Bacterial ‘competence’ genes: signatures of active transformation, or only remnants?

doi:10.1016/S0966-842X(03)00064-7

Trends in Microbiology

Volume 11, Issue 4, April 2003, Pages 161-165

https://doi.org/10.1016/S0966-842X(03)00064-7 Get rights and content

Abstract

An exhaustive review published ten years ago reported natural genetic transformation, a potential mechanism for intra- and interspecies gene transfer, in ∼40 species belonging to different taxonomic and trophic groups. Since then, considerable progress has been made in characterizing DNA-uptake machineries and regulatory circuits controlling their expression in cells competent for genetic transformation. In this article, in light of the recent description of a Group A streptococcal isolate capable of DNA transfer in mixed cultures, we discuss whether the detection in completely sequenced microbial genomes of intact homologues of key competence-regulatory and/or DNA-uptake proteins enables the prediction of new transformable species.

Section snippets

DNA-uptake machines

Most transformable Gram-positive and Gram-negative bacteria share a similar DNA-uptake machine, related to Type II secretion systems and Type IV pili [2] (Fig. 1). After binding to the cell surface, exogenous DNA must first cross the outer membrane of Gram-negative bacteria. This step relies on PilQ in the Gram-negative model, Neisseria gonorrhoeae. Other steps in the process are common to Gram-positive and Gram-negative organisms, and require proteins exhibiting significant similarity (Fig. 1

Competence regulatory circuits

In most transformable species, expression of the genes encoding the DNA-uptake apparatus is tightly regulated. Studies in B. subtilis and S. pneumoniae 8, 9, 10 indicate that the timing of competence development differs between the two species; competence is inhibited in stationary phase in S. pneumoniae, whereas it develops at the onset of the stationary phase in B. subtilis. In addition, competence regulatory circuits are species-specific (Fig. 2).

In S. pneumoniae, the competence pheromone,

Prediction of new transformable species

Genes encoding homologues of components of the DNA-uptake machinery have been detected in completely sequenced genomes of several species not known to be transformable (e.g. Lactococcus lactis [20], Listeria monocytogenes [21], Streptococcus pyogenes [22] and Escherichia coli; see Table 1). Moreover, genes encoding homologues of key competence-regulatory proteins are also present in some of these species: for example, a homologue of the S. pneumoniae competence sigma factor ComX in S. pyogenes

Conclusions

It is amazing that so many intact (i.e. containing no internal stop codons or frameshift mutations) ‘competence’ genes are conserved in bacterial genomes. As for whether these genes are signatures of active transformation or remnants, the observations made in S. pyogenes and E. coli encourage the notion that transformable species are waiting to be found. However, the ease of experimentally demonstrating transformation in any organism will depend on its conservation within the species. The

References (37)

L.C Smeets et al.
Natural transformation in Helicobacter pylori: DNA transport in an unexpected way
Trends Microbiol.
(2002)
B.A Lazazzera et al.
The ins and outs of peptide signaling
Trends Microbiol.
(1998)
R Lange
Domain organization and molecular characterization of 13 two-component systems identified by genome sequencing of Streptococcus pneumoniae
Gene
(1999)
L.S Håvarstein
Identification of a competence regulon in Streptococcus pneumoniae by genomic analysis
Trends Microbiol.
(1998)
M.G Lorenz et al.
Bacterial gene transfer by natural genetic transformation in the environment
Microbiol. Rev.
(1994)
D Dubnau
DNA uptake in bacteria
Annu. Rev. Microbiol.
(1999)
R.J Redfield
Do bacteria have sex?
Nat. Rev. Genet.
(2001)
I Chen et al.
ComE, a competence protein from Neisseria gonorrhoeae with DNA-binding activity
J. Bacteriol.
(2001)
D Hofreuter
Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system
Mol. Microbiol.
(2001)
D.J Bacon
Involvement of a plasmid in virulence of Campylobacter jejuni 81-176
Infect. Immun.
(2000)

A.D Grossman

Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis

Annu. Rev. Genet.

(1995)

J.P Claverys et al.

Extracellular peptide control of competence for genetic transformation in Streptococcus pneumoniae

Front. Biosci.

(2002)

A.M Stock

Two-component signal transduction

Annu. Rev. Biochem.

(2000)

M.S Lee et al.

Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation

J. Bacteriol.

(1999)

P Luo et al.

Transient association of an alternative sigma factor, ComX, with RNA polymerase during the period of competence for genetic transformation in Streptococcus pneumoniae

J. Bacteriol.

(2003)

K Bacon Schneider

Characterization of comQ and comX, two genes required for production of ComX pheromone in Bacillus subtilis

J. Bacteriol.

(2002)

M Ansaldi

Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants

Mol. Microbiol.

(2002)

K Turgay

Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor

EMBO J.

(1998)

Cited by (87)

ComX improves acid tolerance by regulating the expression of late competence proteins in Lactococcus lactis F44
2021, Journal of Dairy Science
Citation Excerpt :
Many studies on Strep. pneumoniae and other naturally transformable bacteria have reported the same phenomenon, that ComX was able to activate the transcription of the late competence genes only after a certain threshold (Claverys and Martin, 2003; Laurenceau et al., 2013). However, the ComX protein can also be rapidly degraded when ClpP is present along with the ATPase subunits ClpC and ClpE in naturally transformable bacteria (Dong et al., 2014; Fontaine et al., 2015).
ComX can improve bacterial competence by modulating global gene expression. Although competence induction may also be a protective mechanism under stress, this has not been investigated in detail. Here, we demonstrated that ComX improved the acid tolerance and nisin yield of Lactococcus lactis, which is an important gram-positive bacterium increasingly used in modern biotechnological applications. We found that overexpression of comX could improve the survival rate up to 36.5% at pH 4.0, compared with only 5.4% and 1.1% with the wild-type and comX knockout strains, respectively. Moreover, quantitative real-time PCR results indicated that comX overexpression stimulated the expression of late competence genes synergistically with exposure to acid stress. Finally, electrophoretic mobility shift assay demonstrated the binding of purified ComX to the cin-box in the promoters of these genes. Taken together, our results reveal a regulation mechanism by which ComX and acid stress can synergistically modulate the expression of late competence genes to enhance cells' acid tolerance and nisin yield.
Horizontal gene transfer: Uptake of extracellular dna by bacteria
2019, Encyclopedia of Microbiology
Competent bacteria can take up extracellular DNA fragments present in several environments during natural transformation. These fragments can recombine with the bacterial chromosome. The stable uptake of DNA over generations depends on the molecular factors governing the integration of DNA into the recipient's chromosome, and the environmental and population factors that determine the long-term survival of the transformant in the population. Here we present experimental models that examine DNA uptake in bacteria, their advantages and limitations. The relationship between transformation frequencies versus selection is examined and the implications for the open release of genetically engineered microorganisms are discussed.
Acid or erythromycin stress significantly improves transformation efficiency through regulating expression of DNA binding proteins in Lactococcus lactis F44
2017, Journal of Dairy Science
Citation Excerpt :
Interestingly, dozens of bacteria could absorb and recombine exogenous DNA into their own genome spontaneously (Fontaine et al., 2015). The recombination process works with the assistance of several DNA binding proteins (DBP), such as DprA, RadA, and RecQ (Claverys and Martin, 2003). Lots of single-strand DNA binding proteins could maintain the stability of genome, and some of them are tightly associated with stress tolerance (Calhoun and Kwon, 2011; Zhu et al., 2015; Riber et al., 2016).
Lactococcus lactis is a gram-positive bacterium used extensively in the dairy industry and food fermentation, and its biological characteristics are usually improved through genetic manipulation. However, poor transformation efficiency was the main restriction factor for the construction of engineered strains. In this study, the transformation efficiency of L. lactis F44 showed a 56.1-fold increase in acid condition (pH 5.0); meanwhile, erythromycin stress (0.04 μg/mL) promoted the transformation efficiency more significantly (76.9-fold). Notably, the transformation efficiency of F44e (L. lactis F44 harboring empty pLEB124) increased up to 149.1-fold under the synergistic stresses of acid and erythromycin. In addition, the gene expression of some DNA binding proteins (DprA, RadA, RadC, RecA, RecQ, and SsbA) changed correspondingly. Especially for radA, 25.1-fold improvement was detected when F44e was exposed to pH 5.0. Overexpression of some DNA binding proteins could improve the transformation efficiency. The results suggested that acid or erythromycin stress could improve the transformation efficiency of L. lactis through regulating gene expression of DNA binding proteins. We have proposed a simple but promising strategy for improving the transformation efficiency of L. lactis and other hard-transformed microorganisms.
Two different routes for double-stranded DNA transfer in natural and artificial transformation of Escherichia coli
2016, Biochemical and Biophysical Research Communications
Citation Excerpt :
Escherichia coli is transformable on agar plates under natural conditions [8–10]. Genomic analysis revealed the presence of a complete set of genes in E. coli homologous to DNA uptake and processing genes conserved in naturally transformable bacterial species [11]. The expression of these genes is controlled by the transcriptional regulator Sxy [12,13], whose homolog regulates natural competence in Haemophilus influenzae [14,15].
Escherichia coli is naturally transformable, independent on the conserved DNA uptake machinery for single-stranded DNA (ssDNA) integration. The transfer of double-stranded DNA (dsDNA) during natural transformation of E. coli is regulated by the alternative sigma factor σ^S. However, it remains mysterious how dsDNA transfers across the membranes and how σ^S regulates natural transformation of E. coli. Here, I screened for σ^S-regulated genes for dsDNA transfer in E. coli. The screening identified the σ^S-regulated genes ydcS and ydcV, both locate on the putative ABC transporter ydcSTUV operon. Considering that ydcS and ydcV are predicted to encode a periplasmic protein and an inner membrane protein for substrate binding and translocation respectively, I propose that they may mediate dsDNA translocation across the inner membrane during natural transformation. In chemical transformation of E. coli, ydcS was but ydcV was not required. Thus, YdcV should not be the channel for dsDNA translocation in artificial transformation. Together with the previous observation that the outer membrane porin OmpA mediates dsDNA transfer across the outer membrane in chemical transformation but not in natural transformation, I conclude that dsDNA transfers across the two membranes through different routes in natural and artificial transformation of E. coli.
Regulation of competence for natural transformation in streptococci
2015, Infection, Genetics and Evolution
Natural DNA transformation is a lateral gene transfer mechanism during which bacteria take up naked DNA from their environment and stably integrate it in their genome. The proteins required for this process are conserved between species and are produced during a specific physiological state known as competence. Although natural transformation drives genome plasticity and adaptability, it is also likely to cause deleterious effects in the chromosome of the recipient bacteria and negatively impact cell growth. The competence window is thus generally tightly regulated in response to species-specific environmental conditions and limited to a proportion of the cell population. In streptococci species, the entry into competence is dictated by the amount of the competence sigma factor σ^X, the master regulator of natural transformation in those species. The Streptococcus genus includes 7 phylogenetic groups that have evolved different regulatory circuits to govern natural transformation. Here, we review the current knowledge on transcriptional and post-transcriptional mechanisms that control the activity of σ^X at the whole population and the single-cell level, with an emphasis on growth conditions that modulate their activation. Recent findings regarding competence regulation by the ComCDE and ComRS cell–cell signalling pathways and the Clp proteolytic system are specifically highlighted.
The oligopeptide ABC-importers are essential communication channels in Gram-positive bacteria
2019, Research in Microbiology
Citation Excerpt :
This process depends on the development of a competent state, triggered by the binding of the signaling peptide ComS to the regulator ComR [49,50]. The ComR–ComS complex induces the transcription of an alternative sigma factor-encoding gene sigX which is the master regulator of competence genes [51–53]. In E. faecalis, 2 pheromones target the same protein resulting in opposite effects.
The transport of peptides in microorganisms plays an important role in their physiology and behavior, both as a nutrient source and as a proxy to sense their environment. This latter function is evidenced in Gram-positive bacteria where cell-cell communication is mediated by small peptides. Here, we highlight the importance of the oligopeptide permease (Opp) systems in the various major processes controlled by signaling peptides, such as sporulation, virulence and conjugation. We underline that the functioning of these communication systems is tightly linked to the developmental status of the bacteria via the regulation of opp gene expression by transition phase regulators.

View all citing articles on Scopus

View full text

Trends in Microbiology

Bacterial ‘competence’ genes: signatures of active transformation, or only remnants?

Abstract

Section snippets

DNA-uptake machines

Competence regulatory circuits

Prediction of new transformable species

Conclusions

Trends Microbiol.

Trends Microbiol.

Gene

Trends Microbiol.

Bacterial gene transfer by natural genetic transformation in the environment

Microbiol. Rev.

DNA uptake in bacteria

Annu. Rev. Microbiol.

Do bacteria have sex?

Nat. Rev. Genet.

ComE, a competence protein from Neisseria gonorrhoeae with DNA-binding activity

J. Bacteriol.

Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system

Mol. Microbiol.

Involvement of a plasmid in virulence of Campylobacter jejuni 81-176

Infect. Immun.

Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis

Annu. Rev. Genet.

Extracellular peptide control of competence for genetic transformation in Streptococcus pneumoniae

Front. Biosci.

Two-component signal transduction

Annu. Rev. Biochem.

Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation

J. Bacteriol.

Transient association of an alternative sigma factor, ComX, with RNA polymerase during the period of competence for genetic transformation in Streptococcus pneumoniae

J. Bacteriol.

Characterization of comQ and comX, two genes required for production of ComX pheromone in Bacillus subtilis

J. Bacteriol.

Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants

Mol. Microbiol.

Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor

EMBO J.