvaT proteins are members of the H-NS family of proteins in pseudomonads. The IncP-7 conjugative plasmid pCAR1 carries an mvaT-homologous gene, pmr. In Pseudomonas putida KT2440 bearing pCAR1, pmr and the chromosomally carried homologous genes, turA and turB, are transcribed at high levels, and Pmr interacts with TurA and TurB in vitro. In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Analyses performed by a modified chromatin immunoprecipitation assay with microarray technology (ChIP-chip) suggested that the binding regions of Pmr, TurA, and TurB in the P. putida KT2440(pCAR1) genome are almost identical; nevertheless, transcriptomic analyses using mutants with deletions of the genes encoding the MvaT proteins during the log and early stationary growth phases clearly suggested that their regulons were different. Indeed, significant regulon dissimilarity was found between Pmr and the other two proteins. Transcription of a larger number of genes was affected by Pmr deletion during early stationary phase than during log phase, suggesting that Pmr ameliorates the effects of pCAR1 on host fitness more effectively during the early stationary phase. Alternatively, the similarity of the TurA and TurB regulons implied that they might play complementary roles as global transcriptional regulators in response to plasmid carriage.
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