Question

how can we induce competence in gram POSITIVE bacteria?

Answer 1

Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple “dialects,” with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.

initiation Se o.m. BI uptake translo- bacation i.m. D recombination

FIG 1

DNA uptake and transformation by competent Gram-negative bacteria. (A) dsDNA is bound at the cell surface. (B) DNA is pulled through the type II secretin pore by retraction of a type 4 pilus (T4P). (C) One strand is translocated intact into the cytoplasm by the Rec2/ComEC protein; the other is degraded. (D) The new strand recombines with a homologous sequence in the chromosome, displacing the resident strand. The abbreviations “o.m.” and “i.m.” refer to the outer and inner cell membranes, respectively.