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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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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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3
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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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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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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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