Systematically Ranking the Tightness of Membrane Association for Peripheral Membrane Proteins (PMPs) *

Abstract

Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic protein complexes as the landmarks, we found that proteins involved in two-component signal transduction systems and transporters are overall tightly associated with the membranes, whereas the associations of ribosomal proteins are much weaker. Moreover, we found that hypothetical proteins containing the same domains generally have similar tightness. This work provided a global view of the structural organization of the membrane proteome with respect to divergent functions, and built the foundation for future investigation of the dynamic membrane proteome reorganization in response to different environmental or internal stimuli. Molecular & Cellular Proteomics

Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium

“…Total proteins extracted from the WCL of three biological replicates of both strains were included for the analysis. Note that we did not separate proteins into membrane and soluble fractions for the quantitative proteomic analysis for the reasons as outlined: Many proteins in Synechocystis, and probably in other cyanobacteria as well, localize both on membranes and in soluble compartments as we described before (33). A protein could be quantified as upregulated in the membrane fraction and downregulated in the soluble fraction or vice versa.…”

“…Grouping the identified proteins according to the functional categories annotated by the CyanoBase revealed that the coverages of identification for all functional categories are higher than 50% except for the category unknown ( Fig. 2B) (35), which presumably contains mainly undetectable low abundance proteins (33,34). Moreover, 457 identified proteins contain one or more transmembrane domains (TM) predicted by the software TMHMM, which is more than 50% of TM-containing proteins encoded by the whole Synechocystis genome (Fig.…”

“…In microarray based analyses, the genes included for analysis are exclusively from chromosome (19,75), which prevents the detection of the expression of plasmid-borne genes. In early gel-based proteomics studies, the relatively low resolution and low throughput nature of this technique limit the analyses to only high abundance proteins (34), which also prevents the identification of most proteins of plasmid origin because they are usually low abundant (33,34). Though the functional significance of these upregulated proteins of plasmid origin is largely unknown, it is conceivable to presume they could complement the functions of some repressed proteins of chromosome origin, as previously observed for the hik31 operon on the plasmid pSYSX (102,103).…”

Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803

“…In our database, the protein ChlD was also observed to interact with SecD, which indicated that it might be functional to deliver chlorophyll to the newly synthesized pD1, carrying a similar role as protein ChlG ( Figure 2D) [34]. Besides, we observed that proteins interacting with photosynthetic proteins are mainly localized in the cytoplasm, while this class of proteins has possible mobility or secretion according to localization identification results [35]. The results provided a clue for understanding how photosynthetic proteins to transmit signals and influence the physiological metabolism in living cells.…”

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

“…PCC 6803 (PCC 6803) proteins with evidence for thylakoid lumen or thylakoid membrane localization (Agarwal et al 2010 ; Aldridge et al 2008 ; Baers et al 2019 ; Fulda et al 2002 ; Heinz et al 2016 ; Herranen et al 2004 ; Kashino et al 2002 , 2006 ; Komenda et al 2006 ; Liberton et al 2016 ; Ohkawa et al 2002 ; Pisareva et al 2011 ; Rajalahti et al 2007 ; Rengstl et al 2011 ; Rowland et al 2010 ; Sacharz et al 2015 ; Schultze et al 2009 ; Srivastava et al 2005 ; Wang et al 2000 ; Xu et al 2008 ; Zak et al 1999 , 2001 ; Zhang et al 2004 ). A false-positive list of PCC 7002 proteins was constructed from homologous proteins found in the soluble proteome of PCC 6803 that do not have signal sequences or transmembrane helices, as these proteins are expected to be cytoplasmic (Baers et al 2019 ; Choi et al 2000 ; Fulda et al 2006 ; Fuszard et al 2013 ; Gan et al 2005 ; Gao et al 2014b , 2015 , 2009 ; Kurian et al 2006b ; Mata-Cabana et al 2007 ; Mehta et al 2014 ; Mikkat et al 2014 ; Pandhal et al 2009 ; Pérez‐Pérez et al 2006 ; Plohnke et al 2015 ; Rowland et al 2011 ; Simon et al 2002 ; Slabas et al 2006 ). As expected, proteins from the true-positive list have significantly higher enrichment values than proteins from the false-positive list (Fig.…”