Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

Abstract Background Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I σ70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the α subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the σ70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions. Conclusion The triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance.</p

Where were the northern elephant seals? Holocene archaeology and biogeography of \u3cem\u3eMirounga angustirostris\u3c/em\u3e

Driven to the brink of extinction during the nineteenth century commercial fur and oil trade, northern elephant seal (NES, Mirounga angustirostris) populations now exceed 100 000 animals in the northeast Pacific from Alaska to Baja California. Because little is known about the biogeography and ecology of NES prior to the mid-nineteenth century, we synthesize and analyze the occurrence of NES remains in North American archaeological sites. Comparing these archaeological data with modern biogeographical, genetic, and behavioral data, we provide a trans-Holocene perspective on NES distribution and abundance. Compared with other pinnipeds, NES bones are relatively rare throughout the Holocene, even in California where they currently breed in large numbers. Low numbers of NES north of California match contemporary NES distribution, but extremely low occurrences in California suggest their abundance in this area was very different during the Holocene than today. We propose four hypotheses to explain this discrepancy, concluding that ancient human settlement and other activities may have displaced NES from many of their preferred modern habitats during much of the Holocene

The Nicoleños in Los Angeles: Documenting the Fate of the Lone Woman’s Community

When the last San Nicolas Island resident, known as the ‘Lone Woman,’ was brought to Santa Barbara in 1853 after 18 years of solitude following the 1835 removal of her people to the mainland, efforts were made to locate speakers who could communicate with her. That search was reported to be unsuccessful, and the Lone Woman died seven weeks later, unable to recount her story. After the Lone Woman’s death, many accounts presumed that everyone from San Nicolas Island had died. Recent research in provincial Mexican papers, Los Angeles documents, American records, and church registers has uncovered original primary source information that details the experience of the Lone Woman’s people in Los Angeles. Five men, women, and children are con rmed or are likely to have come to the Los Angeles area from San Nicolas Island in 1835, and the parents of a newborn girl baptized the following year also may have come from that island

Fundamental relationship between operon organization and gene expression

Half a century has passed since the discovery of operons (groups of genes that are transcribed together as a single mRNA). Despite the importance of operons in bacterial gene networks, the relationship between their organization and gene expression remains poorly understood. Here we show using synthetic operons in Escherichia coli that the expression of a given gene increases with the length of the operon and as its position moves farther from the end of the operon. These findings can be explained by a common mechanism; increasing the distance from the start of a gene to the end of the operon (termed the “transcription distance”) provides more time for translation to occur during transcription, resulting in increased expression. We confirmed experimentally that the increased expression is indeed due to increased translation. Furthermore our analysis indicates the translation initiation rate for an mRNA is sixfold greater during transcription than after its release, which amplifies the impact of the transcription distance on gene expression. As a result of these mechanisms, gene expression increases by ∼40% for each 1,000 nucleotides of transcription distance. In summary, we demonstrate that a fundamental relationship exists between gene expression and the number, length, and order of the genes in an operon. This relationship has important implications for understanding the functional basis of genome organization and practical applications for synthetic biology