Methanobacterium thermoautotrophicum ⌬H, isolated in 1971 from sewage sludge in Urbana, Ill. (72), is a lithoautotrophic, thermophilic archaeon that grows at temperatures ranging from 40 to 70°C and optimally at 65°C. M. thermoautotrophicum conserves energy by using H 2 to reduce CO 2 to CH 4 and synthesizes all of its cellular components from these same gaseous substrates plus N 2 or NH 4 ϩ and inorganic salts, but despite this impressive biosynthetic capacity, M. thermoautotrophicum ⌬H and related strains have very small genomes (ϳ1.7 Ϯ 0.2 Mb [57,58]). M. thermoautotrophicum ⌬H, Marburg, and Winter are the foci of many methanogenesis, archaeal physiology, and molecular biology investigations, and M. thermoautotrophicum ⌬H was chosen as a representative of this group for genome sequencing. These thermophilic methanogens have mesophilic and hyperthermophilic relatives, Methanobacterium formicicum and Methanothermus fervidus, respectively, so that comparisons can be made of homologous

Background: Several high throughput technologies have been employed to identify differentially regulated genes that may be molecular targets for drug discovery. Here we compared the sets of differentially regulated genes discovered using two experimental approaches: a subtracted suppressive hybridization (SSH) cDNA library methodology and Affymetrix GeneChip ® technology. In this "case study" we explored the transcriptional pattern changes during the in vitro differentiation of human monocytes to myeloid dendritic cells (DC), and evaluated the potential for novel gene discovery using the SSH methodology.

An agar-degrading marine bacterium identified as a Microscilla species was isolated from coastal California marine sediment. This organism harbored a single 101-kb circular DNA plasmid designated pSD15. The complete nucleotide sequence of pSD15 was obtained, and sequence analysis indicated a number of genes putatively encoding a variety of enzymes involved in polysaccharide utilization. The most striking feature was the occurrence of five putative agarase genes. Loss of the plasmid, which occurred at a surprisingly high frequency, was associated with loss of agarase activity, supporting the sequence analysis results.Bacteria have long been exploited as a source of natural products for use in medicine, agriculture, and industry. Until recently, most studies utilized microbes that had been isolated from clinical or terrestrial environments. It is now recognized that bacteria living in marine environments provide an abundant and as-yet-untapped source of metabolic properties (8). Marine sediments are rich in bacteria, with reports of 10 8 to 10 10 microbes per g of sediment for the first few centimeters of sediment (21). Estimates of bacterial diversity in natural environments have indicated that, while a few organisms may predominate, such environments still represent a highly complex assemblage of microbes (45).We have initiated a study to identify and characterize the genes present on plasmids isolated from bacteria present in coastal marine sediments. Extrachromosomal elements by definition encode functions that are not essential for cell growth but which provide an advantage to the host bacterium under certain growth conditions. It is therefore not surprising that a wide variety of traits in bacteria have been found to be plasmid encoded. In an earlier study (41), ca. 30% of more than 1,000 aerobic heterotrophic bacteria isolated from coastal California marine sediments contained at least one plasmid that ranged in size from 5 to Ͼ250 kb. These plasmids appeared to contain novel and generally uncharacterized replication regions since no homology was detected between ca. 300 plasmids of marine origin (41) and 15 replicon probes derived from plasmids found in bacteria isolated from mammalian or terrestrial sources (10). These findings suggested that plasmids in marine sediment microbial communities are a unique and diversified set of extrachromosomal elements.We present here the characterization of an agar-degrading marine isolate, Microscilla sp. strain PRE1. This organism contains a 101-kb plasmid, designated pSD15, which potentially encodes five different agarases and is essential for the ability of the bacterium to degrade agar. The complete DNA sequence and analysis of pSD15 are reported. MATERIALS AND METHODSIsolation and characterization of marine bacterial isolate PRE1. Marine sediment associated with the roots of pickleweed (Salicornia virginica) was collected from the Kendall-Frost Mission Bay Marsh Reserve in San Diego, Calif. The sediment was resuspended in artificial seawater (0.3 M NaCl, 0.1 M KCl,...

We report the production and availability of over 7000 fully sequence verified plasmid ORF clones representing over 3400 unique human genes. These ORF clones were derived using the human MGC collection as template and were produced in two formats: with and without stop codons. Thus, this collection supports the production of either native protein or proteins with fusion tags added to either or both ends. The template clones used to generate this collection were enriched in three ways. First, gene redundancy was removed. Second, clones were selected to represent the best available GenBank reference sequence. Finally, a literature-based software tool was used to evaluate the list of target genes to ensure that it broadly reflected biomedical research interests. The target gene list was compared with 4000 human diseases and over 8500 biological and chemical MeSH classes in ∼15 Million publications recorded in PubMed at the time of analysis. The outcome of this analysis revealed that relative to the genome and the MGC collection, this collection is enriched for the presence of genes with published associations with a wide range of diseases and biomedical terms without displaying a particular bias towards any single disease or concept. Thus, this collection is likely to be a powerful resource for researchers who wish to study protein function in a set of genes with documented biomedical significance.