Xanthusbase: adapting wikipedia principles to a model organism database

Abstract

xanthusBase () is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (), and dictyBase (), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.

Isolation and characterization of a suppressor mutation that restores Myxococcus xanthus exopolysaccharide production

“…1). CheW7 is predicted to be 148 amino acids long (Arshinoff et al , 2007; Goldman et al , 2006) and the insertion mutation occurred in the 108 th codon of cheW7 . This frameshift mutation is predicted to result in a polypeptide with 228 amino acids that extended 256 nucleotides into the coding region of mcp7 out of frame.…”

“…To construct the plasmid for a kanamycin-resistance (Kan R ) linked to the che7 locus, a PCR fragment (chromosomal coordinates 8512566 to 8513278) (Arshinoff et al , 2007; Goldman et al , 2006) approximately 2 kb downstream of the che7 locus was amplified and cloned into the Eco RV site of pZErO-2 (Invitrogen) to generate pWB521. To construct the plasmid for a Kan R marker away from the che7 locus, another PCR fragment (chromosomal coordinates 6232354 to 6233024) (Arshinoff et al , 2007; Goldman et al , 2006) about 2·3 Mb away from che7 was amplified and cloned into the Eco RV site of pZErO-2 to generate pWB513.…”

“…To construct the plasmid for a Kan R marker away from the che7 locus, another PCR fragment (chromosomal coordinates 6232354 to 6233024) (Arshinoff et al , 2007; Goldman et al , 2006) about 2·3 Mb away from che7 was amplified and cloned into the Eco RV site of pZErO-2 to generate pWB513. The fragment in pWB513 includes the 3′ end of MXAN4984 and downstream sequence.…”

“…The asterisk (*) marks the approximate location of the cheW7-1 mutation in all panels. cpc7 is predicted to encode a PBS lyase HEAT-like repeat protein (Arshinoff et al , 2007; Goldman et al , 2006). It is likely that there are promoters in the che7 locus, one upstream of MXAN6966 or cheY7 and another within cheW7 (See text for details).…”

The elusive engine in Myxococcus xanthus gliding motility

“…Despite extensive searches, molecular motors that track on the bacterial cytoskeleton have so far not been identified, questioning their existence in prokaryotes. Such motors may exist in M. xanthus but are not readily identified with bioinformatics [42]. It is possible that bacteria evolved distinct ways to power cytoskeletonmediated processes (such as the use of the proton motive force).…”