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Gourgues G, Manso-Silván L, Chamberland C, Sirand-Pugnet P, Thiaucourt F, Blanchard A, Baby V, Lartigue C. A toolbox for manipulating the genome of the major goat pathogen, Mycoplasma capricolum subsp. capripneumoniae. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001423. [PMID: 38193814 PMCID: PMC10866025 DOI: 10.1099/mic.0.001423] [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: 06/08/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024]
Abstract
Mycoplasma capricolum subspecies capripneumoniae (Mccp) is the causative agent of contagious caprine pleuropneumonia (CCPP), a devastating disease listed by the World Organisation for Animal Health (WOAH) as a notifiable disease and threatening goat production in Africa and Asia. Although a few commercial inactivated vaccines are available, they do not comply with WOAH standards and there are serious doubts regarding their efficacy. One of the limiting factors to comprehend the molecular pathogenesis of CCPP and develop improved vaccines has been the lack of tools for Mccp genome engineering. In this work, key synthetic biology techniques recently developed for closely related mycoplasmas were adapted to Mccp. CReasPy-Cloning was used to simultaneously clone and engineer the Mccp genome in yeast, prior to whole-genome transplantation into M. capricolum subsp. capricolum recipient cells. This approach was used to knock out an S41 serine protease gene recently identified as a potential virulence factor, leading to the generation of the first site-specific Mccp mutants. The Cre-lox recombination system was then applied to remove all DNA sequences added during genome engineering. Finally, the resulting unmarked S41 serine protease mutants were validated by whole-genome sequencing and their non-caseinolytic phenotype was confirmed by casein digestion assay on milk agar. The synthetic biology tools that have been successfully implemented in Mccp allow the addition and removal of genes and other genetic features for the construction of seamless targeted mutants at ease, which will pave the way for both the identification of key pathogenicity determinants of Mccp and the rational design of novel, improved vaccines for the control of CCPP.
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Affiliation(s)
- Géraldine Gourgues
- Université de Bordeaux, INRAE, BFP, UMR 1332, F-33140 Villenave d'Ornon, France
| | - Lucía Manso-Silván
- CIRAD, UMR ASTRE, F-34398, Montpellier, France
- ASTRE, Université de Montpellier, CIRAD, INRAE, F-34398, Montpellier, France
| | - Catherine Chamberland
- Université de Sherbrooke, Département de biologie, Sherbrooke, Québec, J1K 2R1, Canada
| | | | - François Thiaucourt
- CIRAD, UMR ASTRE, F-34398, Montpellier, France
- ASTRE, Université de Montpellier, CIRAD, INRAE, F-34398, Montpellier, France
| | - Alain Blanchard
- Université de Bordeaux, INRAE, BFP, UMR 1332, F-33140 Villenave d'Ornon, France
| | - Vincent Baby
- Université de Montréal, Faculté de médecine vétérinaire, Saint-Hyacinthe, Québec, J2S 2M2, Canada
| | - Carole Lartigue
- Université de Bordeaux, INRAE, BFP, UMR 1332, F-33140 Villenave d'Ornon, France
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2
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Nadolinskaia NI, Goncharenko AV. CRISPR Interference in Regulation of Bacterial Gene Expression. Mol Biol 2022. [DOI: 10.1134/s0026893322060139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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3
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Piñero-Lambea C, Garcia-Ramallo E, Miravet-Verde S, Burgos R, Scarpa M, Serrano L, Lluch-Senar M. SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome. Nucleic Acids Res 2022; 50:e127. [PMID: 36215032 PMCID: PMC9825166 DOI: 10.1093/nar/gkac836] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/03/2022] [Accepted: 09/28/2022] [Indexed: 01/29/2023] Open
Abstract
The development of advanced genetic tools is boosting microbial engineering which can potentially tackle wide-ranging challenges currently faced by our society. Here we present SURE editing, a multi-recombinase engineering rationale combining oligonucleotide recombineering with the selective capacity of antibiotic resistance via transient insertion of selector plasmids. We test this method in Mycoplasma pneumoniae, a bacterium with a very inefficient native recombination machinery. Using SURE editing, we can seamlessly generate, in a single step, a wide variety of genome modifications at high efficiencies, including the largest possible deletion of this genome (30 Kb) and the targeted complementation of essential genes in the deletion of a region of interest. Additional steps can be taken to remove the selector plasmid from the edited area, to obtain markerless or even scarless edits. Of note, SURE editing is compatible with different site-specific recombinases for mediating transient plasmid integration. This battery of selector plasmids can be used to select different edits, regardless of the target sequence, which significantly reduces the cloning load associated to genome engineering projects. Given the proven functionality in several microorganisms of the machinery behind the SURE editing logic, this method is likely to represent a valuable advance for the synthetic biology field.
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Affiliation(s)
| | | | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | | | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain,ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Maria Lluch-Senar
- Correspondence may also be addressed to Maria Lluch-Senar. Tel: +34 661963680;
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4
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Genome Editing of Veterinary Relevant Mycoplasmas Using a CRISPR-Cas Base Editor System. Appl Environ Microbiol 2022; 88:e0099622. [PMID: 36000854 PMCID: PMC9469718 DOI: 10.1128/aem.00996-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasmas are minimal bacteria that infect humans, wildlife, and most economically relevant livestock species. Mycoplasma infections cause a large range of chronic inflammatory diseases, eventually leading to death in some animals. Due to the lack of efficient recombination and genome engineering tools for most species, the production of mutant strains for the identification of virulence factors and the development of improved vaccine strains is limited. Here, we demonstrate the adaptation of an efficient Cas9-Base Editor system to introduce targeted mutations into three major pathogenic species that span the phylogenetic diversity of these bacteria: the avian pathogen Mycoplasma gallisepticum and the two most important bovine mycoplasmas, Mycoplasma bovis and Mycoplasma mycoides subsp. mycoides. As a proof of concept, we successfully used an inducible SpdCas9-pmcDA1 cytosine deaminase system to disrupt several major virulence factors in these pathogens. Various induction times and inducer concentrations were evaluated to optimize editing efficiency. The optimized system was powerful enough to disrupt 54 of 55 insertion sequence transposases in a single experiment. Whole-genome sequencing of the edited strains showed that off-target mutations were limited, suggesting that most variations detected in the edited genomes are Cas9-independent. This effective, rapid, and easy-to-use genetic tool opens a new avenue for the study of these important animal pathogens and likely the entire class Mollicutes. IMPORTANCE Mycoplasmas are minimal pathogenic bacteria that infect a wide range of hosts, including humans, livestock, and wild animals. Major pathogenic species cause acute to chronic infections involving still poorly characterized virulence factors. The lack of precise genome editing tools has hampered functional studies of many species, leaving multiple questions about the molecular basis of their pathogenicity unanswered. Here, we demonstrate the adaptation of a CRISPR-derived base editor for three major pathogenic species: Mycoplasma gallisepticum, Mycoplasma bovis, and Mycoplasma mycoides subsp. mycoides. Several virulence factors were successfully targeted, and we were able to edit up to 54 target sites in a single step. The availability of this efficient and easy-to-use genetic tool will greatly facilitate functional studies of these economically important bacteria.
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5
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A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications. Nat Commun 2022; 13:1910. [PMID: 35393441 PMCID: PMC8991246 DOI: 10.1038/s41467-022-29574-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/24/2022] [Indexed: 12/18/2022] Open
Abstract
Mycoplasmas have exceptionally streamlined genomes and are strongly adapted to their many hosts, which provide them with essential nutrients. Owing to their relative genomic simplicity, Mycoplasmas have been used to develop chassis for biotechnological applications. However, the dearth of robust and precise toolkits for genomic manipulation and tight regulation has hindered any substantial advance. Herein we describe the construction of a robust genetic toolkit for M. pneumoniae, and its successful deployment to engineer synthetic gene switches that control and limit Mycoplasma growth, for biosafety containment applications. We found these synthetic gene circuits to be stable and robust in the long-term, in the context of a minimal cell. With this work, we lay a foundation to develop viable and robust biosafety systems to exploit a synthetic Mycoplasma chassis for live attenuated vectors for therapeutic applications. Mycoplasmas are minimal cell model organisms but lack genetic tools. Here the authors provide a robust genetic toolkit for Mycoplasma demonstrating gene circuit engineering applications.
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6
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Ipoutcha T, Gourgues G, Lartigue C, Blanchard A, Sirand-Pugnet P. Genome Engineering in Mycoplasma gallisepticum Using Exogenous Recombination Systems. ACS Synth Biol 2022; 11:1060-1067. [PMID: 35167277 DOI: 10.1021/acssynbio.1c00541] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mycoplasma gallisepticum (Mgal) is a common pathogen of poultry worldwide that has recently spread to North American house finches after a single host shift in 1994. The molecular determinants of Mgal virulence and host specificity are still largely unknown, mostly due to the absence of efficient methods for functional genomics. After evaluating two exogenous recombination systems derived from phages found in the phylogenetically related Spiroplasma phoeniceum and the more distant Bacillus subtilis, the RecET-like system from B. subtilis was successfully used for gene inactivation and targeted replacement in Mgal. In a second step, the Cre-lox recombination system was used for the removal of the antibiotic resistance marker in recombinant mutants. This study therefore describes the first genetic tool for targeted genome engineering of Mgal and demonstrates the efficiency of heterologous recombination systems in minimal bacteria.
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Affiliation(s)
- Thomas Ipoutcha
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Géraldine Gourgues
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Carole Lartigue
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Alain Blanchard
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Pascal Sirand-Pugnet
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
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7
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Chang CW, Wang LS, Pham NN, Shen CC, Hsu MN, Nguyen NTK, Yen CY, Lin MW, Hwu JR, Chang YH, Hu YC. Synthetic biology approach to developing all-in-one baculovirus vector using mammalian introns and miRNA binding sites. J Taiwan Inst Chem Eng 2022. [DOI: 10.1016/j.jtice.2021.104175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Bertram R, Neumann B, Schuster CF. Status quo of tet regulation in bacteria. Microb Biotechnol 2021; 15:1101-1119. [PMID: 34713957 PMCID: PMC8966031 DOI: 10.1111/1751-7915.13926] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 11/27/2022] Open
Abstract
The tetracycline repressor (TetR) belongs to the most popular, versatile and efficient transcriptional regulators used in bacterial genetics. In the tetracycline (Tc) resistance determinant tet(B) of transposon Tn10, tetR regulates the expression of a divergently oriented tetA gene that encodes a Tc antiporter. These components of Tn10 and of other natural or synthetic origins have been used for tetracycline‐dependent gene regulation (tet regulation) in at least 40 bacterial genera. Tet regulation serves several purposes such as conditional complementation, depletion of essential genes, modulation of artificial genetic networks, protein overexpression or the control of gene expression within cell culture or animal infection models. Adaptations of the promoters employed have increased tet regulation efficiency and have made this system accessible to taxonomically distant bacteria. Variations of TetR, different effector molecules and mutated DNA binding sites have enabled new modes of gene expression control. This article provides a current overview of tet regulation in bacteria.
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Affiliation(s)
- Ralph Bertram
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Prof.-Ernst-Nathan-Straße 1, Nuremberg, 90419, Germany
| | - Bernd Neumann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Prof.-Ernst-Nathan-Straße 1, Nuremberg, 90419, Germany
| | - Christopher F Schuster
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Burgstraße 37, Wernigerode, 38855, Germany
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9
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Hill V, Akarsu H, Barbarroja RS, Cippà VL, Kuhnert P, Heller M, Falquet L, Heller M, Stoffel MH, Labroussaa F, Jores J. Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems. PLoS Genet 2021; 17:e1009365. [PMID: 34673769 PMCID: PMC8562856 DOI: 10.1371/journal.pgen.1009365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 11/02/2021] [Accepted: 09/29/2021] [Indexed: 11/19/2022] Open
Abstract
Mycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They encompass several important medical and veterinary pathogens that are often associated with a wide range of chronic diseases. The long persistence of mycoplasma cells in their hosts can exacerbate the spread of antimicrobial resistance observed for many species. However, the nature of the virulence factors driving this phenomenon in mycoplasmas is still unclear. Toxin-antitoxin systems (TA systems) are genetic elements widespread in many bacteria that were historically associated with bacterial persistence. Their presence on mycoplasma genomes has never been carefully assessed, especially for pathogenic species. Here we investigated three candidate TA systems in M. mycoides subsp. capri encoding a (i) novel AAA-ATPase/subtilisin-like serine protease module, (ii) a putative AbiEii/AbiEi pair and (iii) a putative Fic/RelB pair. We sequence analyzed fourteen genomes of M. mycoides subsp. capri and confirmed the presence of at least one TA module in each of them. Interestingly, horizontal gene transfer signatures were also found in several genomic loci containing TA systems for several mycoplasma species. Transcriptomic and proteomic data confirmed differential expression profiles of these TA systems during mycoplasma growth in vitro. While the use of heterologous expression systems based on E. coli and B. subtilis showed clear limitations, the functionality and neutralization capacities of all three candidate TA systems were successfully confirmed using M. capricolum subsp. capricolum as a host. Additionally, M. capricolum subsp. capricolum was used to confirm the presence of functional TA system homologs in mycoplasmas of the Hominis and Pneumoniae phylogenetic groups. Finally, we showed that several of these M. mycoides subsp. capri toxins tested in this study, and particularly the subtilisin-like serine protease, could be used to establish a kill switch in mycoplasmas for industrial applications.
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Affiliation(s)
- Virginia Hill
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Hatice Akarsu
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Valentina L. Cippà
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Martin Heller
- Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Jena, Germany
| | - Laurent Falquet
- Biochemistry Unit, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michael H. Stoffel
- Division of Veterinary Anatomy, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
- * E-mail:
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10
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Burgos R, Weber M, Martinez S, Lluch‐Senar M, Serrano L. Protein quality control and regulated proteolysis in the genome-reduced organism Mycoplasma pneumoniae. Mol Syst Biol 2020; 16:e9530. [PMID: 33320415 PMCID: PMC7737663 DOI: 10.15252/msb.20209530] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Protein degradation is a crucial cellular process in all-living systems. Here, using Mycoplasma pneumoniae as a model organism, we defined the minimal protein degradation machinery required to maintain proteome homeostasis. Then, we conditionally depleted the two essential ATP-dependent proteases. Whereas depletion of Lon results in increased protein aggregation and decreased heat tolerance, FtsH depletion induces cell membrane damage, suggesting a role in quality control of membrane proteins. An integrative comparative study combining shotgun proteomics and RNA-seq revealed 62 and 34 candidate substrates, respectively. Cellular localization of substrates and epistasis studies supports separate functions for Lon and FtsH. Protein half-life measurements also suggest a role for Lon-modulated protein decay. Lon plays a key role in protein quality control, degrading misfolded proteins and those not assembled into functional complexes. We propose that regulating complex assembly and degradation of isolated proteins is a mechanism that coordinates important cellular processes like cell division. Finally, by considering the entire set of proteases and chaperones, we provide a fully integrated view of how a minimal cell regulates protein folding and degradation.
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martinez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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11
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Garcia-Morales L, Ruiz E, Gourgues G, Rideau F, Piñero-Lambea C, Lluch-Senar M, Blanchard A, Lartigue C. A RAGE Based Strategy for the Genome Engineering of the Human Respiratory Pathogen Mycoplasma pneumoniae. ACS Synth Biol 2020; 9:2737-2748. [PMID: 33017534 DOI: 10.1021/acssynbio.0c00263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genome engineering of microorganisms has become a standard in microbial biotechnologies. Several efficient tools are available for the genetic manipulation of model bacteria such as Escherichia coli and Bacillus subtilis, or the yeast Saccharomyces cerevisiae. Difficulties arise when transferring these tools to nonmodel organisms. Synthetic biology strategies relying on genome transplantation (GT) aim at using yeast cells for engineering bacterial genomes cloned as artificial chromosomes. However, these strategies remain unsuccessful for many bacteria, including Mycoplasma pneumoniae (MPN), a human pathogen infecting the respiratory tract that has been extensively studied as a model for systems biology of simple unicellular organisms. Here, we have designed a novel strategy for genome engineering based on the recombinase-assisted genomic engineering (RAGE) technology for editing the MPN genome. Using this strategy, we have introduced a 15 kbp fragment at a specific locus of the MPN genome and replaced 38 kbp from its genome by engineered versions modified either in yeast or in E. coli. A strain harboring a synthetic version of this fragment cleared of 13 nonessential genes could also be built and propagated in vitro. These strains were depleted of known virulence factors aiming at creating an avirulent chassis for SynBio applications. Such a chassis and technology are a step forward to build vaccines or deliver therapeutic compounds in the lungs to prevent or cure respiratory diseases in humans.
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Affiliation(s)
- Luis Garcia-Morales
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Estelle Ruiz
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Géraldine Gourgues
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Fabien Rideau
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Alain Blanchard
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Carole Lartigue
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
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12
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Piñero-Lambea C, Garcia-Ramallo E, Martinez S, Delgado J, Serrano L, Lluch-Senar M. Mycoplasma pneumoniae Genome Editing Based on Oligo Recombineering and Cas9-Mediated Counterselection. ACS Synth Biol 2020; 9:1693-1704. [PMID: 32502342 PMCID: PMC7372593 DOI: 10.1021/acssynbio.0c00022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Mycoplasma species
share a set of features, such as lack of a cell
wall, streamlined genomes, simplified metabolism, and the use of a
deviant genetic code, that make them attractive approximations of
what a chassis strain should ideally be. Among them, Mycoplasma
pneumoniae arises as a candidate for synthetic biology projects,
as it is one of the most deeply characterized bacteria. However, the
historical paucity of tools for editing Mycoplasma genomes has precluded
the establishment of M. pneumoniae as a suitable
chassis strain. Here, we developed an oligonucleotide recombineering
method for this strain based on GP35, a ssDNA recombinase originally
encoded by a Bacillus subtilis-associated phage.
GP35-mediated oligo recombineering is able to carry out point mutations
in the M. pneumoniae genome with an efficiency as
high as 2.7 × 10–2, outperforming oligo recombineering
protocols developed for other bacteria. Gene deletions of different
sizes showed a decreasing power trend between efficiency and the scale
of the attempted edition. However, the editing rates for all modifications
increased when CRISPR/Cas9 was used to counterselect nonedited cells.
This allowed edited clones carrying chromosomal deletions of up to
1.8 kb to be recovered with little to no screening of survivor cells.
We envision this technology as a major step toward the use of M. pneumoniae, and possibly other Mycoplasmas, as synthetic
biology chassis strains.
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Affiliation(s)
- Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Garcia-Ramallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Sira Martinez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Delgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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13
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Weber M, Burgos R, Yus E, Yang J, Lluch‐Senar M, Serrano L. Impact of C-terminal amino acid composition on protein expression in bacteria. Mol Syst Biol 2020; 16:e9208. [PMID: 32449593 PMCID: PMC7246954 DOI: 10.15252/msb.20199208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 11/30/2022] Open
Abstract
The C-terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C-terminal sequence and levels of protein expression remains unknown. Here, we identified C-terminal amino acid biases that are ubiquitous across the bacterial taxonomy (1,582 genomes). We showed that the frequency is higher for positively charged amino acids (lysine, arginine), while hydrophobic amino acids and threonine are lower. We then studied the impact of C-terminal composition on protein levels in a library of Mycoplasma pneumoniae mutants, covering all possible combinations of the two last codons. We found that charged and polar residues, in particular lysine, led to higher expression, while hydrophobic and aromatic residues led to lower expression, with a difference in protein levels up to fourfold. We further showed that modulation of protein degradation rate could be one of the main mechanisms driving these differences. Our results demonstrate that the identity of the last amino acids has a strong influence on protein expression levels.
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Affiliation(s)
- Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Eva Yus
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Jae‐Seong Yang
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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Montero-Blay A, Miravet-Verde S, Lluch-Senar M, Piñero-Lambea C, Serrano L. SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes. DNA Res 2019; 26:327-339. [PMID: 31257417 PMCID: PMC6704405 DOI: 10.1093/dnares/dsz012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/16/2019] [Indexed: 11/17/2022] Open
Abstract
Mycoplasmas are important model organisms for Systems and Synthetic Biology, and are pathogenic to a wide variety of species. Despite their relevance, many of the tools established for genome editing in other microorganisms are not available for Mycoplasmas. The Tn4001 transposon is the reference tool to work with these bacteria, but the transformation efficiencies (TEs) reported for the different species vary substantially. Here, we explore the mechanisms underlying these differences in four Mycoplasma species, Mycoplasma agalactiae, Mycoplasma feriruminatoris, Mycoplasma gallisepticum and Mycoplasma pneumoniae, selected for being representative members of each cluster of the Mycoplasma genus. We found that regulatory regions (RRs) driving the expression of the transposase and the antibiotic resistance marker have a major impact on the TEs. We then designed a synthetic RR termed SynMyco RR to control the expression of the key transposon vector elements. Using this synthetic RR, we were able to increase the TE for M. gallisepticum, M. feriruminatoris and M. agalactiae by 30-, 980- and 1036-fold, respectively. Finally, to illustrate the potential of this new transposon, we performed the first essentiality study in M. agalactiae, basing our study on more than 199,000 genome insertions.
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Affiliation(s)
- Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona, Spain
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15
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Floxed-Cassette Allelic Exchange Mutagenesis Enables Markerless Gene Deletion in Chlamydia trachomatis and Can Reverse Cassette-Induced Polar Effects. J Bacteriol 2018; 200:JB.00479-18. [PMID: 30224436 DOI: 10.1128/jb.00479-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/12/2018] [Indexed: 01/04/2023] Open
Abstract
As obligate intracellular bacteria, Chlamydia spp. have evolved numerous, likely intricate, mechanisms to create and maintain a privileged intracellular niche. Recent progress in elucidating and characterizing these processes has been bolstered by the development of techniques enabling basic genetic tractability. Florescence-reported allelic exchange mutagenesis (FRAEM) couples chromosomal gene deletion with the insertion of a selection cassette encoding antibiotic resistance and green fluorescent protein (GFP). Similar to other bacteria, many chlamydial genes exist within polycistronic operons, raising the possibility of polar effects mediated by insertion cassettes. Indeed, FRAEM-mediated deletion of Chlamydia trachomatis tmeA negatively impacts the expression of tmeB We have adapted FRAEM technology by employing a gfp-bla cassette flanked by loxP sites. Conditional expression of Cre recombinase in Chlamydia tmeA containing a floxed cassette resulted in deletion of the marker and restoration of tmeB expression.IMPORTANCE C. trachomatis infections represent a significant burden to human health. The ability to genetically manipulate Chlamydia spp. is overcoming historic confounding barriers that have impeded rapid progress in understanding overall chlamydial pathogenesis. The current state of genetic manipulation in Chlamydia spp. requires further development, including mechanisms to generate markerless gene disruption. We leveraged a stepwise Cre-lox approach to excise selection marker genes from a deleted gene locus. We found this process to be efficient, and the removal of extraneous elements resulted in the reversal of a negative polar effect on a downstream gene. This technique facilitates a more direct assessment of gene function and adds to the Chlamydia molecular toolbox by facilitating the deletion of genes within operons.
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Mariscal AM, Kakizawa S, Hsu JY, Tanaka K, González-González L, Broto A, Querol E, Lluch-Senar M, Piñero-Lambea C, Sun L, Weyman PD, Wise KS, Merryman C, Tse G, Moore AJ, Hutchison CA, Smith HO, Tomita M, Venter JC, Glass JI, Piñol J, Suzuki Y. Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells. ACS Synth Biol 2018; 7:1538-1552. [PMID: 29786424 DOI: 10.1021/acssynbio.8b00028] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functional genomics studies in minimal mycoplasma cells enable unobstructed access to some of the most fundamental processes in biology. Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in mycoplasmas. Here we demonstrate systems for inducible repression of gene expression based on clustered regularly interspaced short palindromic repeats-mediated interference (CRISPRi) in Mycoplasma pneumoniae and synthetic Mycoplasma mycoides, two organisms with reduced genomes actively used in systems biology studies. In the synthetic cell, we also demonstrate inducible gene expression for the first time. Time-course data suggest rapid kinetics and reversible engagement of CRISPRi. Targeting of six selected endogenous genes with this system results in lowered transcript levels or reduced growth rates that agree with lack or shortage of data in previous transposon bombardment studies, and now produces actual cells to analyze. The ksgA gene encodes a methylase that modifies 16S rRNA, rendering it vulnerable to inhibition by the antibiotic kasugamycin. Targeting the ksgA gene with CRISPRi removes the lethal effect of kasugamycin and enables cell growth, thereby establishing specific and effective gene modulation with our system. The facile methods for conditional gene activation and inactivation in mycoplasmas open the door to systematic dissection of genetic programs at the core of cellular life.
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Affiliation(s)
- Ana M Mariscal
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Shigeyuki Kakizawa
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- National Institute of Advanced Industrial Science and Technology , Tsukuba , Ibaraki 305-8560 , Japan
| | - Jonathan Y Hsu
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093 , United States
| | - Kazuki Tanaka
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Institute for Advanced Biosciences , Keio University , Tsuruoka , Yamagata 997-0035 , Japan
- Faculty of Environment and Information Studies , Keio University , Fujisawa , Kanagawa 252-0882 , Japan
| | - Luis González-González
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Alicia Broto
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Barcelona 08036 , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Barcelona 08036 , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain
| | - Carlos Piñero-Lambea
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Barcelona 08036 , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain
| | - Lijie Sun
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Philip D Weyman
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Kim S Wise
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Chuck Merryman
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Gavin Tse
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093 , United States
| | - Adam J Moore
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
- Department of Bioengineering , University of California, San Diego , La Jolla , California 92093 , United States
| | - Clyde A Hutchison
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Hamilton O Smith
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Masaru Tomita
- Institute for Advanced Biosciences , Keio University , Tsuruoka , Yamagata 997-0035 , Japan
| | - J Craig Venter
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - John I Glass
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina , Universitat Autònoma de Barcelona , Cerdanyola del Vallès, Barcelona 08193 , Spain
| | - Yo Suzuki
- Synthetic Biology Group , J. Craig Venter Institute , La Jolla , California 92037 , United States
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