Detection of Genes with Atypical Nucleotide Sequence in Microbial Genomes

Abstract

Type I signal peptidases (EC 3.4.21.89) are integral membrane proteins responsible for the removal of signal sequences from preproteins following protein translocation across a variety of membranes (Dalbey et al. 1997). Insight into the behavior of signal peptidase has come from the recent description of the crystal structure of the ectodomain of the Escherichia coli enzyme (Paetzel et al. 1998). In E. coli, signal peptidase is composed of two structural components, referred to as domain I and domain II. Corresponding to the “catalytic core” of the enzyme, domain I encompasses boxes A–E, five regions of significant sequence homology preserved throughout evolution (Fig. 1). Box B contains the nucleophilic Ser90 residue (E. coli numbering) and the conserved Met91 residue, while box D contains the proposed general base Lys145 and the conserved Arg146. Ser90 and Lys145 are believed to form the catalytic dyad responsible for enzyme activity (Paetzl et al. 2000). Domain II, corresponding to the stretch of amino acid residues between box D and box E (residues 154–271), folds as a large b-sheet. Sequence alignment studies of signal peptidases from various Gram-negative bacteria (Salmonella typhimurium, Pseudomonas fluorescens, Haemophilus influenzae, Bradyrhizobium japonicum, Borrelia burgdorferi, Phormidum laminosum, Azotobacter vinelandii, Rickettsia prowazekii, Thermotoga maritima, and Rhodobacter capsulatus) reveal the presence of domain II sequences containing between 39 and 152 residues. Examination of the corresponding regions of Gram-positive bacteria (Bacillus subtilis, Staphylococcus aureus, Streptococcus pneumoniae, Aquifex aeolicus, Myobacterium leprae, and Myobacterium tuberculosis) reveals the presence of smaller domain II regions. Despite their omnipresence, the role of domain II in bacterial signal peptidase activity is currently not understood. In contrast to their bacterial homologues, eukaryal signal peptidases do not contain domain II regions. Eukaryal signal peptidases also differ from their bacterial counterparts in that the eukaryal enzyme functions as part of a multisubunit signal peptidase complex (SPC). In Saccharomyces cerevisiae, this complex is comprised of the Sec11, Spc1, Spc2, and Spc3 proteins (YaDeau et al. 1991). Both Sec11 and Spc3 are required for signal sequence cleavage and indeed can be coimmunoprecipitated (Meyer and Hartmann 1997; Fang et al. 1997). While Sec11 contains the evolutionarily conserved boxes A–E sequences (Fig. 1), it has been proposed that Spc3 provides the lysine residue of the catalytic serine/lysine dyad conserved in bacteria (K145) yet absent in eukarya, where it is replaced by a conserved histidine residue. Site-directed mutagenesis of conserved and nonconserved lysine residues as well as of other selected Spc3 amino acids, however, failed to affect enzyme activity (Van Valkenburgh et al. 1999). It appears, therefore, that Correspondence to: Jerry Eichler; email: jeichler@bgumail.bgu.ac.il J Mol Evol (2002) 54:411–415 DOI: 10.1007/s00239-001-0035-8