Amino acid sequence homology among the major outer membrane proteins of Escherichia coli.

Abstract

Analysis of amino acid sequences reported for the major outer membrane proteins of Escherichia coli, including the porins (OmpF, OmpC, and PhoE), the phage A receptor (LamB), and another protein (OmpA), revealed several regions of local homology that is statistically significant.The implications of this observation are discussed in relation to the evolutionary origins of these proteins, as well as to the mechanism of export of these proteins to the outer membrane.All Gram-negative (4,10,11). Third, because all of these proteins are located in the outer membrane, there may be a common "signal" for their translocation. Various observations suggest that if such a signal were present, it likely would be located within the sequence of the mature proteins. For example, it is known that the amino terminal "leader" sequence of the LamB precursor by itself was unable to direct the translocation to the outer membrane of another polypeptide fused to it (12). Fourth, translocation of proteins into the outer membrane could require a complex transport mechanism. It is unlikely that such a mechanism was "reinvented" for each new outer membrane protein as it evolved; therefore, many outer membrane proteins may have been derived from a common ancestral protein.Sequence homologies between E. coli outer membrane proteins have been examined before. Although strong homologies were found among three porins (OmpF, OmpC, and PhoE) (13,14), no significant homology was reported between OmpA and OmpF (15) Searches for Potentially Homologous Regions. All computer programs were written for a Tandy model I personal computer; to speed up the execution, most of the routines were written in Z80 assembly language.t Potentially homologous regions between proteins were identified by a two-step process. (i) Initially, regions of potential homology were searched for by comparisons of short segments without the creation of gaps. Thus, the program compared all possible short segments (e.g., containing seven amino acid residues) from one protein with all or a limited subset of segments of the same length from the second protein. If a comparison revealed a set number (e.g., four) or more of identical amino acids at corresponding positions, the matched region was analyzed further as described below.We emphasize that, for a number of reasons, the matches detected here can serve only as the starting points for the search for homology: homology of short sequences is statistically very unreliable (22); gaps may be needed for optimum alignment, but they were not introduced; and, finally, the search was performed purposefully at low degrees of stringency so as not to miss the real regions of homology. (ii) We then optimized the alignment of the more extended segments containing 11-30 amino acid residues, centered on the short segments of potential match identified above. This procedure permitted the insertion of gaps, if necessary, with a set amount of penalty ("gap penalty factor" of 2) given to the creation of each gap and also another penalty ...

Cloning and nucleotide sequence of the Pseudomonas aeruginosa glucose‐selective OprB porin gene and distribution of OprB within the family Pseudomonadaceae

“…Residues 40-60 of LamB have previously been implicated in LamB function and structure (Chan and Ferenci, 1993, and references therein) and several of the residues within this region are conserved in LamB, OmpA and OmpF, suggesting a general role in porin structure or function (Nikaido and Wu, 1984). Chan and Ferenci (1993) have performed a detailed mutagenic analysis of all the residues within this region of LamB and identified those residues important in the structure and function of this protein.…”

OmpF assembly mutants of Escherichia coli K-12: isolation, characterization, and suppressor analysis

“…How then are outer membrane proteins, which have no obvious mature sequence homology, targeted to the same cellular compartment? The notion that there is a common sorting signal represented in the form of a linear sequence within the mature portion of outer membrane proteins has been proposed (18) but is not yet experimentally proven. It is conceivable that the sorting signal is represented in the form of a secondary or tertiary structure, which may be contained within various partially folded intermediates.…”

Effect of lipopolysaccharide structure on reactivity of antiporin monoclonal antibodies with the bacterial cell surface

“…The Escherichia coli K-12 porins OmpF, OmpC, and PhoE share extensive regions of sequence homology and some limited local homology with OmpA (23,27). E. coli B/r contains a porin that is virtually identical to OmpF, differing in only three residues; it does not have a porin analogous to OmpC (15).…”