Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics

The availability of complete genome sequences of cellular life forms creates the opportunity to explore the functional content of the genomes and evolutionary relationships between them at a new qualitative level. With the advent of these sequences, the construction of a minimal gene set sufficient for sustaining cellular life and reconstruction of the genome of the last common ancestor of bacteria, eukaryotes, and archaea become realistic, albeit challenging, research projects. A version of the minimal gene set for modern-type cellular life derived by comparative analysis of two bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium, consists of ∼250 genes. A comparison of the protein sequences encoded in these genes with those of the proteins encoded in the complete yeast genome suggests that the last common ancestor of all extant life might have had an RNA genome.     

Spectral EEG indicator of pressure to enter into deep sleep: its responsiveness to closing the eyes for just a few minutes exhibits a pure exponential buildup during sleep deprivation

According to the two-process model of sleep–wake regulation, a homeostatic sleep pressure, i.e. a pressure to enter into deep non-rapid eyes movement (NREM) sleep, must exhibit a purely exponential buildup during prolonged wakefulness. However, this pressure is usually measured indirectly, i.e. during the following episode of actual deep NREM sleep. The purpose of this paper was to show that, despite a prominent circadian modulation of time course of any waking EEG index, the model-postulated purely exponential buildup of the homeostatic sleep pressure can be directly confirmed. During two days of sleep deprivation experiments, the EEG of healthy adults (N = 30) was recorded every other hour throughout 5-min eyes closed relaxation. Sixteen ln-transformed single-Hz power densities (from 1 to 16 Hz) were computed for each of 5 one-min intervals. Differences between these densities obtained for the first and the following intervals were calculated and averaged. The obtained 16 values were used as the frequency weighting curve for weighting densities of each set of 16 single-Hz power densities. Summing-up of these weighted densities provided a single measure that was found to co-vary with self-rated sleepiness throughout two-day interval of sleep deprivation, thus reflecting the joint influence of the circadian and homeostatic processes. However, two-day time course of responsiveness of this measure to closing the eyes for just a few minutes exhibited a purely exponential buildup. It was concluded that this result provided a direct experimental confirmation of the model-predicted exponential buildup of the homeostatic sleep pressure across prolonged episode of wakefulness.     

Evolutionary history of bacteriophages with double-stranded DNA genomes

Background

Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned.

Results

We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer.

Conclusion

A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.

Open peer review

This article was reviewed by Eugene Koonin, Nicholas Galtier and Martijn Huynen.     

Role of M3 protein in the adherence and internalization of an invasive Streptococcus pyogenes strain by epithelial cells

Streptococcus pyogenes utilizes multiple mechanisms for adherence to and internalization by epithelial cells. One of the molecules suggested of being involved in adherence and internalization is the M protein. Although strains of the M3 serotype form the second largest group isolated from patients with severe invasive diseases and fatal infections, not much information is known regarding the interactions of M3 protein with mammalian cells. In this study we have constructed an emm3 mutant of an invasive M3 serotype (SP268), and demonstrated that the M3 protein is involved in both adherence to and internalization by HEp-2 cells. Fibronectin promoted both adherence and internalization of SP268 in an M3-independent pathway. Utilizing speB and speB/emm3 double mutants, it was found that M3 protein is not essential for the maturation of SpeB, as was reported for the M1 protein. Increased internalization efficiency observed in both the speB and emm3/speB mutants suggested that inhibition of S. pyogenes internalization by SpeB is not related to the presence of an intact M3 protein. Thus, other proteins in SP268, which serve as targets for SpeB activity, have a prominent role in the internalization process.     

A Novel Serine/Threonine Protein Kinase Homologue of Pseudomonas aeruginosa Is Specifically Inducible within the Host Infection Site and Is Required for Full Virulence in Neutropenic Mice

A genetic locus of Pseudomonas aeruginosa was identified that is highly and specifically inducible during infection of neutropenic mice. This locus, ppkA, encodes a protein that is highly homologous to eukaryote-type serine/threonine protein kinases. A ppkA null mutant strain shows reduced virulence in neutropenic mice compared to the wild type. Overexpression of the PpkA protein greatly inhibited the growth of Escherichia coli or P. aeruginosa. However, a single amino acid change at the catalytic site of the kinase domain eliminated the toxic effect of PpkA on bacterial cells, suggesting that the kinase domain of PpkA is functional within bacterial cells.