Taxonomic comparison of the amino termini of microbial cell proteins

Integration of Multidimensional Chromatographic Protein Separations with a Combined “Top-Down” and “Bottom-Up” Proteomic Strategy

In this paper, we present a combined top-down/bottom-up proteomic analysis workflow for the characterization of proteomic samples. This workflow combines protein fractionation (multidimensional chromatographic separation) with parallel online ESI-TOF-MS intact protein analysis, and fraction collection. Collected fractions were digested and protein identifications were produced using MALDI Q-TOF-MS analysis. These identifications were then linked with corresponding ESI-TOF-MS intact protein mass data to permit full protein characterization. This methodology was applied to an E. coli cytosolic protein fraction, and enabled the identification and characterization of proteins exhibiting co-translational processing, post-translational modification, and proteolytic processing events. The approach also provided the ability to distinguish between closely related protein isoforms. The summary of results from this study indicated that roughly one-third of all detected components generated corresponding data from both top-down and bottom-up analyses, and that significant and novel information can be derived from this application of the hybrid analytical methodology.

Mapping of Chlamydia trachomatis proteins by immobiline-polyacrylamide two-dimensional electrophoresis: spot identification by N-terminal sequencing and immunoblotting

Proteins from purified elementary bodies of Chlamydia trachomatis were separated by two-dimensional gel electrophoresis on nonlinear wide-range immobilized pH gradients in the first dimension and polyacrylamide gradient gels in the second dimension. The maps obtained with this system are highly reproducible and resolve ca. 600 spots. By using immunoblot analysis with specific antibodies and/or N-terminal amino acid sequencing, we established the map positions of a number of described chlamydial proteins, such as the major outer membrane protein (MOMP) the 60 kDa cystein-rich outer membrane protein (OMP2), the DnaK-like, GroEL-like, and macrophage infectivity potentiator (MIP)-like proteins, the plasmid-encoded pgp3 protein, two ribosomal proteins (S1 and L7/L12), and the protein-elongation factor EF-Tu. Other proteins, for which gene assignment was not possible, have been identified by three parameters (Mr, pI and N-terminal sequence). This work provides a preliminary basis for a future and progressive compilation of a genome-linked database of chlamydial proteins.

Humoral immune response to plasmid protein pgp3 in patients with Chlamydia trachomatis infection

We identified, by two-dimensional electrophoretic analysis and microsequencing, a protein of Chlamydia trachomatis elementary bodies which corresponds to the polypeptide (pgp3) encoded by open reading frame 3 (ORF3). Amino acid analysis showed that the first residue (Gly) found in the native protein is the one encoded by the second ORF3 codon, implying a typical bacterial removal of the first Met residue. Relatively large amounts of recombinant pgp3 (r-pgp3) in a stable, water-soluble form were obtained by overexpressing ORF3 in Escherichia coli and purifying the product from periplasmic extracts under nondenaturing conditions. These r-pgp3 preparations allowed specific detection of anti-pgp3 antibodies by enzyme-linked immunosorbent assay. Analysis of a group of 170 sera from healthy blood donors and from patients who were seropositive or -negative for C. trachomatis and Chlamydia pneumoniae showed that an immune response to pgp3 occurs in the majority (ca. 81%) of patients with sexually transmitted diseases who are seropositive for C. trachomatis and generally correlates with the response to cell surface antigens. No reaction between r-pgp3 and C. pneumoniae-positive sera was detected.

Molecular analysis of the Alcaligenes eutrophus poly(3-hydroxybutyrate) biosynthetic operon: identification of the N terminus of poly(3-hydroxybutyrate) synthase and identification of the promoter

Molecular methods have been applied to analyze the expression of the Alcaligenes eutrophus poly(3-hydroxybutyrate) (PHB) synthase gene (phbC). The translational initiation codon was identified by analysis of the amino acid sequence of a PHB synthase-beta-galactosidase fusion protein. This protein was purified to almost gel electrophoretic homogeneity by chromatography on DEAE-Sephacel and on aminophenyl-beta-D-thiogalactopyranoside-Sepharose from cells of A. eutrophus which harbored a phbC'-'lacZ fusion gene. A sequence (TTGACA-18N-AACAAT), exhibiting striking homology to the Escherichia coli sigma 70 promoter consensus sequence, was identified approximately 310 bp 5' upstream from the translation initiation codon. An S1 nuclease protection assay mapped the transcription start point of phbC 6 bp downstream from this promoter. The location of the promoter was confirmed by analyzing the expression of active PHB synthase in clones of E. coli harboring 5' upstream deletions of phbC ligated to the promoter of the lacZ gene (lacZp) in a Bluescript vector. Plasmids do181 and do218, which were deleted for the first 108 or 300 bp of the phbC structural gene, respectively, conferred the ability to synthesize large amounts of different truncated PHB synthase proteins to the cells. These proteins contributed to approximately 10% of the total cellular protein as estimated from sodium dodecyl sulfate-polyacrylamide gels. The modified PHB synthase encoded by plasmid do181 was still active. Clones in which the lacZp-'phbC fusion harbored the complete phbC structural gene plus the phbC ribosome binding site did not overexpress PHB synthase.

Characterization of alcohol dehydrogenase genes of derepressible wild-type Alcaligenes eutrophus H16 and constitutive mutants

The nucleotide sequence of the gene that encodes the fermentative, derepressible alcohol dehydrogenase (ADH) in Alcaligenes eutrophus H16 and of adjacent regions was recently determined. Two potential -10 regions resembling the Escherichia coli sigma 70 consensus sequence were identified 77 and 93 nucleotides upstream of the structural gene. By determination of the 5' mRNA terminus of the wild-type adh gene, the proximal -10 region was identified as responsible for adh expression under derepressive conditions. Transcription started seven nucleotides downstream of this region, at position 388. Sequence analysis of seven mutants expressing the adh gene under aerobic conditions revealed mutations in one or the other potential -10 region. In all seven strains, the mutations restored the invariant T of the E. coli promoter consensus sequence. Mutants altered in the proximal -10 region transcribed the adh gene under aerobic conditions with the same 5' mRNA terminus as in the wild type; gene expression was impaired very little under aerobic conditions. Mutants altered in the distal -10 region also transcribed the adh gene aerobically but were still partially derepressible. The 5' mRNA terminus was seven nucleotides downstream of the distal -10 region, at position 372. When these mutants were cultivated under conditions of restricted oxygen supply, the adh gene was transcribed from both -10 regions, resulting in the synthesis of two mRNA species with different 5' termini.

N-terminal methionine-specific peptidase in Salmonella typhimurium

Crude extracts of a multiply peptidase-deficient strain of Salmonella typhimurium contain an aminopeptidase that specifically removes N-terminal methionine from peptides. This activity shows pronounced specificity for the peptide's second amino acid. Methionine is removed from peptides with alanine, threonine, or glycine in this position but not when the second amino acid is leucine or methionine. The activity is stimulated by Co2+ and is inhibited by EDTA. Mutations that lead to overproduction (up to 30-fold) of the activity have been obtained by selecting for growth on Met-Gly-Gly as a methionine source. These mutations map at approximately 3 map units, phage P22 cotransducible with leu. The overproducer mutations are dominant to wild type, and duplication of the wild-type allele of the locus leads to a gene dosage effect on peptidase levels. This suggests that the locus of the overproducer mutations may be the structural gene for the peptidase. NaDodSO4/PAGE shows an increased level of a single protein (34 kDa) in the overproducer mutant. This protein is highly enriched in a purified preparation of the peptidase. The specificity of this enzyme suggests that it is involved in the cleavage of methionine from newly synthesized peptide chains. This activity can specifically remove methionine from the N terminus of a completed protein. Treatment of purified, unprocessed (N-terminal methionine) interleukin 1 beta with the purified peptidase results in removal of N-terminal methionine with no additional alterations. N-terminal processing of at least this protein can occur after translation is complete. We propose to call this enzyme peptidase M (methionine-specific aminopeptidase).

NH2-terminal amino acid distribution and amino acid composition of Streptococcus faecalis R soluble and ribosomal proteins

The NH(2)-terminal amino acid distribution of Streptococcus faecalis R soluble and ribosomal proteins isolated from cells at different stages of growth on either folate-sufficient or folate-deficient medium was determined by the dinitrophenyl method. The NH(2)-terminal residues do not follow the random distribution observed for the total amino acid composition of S. faecalis soluble and ribosomal proteins. Methionine and alanine occur most frequently; serine, threonine, aspartic and glutamic acids, and glycine are also present at the NH(2)-terminal position of S. faecalis R proteins. The absence of folic acid yields cells that are incapable of formylating methionyl-transfer ribonucelic acid tRNA(f) (Met), but does not affect either the qualitative or quantitative NH(2)-terminal distribution of total soluble or total ribosomal proteins compared to cells grown with folate. A small quantitative difference was observed in the frequency of distribution of certain amino acids at the NH(2)-termini between log and stationary phase soluble proteins. The amino acid residues found at the NH(2)-terminal position of S. faecalis proteins are qualitatively similar to those reported for several other organisms.

NH 2 -terminal residues of Neurospora crassa proteins

The NH(2)-terminal amino acid composition of the soluble and ribosomal proteins from Neurospora crassa mycelia and conidia was determined by the dinitrophenyl method. A nonrandom distribution of NH(2)-terminal amino acids was observed in the complex protein mixtures. Glycine, alanine, and serine accounted for 75% of the NH(2)-terminal amino acids, and glycine appeared most frequently in mature proteins of mycelia. The appearance of phenylalanine as one of the major NH(2)-termini in crude conidial fraction suggests that the composition of proteins may vary in different developmental stages.