Abstract
A systematic comparative genomic analysis of all archaeal membrane proteins that have been projected to the last archaeal common ancestor gene set led to the identification of several novel components of predicted secretion, membrane remodeling, and protein glycosylation systems. Among other findings, most crenarchaea have been shown to encode highly diverged orthologs of the membrane insertase YidC, which is nearly universal in bacteria, eukaryotes, and euryarchaea. We also identified a vast family of archaeal proteins, including the C-terminal domain of N-glycosylation protein AglD, as membrane flippases homologous to the flippase domain of bacterial multipeptide resistance factor MprF, a bifunctional lysylphosphatidylglycerol synthase and flippase. Additionally, several proteins were predicted to function as membrane transporters. The results of this work, combined with our previous analyses, reveal an unexpected diversity of putative archaeal membrane-associated functional systems that remain to be functionally characterized. A more general conclusion from this work is that the currently available collection of archaeal (and bacterial) genomes could be sufficient to identify (almost) all widespread functional modules and develop experimentally testable predictions of their functions.
Highlights
Semipermeable lipid bilayer membranes are a major hallmark of all living cells
We used the results of the reconstruction of the gene complement of Last Archaeal Common Ancestor (LACA) [5] to select 978 archaeal clusters of orthologous genes (arCOGs) that project to LACA with the probability of 90% or greater
It should be noted that the set of 15 arCOGs is the low bound of the uncharacterized conserved membrane proteins because, many other proteins in the 105 arCOGs set have some general function annotation, they have never been studied experimentally and their actual function or specificity might be different from the current assignment
Summary
Semipermeable lipid bilayer membranes are a major hallmark of all living cells. Despite striking differences in membrane lipid structure between archaea and bacteria [1,2,3], these two domains of cellular life share many membrane proteins, including several components of ATP synthase, NADH dehydrogenase, Sec and Tat protein translocase complexes and numerous transporters [4,5,6]. Despite the substantial progress in understanding the organization of biological membranes and membrane proteins over the past several decades, membrane proteins remain notoriously difficult to study both experimentally and computationally These difficulties stem primarily from the fact that most of the membrane proteins are highly hydrophobic and insoluble in aqueous media. This property is reflected in the sequences of membrane proteins that are characterized by high (often up to 90%) content of hydrophobic amino acid residues which typically form clusters corresponding to transmembrane helices (TMs) [10,11] This feature is successfully exploited for membrane protein prediction [9,12,13,14] but makes it difficult to study such proteins using standard methods of sequence comparison. These predictions are intended to guide further experiments with these important archaeal proteins
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
