Bacterial postgenomics: the promise and peril of systems biology.
Explore the source record for details and available documents.
Bacteria↗
Biomedical subjects
Barry S Goldman
Publications and source records attributed to Barry S Goldman.
Functional genome annotation through phylogenomic mapping.
Accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. Here we introduce a genome-scale approach to functional protein annotation--phylogenomic mapping--that requires only sequence data, can be applied equally well to both finished and unfinished genomes, and can be extended beyond single genomes to annotate multiple genomes simultaneously. We have developed and applied it to more than 200 sequenced bacterial genomes. Proteins with similar evolutionary histories were grouped together, placed on a three dimensional map and visualized as a topographical landscape. The resulting phylogenomic maps display thousands of proteins clustered in mountains on the basis of coinheritance, a strong indicator of shared function. In addition to systematic computational validation, we have experimentally confirmed the ability of phylogenomic maps to predict both mutant phenotype and gene function in the delta proteobacterium Myxococcus xanthus.
Bacterial Proteins↗
Genomic analyses of bacterial respiratory and cytochrome c assembly systems: Bordetella as a model for the system II cytochrome c biogenesis pathway.
An analysis of thirty-three genomes of selected bacteria for the presence of specific respiratory pathways and cytochrome c biogenesis systems has led to observations on respiration and biogenesis. A table summarizing these results is presented. The data suggested that Bordetella pertussis would be an excellent genetic model to study the System II cytochrome c biogenesis pathway. These observations are discussed and the results of genetic studies on System II biogenesis in B. pertussis are presented as a case for the power of comparative genomics. System II is present in organisms as diverse as Helicobacter, Neisseria, Porphyromonas, mycobacteria, cyanobacteria, and plants (chloroplasts), indicating this pathway's prominence and that horizontal transfer of system II (and/or System I) must have occurred on multiple occasions.
Bacteria↗