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Deedwania A, Karmakar S, Kumar V, Shefrin S, Sundar D, Srivastava P. Construction and characterization of a temperature-sensitive pRC4 replicon for Rhodococcus and Gordonia. Gene 2024; 896:147990. [PMID: 37977321 DOI: 10.1016/j.gene.2023.147990] [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: 10/17/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Temperature-sensitive plasmids are useful for genome engineering and several synthetic biology applications. There are only limited reports on temperature-sensitive plasmids for Rhodococcus and none for Gordonia. Here, we report the construction of a temperature-sensitive pRC4 replicon that is functional in Rhodococcus and Gordonia. The amino acid residues were predicted for the temperature-sensitive phenotype in the pRC4 replicon using in silico methods and molecular simulation of the DNA-binding replication protein with the origin of replication. The amino acid residues were mutated, and the temperature-sensitive phenotype was validated in Gordonia sp. IITR100. Similar results were also observed in Rhodococcus erythropolis, suggesting that the temperature-sensitive phenotype was exhibited across genera.
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Affiliation(s)
- Agrima Deedwania
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Shreyoshi Karmakar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Vipul Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Seyad Shefrin
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India.
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India.
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2
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Ma J, Zhuang Y, Wang Y, Zhu N, Wang T, Xiao H, Chen J. Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:93345-93362. [PMID: 37548784 DOI: 10.1007/s11356-023-28894-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.
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Affiliation(s)
- Jinglin Ma
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Yan Zhuang
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ning Zhu
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ting Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Hongbin Xiao
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
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3
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Grechishnikova EG, Shemyakina AO, Novikov AD, Lavrov KV, Yanenko AS. Rhodococcus: sequences of genetic parts, analysis of their functionality, and development prospects as a molecular biology platform. Crit Rev Biotechnol 2023; 43:835-850. [PMID: 35786136 DOI: 10.1080/07388551.2022.2091976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/19/2022] [Accepted: 05/12/2022] [Indexed: 12/19/2022]
Abstract
Rhodococcus bacteria are a fast-growing platform for biocatalysis, biodegradation, and biosynthesis, but not a platform for molecular biology. That is, Rhodococcus are not convenient for genetic engineering. One major issue for the engineering of Rhodococcus is the absence of a publicly available, curated, and commented collection of sequences of genetic parts that are functional in biotechnologically relevant species of Rhodococcus (R. erythropolis, R. rhodochrous, R. ruber, and R. jostii). Here, we present a collection of genetic parts for Rhodococcus (vector replicons, promoter regions, regulators, markers, and reporters) supported by a thorough analysis of their functionality. We also highlight and discuss the gaps in Rhodococcus-related genetic parts and techniques, which should be filled in order to make these bacteria a full-fledged molecular biology platform independent of Escherichia coli. We conclude that all major types of required genetic parts for Rhodococcus are available now, except multicopy replicons. As for model Rhodococcus strains, there is a particular shortage of strains with high electrocompetence levels and strains designed for solving specific genetic engineering tasks. We suggest that these obstacles are surmountable in the near future due to an intensification of research work in the field of genetic techniques for non-conventional bacteria.
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Affiliation(s)
- Elena G Grechishnikova
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Anna O Shemyakina
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Andrey D Novikov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Konstantin V Lavrov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Alexander S Yanenko
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
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4
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Jaishankar J, Keshav A, Jayaram B, Chavan S, Srivastava P. Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194843. [PMID: 35840055 DOI: 10.1016/j.bbagrm.2022.194843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Divergent promoters are often responsible for controlling gene expression of related genes of the same pathway or for coordinating regulation at different time points. There are relatively few reports on characterization of divergent promoters in bacteria. In the present study, microarray profiling was carried out to analyze gene expression during growth of Gordonia sp. IITR100, which led to the identification of 35 % of adjacent gene candidates that are divergently transcribed. We focus here on the in-depth characterization of one such pair of genes. Two divergent promoters, PmaiA and Phyd, drive the expression of genes encoding maleate cis-trans isomerase (maiA) and hydantoinase (hyd), respectively. Our findings reveal asymmetric promoter activity with higher activity in the reverse orientation (Phyd) as compared to the forward orientation (PmaiA). Minimal promoter region for each orientation was identified by deletion mapping. Deletion of a 5'-untranslated region of each gene resulted in an increase in promoter activity. A putative binding site for CRP (Catabolite Repressor Protein) transcription regulator was also identified in the 80 bp common regulatory region between the -35 hexamers of the two promoters. The results of this study suggest that CRP-mediated repression of PmaiA occurs only in the cells grown in glucose. Phyd, on the other hand, is not repressed by CRP. However, deletion of the CRP binding site located between -95 to -110 upstream to the transcription start site of the maiA gene resulted in increased activity of PmaiA and decreased activity of Phyd. A single CRP binding site, therefore, affects the two promoters differently.
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Affiliation(s)
- Jananee Jaishankar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Aditi Keshav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Bijjiga Jayaram
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Sourabh Chavan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India.
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5
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Bourigault Y, Rodrigues S, Crépin A, Chane A, Taupin L, Bouteiller M, Dupont C, Merieau A, Konto-Ghiorghi Y, Boukerb AM, Turner M, Hamon C, Dufour A, Barbey C, Latour X. Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching. Int J Mol Sci 2021; 22:ijms22158241. [PMID: 34361010 PMCID: PMC8347015 DOI: 10.3390/ijms22158241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Biofilms are complex structures formed by a community of microbes adhering to a surface and/or to each other through the secretion of an adhesive and protective matrix. The establishment of these structures requires a coordination of action between microorganisms through powerful communication systems such as quorum-sensing. Therefore, auxiliary bacteria capable of interfering with these means of communication could be used to prevent biofilm formation and development. The phytopathogen Rhizobium rhizogenes, which causes hairy root disease and forms large biofilms in hydroponic crops, and the biocontrol agent Rhodococcus erythropolis R138 were used for this study. Changes in biofilm biovolume and structure, as well as interactions between rhizobia and rhodococci, were monitored by confocal laser scanning microscopy with appropriate fluorescent biosensors. We obtained direct visual evidence of an exchange of signals between rhizobia and the jamming of this communication by Rhodococcus within the biofilm. Signaling molecules were characterized as long chain (C14) N-acyl-homoserine lactones. The role of the Qsd quorum-quenching pathway in biofilm alteration was confirmed with an R. erythropolis mutant unable to produce the QsdA lactonase, and by expression of the qsdA gene in a heterologous host, Escherichia coli. Finally, Rhizobium biofilm formation was similarly inhibited by a purified extract of QsdA enzyme.
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Affiliation(s)
- Yvann Bourigault
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Sophie Rodrigues
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Alexandre Crépin
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, F-86073 Poitiers, France;
| | - Andrea Chane
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
| | - Laure Taupin
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Mathilde Bouteiller
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Charly Dupont
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Annabelle Merieau
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Amine M. Boukerb
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
| | - Marie Turner
- Vegenov, F-29250 Saint-Pol-de-Léon, France; (M.T.); (C.H.)
- Biocontrol Consortium, F-75007 Paris, France
| | - Céline Hamon
- Vegenov, F-29250 Saint-Pol-de-Léon, France; (M.T.); (C.H.)
| | - Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Corinne Barbey
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
- Biocontrol Consortium, F-75007 Paris, France
- Correspondence: ; +33-235-146-000
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Liang Y, Yu H. Genetic toolkits for engineering Rhodococcus species with versatile applications. Biotechnol Adv 2021; 49:107748. [PMID: 33823269 DOI: 10.1016/j.biotechadv.2021.107748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 02/09/2023]
Abstract
Rhodococcus spp. are a group of non-model gram-positive bacteria with diverse catabolic activities and strong adaptive capabilities, which enable their wide application in whole-cell biocatalysis, environmental bioremediation, and lignocellulosic biomass conversion. Compared with model microorganisms, the engineering of Rhodococcus is challenging because of the lack of universal molecular tools, high genome GC content (61% ~ 71%), and low transformation and recombination efficiencies. Nevertheless, because of the high interest in Rhodococcus species for bioproduction, various genetic elements and engineering tools have been recently developed for Rhodococcus spp., including R. opacus, R. jostii, R. ruber, and R. erythropolis, leading to the expansion of the genetic toolkits for Rhodococcus engineering. In this article, we provide a comprehensive review of the important developed genetic elements for Rhodococcus, including shuttle vectors, promoters, antibiotic markers, ribosome binding sites, and reporter genes. In addition, we also summarize gene transfer techniques and strategies to improve transformation efficiency, as well as random and precise genome editing tools available for Rhodococcus, including transposition, homologous recombination, recombineering, and CRISPR/Cas9. We conclude by discussing future trends in Rhodococcus engineering. We expect that more synthetic and systems biology tools (such as multiplex genome editing, dynamic regulation, and genome-scale metabolic models) will be adapted and optimized for Rhodococcus.
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Affiliation(s)
- Youxiang Liang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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Singhi D, Parwin S, Srivastava P. Genomic deletions in Rhodococcus based on transformation of linear heterologous DNA. Microbiology (Reading) 2021; 167. [DOI: 10.1099/mic.0.001028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Several genome engineering methods have been developed for
Rhodococcus
. However, they suffer from limitations such as extensive cloning, multiple steps, successful expression of heterologous genes via plasmid etc. Here, we report a rapid method for performing genomic deletions/disruptions in
Rhodococcus
spp. using heterologous linear DNA. The method is cost effective and less labour intensive. The applicability of the method was demonstrated by successful disruption of rodA and orphan parA. None of the disrupted genes were found to be essential for the viability of the cell. Disruption of orphan parA and rodA resulted in elongated cells and short rods, respectively. This is the first report demonstrating disruption of rodA and orphan parA genes by electroporation of heterologous linear DNA in
Rhodococcus
spp.
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Affiliation(s)
- Divya Singhi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Shabnam Parwin
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
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Murarka P, Keshav A, Meena BK, Srivastava P. Functional characterization of the transcription regulator WhiB1 from Gordonia sp. IITR100. MICROBIOLOGY-SGM 2020; 166:1181-1190. [PMID: 33215983 DOI: 10.1099/mic.0.000985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
WhiB is a transcription regulator which has been reported to be involved in the regulation of cell morphogenesis, cell division, antibiotic resistance, stress, etc., in several members of the family Actinomycetes. The present study describes functional characterization of a WhiB family protein, WhiB1 (protein ID: WP_065632651.1), from Gordonia sp. IITR100. We demonstrate that WhiB1 affects chromosome segregation and cell morphology in recombinant Escherichia coli, Gordonia sp. IITR100 as well as in Rhodococcus erythropolis. Multiple sequence alignment suggests that WhiB1 is a conserved protein among members of the family Actinomycetes. It has been reported that overexpression of WhiB1 leads to repression of the biodesulfurization operon in recombinant E. coli, Gordonia sp. IITR100 and R. erythropolis. A WhiB1-mut containing a point mutation Q116A in the DNA binding domain of WhiB1 led to partial alleviation of repression of the biodesulfurization operon. We show for the first time that the WhiB family protein WhiB1 is also involved in repression of the biodesulfurization operon by directly binding to the dsz promoter DNA.
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Affiliation(s)
- Pooja Murarka
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Aditi Keshav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Bintu Kumar Meena
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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9
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Rhodoccoccus erythropolis Is Different from Other Members of Actinobacteria: Monoploidy, Overlapping Replication Cycle, and Unique Segregation Pattern. J Bacteriol 2019; 201:JB.00320-19. [PMID: 31570531 DOI: 10.1128/jb.00320-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/24/2019] [Indexed: 11/20/2022] Open
Abstract
Among actinomycetes, chromosome organization and segregation studies have been limited to Streptomyces coelicolor, Corynebacterium glutamicum, and Mycobacterium spp. There are differences with respect to ploidy and chromosome organization pattern in these bacteria. Here, we report on chromosome replication, organization, and segregation in Rhodococcus erythropolis PR4, which has a circular genome of 6.5 Mbp. The origin of replication of R. erythropolis PR4 was identified, and the DNA content in the cell under different growth conditions was determined. Our results suggest that the number of origins increases as the growth medium becomes rich, suggesting an overlapping replication cell cycle in this bacterium. Subcellular localization of the origin region revealed polar positioning in minimal and rich media. The terminus, which is the last region to be replicated and segregated, was found to be localized at the cell center in large cells. The middle markers corresponding to the 1.5-Mb and 4.7-Mb loci did not overlap, suggesting discontinuity in the segregation of the two arms of the chromosome. Chromosome segregation was not affected by inhibiting cell division. Deletion of parA or parB affected chromosome segregation. Unlike in C. glutamicum and Streptomyces spp., diploidy or polyploidy was not observed in R. erythropolis PR4. Our results suggest that R. erythropolis is different from other members of Actinobacteria; it is monoploid and has a unique chromosome segregation pattern. This is the first report on chromosome organization, replication, and segregation in R. erythropolis PR4.IMPORTANCE Rhodococci are highly versatile Gram-positive bacteria with high bioremediation potential. Some rhodococci are pathogenic and have been suggested as emerging threats. No studies on the replication, segregation, and cell cycle of these bacteria have been reported. Here, we demonstrate that the genus Rhodococcus is different from other actinomycetes, such as members of the genera Corynebacterium, Mycobacterium, and Streptomyces, with respect to ploidy and chromosome organization and segregation. Such studies will be useful not only in designing better therapeutics pathogenic strains in the future but also for studying genome maintenance in strains used for bioremediation.
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10
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Chane A, Barbey C, Robert M, Merieau A, Konto-Ghiorghi Y, Beury-Cirou A, Feuilloley M, Pátek M, Gobert V, Latour X. Biocontrol of Soft Rot: Confocal Microscopy Highlights Virulent Pectobacterial Communication and Its Jamming by Rhodococcal Quorum-Quenching. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:802-812. [PMID: 30645157 DOI: 10.1094/mpmi-11-18-0314-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Confocal laser-scanning microscopy was chosen to observe the colonization and damage caused by the soft rot Pectobacterium atrosepticum and the protection mediated by the biocontrol agent Rhodococcus erythropolis. We developed dual-color reporter strains suited for monitoring quorum-sensing and quorum-quenching activities leading to maceration or biocontrol, respectively. A constitutively expressed cyan or red fluorescent protein served as a cell tag for plant colonization, while an inducible expression reporter system based on the green fluorescent protein gene enabled the simultaneous recording of signaling molecule production, detection, or degradation. The dual-colored pathogen and biocontrol strains were used to coinoculate potato tubers. At cellular quorum, images revealed a strong pectobacterial quorum-sensing activity, especially at the plant cell walls, as well as a concomitant rhodococcal quorum-quenching response, at both the single-cell and microcolony levels. The generated biosensors appear to be promising and complementary tools useful for molecular and cellular studies of bacterial communication and interference.
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Affiliation(s)
- Andrea Chane
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Corinne Barbey
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
- 2 Seeds Innovation Protection Research and Environment, Route de la petite chaussée, 76110 Bretteville du Grand-Caux and Rue des Champs Potez, 62217 Achicourt, France
| | - Magalie Robert
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Annabelle Merieau
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Yoan Konto-Ghiorghi
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Amélie Beury-Cirou
- 2 Seeds Innovation Protection Research and Environment, Route de la petite chaussée, 76110 Bretteville du Grand-Caux and Rue des Champs Potez, 62217 Achicourt, France
- 3 French Federation of seed potato growers (FN3PT/RD3PT), 43-45 rue de Naples, 75008 Paris, France
| | - Marc Feuilloley
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
| | - Miroslav Pátek
- 4 Institute of Microbiology of the CAS, v.v.i. Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Virginie Gobert
- 2 Seeds Innovation Protection Research and Environment, Route de la petite chaussée, 76110 Bretteville du Grand-Caux and Rue des Champs Potez, 62217 Achicourt, France
- 3 French Federation of seed potato growers (FN3PT/RD3PT), 43-45 rue de Naples, 75008 Paris, France
| | - Xavier Latour
- 1 Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)-Normandie Université-LMSM, 55 rue Saint-Germain, 27000 Evreux, France and Structure Fédérative de Recherche Normandie Végétale 4277
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Deletion of pyruvate decarboxylase gene in Zymomonas mobilis by recombineering through bacteriophage lambda red genes. J Microbiol Methods 2018; 151:111-117. [PMID: 29958909 DOI: 10.1016/j.mimet.2018.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/25/2018] [Accepted: 06/25/2018] [Indexed: 11/22/2022]
Abstract
Zymomonas mobilis ZM4 is a gram negative ethanologenic bacterium used in several biotechnological applications. Metabolic engineering in this bacterium is limited because of the available genome engineering tools. In the present study, we report genome engineering in this bacterium using bacteriophage lambda Red genes. Stability of plasmid replicons RK2 (pSIM9) and pBBR1 (pSIM7) containing the lambda Red genes was found to be 78% and 74%, respectively. We demonstrate successful deletion of pyruvate decarboxylase gene by recombineering in Z. mobilis. The deletion was confirmed by PCR and by estimating the metabolites formed. Ethanol, which was the main product in wild type cells, was formed in almost negligible amount in the pdc-deleted mutant. The developed Δpdc Z. mobilis cells can be exploited for production of desired bioproducts by expression of suitable enzymes that can regenerate NAD+.
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Correction: Localization of Low Copy Number Plasmid pRC4 in Replicating Rod and Non-Replicating Cocci Cells of Rhodococcus erythropolis PR4. PLoS One 2017; 12:e0171885. [PMID: 28166281 PMCID: PMC5293212 DOI: 10.1371/journal.pone.0171885] [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] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0166491.].
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