Homologues of the protein constituents of the Klebsiella pneumoniae (Klebsiella oxytoca) type II secreton (T2S), the Pseudomonas aeruginosa type IV pilus/fimbrium biogenesis machinery (T4P) and the Methanococcus voltae flagellum biogenesis machinery (Fla) have been identified. Known constituents of these systems include (1) a major prepilin (preflagellin), (2) several minor prepilins (preflagellins), (3) a prepilin (preflagellin) peptidase/methylase, (4) an ATPase, (5) a multispanning transmembrane (TM) protein, (6) an outer-membrane secretin (lacking in Fla) and (7) several functionally uncharacterized envelope proteins. Sequence and phylogenetic analyses led to the conclusion that, although many of the protein constituents are probably homologous, extensive sequence divergence during evolution clouds this homology so that a common ancestry can be established for all three types of systems for only two constituents, the ATPase and the TM protein. Sequence divergence of the individual T2S constituents has occurred at characteristic rates, apparently without shuffling of constituents between systems. The same is probably also true for the T4P and Fla systems. The family of ATPases is much larger than the family of TM proteins, and many ATPase homologues function in capacities unrelated to those considered here. Many phylogenetic clusters of the ATPases probably exhibit uniform function. Some of these have a corresponding TM protein homologue although others probably function without one. It is further shown that proteins that compose the different phylogenetic clusters in both the ATPase and the TM protein families exhibit unique structural characteristics that are of probable functional significance. The TM proteins are shown to have arisen by at least two dissimilar intragenic duplication events, one in the bacterial kingdom and one in the archaeal kingdom. The archaeal TM proteins are twice as large as the bacterial TM proteins, suggesting an oligomeric structure for the latter. OverviewThree related types of prokaryotic envelope protein complexes include (putative) prepilin proteins with highly similar hydrophobic N-terminal segments of approximately 20 amino acyl residues. These putative prepilins can assemble into filamentous structures which compose parts of (1) the type II secretion system (T2S), (2) the type IV piliation/fimbriation system (T4P) (both of Gramnegative bacteria) and (3) the flagellar system (Fla) of archaea. T2S, also called the type II secreton or the main terminal branch (MTB; TC #3.A.15) of the general secretory pathway (TC #3.A.5;Cao & Saier, 2003), represents the major pathway for exoprotein transport from the periplasm across the outer membrane in a wide variety of Gramnegative bacteria (Pugsley, 1993a). The type II secreton is composed of a core of around 12 proteins, some of which are not present in all type II secretons and others of which appear to be dispensable for secreton function Pugsley, 1993a;Sandkvist, 2001). In this review, secreton components will be referred to accordi...
Previous studies have suggested that the transcription factor CcpA, as well as the coeffectors HPr and Crh, both phosphorylated by the HprK kinase/phosphorylase, are primary mediators of catabolite repression and catabolite activation in Bacillus subtilis. We here report whole transcriptome analyses that characterize glucosedependent gene expression in wild-type cells and in isogenic mutants lacking CcpA, HprK, or the HprK phosphorylatable serine in HPr. Binding site identification revealed which genes are likely to be primarily or secondarily regulated by CcpA. Most genes subject to CcpA-dependent regulation are regulated fully by HprK and partially by serine-phosphorylated HPr [HPr(Ser-P)]. A positive linear correlation was noted between the dependencies of catabolite-repressible gene expression on CcpA and HprK, but no such relationship was observed for catabolite-activated genes, suggesting that large numbers of the latter genes are not regulated by the CcpA-HPr(Ser-P) complex. Many genes that mediate nitrogen or phosphorus metabolism as well as those that function in stress responses proved to be subject to CcpA-dependent glucose control. While nitrogenmetabolic genes may be subject to either glucose repression or activation, depending on the gene, almost all glucose-responsive phosphorus-metabolic genes exhibit activation while almost all glucose-responsive stress genes show repression. These responses are discussed from physiological standpoints. These studies expand our appreciation of CcpA-mediated catabolite control and provide insight into potential interregulon control mechanisms in gram-positive bacteria.
SugE of Escherichia coli, first identified as a suppressor of groEL mutations but a member of the small multidrug resistance family, has not previously been shown to confer a drug resistance phenotype. We show that high-level expression of sugE leads to resistance to a subset of toxic quaternary ammonium compounds.
Sequence analysis upstream from the subtilin structural gene (spaS) puter Group (University of Wisconsin) program package. The best homologies were found with the deduced SpaB protein sequence, which showed extensive homologies to a variety of membrane translocator proteins, such as the HlyB protein, which is involved with export of the hemolysin A protein (hemolysin toxin) in E. coli (6). The homologies between SpaB and HlyB are shown in Fig. 3. Included in the regions of homology are five transmembrane helices and an ATP-binding region. The HlyB protein has previously been shown to have homologies to many different membrane translocators, including human and other mammalian proteins involved with multidrug resistance (3). As would be expected, the SpaB protein also shows homologies to these proteins (data not shown).spaB and spaC have overlapping reading frames. The overlap shown for the SpaB and SpaC ORFs (Fig. 2) is unusual in prokaryotes. The overlapping region contains a sequence that could act as a ribosome binding site for spaC, but it also has characteristics of a frameshift sequence (see the legend to Fig. 2 (Fig. 3). One involves a 30-residue region located about 12 residues from the N terminus of SpaD and a region located about 15 residues from the C terminus of HlyD. The second homology was between a 45-residue region in the
Integral membrane proteins from over 20 ubiquitous families of channels, secondary carriers, and primary active transporters were analyzed for average size differences between homologues from the three domains of life: Bacteria, Archaea, and Eucarya. The results showed that while eucaryotic homologues are consistently larger than their bacterial counterparts, archaeal homologues are significantly smaller. These size differences proved to be due primarily to variations in the sizes of hydrophilic domains localized to the N termini, the C termini, or specific loops between transmembrane ␣-helical spanners, depending on the family. Within the Eucarya domain, plant homologues proved to be substantially smaller than their animal and fungal counterparts. By contrast, extracytoplasmic receptors of ABC-type uptake systems in Archaea proved to be larger on average than those of their bacterial homologues, while cytoplasmic enzymes from different organisms exhibited little or no significant size differences. These observations presumably reflect evolutionary pressure and molecular mechanisms that must have been operative since these groups of organisms diverged from each other.
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