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Gibson PS, Bexkens E, Zuber S, Cowley LA, Veening JW. The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci. PLoS Pathog 2022; 18:e1010727. [PMID: 35877768 PMCID: PMC9352194 DOI: 10.1371/journal.ppat.1010727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/04/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae, resistance to β-lactam antibiotics is mediated by recombination events in genes encoding the target proteins, resulting in reduced drug binding affinity. However, for the front-line antibiotic amoxicillin, the exact mechanism of resistance still needs to be elucidated. Through successive rounds of transformation with genomic DNA from a clinically resistant isolate, we followed amoxicillin resistance development. Using whole genome sequencing, we showed that multiple recombination events occurred at different loci during one round of transformation. We found examples of non-contiguous recombination, and demonstrated that this could occur either through multiple D-loop formation from one donor DNA molecule, or by the integration of multiple DNA fragments. We also show that the final minimum inhibitory concentration (MIC) differs depending on recipient genome, explained by differences in the extent of recombination at key loci. Finally, through back transformations of mutant alleles and fluorescently labelled penicillin (bocillin-FL) binding assays, we confirm that pbp1a, pbp2b, pbp2x, and murM are the main resistance determinants for amoxicillin resistance, and that the order of allele uptake is important for successful resistance evolution. We conclude that recombination events are complex, and that this complexity contributes to the highly diverse genotypes of amoxicillin-resistant pneumococcal isolates.
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Affiliation(s)
- Paddy S. Gibson
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Evan Bexkens
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sylvia Zuber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Lauren A. Cowley
- Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Di Giacomo S, Toussaint F, Ledesma-García L, Knoops A, Vande Capelle F, Fremaux C, Horvath P, Ladrière JM, Ait-Abderrahim H, Hols P, Mignolet J. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6543703. [PMID: 35254446 PMCID: PMC9300618 DOI: 10.1093/femsre/fuac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 11/14/2022] Open
Abstract
Nowadays, the growing human population exacerbates the need for sustainable resources. Inspiration and achievements in nutrient production or human/animal health might emanate from microorganisms and their adaptive strategies. Here, we exemplify the benefits of lactic acid bacteria (LAB) for numerous biotechnological applications and showcase their natural transformability as a fast and robust method to hereditarily influence their phenotype/traits in fundamental and applied research contexts. We described the biogenesis of the transformation machinery and we analyzed the genome of hundreds of LAB strains exploitable for human needs to predict their transformation capabilities. Finally, we provide a stepwise rational path to stimulate and optimize natural transformation with standard and synthetic biology techniques. A comprehensive understanding of the molecular mechanisms driving natural transformation will facilitate and accelerate the improvement of bacteria with properties that serve broad societal interests.
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Affiliation(s)
- Stefano Di Giacomo
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Frédéric Toussaint
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Laura Ledesma-García
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Adrien Knoops
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Florence Vande Capelle
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Christophe Fremaux
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | - Philippe Horvath
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | - Jean-Marc Ladrière
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | | | - Pascal Hols
- Corresponding author: Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5 (box L7.07.06), B-1348 Louvain-La-Neuve, Belgium. Tel: +3210478896; Fax: +3210472825; E-mail:
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3
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Waldern JM, Smith D, Piazza CL, Bailey EJ, Schiraldi NJ, Nemati R, Fabris D, Belfort M, Novikova O. Methylation of rRNA as a host defense against rampant group II intron retrotransposition. Mob DNA 2021; 12:9. [PMID: 33678171 PMCID: PMC7938551 DOI: 10.1186/s13100-021-00237-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Group II introns are mobile retroelements, capable of invading new sites in DNA. They are self-splicing ribozymes that complex with an intron-encoded protein to form a ribonucleoprotein that targets DNA after splicing. These molecules can invade DNA site-specifically, through a process known as retrohoming, or can invade ectopic sites through retrotransposition. Retrotransposition, in particular, can be strongly influenced by both environmental and cellular factors. RESULTS To investigate host factors that influence retrotransposition, we performed random insertional mutagenesis using the ISS1 transposon to generate a library of over 1000 mutants in Lactococcus lactis, the native host of the Ll.LtrB group II intron. By screening this library, we identified 92 mutants with increased retrotransposition frequencies (RTP-ups). We found that mutations in amino acid transport and metabolism tended to have increased retrotransposition frequencies. We further explored a subset of these RTP-up mutants, the most striking of which is a mutant in the ribosomal RNA methyltransferase rlmH, which exhibited a reproducible 20-fold increase in retrotransposition frequency. In vitro and in vivo experiments revealed that ribosomes in the rlmH mutant were defective in the m3Ψ modification and exhibited reduced binding to the intron RNA. CONCLUSIONS Taken together, our results reinforce the importance of the native host organism in regulating group II intron retrotransposition. In particular, the evidence from the rlmH mutant suggests a role for ribosome modification in limiting rampant retrotransposition.
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Affiliation(s)
- Justin M. Waldern
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Department of Biology, University of North Carolina, 270 Bell Tower Drive, Chapel Hill, NC 27599 USA
| | - Dorie Smith
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Carol Lyn Piazza
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - E. Jake Bailey
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Nicholas J. Schiraldi
- Academic and Research Computing Center, Information Technology Services, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Reza Nemati
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Biogen, 125 Broadway, Cambridge, MA 02142 USA
| | - Dan Fabris
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, Storrs, CT 06268 USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Biology Department, SUNY Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222 USA
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Cesinger MR, Thomason MK, Edrozo MB, Halsey CR, Reniere ML. Listeria monocytogenes SpxA1 is a global regulator required to activate genes encoding catalase and heme biosynthesis enzymes for aerobic growth. Mol Microbiol 2020; 114:230-243. [PMID: 32255216 PMCID: PMC7496741 DOI: 10.1111/mmi.14508] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/24/2022]
Abstract
An imbalance of cellular oxidants and reductants causes redox stress, which must be rapidly detected to restore homeostasis. In bacteria, the Firmicutes encode conserved Spx-family transcriptional regulators that modulate transcription in response to redox stress. SpxA1 is an Spx-family orthologue in the intracellular pathogen Listeria monocytogenes that is essential for aerobic growth and pathogenesis. Here, we investigated the role of SpxA1 in growth and virulence by identifying genes regulated by SpxA1 in broth and during macrophage infection. We found SpxA1-activated genes encoding heme biosynthesis enzymes and catalase (kat) were required for L. monocytogenes aerobic growth in rich medium. An Spx-recognition motif previously defined in Bacillus subtilis was identified in the promoters of SpxA1-activated genes and proved necessary for the proper activation of two genes, indicating this regulation by SpxA1 is likely direct. Together, these findings elucidated the mechanism of spxA1 essentiality in vitro and demonstrated that SpxA1 is required for basal expression of scavenging enzymes to combat redox stress generated in the presence of oxygen.
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Affiliation(s)
- Monica R. Cesinger
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Maureen K. Thomason
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Mauna B. Edrozo
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Cortney R. Halsey
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Michelle L. Reniere
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
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5
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Robinson J, Rostami N, Casement J, Vollmer W, Rickard A, Jakubovics N. ArcR modulates biofilm formation in the dental plaque colonizerStreptococcus gordonii. Mol Oral Microbiol 2018; 33:143-154. [DOI: 10.1111/omi.12207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 01/20/2023]
Affiliation(s)
- J.C. Robinson
- School of Dental Sciences; Newcastle University; Newcastle upon Tyne UK
| | - N. Rostami
- School of Dental Sciences; Newcastle University; Newcastle upon Tyne UK
| | - J. Casement
- Bioinformatics Support Unit; Newcastle University; Newcastle upon Tyne UK
| | - W. Vollmer
- Centre for Bacterial Cell Biology; Newcastle University; Newcastle upon Tyne UK
| | - A.H. Rickard
- Department of Epidemiology; School of Public Health; University of Michigan; Ann Arbor MI USA
| | - N.S. Jakubovics
- School of Dental Sciences; Newcastle University; Newcastle upon Tyne UK
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6
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Transcriptome analysis of Streptococcus pneumoniae treated with the designed antimicrobial peptides, DM3. Sci Rep 2016; 6:26828. [PMID: 27225022 PMCID: PMC4881017 DOI: 10.1038/srep26828] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/09/2016] [Indexed: 11/18/2022] Open
Abstract
In our previous studies, we generated a short 13 amino acid antimicrobial peptide (AMP), DM3, showing potent antipneumococcal activity in vitro and in vivo. Here we analyse the underlying mechanisms of action using Next-Generation transcriptome sequencing of penicillin (PEN)-resistant and PEN-susceptible pneumococci treated with DM3, PEN, and combination of DM3 and PEN (DM3PEN). DM3 induced differential expression in cell wall and cell membrane structural and transmembrane processes. Notably, DM3 altered the expression of competence-induction pathways by upregulating CelA, CelB, and CglA while downregulating Ccs16, ComF, and Ccs4 proteins. Capsular polysaccharide subunits were downregulated in DM3-treated cells, however, it was upregulated in PEN- and DM3PEN-treated groups. Additionally, DM3 altered the amino acids biosynthesis pathways, particularly targeting ribosomal rRNA subunits. Downregulation of cationic AMPs resistance pathway suggests that DM3 treatment could autoenhance pneumococci susceptibility to DM3. Gene enrichment analysis showed that unlike PEN and DM3PEN, DM3 treatment exerted no effect on DNA-binding RNA polymerase activity but observed downregulation of RpoD and RNA polymerase sigma factor. In contrast to DM3, DM3PEN altered the regulation of multiple purine/pyrimidine biosynthesis and metabolic pathways. Future studies based on in vitro experiments are proposed to investigate the key pathways leading to pneumococcal cell death caused by DM3.
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Straume D, Stamsås GA, Håvarstein LS. Natural transformation and genome evolution in Streptococcus pneumoniae. INFECTION GENETICS AND EVOLUTION 2014; 33:371-80. [PMID: 25445643 DOI: 10.1016/j.meegid.2014.10.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/16/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023]
Abstract
Streptococcus pneumoniae is a frequent colonizer of the human nasopharynx that has the potential to cause severe infections such as pneumonia, bacteremia and meningitis. Despite considerable efforts to reduce the burden of pneumococcal disease, it continues to be a major public health problem. After the Second World War, antimicrobial therapy was introduced to fight pneumococcal infections, followed by the first effective vaccines more than half a century later. These clinical interventions generated a selection pressure that drove the evolution of vaccine-escape mutants and strains that were highly resistant against antibiotics. The remarkable ability of S. pneumoniae to acquire drug resistance and evade vaccine pressure is due to its recombination-mediated genetic plasticity. S. pneumoniae is competent for natural genetic transformation, a property that enables the pneumococcus to acquire new traits by taking up naked DNA from the environment and incorporating it into its genome through homologous recombination. In the present paper, we review current knowledge on pneumococcal transformation, and discuss how the pneumococcus uses this mechanism to adapt and survive under adverse and fluctuating conditions.
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Affiliation(s)
- Daniel Straume
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Gro Anita Stamsås
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Leiv Sigve Håvarstein
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway.
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8
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Fagerlund A, Granum PE, Håvarstein LS. Staphylococcus aureus competence genes: mapping of the SigH, ComK1 and ComK2 regulons by transcriptome sequencing. Mol Microbiol 2014; 94:557-79. [PMID: 25155269 DOI: 10.1111/mmi.12767] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2014] [Indexed: 01/17/2023]
Abstract
Staphylococcus aureus is a major human pathogen. Hospital infections caused by methicillin-resistant strains (MRSA), which have acquired resistance to a broad spectrum of antibiotics through horizontal gene transfer (HGT), are of particular concern. In S. aureus, virulence and antibiotic resistance genes are often encoded on mobile genetic elements that are disseminated by HGT. Conjugation and phage transduction have long been known to mediate HGT in this species, but it is unclear whether natural genetic transformation contributes significantly to the process. Recently, it was reported that expression of the alternative sigma factor SigH induces the competent state in S. aureus. The transformation efficiency obtained, however, was extremely low, indicating that the optimal conditions for competence development had not been found. We therefore used transcriptome sequencing to determine whether the full set of genes known to be required for competence in other naturally transformable bacteria is part of the SigH regulon. Our results show that several essential competence genes are not controlled by SigH. This presumably explains the low transformation efficiency previously reported, and demonstrates that additional regulating mechanisms must be involved. We found that one such mechanism involves ComK1, a transcriptional activator that acts synergistically with SigH.
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Affiliation(s)
- Annette Fagerlund
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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9
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Johnston C, Campo N, Bergé MJ, Polard P, Claverys JP. Streptococcus pneumoniae, le transformiste. Trends Microbiol 2014; 22:113-9. [PMID: 24508048 DOI: 10.1016/j.tim.2014.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Natural genetic transformation, which was discovered in this species, involves internalization of exogenous single-stranded DNA and its incorporation into the chromosome. It allows acquisition of pathogenicity islands and antibiotic resistance and promotes vaccine escape via capsule switching. This opinion article discusses how recent advances regarding several facets of pneumococcal transformation support the view that the process has evolved to maximize plasticity potential in this species, making the pneumococcus le transformiste of the bacterial kingdom and providing an advantage in the constant struggle between this pathogen and its host.
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Affiliation(s)
- Calum Johnston
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Nathalie Campo
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Matthieu J Bergé
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Patrice Polard
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Jean-Pierre Claverys
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France.
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Kidane D, Ayora S, Sweasy JB, Graumann PL, Alonso JC. The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery. Crit Rev Biochem Mol Biol 2012; 47:531-55. [PMID: 23046409 DOI: 10.3109/10409238.2012.729562] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.
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Affiliation(s)
- Dawit Kidane
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, CT, USA
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Kovács AT, Smits WK, Mirończuk AM, Kuipers OP. Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries. Environ Microbiol 2009; 11:1911-22. [PMID: 19453701 DOI: 10.1111/j.1462-2920.2009.01937.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural competence for genetic transformation, i.e. the ability to take up DNA and stably integrate it in the genome, has so far only been observed in the bacterial kingdom (both in gram-negative and gram-positive species) and may contribute to survival under adverse growth conditions. Bacillus subtilis, the model organism for the Bacillus genus, possesses a well-characterized competence machinery. Phylogenetic analysis of several genome sequences of different Bacillus species reveals the presence of many, but not all genes potentially involved in competence and its regulation. The recent demonstration of functional DNA uptake by B. cereus supports the significance of our genome analyses and shows that the ability for functional DNA uptake might be widespread among Bacilli.
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Affiliation(s)
- Akos T Kovács
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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12
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Claverys JP, Martin B, Polard P. The genetic transformation machinery: composition, localization, and mechanism. FEMS Microbiol Rev 2009; 33:643-56. [DOI: 10.1111/j.1574-6976.2009.00164.x] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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13
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Identification by genomic and genetic analysis of two new genes playing a key role in intermediate glycopeptide resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2008; 53:903-11. [PMID: 19104009 DOI: 10.1128/aac.01287-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Endogenous, low-level glycopeptide resistance in Staphylococcus aureus results from multifactorial genetic changes. Comparative genomic hybridization analysis revealed the specific deletion of a 1.8-kb segment encompassing two adjacent open reading frames (ORFs) of unknown function in a teicoplanin-susceptible revertant (strain 14-4rev) compared to the sequence of its isogenic, teicoplanin-resistant parental strain, strain 14-4. This provocative finding prompted us to perform a detailed genetic analysis of the contribution of this genomic segment to glycopeptide resistance. Despite repeated efforts in our laboratory, 14-4 and 14-4rev have proven refractory to most genetic manipulations. To circumvent this difficulty, we evaluated the contribution of both putative ORFs (designated teicoplanin resistance factors trfA and trfB) on teicoplanin resistance in a different, genetically tractable background. Genetic analysis showed that single or double trfA and/or trfB mutations abolished teicoplanin resistance in two independent teicoplanin-resistant derivatives of NCTC8325 strain ISP794 generated by two-step passages with the drug. The frequency of teicoplanin-resistant mutants was markedly decreased by the absence of trfAB in the teicoplanin-susceptible ISP794 background. Nevertheless, a low rate of teicoplanin-resistant mutants was selected from ISP794 trfAB, thus indicating an additional contribution of trfAB-independent pathways in the emergence of low-level glycopeptide resistance. Further experiments performed with clinical glycopeptide-intermediate S. aureus isolate NRS3 indicated that the trfAB mutation could affect not only teicoplanin resistance but also vancomycin and oxacillin resistance. In conclusion, our study demonstrates the key role of two novel loci in endogenous, low-level glycopeptide resistance in S. aureus whose precise molecular functions warrant further investigation.
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Mortier-Barrière I, Velten M, Dupaigne P, Mirouze N, Piétrement O, McGovern S, Fichant G, Martin B, Noirot P, Le Cam E, Polard P, Claverys JP. A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell 2007; 130:824-36. [PMID: 17803906 DOI: 10.1016/j.cell.2007.07.038] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 05/25/2007] [Accepted: 07/13/2007] [Indexed: 11/15/2022]
Abstract
Natural transformation is a mechanism for genetic exchange in many bacterial genera. It proceeds through the uptake of exogenous DNA and subsequent homology-dependent integration into the genome. In Streptococcus pneumoniae, this integration requires the ubiquitous recombinase, RecA, and DprA, a protein of unknown function widely conserved in bacteria. To unravel the role of DprA, we have studied the properties of the purified S. pneumoniae protein and its Bacillus subtilis ortholog (Smf). We report that DprA and Smf bind cooperatively to single-stranded DNA (ssDNA) and that these proteins both self-interact and interact with RecA. We demonstrate that DprA-RecA-ssDNA filaments are produced and that these filaments catalyze the homology-dependent formation of joint molecules. Finally, we show that while the Escherichia coli ssDNA-binding protein SSB limits access of RecA to ssDNA, DprA lowers this barrier. We propose that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation.
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Affiliation(s)
- Isabelle Mortier-Barrière
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100 CNRS-Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 09, France
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15
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Johnsborg O, Eldholm V, Håvarstein LS. Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol 2007; 158:767-78. [PMID: 17997281 DOI: 10.1016/j.resmic.2007.09.004] [Citation(s) in RCA: 229] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 09/04/2007] [Accepted: 09/21/2007] [Indexed: 02/02/2023]
Abstract
Studies show that gene acquisition through natural transformation has contributed significantly to the adaptation and ecological diversification of several bacterial species. Relatively little is still known, however, about the prevalence and phylogenetic distribution of organisms possessing this property. Thus, whether natural transformation only benefits a limited number of species or has a large impact on lateral gene flow in nature remains a matter of speculation. Here we will review the most recent advances in our understanding of the phenomenon and discuss its possible biological functions.
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Affiliation(s)
- Ola Johnsborg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
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Morrison DA, Mortier-Barrière I, Attaiech L, Claverys JP. Identification of the major protein component of the pneumococcal eclipse complex. J Bacteriol 2007; 189:6497-500. [PMID: 17601792 PMCID: PMC1951911 DOI: 10.1128/jb.00687-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 06/19/2007] [Indexed: 11/20/2022] Open
Abstract
During genetic transformation of Streptococcus pneumoniae, single strands from native donor DNA enter competent cells, where they associate with an unidentified protein with a molecular mass of 15 to 20 kDa to form the eclipse complex. Using Western blotting, we identify the principal protein cofractionating with donor DNA in this complex as SsbB.
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Affiliation(s)
- Donald A Morrison
- Laboratory for Molecular Biology, Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Ave., Chicago, IL 60607, USA.
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Abstract
Proteins required for transformation of Bacillus subtilis and other competent bacteria are associated with the membrane or reside in the cytosol. Previous work has shown that RecA, ComGA, ComFA and SsbB are directed to the cell poles in competent cells, and that the uptake of transforming DNA occurs preferentially at the poles. We show that ComGA, ComFA, DprA (Smf), SsbB (YwpH), RecA and YjbF (CoiA) are located at the cell poles, where they appear to colocalize. Using fluorescence resonance energy transfer, we have shown that these six competent (Com) proteins reside in close proximity to one another. This conclusion was supported by the effects of com gene knockouts on the stabilities of Com proteins. Data obtained from the com gene knockout studies, as well as information from other sources, extend the list of proteins in the transformation complex to include ComEC and ComEA. Because ComGA and ComFA are membrane-associated, while DprA, SsbB, RecA and YjbF are soluble, a picture emerges of a large multiprotein polar complex, involving both cytosolic and membrane proteins. This complex mediates the binding and uptake of single-stranded DNA, the protection of this DNA from cellular nucleases and its recombination with the recipient chromosome.
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Affiliation(s)
- Naomi Kramer
- Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
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