Efficient profiling of detergent-assisted membrane proteome in cyanobacteria

Membrane proteins play key roles in cellular functions like transport of molecules, perception of environmental cues, and signal transduction into the intracellular compartment. However, the profiling of membrane proteins is still a daunting task because of the hydrophobicity, restricting our knowledge of membrane proteins. Thus, we attempted to develop a novel detergent-based approach to uncover membrane proteins using cyanobacteria. We investigated the effect of five different detergents on the profiling of the cyanobacterial membrane proteome. The application of either amidosulfobetaine-14 (ASB14) or N-lauroylsarcosine (NL) doubled the number of the identified integral membrane proteins compared with the control. Extraction with ASB14 increased the number of transmembrane helices over four times. The quantitative index (mol%) of membrane proteins also increased from 13 to 22% when ASB14, NL, and benzyldimethyl-n-hexadecylammonium chloride (BAC) were used. ASB14 treatment was particularly useful for identifying membrane proteins with higher molecular weights (Mr), and the addition of BAC to the cyanobacterial membrane could identify the membrane proteins with acidic isoelectric points (pI). To validate the efficiency of the detergent-based proteomics, the functional membrane protein complexes involved in energy metabolism were selected as an example and shown to be successful with the combined data of ASB14, NL, and zwittergent 3-10 (ZW3-10). Taken together, we suggest that the use of a specific detergent and the subsequent combination of proteome data is critical for detailed profiling of cyanobacterial functional membrane proteins.