Frequency and Distribution of DNA Uptake Signal Sequences in the Haemophilus influenzae Rd Genome

Abstract

The naturally transformable, Gram-negative bacterium Haemophilus influenzae Rd preferentially takes up DNA of its own species by recognizing a 9-base pair sequence, 5'-AAGTGCGGT, carried in multiple copies in its chromosome. With the availability of the complete genome sequence, 1465 copies of the 9-base pair uptake site have been identified. Alignment of these sites unexpectedly reveals an extended consensus region of 29 base pairs containing the core 9-base pair region and two downstream 6-base pair A/T-rich regions, each spaced about one helix turn apart. Seventeen percent of the sites are in inverted repeat pairs, many of which are located downstream to gene termini and are capable of forming stem-loop structures in messenger RNA that might function as signals for transcription termination.

Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae

“…Thus under this model accumulation of USSs in the genome might be expected to require (at least) strong kin selection, if not the extreme altruism of programmed cell death (23). However the problem can be greatly simplified by recognizing that, provided the uptake machinery is biased, USSs may be maintained (14,19) or even increase (24) without being beneficial. Instead USSs will accumulate as a direct consequence of the uptake bias, in a form of what is often called ''molecular drive'' (25).…”

“…Because closely spaced USSs are less common in the H. influenzae genome than predicted for randomly located sequence elements, Karlin et al (27) proposed that USSs have a structural function in the compaction of the chromosome or in DNA replication or repair. However, no intracellular USS-binding proteins are known (19), and the H. influenzae and N. meningitidis USSs show no orientation bias around the chromosome, such as would be expected for a sequence that interacts with DNA replication machinery. Furthermore, this nonrandom distribution can also be explained by biased uptake, because molecular drive will act less strongly on two closely spaced USSs than on two isolated ones.…”

“…6), and Danner et al (14) have shown that DNA uptake is specifically blocked by ethylation of bases in the USS. Second, the genomes of these species are highly enriched for their preferred sequence, so most fragments larger than 2 kb will contain one or more USSs (18)(19)(20). In the Neisseriaceae species N. gonorrhoeae and Neisseria meningitidis the highly conserved core of the USS is the 10-bp sequence GCCGTCTGAA, present in 1,891 copies in the 2.18-megabase (Mb) N. meningitidis Z2491 genome (18,20).…”

Yeasties and beasties: 7 years of genome sequencing

“…Not least of these, J. Craig Venter's laboratory at the Institute of Genome Research (TIGR), completed the first bacterial genomes; Haemophilus influenzae and M. genitalium for which whole genome shotgun sequencing was employed [10][11][12]. As can be seen from Random sequencing using universal primers either using flourent or radioactive labelling assemble overlapping clones to form "contigs" directed finishing stage involving custom primers and modified chemistry genome projects use shotgun methodology, including that of C. elegans.…”

Evaluation of the current models for the evolution of bacterial DNA uptake signal sequences

“…There have been thorough investigations of the statistical properties of USS, particularly in Haemophilus influenzae (HI); an exhaustive review of the literature (Smith et al, 1995(Smith et al, , 1999Karlin et al, 1996) would go beyond the scope of this article. Here, we only mention that the USS is highly over-represented.…”