Natural competence

In microbiology, genetics, cell biology and molecular biology, competence is the ability of a cell to take up extracellular ("naked") DNA from its environment. Competence may be differentiated between natural competence, a genetically specified ability of bacteria which is thought to occur under natural conditions as well as in the laboratory, and induced or artificial competence, which arises when cells in laboratory cultures are treated to make them transiently permeable to DNA. This article primarily deals with natural competence in bacteria. Information about artificial competence is provided in the article Transformation (genetics).

History

Natural competence was discovered by Frederick Griffith in 1928, when he showed that a preparation of killed cells of a pathogenic bacterium contained something that could transform related non-pathogenic cells into the pathogenic type. In 1944 Oswald Avery, Colin MacLeod, and Maclyn McCarty demonstrated that this 'transforming factor' was pure DNA. This was the first compelling evidence that DNA carries the genetic information of the cell.

Since then, natural competence has been studied in a number of different bacteria, particularly Bacillus subtilis, Streptococcus pneumoniae (Griffith's "pneumococcus"), Neisseria gonorrhoeae and Haemophilus influenzae. Areas of active research include the mechanisms of DNA transport, the regulation of competence in different bacteria, and the evolutionary function of competence.

Mechanisms of DNA uptake

In the natural world DNA usually becomes available by death and lysis of other cells, but in the laboratory it is provided by the researcher, often as a genetically engineered fragment or plasmid. During uptake, DNA is transported across the cell membrane(s), and the cell wall if one is present. Once the DNA is inside the cell it may be degraded to nucleotides, which are reused for DNA replication and other metabolic functions. Alternatively it may be recombined into the cell’s genome by its DNA repair enzymes. If this recombination changes the cell’s genotype the cell is said to have been transformed. Artificial competence and transformation are used as research tools in many organisms (see Transformation (genetics)).^[1]

In almost all naturally competent bacteria components of extracellular filaments called type 4 pili (a type of fimbria) are involved in the transformation process, and DNA may enter the cells via DNA translocase. Some bacteria cut the DNA into short pieces before transporting it; others can take up very long intact fragments and circular plasmids. The details of the uptake machinery are not yet fully characterized in any system.

Regulation of competence

In laboratory cultures natural competence is usually tightly regulated and often triggered by nutritional shortages or adverse conditions. However the specific inducing signals and regulatory machinery are much more variable than the uptake machinery, and little is known about the regulation of competence in the natural environments of these bacteria.^[2] Transcription factors have been discovered which regulate competence; an example is sxy (also known as tfoX) which has been found to be regulated in turn by a 5' non-coding RNA element.^[3] In bacteria capable of forming spores, conditions inducing sporulation often overlap with those inducing competence. Thus cultures or colonies containing sporulating cells often also contain competent cells. Recent research by Süel et al. has identified an excitable core module of genes which can explain entry into and exit from competence when cellular noise is taken into account.^[4]

Most competent bacteria are thought to take up all DNA molecules with roughly equal efficiencies, but bacteria in the families Neisseriaceae and Pasteurellaceae preferentially take up DNA fragments containing short DNA sequences, termed DNA uptake sequence (DUS), that are very frequent in their own genomes. Neisserial genomes contain thousands of copies of the preferred sequence GCCGTCTGAA, and Pasteurellacean genomes contain either AAGTGCGGT or ACAAGCGGT.^[1][5]

Evolutionary functions and consequences of competence

The evolutionary functions of natural competence are controversial. Competence has conventionally been viewed as a mechanism that cells evolved to provide themselves with novel genetic information. However the theoretical difficulties associated with the evolution of sex suggest that this explanation is problematic. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesize, these may make a significant contribution to the cell's energy budget.^[6] In principle, competence could also allow cells to replace heavily damaged DNA in the cell's genome if needed.

Regardless of the nature of selection for competence, the composite nature of bacterial genomes provides abundant evidence that the lateral gene transfer caused by competence contributes to the genetic diversity that makes evolution possible.

References

1. ^ ^{a b} Chen I, Dubnau D (2004). "DNA uptake during bacterial transformation". Nat. Rev. Microbiol. 2 (3): 241–9. doi:10.1038/nrmicro844. PMID 15083159. 
2. ^ Solomon JM, Grossman AD (1996). "Who's competent and when: regulation of natural genetic competence in bacteria". Trends Genet. 12 (4): 150–5. doi:10.1016/0168-9525(96)10014-7. PMID 8901420. 
3. ^ Redfield RJ (September 1991). "sxy-1, a Haemophilus influenzae mutation causing greatly enhanced spontaneous competence". J. Bacteriol. 173 (18): 5612–8. PMC 208288. PMID 1653215. http://jb.asm.org/cgi/pmidlookup?view=long&pmid=1653215. 
4. ^ Süel GM, Garcia-Ojalvo J, Liberman LM, and Elowitz MB (2006). "An excitable gene regulatory circuit induces transient cellular differentiation". Nature 440 (7083): 545–50. doi:10.1038/nature04588. PMID 16554821. 
5. ^ Full text at PMC: / 2817400 Findlay, W. A.; Redfield, R. J. (2009). "Coevolution of DNA Uptake Sequences and Bacterial Proteomes". Genome Biology and Evolution 1: 45–55. doi:10.1093/gbe/evp005. PMC 2817400. PMID 20333176. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2817400.  edit
6. ^ Redfield RJ (2001). "Do bacteria have sex?". Nat. Rev. Genet. 2 (8): 634–9. doi:10.1038/35084593. PMID 11483988. 

See also

• Transformation (genetics)