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Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium

Micrococcus luteus (NCTC2665, “Fleming strain”) has one of the smallest genomes of free-living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to encode 2,403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently…. [Read More]

Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy

Forward genetic screens with ENU (N-ethyl-N-nitrosourea) mutagenesis can facilitate gene discovery, but mutation identification is often difficult. We present the first study in which an ENU-induced mutation was identified by massively parallel DNA sequencing. This mutation causes heterotaxy and complex congenital heart defects and was mapped to a 2.2-Mb interval on mouse chromosome 7. Massively… [Read More]

Proteomics for validation of automated gene model predictions

High-throughput liquid chromatography mass spectrometry (LC-MS)-based proteomic analysis has emerged as a powerful tool for functional annotation of genome sequences. These analyses complement the bioinformatic and experimental tools used for deriving, verifying, and functionally annotating models of genes and their transcripts. Furthermore, proteomics extends verification and functional annotation to the level of the translation product… [Read More]

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575(T))

Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on… [Read More]

Novel function of the human presqualene diphosphate phosphatase as a type II phosphatidate phosphatase in phosphatidylcholine and triacylglyceride biosynthesis pathways

Phosphatidate phosphatases, PAPs, are key enzymes in lipid biosynthesis and signaling. Type I PAP enzymes participate in de-novo phospholipid biosynthesis, whereas type II PAP enzymes have an established role in lipid signaling. To identify novel human type II PAPs potentially involved in de-novo phospholipid synthesis we used bioinformatics to screen for enzymes with an active… [Read More]

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2)

Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus Halomicrobium. It is of phylogenetic interest because of its isolated location within the large euryarchaeal family Halobacteriaceae. H. mukohataei is an extreme halophile that grows essentially aerobically, but can also grow anaerobically under a change of morphology and… [Read More]

Prepublication data sharing

Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets. [Read More]

A renaissance for the pioneering 16S rRNA gene

Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community’s functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene… [Read More]

Prokaryotic community profiles at different operational stages of a Greek solar saltern

A combination of culture-dependent and independent approaches was employed to identify the microbial community structure in a Greek solar saltem. A total of 219 and 132 isolates belonging, respectively, to Bacteria and Archaea, were recovered. All bacterial isolates were phylogenetically related to 43 members of Actinobacteria, Firmicutes and gamma-Proteobacteria. The archaeal isolates were placed within… [Read More]