1
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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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2
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Billane K, Harrison E, Cameron D, Brockhurst MA. Why do plasmids manipulate the expression of bacterial phenotypes? Philos Trans R Soc Lond B Biol Sci 2022; 377:20200461. [PMID: 34839708 PMCID: PMC8628079 DOI: 10.1098/rstb.2020.0461] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Conjugative plasmids play an important role in bacterial evolution by transferring niche-adaptive traits between lineages, thus driving adaptation and genome diversification. It is increasingly clear, however, that in addition to this evolutionary role, plasmids also manipulate the expression of a broad range of bacterial phenotypes. In this review, we argue that the effects that plasmids have on the expression of bacterial phenotypes may often represent plasmid adaptations, rather than mere deleterious side effects. We begin by summarizing findings from untargeted omics analyses, which give a picture of the global effects of plasmid acquisition on host cells. Thereafter, because many plasmids are capable of both vertical and horizontal transmission, we distinguish plasmid-mediated phenotypic effects into two main classes based upon their potential fitness benefit to plasmids: (i) those that promote the competitiveness of the host cell in a given niche and thereby increase plasmid vertical transmission, and (ii) those that promote plasmid conjugation and thereby increase plasmid horizontal transmission. Far from being mere vehicles for gene exchange, we propose that plasmids often act as sophisticated genetic parasites capable of manipulating their bacterial hosts for their own benefit. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
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Affiliation(s)
- Kathryn Billane
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Duncan Cameron
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK
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3
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Nakamura T, Suzuki-Minakuchi C, Kawano H, Kanesaki Y, Kawasaki S, Okada K, Nojiri H. H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1. Front Microbiol 2020; 11:1099. [PMID: 32547524 PMCID: PMC7273181 DOI: 10.3389/fmicb.2020.01099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/04/2020] [Indexed: 01/20/2023] Open
Abstract
H-NS family proteins regulate the expression of many genes by preferably binding to AT-rich genomic regions and altering DNA topology. They are found in both bacterial chromosomes and plasmids, and plasmid-encoded H-NS family proteins have sometimes been suggested to act as a molecular backup of the chromosomally encoded ones. Pmr is an H-NS family protein encoded on the catabolic plasmid pCAR1, which belongs to incompatibility P-7 group. We have investigated the function of Pmr in Pseudomonas putida KT2440, where two H-NS family proteins (TurA and TurB) encoded on the chromosome are expressed predominantly. Previous transcriptome analyses suggested that TurA, TurB, and Pmr cooperatively regulate numerous genes, but the differentially transcribed genes in KT2440ΔturA(pCAR1), KT2440ΔturB(pCAR1), and KT2440(pCAR1Δpmr) compared with those in KT2440(pCAR1) were somewhat different. Here, we performed RNA sequencing analyses to compare the differentially transcribed genes after the deletion of turA or turB in KT2440, and turA, turB or pmr in KT2440(pCAR1). Three pCAR1-free strains (KT2440, KT2440ΔturA, KT2440ΔturB) and four pCAR1-harboring strains [KT2440(pCAR1), KT2440ΔturA(pCAR1), KT2440ΔturB(pCAR1), KT2440(pCAR1Δpmr)], grown until the log and stationary phases, were used. In KT2440, TurA was the major H-NS family protein regulating a large number and wide range of genes, and both TurA and TurB were suggested to functionally compensate each other, particularly during the stationary phase. In KT2440(pCAR1), the numbers of differentially transcribed genes after the deletion of turA or turB drastically increased compared to those in KT2440. Notably, more than half of the differentially transcribed genes in KT2440ΔturA and KT2440ΔturB did not overlap with those in KT2440ΔturA(pCAR1) and KT2440ΔturB(pCAR1). This dynamic change could be explained by the acquisition of pCAR1 itself and the expression of Pmr. After pCAR1 was transferred into the host, TurA and TurB could be detached from the chromosome of KT2440 and they could newly bind to pCAR1. Moreover, Pmr could reconstitute the chromosome-binding heteromeric oligomers which were formed by TurA and TurB. Our study revealed that horizontal transfer of a plasmid changes the transcriptional network of the chromosomally encoded H-NS family proteins.
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Affiliation(s)
- Taisuke Nakamura
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hibiki Kawano
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Shinji Kawasaki
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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4
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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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5
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Vial L, Hommais F. Plasmid-chromosome cross-talks. Environ Microbiol 2019; 22:540-556. [PMID: 31782608 DOI: 10.1111/1462-2920.14880] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
Abstract
Plasmids can be acquired by recipient bacteria at a significant cost while conferring them advantageous traits. To counterbalance the costs of plasmid carriage, both plasmids and host bacteria have developed a tight regulatory network that may involve a cross-talk between the chromosome and the plasmids. Although plasmid regulation by chromosomal regulators is generally well known, chromosome regulation by plasmid has been far less investigated. Yet, a growing number of studies have highlighted an impact of plasmids on their host bacteria. Here, we describe the plasmid-chromosome cross-talk from the plasmid point of view. We summarize data about the chromosomal adaptive mutations generated by plasmid carriage; the impact of the loss of a domesticated plasmid or the gain of a new plasmid. Then, we present the control of plasmid-encoded regulators on chromosomal gene expression. The involvement of regulators homologous to chromosome-encoded proteins is illustrated by the H-NS-like proteins, and by the Rap-Phr system. Finally, plasmid-specific regulators of chromosomal gene expression are presented, which highlight the involvement of transcription factors and sRNAs. A comprehensive analysis of the mechanisms that allow a given plasmid to impact the chromosome of bacterium will help to understand the tight cross-talk between plasmids and the chromosome.
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Affiliation(s)
- Ludovic Vial
- Université de Lyon, 69622, Lyon, France.,Université Lyon 1, 69622, Villeurbanne, France.,CNRS, UMR 5557 Ecologie Microbienne, 69622, Villeurbanne, France.,INRA, UMR1418 Ecologie Microbienne, 69622, Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, 69622, Lyon, France.,Université Lyon 1, 69622, Villeurbanne, France.,CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, 69622, Villeurbanne, France
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6
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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: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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7
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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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8
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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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9
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Yano H, Shintani M, Tomita M, Suzuki H, Oshima T. Reconsidering plasmid maintenance factors for computational plasmid design. Comput Struct Biotechnol J 2018; 17:70-81. [PMID: 30619542 PMCID: PMC6312765 DOI: 10.1016/j.csbj.2018.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/08/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, 5180, Kurokawa, Imizu, Toyama 939-0398, Japan
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10
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García-Pastor L, Sánchez-Romero MA, Gutiérrez G, Puerta-Fernández E, Casadesús J. Formation of phenotypic lineages in Salmonella enterica by a pleiotropic fimbrial switch. PLoS Genet 2018; 14:e1007677. [PMID: 30252837 PMCID: PMC6173445 DOI: 10.1371/journal.pgen.1007677] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/05/2018] [Accepted: 09/05/2018] [Indexed: 11/29/2022] Open
Abstract
The std locus of Salmonella enterica, an operon acquired by horizontal transfer, encodes fimbriae that permit adhesion to epithelial cells in the large intestine. Expression of the std operon is bistable, yielding a major subpopulation of StdOFF cells (99.7%) and a minor subpopulation of StdON cells (0.3%). In addition to fimbrial proteins, the std operon encodes two proteins, StdE and StdF, that have DNA binding capacity and control transcription of loci involved in flagellar synthesis, chemotaxis, virulence, conjugal transfer, biofilm formation, and other cellular functions. As a consequence of StdEF pleiotropic transcriptional control, StdON and StdOFF subpopulations may differ not only in the presence or absence of Std fimbriae but also in additional phenotypic traits. Separation of StdOFF and StdON lineages by cell sorting confirms the occurrence of lineage-specific features. Formation of StdOFF and StdON lineages may thus be viewed as a rudimentary bacterial differentiation program. We show that the std fimbrial operon of Salmonella enterica undergoes bistable expression, a trait far from exceptional among loci that encode components of the bacterial envelope. However, an unsuspected trait of the std operon is the presence of two genes that encode pleiotropic regulators of gene expression. Indeed, StdE and StdF are DNA-binding proteins that control transcription of hundreds of genes. As a consequence, StdEF govern multiple phenotypic traits, and the fimbriated and non-fimbriated Salmonella lineages may differ in motility, virulence, conjugal transfer, biofilm formation, and potentially in other phenotypic features. We hypothesize that pleiotropic control of gene expression by StdEF may contribute to adapt the non-fimbriated lineage to acute infection and the fimbriated lineage to chronic infection.
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Affiliation(s)
- Lucía García-Pastor
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | | | - Gabriel Gutiérrez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Elena Puerta-Fernández
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS, CSIC), Sevilla, Spain
- * E-mail: (EPF); (JC)
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- * E-mail: (EPF); (JC)
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11
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Sun Z, Vasileva D, Suzuki-Minakuchi C, Okada K, Luo F, Igarashi Y, Nojiri H. Differential protein-protein binding affinities of H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440 and IncP-7 plasmid pCAR1. Biosci Biotechnol Biochem 2018; 82:1640-1646. [PMID: 29924693 DOI: 10.1080/09168451.2018.1484277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440 (TurA and TurB) and the IncP-7 plasmid pCAR1 (Pmr) commonly have an N-terminal dimerization/oligomerization domain constituted by a central and a terminal dimerization sites. To clarify the dimerization manner at the central dimerization sites of the three homologs, we performed chemical cross-linking analyses with protein variants inactivated at the terminal dimerization site. Comparison of the hetero-dimer ratios among them suggested stronger affinities between the central dimerization sites of TurA and TurB monomers than between TurA and Pmr or TurB and Pmr. Furthermore, analyses of the interaction between truncated TurB containing only a functional terminal dimerization site and full-length proteins suggested that TurB exhibited higher affinities for oligomer complex formation with TurB itself and TurA but not Pmr. Altogether, we revealed stronger interaction between the N-terminal domains of TurA and TurB than between either of them and Pmr.
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Affiliation(s)
- Zongping Sun
- a Research Center of Bioenergy & Bioremediation, College of Resources and Environment , Southwest University , Chongqing , China.,b Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Delyana Vasileva
- b Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | | | - Kazunori Okada
- b Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Feng Luo
- a Research Center of Bioenergy & Bioremediation, College of Resources and Environment , Southwest University , Chongqing , China
| | - Yasuo Igarashi
- a Research Center of Bioenergy & Bioremediation, College of Resources and Environment , Southwest University , Chongqing , China
| | - Hideaki Nojiri
- a Research Center of Bioenergy & Bioremediation, College of Resources and Environment , Southwest University , Chongqing , China.,b Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
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12
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Vasileva D, Suzuki-Minakuchi C, Kosono S, Yoshida M, Okada K, Nojiri H. Proteome and acylome analyses of the functional interaction network between the carbazole-degradative plasmid pCAR1 and host Pseudomonas putida KT2440. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:299-309. [PMID: 29573367 DOI: 10.1111/1758-2229.12639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 06/08/2023]
Abstract
Understanding the interplay between a plasmid and its host system is a bottleneck towards prediction of the fate of plasmid-harbouring strains in the natural environments. Here, we studied the impact of the conjugative plasmid pCAR1, involved in carbazole degradation, on the proteome of Pseudomonas putida KT2440 using SILAC method. Furthermore, we investigated two acyl lysine modifications (acetylation and succinylation) that respond to the metabolic status of the cell and are implicated in regulation of various cellular processes. The total proteome analysis revealed that the abundance of key proteins involved in metabolism, signal transduction and motility was affected by pCAR1 carriage. In total, we identified 1359 unique acetylation sites on 637 proteins and 567 unique succinylation sites on 259 proteins. Changes in the acylation status of proteins involved in metabolism and translation by pCAR1 carriage were detected. Remarkably, acylation was identified on proteins involved in important plasmid functions, including partitioning and carbazole degradation, and on nucleoid-associated proteins that play a key role in the functional interaction with the chromosome. This study provides a novel insight on the functional consequences of plasmid carriage and improves our understanding of the plasmid-host cross-talk.
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Affiliation(s)
- Delyana Vasileva
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | | | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science Wako, Saitama, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science Wako, Saitama, Japan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
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13
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Hüttener M, Prieto A, Aznar S, Dietrich M, Paytubi S, Juárez A. Tetracycline alters gene expression in Salmonella strains that harbor the Tn10 transposon. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:202-209. [PMID: 29393572 DOI: 10.1111/1758-2229.12621] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this report, we show that bacterial plasmids that harbor the Tn10 transposon (i.e., the IncHI1 plasmid R27) modify expression of different Salmonella regulons responding to the presence of tetracycline (Tc) in the medium. By using as a model the Tc-dependent upregulation of the ibpAB operon (which belongs to the heat shock regulon), we have identified Tn10-tetA (coding for a Tc efflux pump) and adjacent tetC sequences as required for ibpAB upregulation. Characterization of transcripts in the tetAC region showed that tetA transcription can continue into tetC sequences, generating a long 3'UTR sequence, which can protect transcripts from RNA processing, thus increasing the expression of TetA protein. In the presence of Tc, the DnaK and IbpA chaperones are overexpressed and translocated to the periplasm and to the membrane fraction respectively. DnaK targeting unfolded proteins is known to induce heat shock by avoiding RpoH proteolysis. We correlate expression levels of Tn10-encoded TetA protein with heat shock induction in Salmonella, likely because TetA activity compromises protein secretion.
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Affiliation(s)
- M Hüttener
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - A Prieto
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - S Aznar
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - M Dietrich
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - S Paytubi
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - A Juárez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and technology, Barcelona, Spain
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14
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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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15
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Shintani M. The behavior of mobile genetic elements (MGEs) in different environments. Biosci Biotechnol Biochem 2017; 81:854-862. [PMID: 28077029 DOI: 10.1080/09168451.2016.1270743] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Mobile genetic elements (MGEs) including plasmids have an important role in the rapid evolution and adaptation of bacteria. Here, the behavior of MGEs in different environments is reviewed, in particular, behavior of the plasmid pCAR1, a carbazole-degradative plasmid isolated from Pseudomonas resinovorans CA10. pCAR1 belongs to incompatibility P-7 group and is self-transmissible among different bacteria. Comparisons of changes in the transcriptome of different host strains caused by carrying pCAR1 revealed common responses in the hosts and host-specific responses. Monitoring the survival of the host and transfer of the plasmid in artificial and natural environmental samples revealed several environmental factors, including cations and water content, which changed the behavior of both the host and its plasmid. Single-cell level analysis to detect the transconjugants of different plasmids successfully determined the transfer range of the plasmids. Three nucleoid-associated proteins encoded on pCAR1 are important factors affecting its genetic stability, maintenance, and transfer.
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Affiliation(s)
- Masaki Shintani
- a Department of Engineering , Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu , Japan.,b Department of Bioscience , Graduate School of Science and Technology, Shizuoka University , Hamamatsu , Japan.,c Japan Collection of Microorganisms , RIKEN BioResource Center , Tsukuba , Japan
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16
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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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17
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Lee S, Takahashi Y, Oura H, Suzuki-Minakuchi C, Okada K, Yamane H, Nomura N, Nojiri H. Effects of carbazole-degradative plasmid pCAR1 on biofilm morphology in Pseudomonas putida KT2440. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:261-271. [PMID: 26743211 DOI: 10.1111/1758-2229.12376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/31/2015] [Accepted: 12/31/2015] [Indexed: 06/05/2023]
Abstract
Bacteria typically form biofilms under natural conditions. To elucidate the effect of the carriage of carbazole-degradative plasmid pCAR1 on biofilm formation by host bacteria, we compared the biofilm morphology, using confocal laser scanning microscopy, of three pCAR1-free and pCAR1-carrying Pseudomonas hosts: P. putida KT2440, P. aeruginosa PAO1 and P. fluorescens Pf0-1. Although pCAR1 did not significantly affect biofilm formation by PAO1 or Pf0-1, pCAR1-carrying KT2440 became filamentous and formed flat biofilms, whereas pCAR1-free KT2440 formed mushroom-like biofilms. pCAR1 contains three genes encoding nucleoid-associated proteins (NAPs), namely, Pmr, Pnd and Phu. The enhanced filamentous morphology was observed in two double mutants [KT2440(pCAR1ΔpmrΔpnd) and KT2440(pCAR1ΔpmrΔphu)], suggesting that these NAPs are involved in modulating the filamentous phenotype. Transcriptome analyses of the double mutants identified 32 candidate genes that may be involved in filamentation of KT2440. Overexpression of PP_2193 in KT2440 induced filamentation and overexpression of PP_0308 or PP_0309 in KT2440(pCAR1) enhanced filamentation of cells over time. This suggests that pCAR1 induces development of an abnormal filamentous morphology by KT2440 via a process involving overexpression of several genes, such as PP_2193. In addition, pCAR1-encoded NAPs partly suppress too much filamentation of KT2440(pCAR1) by repressing transcription of some genes, such as PP_0308 and PP_0309.
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Affiliation(s)
- Seunguk Lee
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yurika Takahashi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiromu Oura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, 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
| | - Hisakazu Yamane
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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