Life at depth: Photobacterium profundum genome sequence and expression analysis

Deep-sea life requires adaptation to high pressure, an extreme yet common condition given that oceans cover 70% of Earth's surface and have an average depth of 3800 meters. Survival at such depths requires specific adaptation but, compared with other extreme conditions, high pressure has received little attention. Recently, Photobacterium profundum strain SS9 has been adopted as a model for piezophily. Here we report its genome sequence (6.4 megabase pairs) and transcriptome analysis. The results provide a first glimpse into the molecular basis for life in the largest portion of the biosphere, revealing high metabolic versatility.

A comprehensive, high-resolution genomic transcript map of human skeletal muscle

We present the Human Muscle Gene Map (HMGM), the first comprehensive and updated high-resolution expression map of human skeletal muscle. The 1078 entries of the map were obtained by merging data retrieved from UniGene with the RH mapping information on 46 novel muscle transcripts, which showed no similarity to any known sequence. In the map, distances are expressed in megabase pairs. About one-quarter of the map entries represents putative novel genes. Genes known to be specifically expressed in muscle account for <4% of the total. The genomic distribution of the map entries confirmed the previous finding that muscle genes are selectively concentrated in chromosomes 17, 19, and X. Five chromosomal regions are suspected to have a significant excess of muscle genes. Present data support the hypothesis that the biochemical and functional properties of differentiated muscle cells may result from the transcription of a very limited number of muscle-specific genes along with the activity of a large number of genes, shared with other tissues, but showing different levels of expression in muscle. [The sequence data described in this paper have been submitted to the EMBL data library under accession nos. F23198-F23242.]

Characterization of 16 novel human genes showing high similarity to yeast sequences

The entire set of open reading frames (ORFs) of Saccharomyces cerevisiae has been used to perform systematic similarity searches against nucleic acid and protein databases: with the aim of identifying interesting homologies between yeast and mammalian genes. Many similarities were detected: mostly with known genes. However: several yeast ORFs were only found to match human partial sequence tags: indicating the presence of human transcripts still uncharacterized that have a homologous counterpart in yeast. About 30 such transcripts were further studied and named HUSSY (human sequence similar to yeast). The 16 most interesting are presented in this paper along with their sequencing and mapping data. As expected: most of these genes seem to be involved in basic metabolic and cellular functions (lipoic acid biosynthesis: ribulose-5-phosphate-3-epimerase: glycosyl transferase: beta-transducin: serine-threonine-kinase: ABC proteins: cation transporters). Genes related to RNA maturation were also found (homologues to DIM1: ROK1-RNA-elicase and NFS1). Furthermore: five novel human genes were detected (HUSSY-03: HUSSY-22: HUSSY-23: HUSSY-27: HUSSY-29) that appear to be homologous to yeast genes whose function is still undetermined. More information on this work can be obtained at the website http://grup.bio.unipd.it/hussy