Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations

摘要: The -proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce wide range of organic compounds, metal ions, and radionuclides. Similar to most other sequenced organisms, 40% the predicted ORFs in S. genome were annotated as uncharacterized ‘‘hypothetical’’ genes. We implemented an integrative approach by using experimental computational analyses provide more detailed insight into gene function. Global expression profiles determined for cells after UV irradiation under aerobic suboxic growth conditions. Transcriptomic proteomic confidently identified 538 hypothetical genes expressed both mRNAs proteins (33% all proteins). Publicly available analysis tools databases data applied improve annotation these results scored seven-category schema ranked confidence precision functional assignment. able identify homologs nearly (97%), but could assign exact biochemical functions only 16 (category 1; 3%). Altogether, evidence provided assignments or insights 240 (categories 2–5; 45%). These annotations advance our understanding involved vital cellular processes, including energy conversion, ion transport, secondary metabolism, signal transduction. propose this offers valuable means undertake enormous challenge characterizing rapidly growing number with each newly genome. biology microarrays proteomics microbiology