In this week's PNAS Early Edition, Eugene Gladyshev and Irina Arkhipova at the Marine Biological Laboratory in Woods Hole, Mass., present evidence that suggests the class of class of reverse transcriptase-related cellular genes collectively called rvts "are not components of retrotransposons or viruses, but [are] single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection." Gladyshev and Arkhipova show that these genes "can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria," and add their very existence — as a previously unknown class of single-copy reverse transcriptase-related genes — "calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells."
Elsewhere in the Early Edition, an international team led by investigators at the John Innes Centre in the UK discusses the "formation of plant metabolic gene clusters within dynamic chromosomal regions." In its paper, the team suggests "common mechanisms are likely to underlie the assembly and control of operon-like gene clusters in plants."
Researchers in Mexico this week present COIN-VGH, "a unique strategy for identifying SNPs … that largely minimizes the presence of false-positives in the generated data." The team developed the COIN-VGH algorithm — which is "based on the concept that a nucleotide can be individualized if it is analyzed in the context of its surrounding genomic sequence" — using "X-chromosome-specific regions from the previously sequenced genomes of Craig Venter and James Watson."
Boston University's James Collins and his colleagues report their use of gene expression profiles and a network biology approach to predict functional roles and regulatory interactions for small RNAs in E. coli. "This work shows that a network-based approach can be used to identify the cellular function of sRNAs and characterize the relationship between sRNAs and transcription factors," Collins et al. write in PNAS.