In silico analysis of haloarchaeal intramembrane proteases of the Rhomboid family

GIMÉNEZ M.I.; DE CASTRO R.E.

Villa Carlos Paz, Córdoba, Argentina.

Congreso; VI Congreso Argentino de Microbiología General; 2009

Sociedad Argentina de Microbiología General

Rhomboids are intramembrane proteases which are conserved in the three domains of life. Even though they share topological traits, their roles in different organisms, when known, are very diverse. Particularly, nothing is known on the biology of rhomboid proteases in archaea. Haloarchaea belong to the Archaea domain and thrive in high salt (1.5 M to saturation NaCl) environments. As a first approach to study rhomboid proteases in this group of extremophilic microorganisms, we performed a bioinformatics survey for haloarchaeal intramembrane proteases, focusing on the rhomboid family, in publicly available haloarchaeal genome sequences. Haloarchaeal genomes encode two or three rhomboid proteases, depending the organism. Predicted protein sequence analysis showed that some rhomboid proteases of halophilic archaea show the canonical 6 transmembrane segment (TMS) topology whereas others have unique traits, including extra TMSs for one group of proteases and an N-terminal AN-1 Zn-finger motif for another. The domain combination of the Zn-finger-rhomboid proteases is unique and suggests a novel function for these proteases in haloarchaea. Zn-fingers are protein motifs initially described as DNA interacting domains, which can also interact with other molecules as RNA, lipids and proteins. Interestingly, in all studied genomes, we found that the gene encoding the Zn-finger motif-containing rhomboid is in the same operon with a predicted endonuclease V gene, suggesting the participation of rhomboid proteases in DNA related mechanisms.  In an attempt to search for potential substrates of rhomboid proteases in archaea, we looked for an N-terminal extension on the TatA protein, a component of the Tat protein translocation system, which was previously reported to be processed by a rhomboid protease in the bacterium Providencia stuartii. We observed that all haloarchaeal TatA homologs show an extension of 5-11 aminoacid residues followed by a predicted serine protease cleavage site, anticipating that the TatA component is also processed by rhomboid proteases in haloarchaea. All the data compiled in this work suggest that haloarchaeal rhomboid proteases may have unique as well as common roles and features compared to their non-haloarchaeal counterparts. Current experimental work in our laboratory is aimed to confirm this hypothesis. Supported by UNMDP and ANPCyT.