Biogenesis of E. coli Pap pili: papH, a minor pilin subunit involved in cell anchoring and length modulation

The biogenesis of Escherichia coli Pap pili, encoded by the pap gene cluster, was studied. A novel gene, papH, was identified and found to encode a weakly expressed pilin-like protein. PapH was dispensable for digalactoside-specific binding and for formation of Pap pili. However, in papH deletion mutants 50%-70% of total pilus antigen was found free of the cells. We present evidence showing coregulation of papH and the adjacent gene, papA, which encodes the major pilin subunit. A decrease in the PapA to PapH ratio resulted in a large fraction of cells producing shortened pili, whereas overproduction of PapA relative to PapH resulted in cells with lengthened pili. The data show that PapH has roles in anchoring the pilus to the cell and in modulating pilus length.     

Crystal structure of the P pilus rod subunit PapA

P pili are important adhesive fibres involved in kidney infection by uropathogenic Escherichia coli strains. P pili are assembled by the conserved chaperone-usher pathway, which involves the PapD chaperone and the PapC usher. During pilus assembly, subunits are incorporated into the growing fiber via the donor-strand exchange (DSE) mechanism, whereby the chaperone's G1 beta-strand that complements the incomplete immunoglobulin-fold of each subunit is displaced by the N-terminal extension (Nte) of an incoming subunit. P pili comprise a helical rod, a tip fibrillum, and an adhesin at the distal end. PapA is the rod subunit and is assembled into a superhelical right-handed structure. Here, we have solved the structure of a ternary complex of PapD bound to PapA through donor-strand complementation, itself bound to another PapA subunit through DSE. This structure provides insight into the structural basis of the DSE reaction involving this important pilus subunit. Using gel filtration chromatography and electron microscopy on a number of PapA Nte mutants, we establish that PapA differs in its mode of assembly compared with other Pap subunits, involving a much larger Nte that encompasses not only the DSE region of the Nte but also the region N-terminal to it.     

Mitochondrial import of cytochrome c oxidase subunit VIIa in Saccharomyces cerevisiae. Identification of sequences required for mitochondrial localization in vivo

Subunit VIIa of yeast cytochrome c oxidase is a small (59 amino acids) protein of the inner mitochondrial membrane that lacks a cleavable amino-terminal presequence. To identify regions within this polypeptide that are essential for its import, gene fusions were constructed using a leader peptide substitution vector (pLPS) developed in this laboratory (Glaser, S. M., Trueblood, C. E., Dircks, L. K., Poyton, R. O., and Cumsky, M. G. (1988) J. Cell. Biochem. 36, 275-287). In this vector, oligonucleotide sequences encoding all or part of subunit VIIa were fused in-frame with the coding region of mature cytochrome c oxidase subunit Va. The plasmid pLPS is ideal for assaying protein sequences for their ability to direct mitochondrial import in vivo since subunit Va's leader peptide is essential for import and because subunit V is required for cytochrome c oxidase activity and respiration. Strains containing these fusions but lacking both subunit V genes (COX5a and COX5b) were analyzed to determine whether the chimeric protein is directed to mitochondria. Our findings indicate that the amino-terminal 17 amino acids of subunit VIIa are sufficient to localize subunit Va to the mitochondrion and that a 6-amino acid-long region within the amino terminus (Gly8-Arg13) is essential. In addition, some import (approximately 10% of wild type) is observed with the highly charged carboxyl terminus of subunit VIIa, suggesting that the subunit may contain redundancy in its import information.     

New tools in an old trade: CS1 pilus morphogenesis

CS1 pili serve as the prototype for a large class of serologically distinct pili associated with enterotoxigenic Escherichia coli that cause diarrhoea in humans. The four genes essential for CS1 pilus morphogenesis, cooB, A, C and D, are arranged in an operon and encode structural and assembly proteins unlike those of other pilus systems commonly associated with Gram-negative bacteria. CS1 pili are composed primarily of the major pilin subunit, CooA, which determines the serological type of the pilus. The major pilin subunit is assembled into pili by the proteins CooB, CooC and CooD. CooD is both a minor component found at the pilus tip and an essential assembly protein, whereas CooC is an outer membrane protein thought to be involved in pilin transport. CooB is a novel periplasmic chaperone-like protein that forms intermolecular complexes with and stabilizes the major and minor pilins. Unlike other pilin chaperones, CooB also stabilizes the outer membrane component of the assembly system, CooC. The proteins of CS1 pili have no significant homology to those of the well-characterized Pap (pyelonephritis-associated) pili and related systems, although most of the features of pilus morphogenesis are similar. Therefore, these appear to be among the rare cases of convergent evolution. Thus, for CS1 pili, enterotoxigenic E. coli use new protein 'tools' in the old 'trade' of forming functional pili.     

A single-step isolation of K99 pili from B-44 strain of Escherichia coli

A single-step procedure has been developed to isolate pili from enterotoxigenic Escherichia coli strain B44 of calf origin. Pili, removed from the bacteria by heat shock treatment, were allowed to aggregate at 4 degrees C for 16 h. The precipitated pili, isolated by centrifugation, had typical pili morphology as shown by electron microscopy; ability to bind pig brush border; molecular weight greater than 6 million; and predominance of hydrophobic amino acids. On sodium dodecyl sulfate gel electrophoresis, the subunit pilin migrated as a single polypeptide of molecular weight 17,000.     

Biochemical studies on pili isolated from Pseudomonas aeruginosa strain PAO.

Pseudomonas aeruginosa strains PAO and PAK bear polar pili which are flexible filaments having a diameter of 6 nm and an average length of 2500 nm. Both types of pili are retractile and promote infection by a number of bacteriophages. The present communication describes the partial biochemical characterization of PAO pili isolated from a multipiliated nonretractile mutant of PAO. The observed properties are compared to those of PAK pili which were characterized previously. PAO pili were found to contain a single polypeptide subunit of 18 700 daltons. This is similar to PAK pili which contain a single polypeptide of 18 100 daltons. The amino acid composition of PAO pilin was also similar to that of PAK pilin. Neither protein contained phosphate or carbohydrate residues and both were found to contain N-methylphenylalanine at the amino terminus. Sequencing of 20 amino acid residues at the amino terminal end of PAO pilin revealed the sequence to be identical with that of PAK pilin, while tryptic peptide analyses of PAO and PAK pilin indicated that the two proteins probably contain a number of homologous regions within the polypeptide. It was concluded that PAO and PAK pili were closely related structures.     

Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the beta subunit of Escherichia coli RNA polymerase.

We have mapped principal sites in the Escherichia coli RNA polymerase molecule that are exposed to attack by trypsin under limited proteolysis conditions. The 1342-amino acid-long beta subunit is alternatively cleaved at Arg903 or Lys909. The cleavage occurs adjacent to a dispensable domain (residues 940-1040) that is absent in the homologous RNA polymerase subunits from chloroplasts, eukaryotes, and archaebacteria. In E. coli, this region can be disrupted with genetic deletions and insertions without the loss of RNA polymerase function. Insertion of 127 amino acids into this region introduces a new highly labile site for trypsin proteolysis. The dispensable domain carries the epitope for monoclonal antibody PYN-6 (near residue 1000), which can be used for anchoring the catalytically active enzyme on a solid support. We also report the identification of a secondary trypsin cleavage at Arg81 of the beta' subunit within a putative zinc-binding domain that is conserved in prokaryotes and chloroplasts.     

Human and mouse mitochondrial orthologs of bacterial ClpX

We have determined the cDNA sequence and exon/intron structure of the human CLPX gene encoding a human ortholog of the E. coli ClpX chaperone and protease subunit. The CLPX gene comprises 14 exons and encodes a 633-amino acid-long precursor polypeptide. The polypeptide contains an N-terminal putative mitochondrial transit peptide, and expression of a full-length ClpX cDNA tagged at its C-terminus (Myc-His) shows that the polypeptide is transported into mitochondria. FISH analysis localized the CLPX gene to human Chromosome (Chr) 15q22.1-22.32. This localization was refined by radiation hybrid mapping placing the CLPX gene 4.6 cR distal to D15S159. Murine ClpX cDNA was sequenced, and the mouse Clpx locus was mapped to a position between 31 and 42 cM offset from the centromere on mouse Chr 9. Experimental observations indicate the presence of a pseudogene in the mouse genome and sequence variability between mouse ClpX cDNAs from different strains. Alignment of the human and mouse ClpX amino acid sequences with ClpX sequences from other organisms shows that they display the typical modular organization of domains with one AAA⁺ domain common to a large group of ATPases and several other domains conserved in ClpX orthologs linked by non-conserved sequences. Notably, a C-4 zinc finger type motif is recognized in human and mouse ClpX. This motif of so far unknown function is present only in a subset of the known ClpX sequences. Received: 5 April 2000 / Accepted: 14 June 2000     

Purification of pili from Bacteroides nodosus and an examination of their chemical, physical and serological properties.

Pili from Bacteroides nodosus were purified to greater than 99% homogeneity by precipitation at pH 4.0 and in MgCl2 followed by chromatography on BioGel A150. The pili were composed entirely of one type of polypeptide subunit, pilin. No carbohydrates, nucleic acid, lipid, lipopolysaccharide or phosphate could be detected in purified pili preparations. The molecular weight of pilin from B. nodosus strains 91B and 198 was 18,400 and from strain 80 was 19,300. The isoelectric points of pili from B. nodosus strains 91B and 80 were both 4.5. The buoyant densities of pili from strains 91B, 80 and 198 were 1.287, 1.284 and 1.286 g ml-1, respectively. The three strains of B. nodosus did not cross-react in K-agglutination tests and produced pili which did not cross-react in immunodiffusion tests. Antiserum to highly purified pili caused a characteristic K-type agglutination reaction. It was concluded that pili are the K-agglutinogen.     

Assembly proteins of CS1 pili of enterotoxigenic Escherichia coli

Some strains of enterotoxigenic Escherichia coli associated with human diarrhoeal disease produce a class of pili represented by those called CS1. For the assembly of the major-pilin subunit, CooA, into pili, each of four linked genes, cooB,A,C, and D, is required. In this study, we have determined the subcellular localization of CooB, C and D, and investigated the molecular interactions of these proteins using specific antisera. CooD appears to be an integral pilus protein because it co-purifies with, and is strongly associated with, CS1 pili. In keeping with its role as an assembly protein, the CooD minor pilin (when overexpressed in CS1-piliated strains) was detected in periplasmic inter-molecular complexes with the major-pilin subunit CooA. CooB is an assembly protein found exclusively in the periplasm of CS1-piliated strains. CooB also forms periplasmic intermolecular complexes with CooA, but does not constitute part of the final pilus structure. Immunoblot analysis of cell fractions showed that CooC is an outer membrane protein of CS1-piliated E. coli. Based on this information, we have proposed a model for CS1 -pilus assembly which is very similar to the model for polymerization of the PapA pilin of uropathogenic E. coli. As the assembly proteins of Pap and CS1 pili are structurally unrelated, this may represent a case of convergent evolution.     

A human polyadenylation factor is a G protein beta-subunit homologue.

Cleavage stimulation factor (CstF) is one of the multiple factors required for polyadenylation of mammalian pre-mRNAs in vitro. We have shown previously that this factor is composed of three distinct subunits of 77, 64, and 50 kDa, and that the 64-kDa subunit can be UV-cross-linked to RNA in a polyadenylation signal (AAUAAA)-dependent manner. By molecular cloning, the 64-kDa subunit was shown to contain a ribonucleoprotein-type RNA binding domain and a novel repeat structure. To study the functions of the other subunits, we have now isolated cDNAs encoding the 50-kDa subunit of human CstF. This subunit shares extensive homology with mammalian G protein beta-subunits and has a characteristic repeat structure (transducin repeat), in which an approximately 44-amino acid-long sequence is repeated seven times. To our knowledge, the 50-kDa subunit is the first example of a functional beta-subunit-like protein in vertebrates. Possible roles of the transducin repeat, both in CstF function specifically and in other beta-subunit homologues more generally, are discussed.     

Composition and molecular weight of pili purified from Pseudomonas aeruginosa K.

Pseudomonas aeruginosa strain K (PAK) bears polar pili that promote infection by at least six bacteriophages. Moreover, a recently isolated mutant of strain K (PAK/2PfS) is many times more piliated than the wild-type strain and facilitates the preparation of large amounts of pure pili for biochemical studies. The present investigation was carried out to establish the structural relatedness of PAK and PAK/2PfS pili and to determine their biochemical composition. A purfication procedure is described for PAK and PAK/2PfS pili that yields about 8 mg of pure pili per 100 g (wet weight) of PAK/2PfS cells and 0.8 mg of pure pili per 100 g (wet weight) of PAK cells. PAK and PAK/2PfS pili were found to be free from phosphate, carbohydrate, and lipid and to contain a single polypeptide subunit of 17,800 daltons. Isopycnic centrifugation studies revealed that PAK and PAK(2PfS pili have the same buoyant density in sucrose (1.221) and CsC1 (1.295). Both types of pili banded at pH 3.9 when subjected to isoelectric focusing. Amino acid analyses showed that PAK and PAK/2PfS pili have identical amino acid compositions, whereas microimmunodiffusion studies revealed that the two types of pili are immunologically indistinguishable. It was concluded that PAK and PAK/2PfS pili are identical and that the mutation responsible for producing the multipiliated state in PAK/2PfS is probably located outside the structural gene for PAK pili.     

Genes of pyelonephritogenic E. coli required for digalactoside-specific agglutination of human cells.

Most pyelonephritic Escherichia coli strains bind to digalactoside-containing glycolipids on uroepithelial cells. Purified Pap pili (pili associated with pyelonephritis) show the same binding specificity. A non-polar mutation early in the papA pilin gene abolishes formation of Pap pili but does not affect the degree of digalactoside-specific hemagglutination. Three novel pap genes, papE , papF and papG are defined in this report. The papF and papG gene products are both required for digalactoside-specific agglutination by whole bacteria cells as well as for agglutination by pilus preparations. Pili prepared from a papE mutant have lost their binding ability although whole cells from this mutant retain it, implying an adhesin anchoring role for the papE gene product. A mutant with lesions both in the papA and the papE genes does not mediate digalactoside-specific agglutination. The implications of this finding for pilus biogenesis are discussed.     

Molecular cloning and tissue-specific expression of a novel murine laminin gamma3 chain.

A novel laminin gamma3 chain was identified from the expressed sequence tag data base at the National Center for Biotechnology Information. A complete cDNAderived peptide sequence reveals a 1592-amino acid-long primary translation product, including a tentative 33-amino acid-long signal peptide. Comparison with the laminin gamma1 chain predicts that the two polypeptides have equal spatial dimensions. In addition, the well conserved domains VI and III(LE4) predict that gamma3 containing laminins are able to integrate to the laminin network and also via nidogen connect to other protein networks in the basement membranes. Combination of Northern analysis and in situ hybridization experiments indicate that expression of the gamma3 chain is highly tissue- and cell-specific, being significantly strong in capillaries and arterioles of kidney as well as in interstitial Leydig cells of testis.     

Mechanism of fibre assembly through the chaperone-usher pathway

The chaperone-usher pathway directs the formation of adhesive surface fibres in numerous pathogenic Gram-negative bacteria. The fibres or pili consist exclusively of protein subunits that, before assembly, form transient complexes with a chaperone in the periplasm. In these chaperone:subunit complexes, the chaperone donates one beta-strand to complete the imperfect immunoglobulin-like fold of the subunit. During pilus assembly, the chaperone is replaced by a polypeptide extension of another subunit in a process termed 'donor strand exchange' (DSE). Here we show that DSE occurs in a concerted reaction in which a chaperone-bound acceptor subunit is attacked by another chaperone-bound donor subunit. We provide evidence that efficient DSE requires interactions between the reacting subunits in addition to those involving the attacking donor strand. Our results indicate that the pilus assembly platforms in the outer membrane, referred to as ushers, catalyse fibre formation by increasing the effective concentrations of donor and acceptor subunits.     

Nucleotide sequence, regulation and functional analysis of the papC gene required for cell surface localization of Pap pili of uropathogenic Escherichia coli

The papC gene of uropathogenic Escherichia coli is required for the formation of digalactoside-binding Pap pili. papC forms part of an operon wherein the regulatory gene papB, the major pilin gene papA, a minor pilin-like gene papH, and papC are co-transcribed. Furthermore, the extent of PapC synthesis was found to affect the number of pili expressed on the cell surface. The DNA sequence of the papC gene is presented and its deduced amino acid sequence is compared to that of the FaeD protein encoded by the K88 pili gene cluster. The PapC protein was localized to the E. coli outer membrane where it may form a trans-membrane channel through which pilin subunits are surface localized.     

Myeloperoxidase precursors incorporate heme

Myeloperoxidase of neutrophil granulocytes is synthesized as a larger molecular weight precursor, which is processed to yield mature polypeptides with molecular weights of 62,000 and 12,000. We have investigated the incorporation of heme into myeloperoxidase of the human promyelocytic HL-60 cell line labeled with 5-amino[14C]levulinic acid. Myeloperoxidase was isolated by immunoprecipitation followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and radiolabeled myeloperoxidase was visualized by fluorography. A 3-h pulse labeling with 5-amino[14C]levulinic acid resulted in labeling of the Mr 90,000 and Mr 82,000 precursor polypeptides. During subsequent chase of the label, conversion to mature radioactive heavy Mr 62,000 subunit was observed but no radioactivity was associated with the mature small Mr 12,000 subunit. Peptide mapping after proteolytic cleavage with V8 proteinase showed that 5-amino[14C]levulinic acid was associated with a single Mr 23,000 polypeptide while multiple radioactive fragments were visible after proteolytic cleavage of myeloperoxidase biosynthetically labeled with [14C]leucine. That 5-amino[14C]levulinic acid was specifically incorporated into heme of myeloperoxidase was also demonstrated by dissociation under reducing conditions which yielded 14C-labeled heme as indicated by reversed phase high pressure liquid chromatography. The ionophore monensin and the base chloroquine, which block processing of myeloperoxidase, did not affect the incorporation of 5-amino[14C]levulinic acid, further supporting the notion that the incorporation of heme is independent of final processing of the polypeptide. Our data establish that heme is incorporated into myeloperoxidase already at the level of the precursor and that processing yields a heme-containing heavy subunit and a heme-free small subunit.     

The role of chaperone-subunit usher domain interactions in the mechanism of bacterial pilus biogenesis revealed by ESI-MS

The PapC usher is a β-barrel outer membrane protein essential for assembly and secretion of P pili that are required for adhesion of pathogenic E. coli, which cause the development of pyelonephritis. Multiple protein subunits form the P pilus, the highly specific assembly of which is coordinated by the usher. Despite a wealth of structural knowledge, how the usher catalyzes subunit polymerization and orchestrates a correct and functional order of subunit assembly remain unclear. Here, the ability of the soluble N-terminal (UsherN), C-terminal (UsherC2), and Plug (UsherP) domains of the usher to bind different chaperone-subunit (PapDPapX) complexes is investigated using noncovalent electrospray ionization mass spectrometry. The results reveal that each usher domain is able to bind all six PapDPapX complexes, consistent with an active role of all three usher domains in pilus biogenesis. Using collision induced dissociation, combined with competition binding experiments and dissection of the adhesin subunit, PapG, into separate pilin and adhesin domains, the results reveal why PapG has a uniquely high affinity for the usher, which is consistent with this subunit always being displayed at the pilus tip. In addition, we show how the different soluble usher domains cooperate to coordinate and control efficient pilus assembly at the usher platform. As well as providing new information about the protein-protein interactions that determine pilus biogenesis, the results highlight the power of noncovalent MS to interrogate biological mechanisms, especially in complex mixtures of species.