The primary structures of helices A to G of three new bacteriorhodopsin-like retinal proteins.
The primary structures of helices A to G of all bacteriorhodopsin (BR)-like retinal proteins identified in newly isolated halobacteria have been determined from the nucleotide sequence of the BR-like protein genes. Using PCR methods, gene fragments encoding the A- to G-helix region of BR-like proteins were directly amplified from the total genomic DNA of the seven new halobacterial strains. Oligonucleotide primers corresponding to highly conserved regions in the helices A to G were designed from the nucleotide sequences of bacterioopsin (bop) and archaeopsin-I (aop-I), and some primers were effective for the amplification of the gene encoding C- to G-helix region of all new BR-like proteins. The primer corresponding to A-helix region was designed either from the nucleotide sequence of bop and aop-I or from the N-terminus amino acid sequence of a BR-like protein. Three new BR-like proteins were identified from the amino acid sequence, which was deduced from the nucleotide sequence of the genes encoding A- to G-helix region of the BR-like proteins. It was found that not only the amino acid sequence, but also the nucleotide sequence of the gene encoding the C- and G-helix region, in which a number of important residues for proton translocation are located, is highly conserved in three new BR-like proteins. Analysis of the primary structures of the A- to G-helix region of new BR-like proteins revealed that one has about 85% homology with aR-I and aR-II, and the rest have about 55% homology with halobium BR, aR-I and aR-II.(ABSTRACT TRUNCATED AT 250 WORDS)
Otomo
J
J
Frontier Research Program, RIKEN Institute, Saitama, Japan.
Urabe
Y
Y
Tomioka
H
H
Sasabe
H
H
D000595:Amino Acid Sequence; D001436:Bacteriorhodopsins / Q000235:genetics*; D001483:Base Sequence; D005798:Genes, Bacterial / Q000235:genetics*; D014644:Genetic Variation; D016931:Halobacteriales / Q000235:genetics*; D006217:Halobacterium / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid
D001436:Bacteriorhodopsins