1
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. PLoS Genet 2024; 20:e1011287. [PMID: 38768229 PMCID: PMC11142719 DOI: 10.1371/journal.pgen.1011287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/31/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint residues in QueE that contribute distinctly to each of its functions-Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE's secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of "one gene, one enzyme, one function", which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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Affiliation(s)
- Samuel A. Adeleye
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
| | - Srujana S. Yadavalli
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
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2
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Zuke JD, Burton BM. From isotopically labeled DNA to fluorescently labeled dynamic pili: building a mechanistic model of DNA transport to the cytoplasmic membrane. Microbiol Mol Biol Rev 2024; 88:e0012523. [PMID: 38466096 PMCID: PMC10966944 DOI: 10.1128/mmbr.00125-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
SUMMARYNatural competence, the physiological state wherein bacteria produce proteins that mediate extracellular DNA transport into the cytosol and the subsequent recombination of DNA into the genome, is conserved across the bacterial domain. DNA must successfully translocate across formidable permeability barriers during import, including the cell membrane(s) and the cell wall, that are normally impermeable to large DNA polymers. This review will examine the mechanisms underlying DNA transport from the extracellular space to the cytoplasmic membrane. First, the challenges inherent to DNA movement through the cell periphery will be discussed to provide context for DNA transport during natural competence. The following sections will trace the development of a comprehensive model for DNA translocation to the cytoplasmic membrane, highlighting the crucial studies performed over the last century that have contributed to building contemporary DNA import models. Finally, this review will conclude by reflecting on what is still unknown about the process and the possible solutions to overcome these limitations.
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Affiliation(s)
- Jason D. Zuke
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Briana M. Burton
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
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3
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Morgene F, Rizoug Zeghlache C, Feng SY, Hauck Y, Mirouze N. Natural transformation and cell division delay in competent Staphylococcus aureus. Microbiol Spectr 2023; 11:e0280723. [PMID: 37831481 PMCID: PMC10714784 DOI: 10.1128/spectrum.02807-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Natural transformation, considered one of the three main mechanisms leading to horizontal gene transfer in bacteria, is able to promote genomic plasticity and foster antibiotic resistance spreading. Conserved machinery and actors required to perform natural transformation have been shown to accumulate at different cellular localizations depending on the model organism considered. Here, we show in the human pathogen Staphylococcus aureus that DNA binding, uptake, and recombination are spatially and temporally coordinated to ensure S. aureus natural transformation. We also reveal that localization of natural transformation proteins occurs in the vicinity of the division septum allowing S. aureus competent cells to block cell division to ensure the success of natural transformation before the final constriction of the cytokinetic ring.
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Affiliation(s)
- Fedy Morgene
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Célia Rizoug Zeghlache
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Shi Yuan Feng
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yolande Hauck
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nicolas Mirouze
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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4
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Zuke JD, Erickson R, Hummels KR, Burton BM. Visualizing dynamic competence pili and DNA capture throughout the long axis of Bacillus subtilis. J Bacteriol 2023; 205:e0015623. [PMID: 37695859 PMCID: PMC10521363 DOI: 10.1128/jb.00156-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 09/13/2023] Open
Abstract
The first step in the process of bacterial natural transformation is DNA capture. Although long hypothesized based on genetics and functional experiments, the pilus structure responsible for initial DNA binding had not yet been visualized for Bacillus subtilis. Here, we visualize functional competence pili in Bacillus subtilis using fluorophore-conjugated maleimide labeling in conjunction with epifluorescence microscopy. In strains that produce pilin monomers within tenfold of wild-type levels, the median length of detectable pili is 300 nm. These pili are retractile and associate with DNA. The analysis of pilus distribution at the cell surface reveals that they are predominantly located along the long axis of the cell. The distribution is consistent with localization of proteins associated with subsequent transformation steps, DNA binding, and DNA translocation in the cytosol. These data suggest a distributed model for B. subtilis transformation machinery, in which initial steps of DNA capture occur throughout the long axis of the cell and subsequent steps may also occur away from the cell poles. IMPORTANCE This work provides novel visual evidence for DNA translocation across the cell wall during Bacillus subtilis natural competence, an essential step in the natural transformation process. Our data demonstrate the existence of natural competence-associated retractile pili that can bind exogenous DNA. Furthermore, we show that pilus biogenesis occurs throughout the cell long axis. These data strongly support DNA translocation occurring all along the lateral cell wall during natural competence, wherein pili are produced, bind to free DNA in the extracellular space, and finally retract to pull the bound DNA through the gap in the cell wall created during pilus biogenesis.
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Affiliation(s)
- Jason D. Zuke
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rachel Erickson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katherine R. Hummels
- Department of Microbiology and Immunology, Harvard Medical School, Boston, MA, USA
| | - Briana M. Burton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Zuke JD, Erickson R, Hummels KR, Burton BM. Visualizing dynamic competence pili and DNA capture throughout the long axis of Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542325. [PMID: 37292776 PMCID: PMC10246001 DOI: 10.1101/2023.05.26.542325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The first step in the process of bacterial natural transformation is DNA capture. Although long-hypothesized based on genetics and functional experiments, the pilus structure responsible for initial DNA-binding had not yet been visualized for Bacillus subtilis. Here, we visualize functional competence pili in Bacillus subtilis using fluorophore-conjugated maleimide labeling in conjunction with epifluorescence microscopy. In strains that produce pilin monomers within ten-fold of wild type levels, the median length of detectable pili is 300nm. These pili are retractile and associate with DNA. Analysis of pilus distribution at the cell surface reveals that they are predominantly located along the long axis of the cell. The distribution is consistent with localization of proteins associated with subsequent transformation steps, DNA-binding and DNA translocation in the cytosol. These data suggest a distributed model for B. subtilis transformation machinery, in which initial steps of DNA capture occur throughout the long axis of the cell and subsequent steps may also occur away from the cell poles.
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Affiliation(s)
- Jason D. Zuke
- Department of Bacteriology, University of Wisconsin - Madison
- Microbiology Doctoral Training Program, University of Wisconsin - Madison
| | - Rachel Erickson
- Department of Bacteriology, University of Wisconsin - Madison
| | - Katherine R. Hummels
- Current address: Department of Microbiology and Immunology, Harvard Medical School
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6
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ComFC mediates transport and handling of single-stranded DNA during natural transformation. Nat Commun 2022; 13:1961. [PMID: 35414142 PMCID: PMC9005727 DOI: 10.1038/s41467-022-29494-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes and virulence factors across bacteria. However, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is involved in DNA transport through the cell membrane, and is required for the handling of the single-stranded DNA once it is delivered into the cytoplasm. The crystal structure of ComFC includes a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for the protein's in vivo activity. Furthermore, we show that ComFC is a membrane-associated protein with affinity for single-stranded DNA. Our results suggest that ComFC provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.
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7
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Zhou P, Chen W, Zhu Z, Zhou K, Luo S, Hu S, Xia L, Ding X. Comparative Study of Bacillus amyloliquefaciens X030 on the Intestinal Flora and Antibacterial Activity Against Aeromonas of Grass Carp. Front Cell Infect Microbiol 2022; 12:815436. [PMID: 35145928 PMCID: PMC8821659 DOI: 10.3389/fcimb.2022.815436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/03/2022] [Indexed: 01/16/2023] Open
Abstract
Beneficial microorganisms to control bacterial diseases has been widely used in aquaculture, Bacillus amyloliquefaciens (BaX030) as a probiotic feed additive was a commonly biological control method. Added sucrose promoted the growth of BaX030, and the yield of its antibacterial substance macrolactin A was enhanced by 1.46-fold. A total of 2055 proteins were screened through proteomics, with 143 upregulated and 307 downregulated. Differential protein expression analysis and qRT-PCR verification showed that the pentose phosphate pathway and the fatty acid synthesis pathway were upregulated, thereby providing sufficient energy and precursors for the synthesis of macrolactin A. The influence of some potential regulatory factors (SecG, LiaI, MecG and ComG) on macrolactin A was discovered. After grass carp were fed with BaX030, the abundance of probiotics (Fusobacterium, Proteobacteria, Gemmobacter) were higher than the control group, and the abundance of potential pathogenic bacteria (Planctomycetes, Aeromonas) were significantly lower than the control group. The cell and challenge experiments showed that BaX030 can significantly increase the expression of C3 and IL8 in the liver and kidney, which decreases the risk of immune organ disease. Moreover, BaX030 effectively reduced the mortality of grass carp. The results revealed that BaX030 can significantly improve the structure of the intestinal flora, enhance immunity and it is beneficial to the control of grass carp Aeromonas.
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8
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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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9
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Hahn J, DeSantis M, Dubnau D. Mechanisms of Transforming DNA Uptake to the Periplasm of Bacillus subtilis. mBio 2021; 12:e0106121. [PMID: 34126763 PMCID: PMC8262900 DOI: 10.1128/mbio.01061-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
We demonstrate here that the acquisition of DNase resistance by transforming DNA, often assumed to indicate transport to the cytoplasm, reflects uptake to the periplasm, requiring a reevaluation of conclusions about the roles of several proteins in transformation. The new evidence suggests that the transformation pilus is needed for DNA binding to the cell surface near the cell poles and for the initiation of uptake. The cellular distribution of the membrane-anchored ComEA of Bacillus subtilis does not dramatically change during DNA uptake as does the unanchored ComEA of Vibrio and Neisseria. Instead, our evidence suggests that ComEA stabilizes the attachment of transforming DNA at localized regions in the periplasm and then mediates uptake, probably by a Brownian ratchet mechanism. Following that, the DNA is transferred to periplasmic portions of the channel protein ComEC, which plays a previously unsuspected role in uptake to the periplasm. We show that the transformation endonuclease NucA also facilitates uptake to the periplasm and that the previously demonstrated role of ComFA in the acquisition of DNase resistance derives from the instability of ComGA when ComFA is deleted. These results prompt a new understanding of the early stages of DNA uptake for transformation. IMPORTANCE Transformation is a widely distributed mechanism of bacterial horizontal gene transfer that plays a role in the spread of antibiotic resistance and virulence genes and more generally in evolution. Although transformation was discovered nearly a century ago and most, if not all the proteins required have been identified in several bacterial species, much remains poorly understood about the molecular mechanism of DNA uptake. This study uses epifluorescence microscopy to investigate the passage of labeled DNA into the compartment between the cell wall and the cell membrane of Bacillus subtilis, a necessary early step in transformation. The roles of individual proteins in this process are identified, and their modes of action are clarified.
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Affiliation(s)
- Jeanette Hahn
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Micaela DeSantis
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - David Dubnau
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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10
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Burghard-Schrod M, Altenburger S, Graumann PL. The Bacillus subtilis dCMP deaminase ComEB acts as a dynamic polar localization factor for ComGA within the competence machinery. Mol Microbiol 2020; 113:906-922. [PMID: 31954084 DOI: 10.1111/mmi.14457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 01/15/2023]
Abstract
Bacillus subtilis can import DNA from the environment by an uptake machinery that localizes to a single cell pole. We investigated the roles of ComEB and of the ATPase ComGA during the state of competence. We show that ComEB plays an important role during competence, possibly because it is necessary for the recruitment of GomGA to the cell pole. ComEB localizes to the cell poles even upon expression during exponential phase, indicating that it can serve as polar marker. ComEB is also a deoxycytidylate monophosphate (dCMP) deaminase, for the function of which a conserved cysteine residue is important. However, cysteine-mutant ComEB is still capable of natural transformation, while a comEB deletion strain is highly impaired in competence, indicating that ComEB confers two independent functions. Single-molecule tracking (SMT) reveals that both proteins exchange at the cell poles between bound and unbound in a time scale of a few milliseconds, but turnover of ComGA increases during DNA uptake, whereas the mobility of ComEB is not affected. Our data reveal a highly dynamic role of ComGA during DNA uptake and an unusual role for ComEB as a mediator of polar localization, localizing by diffusion-capture on an extremely rapid time scale and functioning as a moonlighting enzyme.
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Affiliation(s)
- Marie Burghard-Schrod
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Stephan Altenburger
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
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11
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Abstract
Transformation is a widespread mechanism of horizontal gene transfer in bacteria. DNA uptake to the periplasmic compartment requires a DNA-uptake pilus and the DNA-binding protein ComEA. In the gram-negative bacteria, DNA is first pulled toward the outer membrane by retraction of the pilus and then taken up by binding to periplasmic ComEA, acting as a Brownian ratchet to prevent backward diffusion. A similar mechanism probably operates in the gram-positive bacteria as well, but these systems have been less well characterized. Transport, defined as movement of a single strand of transforming DNA to the cytosol, requires the channel protein ComEC. Although less is understood about this process, it may be driven by proton symport. In this review we also describe various phenomena that are coordinated with the expression of competence for transformation, such as fratricide, the kin-discriminatory killing of neighboring cells, and competence-mediated growth arrest.
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Affiliation(s)
- David Dubnau
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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12
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Stingl K, Koraimann G. Prokaryotic Information Games: How and When to Take up and Secrete DNA. Curr Top Microbiol Immunol 2019. [PMID: 29536355 DOI: 10.1007/978-3-319-75241-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Besides transduction via bacteriophages natural transformation and bacterial conjugation are the most important mechanisms driving bacterial evolution and horizontal gene spread. Conjugation systems have evolved in eubacteria and archaea. In Gram-positive and Gram-negative bacteria, cell-to-cell DNA transport is typically facilitated by a type IV secretion system (T4SS). T4SSs also mediate uptake of free DNA in Helicobacter pylori, while most transformable bacteria use a type II secretion/type IV pilus system. In this chapter, we focus on how and when bacteria "decide" that such a DNA transport apparatus is to be expressed and assembled in a cell that becomes competent. Development of DNA uptake competence and DNA transfer competence is driven by a variety of stimuli and often involves intricate regulatory networks leading to dramatic changes in gene expression patterns and bacterial physiology. In both cases, genetically homogeneous populations generate a distinct subpopulation that is competent for DNA uptake or DNA transfer or might uniformly switch into competent state. Phenotypic conversion from one state to the other can rely on bistable genetic networks that are activated stochastically with the integration of external signaling molecules. In addition, we discuss principles of DNA uptake processes in naturally transformable bacteria and intend to understand the exceptional use of a T4SS for DNA import in the gastric pathogen H. pylori. Realizing the events that trigger developmental transformation into competence within a bacterial population will eventually help to create novel and effective therapies against the transmission of antibiotic resistances among pathogens.
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Affiliation(s)
- Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany.
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
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13
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Abstract
ABSTRACT
Type IV pili (T4P) are remarkable bacterial surface appendages that carry out a range of functions. Various types of T4P have been identified in bacteria and archaea, making them almost universal structures in prokaryotes. T4P are best characterized in Gram-negative bacteria, in which pilus biogenesis and T4P-mediated functions have been studied for decades. Recent advances in microbial whole-genome sequencing have provided ample evidence for the existence of T4P also in many Gram-positive species. However, comparatively little is known, and T4P in Gram-positive bacteria are just beginning to be dissected. So far, they have mainly been studied in
Clostridium
and
Streptococcus
spp. and are involved in diverse cellular processes such as adhesion, motility, and horizontal gene transfer. Here we summarize the current understanding of T4P in Gram-positive species and their functions, with particular focus on the type IV competence pilus produced by the human pathogen
Streptococcus pneumoniae
and its role in natural transformation.
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14
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Mirouze N, Ferret C, Cornilleau C, Carballido-López R. Antibiotic sensitivity reveals that wall teichoic acids mediate DNA binding during competence in Bacillus subtilis. Nat Commun 2018; 9:5072. [PMID: 30498236 PMCID: PMC6265299 DOI: 10.1038/s41467-018-07553-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 10/22/2018] [Indexed: 12/02/2022] Open
Abstract
Despite decades of investigation of genetic transformation in the model Gram-positive bacterium Bacillus subtilis, the factors responsible for exogenous DNA binding at the surface of competent cells remain to be identified. Here, we report that wall teichoic acids (WTAs), cell wall-anchored anionic glycopolymers associated to numerous critical functions in Gram-positive bacteria, are involved in this initial step of transformation. Using a combination of cell wall-targeting antibiotics and fluorescence microscopy, we show that competence-specific WTAs are produced and specifically localized in the competent cells to mediate DNA binding at the proximity of the transformation apparatus. Furthermore, we propose that TuaH, a putative glycosyl transferase induced during competence, modifies competence-induced WTAs in order to promote (directly or indirectly) DNA binding. On the basis of our results and previous knowledge in the field, we propose a model for DNA binding and transport during genetic transformation in B. subtilis. Natural genetic transformation in bacteria requires DNA binding at the surface of competent cells. Here, Mirouze et al. show that wall teichoic acids are specifically produced or modified during competence in Bacillus subtilis and promote (directly or indirectly) DNA binding at the cell surface.
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Affiliation(s)
- Nicolas Mirouze
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Institute for Integrative Biology of the Cell (I2BC), INSERM, CEA, CNRS, Université Paris-Sud, Orsay, 91190, Gif sur Yvette, France.
| | - Cécile Ferret
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Charlène Cornilleau
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Inovarion, 75013, Paris, France
| | - Rut Carballido-López
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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15
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Ibáñez de Aldecoa AL, Zafra O, González-Pastor JE. Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities. Front Microbiol 2017; 8:1390. [PMID: 28798731 PMCID: PMC5527159 DOI: 10.3389/fmicb.2017.01390] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022] Open
Abstract
The capacity to release genetic material into the extracellular medium has been reported in cultures of numerous species of bacteria, archaea, and fungi, and also in the context of multicellular microbial communities such as biofilms. Moreover, extracellular DNA (eDNA) of microbial origin is widespread in natural aquatic and terrestrial environments. Different specific mechanisms are involved in eDNA release, such as autolysis and active secretion, as well as through its association with membrane vesicles. It is noteworthy that in microorganisms, in which DNA release has been studied in detail, the production of eDNA is coordinated by the population when it reaches a certain cell density, and is induced in a subpopulation in response to the accumulation of quorum sensing signals. Interestingly, in several bacteria there is also a relationship between eDNA release and the development of natural competence (the ability to take up DNA from the environment), which is also controlled by quorum sensing. Then, what is the biological function of eDNA? A common biological role has not been proposed, since different functions have been reported depending on the microorganism. However, it seems to be important in biofilm formation, can be used as a nutrient source, and could be involved in DNA damage repair and gene transfer. This review covers several aspects of eDNA research: (i) its occurrence and distribution in natural environments, (ii) the mechanisms and regulation of its release in cultured microorganisms, and (iii) its biological roles. In addition, we propose that eDNA release could be considered a social behavior, based on its quorum sensing-dependent regulation and on the described functions of eDNA in the context of microbial communities.
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Affiliation(s)
- Alejandra L Ibáñez de Aldecoa
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (Consejo Superior de Investigaciones Científicas/Instituto Nacional de Técnica Aeroespacial)Madrid, Spain
| | - Olga Zafra
- Experimental Sciences Faculty, Francisco de Vitoria UniversityMadrid, Spain
| | - José E González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (Consejo Superior de Investigaciones Científicas/Instituto Nacional de Técnica Aeroespacial)Madrid, Spain
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Fontaine L, Wahl A, Fléchard M, Mignolet J, Hols P. Regulation of competence for natural transformation in streptococci. INFECTION GENETICS AND EVOLUTION 2015; 33:343-60. [DOI: 10.1016/j.meegid.2014.09.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/28/2014] [Accepted: 09/07/2014] [Indexed: 02/02/2023]
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MreB-Dependent Inhibition of Cell Elongation during the Escape from Competence in Bacillus subtilis. PLoS Genet 2015; 11:e1005299. [PMID: 26091431 PMCID: PMC4474612 DOI: 10.1371/journal.pgen.1005299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/26/2015] [Indexed: 02/02/2023] Open
Abstract
During bacterial exponential growth, the morphogenetic actin-like MreB proteins form membrane-associated assemblies that move processively following trajectories perpendicular to the long axis of the cell. Such MreB structures are thought to scaffold and restrict the movement of peptidoglycan synthesizing machineries, thereby coordinating sidewall elongation. In Bacillus subtilis, this function is performed by the redundant action of three MreB isoforms, namely MreB, Mbl and MreBH. mreB and mbl are highly transcribed from vegetative promoters. We have found that their expression is maximal at the end of exponential phase, and rapidly decreases to a low basal level upon entering stationary phase. However, in cells developing genetic competence, a stationary phase physiological adaptation, expression of mreB was specifically reactivated by the central competence regulator ComK. In competent cells, MreB was found in complex with several competence proteins by in vitro pull-down assays. In addition, it co-localized with the polar clusters formed by the late competence peripheral protein ComGA, in a ComGA-dependent manner. ComGA has been shown to be essential for the inhibition of cell elongation characteristic of cells escaping the competence state. We show here that the pathway controlling this elongation inhibition also involves MreB. Our findings suggest that ComGA sequesters MreB to prevent cell elongation and therefore the escape from competence. In bacterial cells, like in their eukaryotic counterparts, precise spatiotemporal localization of proteins is critical for their cellular function. This study shows that the expression and the localization of the bacterial actin-like MreB protein are growth phase-dependent. During exponential growth, we previously showed that MreB, together with other morphogenetic factors, forms discrete assemblies that move in a directed manner along peripheral tracks. Here, we demonstrate that in cells that develop genetic competence during stationary phase, transcription of mreB is specifically activated and MreB relocalizes to the cell poles. Our findings suggest a model in which MreB sequestration by the late competence protein ComGA prevents cell elongation during the escape from competence.
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Hahn J, Tanner AW, Carabetta VJ, Cristea IM, Dubnau D. ComGA-RelA interaction and persistence in the Bacillus subtilis K-state. Mol Microbiol 2015; 97:454-71. [PMID: 25899641 DOI: 10.1111/mmi.13040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2015] [Indexed: 01/17/2023]
Abstract
The bistably expressed K-state of Bacillus subtilis is characterized by two distinct features; transformability and arrested growth when K-state cells are exposed to fresh medium. The arrest is manifested by a failure to assemble replisomes and by decreased rates of cell growth and rRNA synthesis. These phenotypes are all partially explained by the presence of the AAA(+) protein ComGA, which is also required for the binding of transforming DNA to the cell surface and for the assembly of the transformation pilus that mediates DNA transport. We have discovered that ComGA interacts with RelA and that the ComGA-dependent inhibition of rRNA synthesis is largely bypassed in strains that cannot synthesize the alarmone (p)ppGpp. We propose that the interaction of ComGA with RelA prevents the hydrolysis of (p)ppGpp in K-state cells, which are thus trapped in a non-growing state until ComGA is degraded. We show that some K-state cells exhibit tolerance to antibiotics, a form of type 1 persistence, and we propose that the bistable expression of both transformability and the growth arrest are bet-hedging adaptations that improve fitness in the face of varying environments, such as those presumably encountered by B. subtilis in the soil.
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Affiliation(s)
- Jeanette Hahn
- Public Health Research Institute Center of New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Andrew W Tanner
- Public Health Research Institute Center of New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Valerie J Carabetta
- Public Health Research Institute Center of New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - David Dubnau
- Public Health Research Institute Center of New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
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Muschiol S, Balaban M, Normark S, Henriques-Normark B. Uptake of extracellular DNA: competence induced pili in natural transformation of Streptococcus pneumoniae. Bioessays 2015; 37:426-35. [PMID: 25640084 PMCID: PMC4405041 DOI: 10.1002/bies.201400125] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Transport of DNA across bacterial membranes involves complex DNA uptake systems. In Gram-positive bacteria, the DNA uptake machinery shares fundamental similarities with type IV pili and type II secretion systems. Although dedicated pilus structures, such as type IV pili in Gram-negative bacteria, are necessary for efficient DNA uptake, the role of similar structures in Gram-positive bacteria is just beginning to emerge. Recently two essentially very different pilus structures composed of the same major pilin protein ComGC were proposed to be involved in transformation of the Gram-positive bacterium Streptococcus pneumoniae – one is a long, thin, type IV pilus-like fiber with DNA binding capacity and the other one is a pilus structure that was thicker, much shorter and not able to bind DNA. Here we discuss how competence induced pili, either by pilus retraction or by a transient pilus-related opening in the cell wall, may mediate DNA uptake in S. pneumoniae.
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Affiliation(s)
- Sandra Muschiol
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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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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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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Mann JM, Carabetta VJ, Cristea IM, Dubnau D. Complex formation and processing of the minor transformation pilins of Bacillus subtilis. Mol Microbiol 2013; 90:1201-15. [PMID: 24164455 PMCID: PMC5687075 DOI: 10.1111/mmi.12425] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2013] [Indexed: 01/06/2023]
Abstract
Transformation in most bacteria is dependent on orthologues of Type 2 secretion and Type 4 pilus system proteins. In each system, pilin proteins (major and minor) are required to make the pilus structure and are essential to the process, although the precise roles of the minor pilins remain unclear. We have explored protein-protein interactions among the competence minor pilins of Bacillus subtilis through in vitro binding studies, immunopurification and mass spectrometry. We demonstrate that the minor pilins directly interact, and the minor pilin ComGG interacts with most of the known proteins required for transformation. We find that ComGG requires other ComG proteins for its stabilization and for processing by the pre-pilin peptidase. These observations, C-terminal mutations in ComGG that prevent processing and the inaccessibility of pre-ComGG to externally added protease suggest a model in which pre-ComGG must be associated with other minor pilins for processing to take place. We propose that ComGG does not become a transmembrane protein until after processing. These behaviours contrast with that of pre-ComGC, the major pilin, which is accessible to externally added protease and requires only the peptidase to be processed. The roles of the pilins and of the pilus in transformation are discussed.
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Affiliation(s)
- Jessica M. Mann
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
| | - Valerie J. Carabetta
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - David Dubnau
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
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Plasmid-encoded ComI inhibits competence in the ancestral 3610 strain of Bacillus subtilis. J Bacteriol 2013; 195:4085-93. [PMID: 23836866 DOI: 10.1128/jb.00696-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Natural competence is a process by which bacteria construct a membrane-associated machine for the uptake and integration of exogenous DNA. Many bacteria harbor genes for the DNA uptake machinery and yet are recalcitrant to DNA uptake for unknown reasons. For example, domesticated laboratory strains of Bacillus subtilis are renowned for high-frequency natural transformation, but the ancestral B. subtilis strain NCIB3610 is poorly competent. Here we find that endogenous plasmid pBS32 encodes a small protein, ComI, that inhibits transformation in the 3610 strain. ComI is a single-pass trans-membrane protein that appears to functionally inhibit the competence DNA uptake machinery. Functional inhibition of transformation may be common, and abolishing such inhibitors could be the key to permitting convenient genetic manipulation of a variety of industrially and medically relevant bacteria.
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A type IV pilus mediates DNA binding during natural transformation in Streptococcus pneumoniae. PLoS Pathog 2013; 9:e1003473. [PMID: 23825953 PMCID: PMC3694846 DOI: 10.1371/journal.ppat.1003473] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/17/2013] [Indexed: 02/05/2023] Open
Abstract
Natural genetic transformation is widely distributed in bacteria and generally occurs during a genetically programmed differentiated state called competence. This process promotes genome plasticity and adaptability in Gram-negative and Gram-positive bacteria. Transformation requires the binding and internalization of exogenous DNA, the mechanisms of which are unclear. Here, we report the discovery of a transformation pilus at the surface of competent Streptococcus pneumoniae cells. This Type IV-like pilus, which is primarily composed of the ComGC pilin, is required for transformation. We provide evidence that it directly binds DNA and propose that the transformation pilus is the primary DNA receptor on the bacterial cell during transformation in S. pneumoniae. Being a central component of the transformation apparatus, the transformation pilus enables S. pneumoniae, a major Gram-positive human pathogen, to acquire resistance to antibiotics and to escape vaccines through the binding and incorporation of new genetic material.
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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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Seventeen Sxy-dependent cyclic AMP receptor protein site-regulated genes are needed for natural transformation in Haemophilus influenzae. J Bacteriol 2012; 194:5245-54. [PMID: 22821979 DOI: 10.1128/jb.00671-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Natural competence is the ability of bacteria to actively take up extracellular DNA. This DNA can recombine with the host chromosome, transforming the host cell and altering its genotype. In Haemophilus influenzae, natural competence is induced by energy starvation and the depletion of nucleotide pools. This induces a 26-gene competence regulon (Sxy-dependent cyclic AMP receptor protein [CRP-S] regulon) whose expression is controlled by two regulators, CRP and Sxy. The role of most of the CRP-S genes in DNA uptake and transformation is not known. We have therefore created in-frame deletions of each CRP-S gene and studied their competence phenotypes. All but one gene (ssb) could be deleted. Although none of the remaining CRP-S genes were required for growth in rich medium or survival under starvation conditions, DNA uptake and transformation were abolished or reduced in most of the mutants. Seventeen genes were absolutely required for transformation, with 14 of these genes being specifically required for the assembly and function of the type IV pilus DNA uptake machinery. Only five genes were dispensable for both competence and transformation. This is the first competence regulon for which all genes have been mutationally characterized.
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Allemand JF, Maier B, Smith DE. Molecular motors for DNA translocation in prokaryotes. Curr Opin Biotechnol 2012; 23:503-9. [PMID: 22226958 DOI: 10.1016/j.copbio.2011.12.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/08/2011] [Accepted: 12/19/2011] [Indexed: 11/25/2022]
Abstract
DNA transport is an essential life process. From chromosome separation during cell division or sporulation, to DNA virus ejection or encapsidation, to horizontal gene transfer, it is ubiquitous in all living organisms. Directed DNA translocation is often energetically unfavorable and requires an active process that uses energy, namely the action of molecular motors. In this review we present recent advances in the understanding of three molecular motors involved in DNA transport in prokaryotes, paying special attention to recent studies using single-molecule techniques. We first discuss DNA transport during cell division, then packaging of DNA in phage capsids, and then DNA import during bacterial transformation.
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Affiliation(s)
- Jean-François Allemand
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, UMR 8550 CNRS, Universités Pierre et Marie Curie and Paris Diderot, Département de Physique, 24 rue Lhomond, 75231 Paris Cedex 05, France.
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