Comparative proteomics of related symbiotic mussel species reveals high variability of host–symbiont interactions

摘要

Relative abundance of proteins in major metabolic categories in ( ) and ( ). Bubble size corresponds to protein abundance in %OrgNSAF (average values, for replicate numbers see Supplementary Table  ; see Supplementary Tables  and for a complete list of all identified proteins). Sample types: we analyzed the soluble proteome of symbiont-containing whole gill tissue (Gill) and symbiont-free foot tissue (Foot). In addition, we selectively enriched symbiont fractions (symbiont cell pellet, Sym) and host proteins (host-enriched supernatant, Host, only) from gill tissue using gradient centrifugation, and analyzed their soluble proteome. For enhanced identification of membrane-associated symbiont proteins, we additionally analyzed the membrane proteome of whole gill tissue samples (gill membrane fraction, GM) and enriched symbionts (symbiont membrane fraction, SM, only). Sym samples were analyzed in an LTQ-Orbitrap Velos (V) mass spectrometer and in an LTQ-Orbitrap Classic (O) mass spectrometer. The heat map in the center shows ratios of symbiont protein abundance in and Gill and Sym samples (Velos measurements only). Ratios were calculated from CLR-transformed %OrgNSAF values (see ). Negative ratios (red cells) indicate higher abundance in , while positive ratios (blue cells) indicate higher abundance in . Gray cells (NA) indicate proteins that were either not compared, or that lacked the minimum number of valid values for reliable ratio calculations (see also Supplementary Table  ). Major metabolic categories are indicated on the right. H hydrogen oxidation, P phage defense