an empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences实证的策略描述细菌蛋白质组跨物种的基因组序列的缺失.pdfVIP

An Empirical Strategy for Characterizing Bacterial Proteomes across Species in the Absence of Genomic Sequences ¤ Joshua E. Turse , Matthew J. Marshall, James K. Fredrickson, Mary S. Lipton, Stephen J. Callister* Biological Sciences and Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America Abstract Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300–500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide syn