Advances of genetic engineering in streptococci and enterococci.
CRISPR\Cas
conjugation
enterococci
genome editing
horizontal gene transfer
natural transformation
streptococci
Journal
Microbiology and immunology
ISSN: 1348-0421
Titre abrégé: Microbiol Immunol
Pays: Australia
ID NLM: 7703966
Informations de publication
Date de publication:
Sep 2022
Sep 2022
Historique:
revised:
09
06
2022
received:
01
05
2022
accepted:
11
06
2022
pubmed:
16
6
2022
medline:
14
9
2022
entrez:
15
6
2022
Statut:
ppublish
Résumé
In the post-genome era, reverse genetic engineering is an indispensable methodology for experimental molecular biology to provide a deeper understanding of the principal relationship between genomic features and biological phenotypes. Technically, genetic engineering is carried out through allele replacement of a target genomic locus with a designed nucleotide sequence, so called site-directed mutagenesis. To artificially manipulate allele replacement through homologous recombination, researchers have improved various methodologies that are optimized to the bacterial species of interest. Here, we review widely used genetic engineering technologies, particularly for streptococci and enterococci, and recent advances that enable more effective and flexible manipulation. The development of genetic engineering has been promoted by synthetic biology approaches based on basic biological knowledge of horizontal gene transfer systems, such as natural conjugative transfer, natural transformation, and the CRISPR/Cas system. Therefore, this review also describes basic insights into molecular biology that underlie improvements in genetic engineering technology.
Identifiants
pubmed: 35703039
doi: 10.1111/1348-0421.13015
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
411-417Subventions
Organisme : The Naito Foundation
Organisme : Japan Society for Promotion of Science (JSPS) KAKENHI
ID : 22K07052
Organisme : Japan Society for Promotion of Science (JSPS) KAKENHI
ID : 22K07067
Organisme : Japanese Ministry of Health, Labor and Welfare (Research Program on ensuring Food Safety)
ID : 21KA1004
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP22fk0108604h0902
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP22wm0225008h0203
Organisme : Ohyama Health Foundation Inc.
Organisme : GSK Japan research grant
Informations de copyright
© 2022 The Societies and John Wiley & Sons Australia, Ltd.
Références
Aghababa H, Ting YT, Pilapitiya D, Loh JMS, Young PG, Proft T. Complement evasion factor (CEF), a novel immune evasion factor of Streptococcus pyogenes. Virulence. 2022;13:225-40.
Maguin E, Prévost H, Ehrlich SD, Gruss A. Efficient insertional mutagenesis in lactococci and other gram-positive bacteria. J Bacteriol. 1996;178:931-5.
Otto R, de Vos WM, Gavrieli J. Plasmid DNA in Streptococcus cremoris Wg2: influence of pH on selection in chemostats of a variant lacking a protease plasmid. Appl Environ Microbiol. 1982;43:1272-77.
Takamatsu D, Osaki M, Sekizaki T. Thermosensitive suicide vectors for gene replacement in Streptococcus suis. Plasmid. 2001;46:140-8.
Roobthaisong A, Aikawa C, Nozawa T, Maruyama F, Nakagawa I. YvqE and CovRS of group A streptococcus play a pivotal role in viability and phenotypic adaptations to multiple environmental stresses. PLoS One. 2017;12:e0170612.
Liu G, Gao T, Zhong X, et al. The novel streptococcal transcriptional regulator XtgS negatively regulates bacterial virulence and directly represses PseP transcription. Infect Immun. 2020;88:e00035-20.
D'gama JD, Ma Z, Zhang H, et al. A conserved streptococcal virulence regulator controls the expression of a distinct class of M-like proteins. mBio. 2019;10:e02500.
Tomoyasu T, Imaki H, Masuda S, et al. LacR mutations are frequently observed in Streptococcus intermedius and are responsible for increased intermedilysin production and virulence. Infect Immun. 2013;81:3276-86.
Kristich CJ, Chandler JR, Dunny GM. Development of a host-genotype-independent counterselectable marker and a high-frequency conjugative delivery system and their use in genetic analysis of Enterococcus faecalis. Plasmid. 2007;57:131-44.
Barnes AMT, Frank KL, Dunny GM. Enterococcal endocarditis: hiding in plain sight. Front Cell Infect Microbiol. 2021;11:722482.
Arias CA, Murray BE. The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol. 2012;10:266-78. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=22421879&retmode=ref&cmd=prlinks
Dunny GM, Berntsson RP-A. Enterococcal sex pheromones: evolutionary pathways to complex, two-signal systems. J Bacteriol. 2016;198:1556-62.
Clewell DB, Weaver KE, Dunny GM, et al. Extrachromosomal and mobile elements in enterococci: transmission, maintenance, and epidemiology. In: Gilmore MS, Clewell DB, Ike Y, et al., eds. Enterococci: from commensals to leading causes of drug resistant infection [Internet]. Boston: Massachusetts Eye and Ear Infirmary; 2014. Available from: https://www.ncbi.nlm.nih.gov/books/NBK190430/
Clewell DB. Bacterial sex pheromone-induced plasmid transfer. Cell. 1993;73:9-12.
Chung JW, Dunny GM. Transcriptional analysis of a region of the Enterococcus faecalis plasmid pCF10 involved in positive regulation of conjugative transfer functions. J Bacteriol. 1995;177:2118-24.
Hirt H, Manias DA, Bryan EM, et al. Characterization of the pheromone response of the Enterococcus faecalis conjugative plasmid pCF10: complete sequence and comparative analysis of the transcriptional and phenotypic responses of pCF10-containing cells to pheromone induction. J Bacteriol. 2005;187:1044-54.
Clewell DB. Tales of conjugation and sex pheromones. Mob Genetic Elements. 2011;1:38-54.
Järvå MA, Hirt H, Dunny GM, Berntsson RP-A. Polymer adhesin domains in gram-positive cell surface proteins. Front Microbiol. 2020;11:599899.
Schmitt A, Jiang K, Camacho MI, et al. PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction. Mol Microbiol. 2018;109:291-305.
Sterling AJ, Snelling WJ, Naughton PJ, Ternan NG, Dooley JSG. Competent but complex communication: the phenomena of pheromone-responsive plasmids. PLoS Pathog. 2020;16:e1008310.
Gay P, Coq DL, Steinmetz M, Ferrari E, Hoch JA. Cloning structural gene sacB, which codes for exoenzyme levansucrase of Bacillus subtilis: expression of the gene in Escherichia coli. J Bacteriol. 1983;153:1424-31.
Gay P, Coq DL, Steinmetz M, Berkelman T, Kado CI. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J Bacteriol. 1985;164:918-21.
Hooven TA, Bonakdar M, Chamby AB, Ratner AJ. A counterselectable sucrose sensitivity marker permits efficient and flexible mutagenesis in Streptococcus agalactiae. Appl Environ Microbiol. 2019;85:e03009-18.
Ibba M, Kast P, Hennecke H. Substrate specificity is determined by amino acid binding pocket size in Escherichia coli phenylalanyl-tRNA synthetase. Biochemistry. 1994;33:7107-12.
Sung CK, Li H, Claverys JP, Morrison DA. An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl Environ Microbiol. 2001;67:5190-96.
Charpentier X, Polard P, Claverys J-P. Induction of competene for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS? Current Opinion in Microbiology. 2012;15:570-6.
Blokesch M. Natural competence for transformation. Current Biology. 2016;B26:R1126-R1130.
Griffith F. The significance of pneumococcal types. J Hyg (Lond). 1928;27:113-59.
Dubnau D, Blokesch M. Mechanisms of DNA uptake by naturally competent bacteria. Annu Rev Genet. 2019;53:217-37.
Mortier-Barrière I, Campo N, Bergé MA, Prudhomme M, Polard P. Natural genetic transformation: a direct route to easy insertion of chimeric genes into the pneumococcal chromosome. Methods Mol Biol. 2019;1968:63-78.
O'Connell LM, Kelleher P, Rijswijck IMH, et al. Natural transformation in gram-positive bacteria and its biotechnological relevance to lactic acid bacteria. Annu Rev Food Sci Technol. 2022;13:409-31.
Johnston C, Campo N, Bergé MJ, Polard P, Claverys J-P. Streptococcus pneumoniae, le transformiste. Trends Microbiol. 2014;22:113-9.
Slager J, Aprianto R, Veening J-W. Refining the pneumococcal competence regulon by RNA-sequencing. J Bacteriol. 2019;201:e00780-18.
Domenech A, Slager J, Veening J. Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine-like signaling. Cell Rep. 2018;25:2390-400.e3.
Moreno-Gámez S, Sorg RA, Domenech A, et al. Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence. Nat Commun. 2017;8:854.
Prudhomme M, Berge M, Martin B, Polard P. Pneumococcal competence coordination relies on a cell-contact sensing mechanism. PLoS Genet. 2016;12:e1006113.
Alloing G, Granadel C, Morrison DA, Claverys JP. Competence pheromone, oligopeptide permease, and induction of competence in Streptococcus pneumoniae. Mol Microbiol. 1996;21:471-8.
Håvarstein LS, Gaustad P, Nes IF, Morrison DA. Identification of the streptococcal competence-pheromone receptor. Mol Microbiol. 1996;21:863-9.
Chandler MS, Morrison DA. Identification of two proteins encoded by com, a competnece control locus of Streptococcus pneumoniae. J Bacteriol. 1988;170:3136-41.
Håvarstein LS, Coomaraswamy G, Morrison DA. An unmodified heptadecapeptide pheromone induces competence for genetic transformation in Streptococcus pneumoniae. Proc Natl Acad Sci USA. 1995;92:11140-4.
Hui FM, Zhou L, Morrison DA. Competence for genetic transformation in Streptococcus pneumoniae: organization of a regulatory locus with homology to two lactococcin A secretion genes. Gene. 1995;153:25-31.
Martin B, Soulet A-L, Mirouze N, et al. ComE/ComE~P interplay dictates activation or extinction status of pneumococcal X-state (competence). Mol Microbiol. 2013;87:394-411.
Campbell EA, Choi SY, Masure HR. A competence regulon in Streptococcus pneumoniae revealed by genomic analysis. Molecular Microbiology. 1998;27:929-39.
Laurenceau R, Péhau-Arnaudet G, Baconnais S, et al. A type IV pilus mediates DNA binding during natural transformation in Streptococcus pneumoniae. PLoS Pathog. 2013;9:e1003473.
Attaiech L, Olivier A, Mortier-Barrière I, et al. Role of the single-stranded DNA-binding protein SsbB in pneumococcal transformation: maintenance of a reservoir for genetic plasticity. PLoS Genet. 2011;7:e1002156.
Berge M, Mortier-Barrière I, Martin B, Claverys J-P. Transformation of Streptococcus pneumoniae relies on DprA- and RecA-dependent protection of incoming DNA single strands. Mol Microbiol. 2003;50:527-36.
Marie L, Rapisarda C, Morales V, et al. Bacterial RadA is a DnaB-type helicase interacting with RecA to promote bidirectional D-loop extension. Nat Commun. 2017;8:15638-14.
Mortier-Barrière I, Velten M, Dupaigne P, et al. A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell. 2007;130:824-36.
Johnston C, Martin B, Fichant G, Polard P, Claverys J-P. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat Rev Microbiol. 2014;12:181-96.
Jim KK, Engelen-Lee J, van der Sar AM, et al. Infection of zebrafish embryos with live fluorescent Streptococcus pneumoniae as a real-time pneumococcal meningitis model. J Neuroinflammation. 2016;13:188.
Håvarstein LS, Hakenbeck R, Gaustad P. Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges. J Bacteriol. 1997;179:6589-94.
Salvadori G, Junges R, Khan R, Åmdal HA, Morrison DA, Petersen FC. Oral biology: molecular techniques and applications. Humana; 2016. p. 219-32.
Keller L, Rueff A, Kurushima J, Veening J. Three new integration vectors and fluorescent proteins for use in the opportunistic human pathogen Streptococcus pneumoniae. Genes (Basel). 2019;10:394.
Reck M, Tomasch J, Wagner-Döbler I. The alternative sigma factor SigX controls bacteriocin synthesis and competence, the two quorum sensing regulated traits in Streptococcus mutans. PLoS Genet. 2015;11:e1005353.
Kurushima J, Campo N, Raaphorst R, van, Cerckel G, Polard P, Veening J-W. Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events. eLife. 2020;9:e58771.
Bourgogne A, Garsin DA, Qin X, et al. Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biology. 2008;9:R110.
Dale JL, Beckman KB, Willett JLE, et al. Comprehensive functional analysis of the Enterococcus faecalis core genome using an ordered, sequence-defined collection of insertional mutations in strain OG1RF. Msystems. 2018;3:e00062-18.
Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315:1709-12.
Lemaire C, Gallou BL, Lanotte P, Mereghetti L, Pastuszka A. Distribution, diversity and roles of CRISPR-Cas systems in human and animal pathogenic streptococci. Front Microbiol. 2022;13:828031.
Mojica FJM, Díez-Villaseñor C, Soria E, Juez G. Biological significance of a family of regularly spaced repeats in the genomes of archaea, bacteria and mitochondria. Mol Microbiol. 2000;36:244-6.
Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169:5429-33.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816-21.
Adli M. The CRISPR tool kit for genome editing and beyond. Nat Commun. 2018;9:1911.
Synefiaridou D, Veening J-W. Harnessing CRISPR-Cas9 for genome editing in Streptococcus pneumoniae D39V. Appl Environ Microbiol. 2021;87:e02762-20.
Afonina I, Ong J, Chua J, Lu T, Kline KA. Multiplex CRISPRi system enables the study of stage-specific biofilm genetic requirements in Enterococcus faecalis. mBio. 2020;11:e01101.
de Maat V, Stege PB, Dedden M, et al. CRISPR-Cas9-mediated genome editing in vancomycin-resistant Enterococcus faecium. FEMS Microbiol Lett. 2019;366:fnz256.
Bakker V, de, Liu X, Bravo AM, Veening J-W. CRISPRi-seq for genome-wide fitness quantification in bacteria. Nat Protoc. 2022;17:252-81.
Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 2012;482:331-8.
Liu X, Gallay C, Kjos M, et al. High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae. Mol Syst Biol. 2017;13:931.
Liu X, Kimmey JM, Matarazzo L, et al. Exploration of bacterial bottlenecks and Streptococcus pneumoniae pathogenesis by CRISPRi-seq. Cell Host Microbe. 2021;29:107-20.e6.