PubMed · 7919792
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N C Seeman, N R Kallenbach. 1994. DNA branched junctions.. https://doi.org/10.1146/annurev.bb.23.060194.000413
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A sequence similarity metric operating on 10 kb upstream regions of gene pairs quantitatively predicts a portion of co-variation of expression of gene pairs in large-scale gene expression studies in human tumors and tumor-derived cell lines. The signal on which the metric depends most strongly originates in the compositional structure of repetitive genomic sequences (particularly Alu elements) present in these upstream regions. This effect is completely separable from effects of isochore composition on gene expression. The results implicate repetitive elements with some functional role in transcriptional regulation of the specific genes in whose promoter regions they reside and lend credence to suggestions that the general phenomenon of repetitive element insertions may be a fundamental evolutionary mechanism for modulating gene transcription.
A novel thermoacidophilic strain, designated RT8-4, was isolated from an acidic hot spring in Tengchong, Yunnan, China, and characterized phenotypically and phylogenetically. Cells of strain RT8-4 are irregular cocci with peritrechous flagella. The strain grows aerobically in either a lithotrophic or a heterotrophic mode. No anaerobic growth is apparent. Growth on elemental sulfur occurs through the oxidation of sulfur. Strain RT8-4 is capable of utilizing tryptone, d-xylose, d-arabinose, d-galactose, maltose, sucrose, d-fructose, or l-glutamic acid as the sole source of carbon. d-Glucose and d-mannose are not utilized. RT8-4 grows optimally at 85 degrees C and pH 3.5. The G+C content of the genome of RT8-4 is 34.4 mol%. Phylogenetic analysis based on 16S rDNA sequence as well as DNA-DNA hybridization and phenotypic characterization identifies strain RT8-4 as a novel species in the genus Sulfolobus. It is proposed that strain RT8-4 be designated as Sulfolobus tengchongensis sp. nov. The type strain is RT8-4(T).
We describe a query-based web-accessible system (www.neurogadgets.com/bws.php) for facilitating comparative microbial genomics. A variety of query pages are available, each with numerous options, that allow a biologist to pose relevant questions of genomic data. We illustrate with a characterization of species-specific protein-coding genes (so-called "ORFans"), finding that they are on average smaller, faster evolving, and less G+C-rich, and that they encode proteins more basic in their predicted isoelectric point, compared with non-species-specific genes. Using a dual-threshold approach, we conclude that these are characteristics of true species-specific genes, rather than artifacts of mis-annotation.