The functional proteome landscape of a cosmopolitan oceanic bacterium

SAR11 bacteria, the most abundant organisms in the global ocean, are an extensively studied example of streamlining, an adaptation to extremely low nutrient levels. To understand the regulation of gene function in streamlined cells, we developed a proteome map for the SAR11 type strain HTCC1062 under 13 growth conditions. We detected 95% (1284 out of 1354) of the previously predicted proteins from the HTCC1062 genome, corrected 24 predicted coding regions, and discovered 80 previously unannotated proteins, many of which had frame-shifted or overlapping reading frames. HTCC1062 cells expressed almost their entire genome (> 87.7% of predicted proteins) under all growth conditions, demonstrating that they allocate relatively little coding capacity to auxiliary functions that are deployed infrequently in response to environmental challenges. Most proteins involved in fundamental cellular processes were stable. A highly compact genome and relatively stable proteome are critical for the organization of these simple, free-living planktonic cells, providing a unique model for interpreting the cell biology of a larger number of uncultured cell types.