Showing papers by "Nikos C. Kyrpides published in 2001"

Genomes OnLine Database (GOLD): a monitor of genome projects world-wide

Abstract: GOLD is a comprehensive resource for accessing information related to completed and ongoing genome projects world-wide. The database currently provides information on 350 genome projects, of which 48 have been completely sequenced and their analysis published. GOLD was created in 1997 and since April 2000 it has been licensed to Integrated Genomics. The database is freely available through the URL: http://igweb.integratedgenomics.com/GOLD/.

Cross-talk between catalytic and regulatory elements in a DEAD motor domain is essential for SecA function

Abstract: SecA, the motor subunit of bacterial polypeptide translocase, is an RNA helicase. SecA comprises a dimerization C‐terminal domain fused to an ATPase N‐terminal domain containing conserved DEAD helicase motifs. We show that the N‐terminal domain is organized like the motor core of DEAD proteins, encompassing two subdomains, NBD1 and IRA2. NBD1, a rigid nucleotide‐binding domain, contains the minimal ATPase catalytic machinery. IRA2 binds to NBD1 and acts as an intramolecular regulator of ATP hydrolysis by controling ADP release and optimal ATP catalysis at NBD1. IRA2 is flexible and can undergo changes in its α‐helical content. The C‐terminal domain associates with NBD1 and IRA2 and restricts IRA2 activator function. Thus, cytoplasmic SecA is maintained in the thermally stabilized ADP‐bound state and unnecessary ATP hydrolysis cycles are prevented. Two DEAD family motifs in IRA2 are essential for IRA2–NBD1 binding, optimal nucleotide turnover and polypeptide translocation. We propose that translocation ligands alleviate C‐terminal domain suppression, allowing IRA2 to stimulate nucleotide turnover at NBD1. DEAD motors may employ similar mechanisms to translocate different enzymes along chemically unrelated biopolymers.

The Rhodobacter capsulatus genome

Abstract: The genome of Rhodobacter capsulatus has been completely sequenced. It consists of a single chromosome containing 3.5 Mb and a circular plasmid of 134 kb. This effort, started in 1992, began with a fine-structure restriction map of an overlapping set of cosmids that covered the genome. Cosmid sequencing led to a gapped genome that was filled by primer walking on the chromosome and by using lambda clones. Methods had to be developed to handle strong stops in the high GC (68%) inserts. Annotation was done with the ERGO system at Integrated Genomics, as was the reconstruction of the cell's metabolism. It was possible to recognize 3709 orfs of which functional assignments could be made with high confidence to 2392 (65%). Unusual features include the presence of numerous cryptic phage genomes embedded in the chromosome.

Genome of Methanocaldococcus (Methanococcus) jannaschii.

Abstract: Publisher Summary Methanocaldococcus ( Methanococcus ) jannaschii strain JAL-1 is a hyperthermophilic methanogenic archaeon that was isolated from surface material collected at a “white smoker” chimney at a depth of 2600 m in the East Pacific Rise near the western coast of Mexico. Cells are irregular cocci possessing polar bundles of flagella. The cell envelope is composed of a cytoplasmic membrane and a protein surface layer. Similar isolates have been obtained from hydrothermally active sediments in the Guaymas Basin and the Mid-Atlantic Ridge, and related species have been found at other marine hydrothermal vents. Because these hyperthermophilic species are very different from the mesophilic methanococci, they have been reclassified into a new family, Methanocaldococcaceae , and two new genera, Methanocaldococcus and Methanotorris . The characteristics of the source material for these isolates suggest that they possess adaptations for growth at high temperature and pressure as well as moderate salinity.