DNA as a nutrient: novel role for bacterial competence gene homologs - PubMed (original) (raw)

DNA as a nutrient: novel role for bacterial competence gene homologs

S E Finkel et al. J Bacteriol. 2001 Nov.

Abstract

The uptake and stable maintenance of extracellular DNA, genetic transformation, is universally recognized as a major force in microbial evolution. We show here that extracellular DNA, both homospecific and heterospecific, can also serve as the sole source of carbon and energy supporting microbial growth. Mutants unable to consume DNA suffer a significant loss of fitness during stationary-phase competition. In Escherichia coli, the use of DNA as a nutrient depends on homologs of proteins involved in natural genetic competence and transformation in Haemophilus influenzae and Neisseria gonorrhoeae. Homologs of these E. coli genes are present in many members of the gamma subclass of Proteobacteria, suggesting that the mechanisms for consumption of DNA may have been widely conserved during evolution.

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Figures

FIG. 1

FIG. 1

Survival patterns of yhiR and the wild-type (WT) parental strain in the presence or absence of competition. LB cultures were incubated for 12 days. (A) Cells grown in coculture; (B) cells grown separately. The asterisk indicates no detectable counts (limit of detection of <100 CFU/ml).

FIG. 2

FIG. 2

Growth yields for overnight cultures of wild-type (WT) or yhiR cells incubated in conditioned medium. Culture medium was prepared from 5-day-old LB cultures without or with DNase I treatment prior to inoculation. Results are the averages of four experiments.

FIG. 3

FIG. 3

Growth of E. coli utilizing DNA as the sole carbon source. Cells were grown in M63 minimal medium in the presence or absence of purified E. coli chromosomal DNA as the sole carbon source. Results are averages of three experiments. WT, wild type.

FIG. 4

FIG. 4

Genetic maps of the H. influenzae com locus genes and their homologs. Dashed lines indicate the limits of gene clusters between H. influenzae and E. coli. Arrows indicate direction of transcription, and arrow length is proportional to gene length (with the exception of ponA/mrcA homologs, which are not to scale). Genes that are not contiguous are indicated by breaks between genes or clusters. Annotated sequence information from the completed genomes of H. influenzae and E. coli was obtained from The Institute for Genomic Research (

www.tigr.org

) and the University of Wisconsin (

www.genetics.wisc.edu

) websites, respectively. Except for the published pil locus sequences (6, 18, 25), unannotated sequence data were obtained as follows: for S. enterica serovar Typhi,

www.sanger.ac.uk/projects/S.typhi

; for V. cholerae and S. putrefaciens,

www.tigr.org

; for N. gonorrhoeae,

dna1.chem.ou.edu/gono.html

; for P. aeruginosa,

www.pseudomonas.com

; for K. pneumoniae,

genome.wustl.edu/gsc/Projects/bacterial/klebsiella/klebsiella.shtml

.

FIG. 5

FIG. 5

Survival patterns of the hofQ mutant and the wild-type parental strain (WT) during competition in stationary phase. LB cultures were incubated for 12 days.

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