Deduced Peptide Sequence Research Articles

Isolation of an extracellular protease gene of Erwinia carotovora subsp. carotovora strain SCC3193 by transposon mutagenesis and the role of protease in phytopathogenicity.

Using mini-Tn5CmR::gusA, a transposon that allows transcriptional fusions to a promoterless beta-glucuronidase gene, a mutant of Erwinia carotovora subsp. carotovora SCC3193 deficient in extracellular protease production and soft-rot pathogenicity in plants was isolated. The mutant, designated SCC6004, produced normal levels of pectate lyase, polygalacturonase and cellulase. The region of the transposon insertion was partially sequenced to permit the design of specific oligonucleotide primers to amplify a 2.7 kb Clal fragment from E. carotovora subsp. carotovora SCC3193. The DNA sequence of the cloned fragment contained two complete and one partial ORFs. One of the complete ORFs (ORF1) was designated prtW and encodes a secreted protease. The deduced amino acid sequence of PrtW showed a high overall identify of 60-66% to the previously described Erwinia chrysanthemi proteases, but no homology to other proteases isolated from different E. carotovora strains. Downstream from ORF1, a further complete ORF (ORF2) and a partial ORF (ORF3) were found, with deduced peptide sequences that have significant similarity to the Inh and PrtD proteins, respectively, from E. chrysanthemi, which are involved in protease secretion. Gene fusion to the gusA reporter was employed to charaterize the regulation of prtW. The prtW gene was found to be strongly induced in the presence of plant extracts. The mutant exhibited reduced virulence, suggesting that PrtW enhances the ability of strain SCC3193 to macerate plant tissue.

Two novel Xenopus frizzled genes expressed in developing heart and brain

A family of genes related to the Drosophila wingless receptor frizzled have been found in vertebrates. We have cloned full length cDNAs of two novel frizzled genes from embryonic Xenopus tissue. We are calling them X fz7 and X fz9 (for Xenopus fri zzled) because their deduced peptide sequences show extensive similarity to other vertebrate frizzled molecules. X fz7 is closely related to human, chick and mouse frz-7 and X fz9 is most related to human FZD9 and mouse fzd9. X fz7 is expressed in a broad, complex and dynamic pattern beginning at gastrulation. At later stages X fz7 expression is found in neural crest, neural tube, eye, pronephric duct and the heart. X fz9 expression in contrast is more restricted to the neuroectoderm and, at later stages of development, to the dorsal regions of the mid- and hindbrain.

Purification of Tomato Sucrose Synthase Phosphorylated Isoforms by Fe(III)-Immobilized Metal Affinity Chromatography

The major phosphorylation site of maize sucrose synthase (SuSy) is well conserved among plant species but absent in the deduced peptide sequence of the tomato SuSy cDNA (TOMSSF). In this study, we report thein vitrophosphorylation of 25-day-old tomato fruits SuSy on seryl residue(s) by an endogenous Ca2+-dependent protein kinase activity. Two distinct32P-labeled peptides detected in the tryptic peptide map ofin vitro32P-radiolabeled tomato fruit SuSy were purified. Amino acid sequencing and phosphoamino acid analysis of the major32P-labeled peptide revealed the presence of a SuSy isozyme in young tomato fruit having the N-terminus phosphorylation site present in other plant species. By using Fe(III)-immobilized metal affinity chromatography [Fe(III)-IMAC] as a final purification step of tomato fruit SuSy, two32P-labeled tomato SuSy isoforms were separated from a nonradiolabeled SuSy fraction by using a pH gradient. The major32P-SuSy isoform was phosphorylated exclusively at the seryl residue related to the phosphorylation site of maize SuSy. The multiphosphorylated state of the second radiolabeled SuSy fraction was indicated by a higher retention during Fe(III)-IMAC and by tryptic peptide mapping analysis. Kinetic analyses of SuSy isoforms purified by Fe(III)-IMAC have revealed that phosphorylation of the major phosphorylation site of tomato fruit SuSy was not sufficient by itself to modulate tomato SuSy activity, whereas the affinity for UDP increased about threefold for the multiphosphorylated SuSy isoform.

RFLP- and physical mapping of resistance gene homologues in rice (O. sativa) and Barley (H. vulgare)

The deduced peptide sequences of 25 gene fragments of NBS-LRR resistance (R) gene homologues from rice and barley and of characterized R genes were compared, revealing a string of six conserved motifs. Mapping of the R-gene candidates in rice showed linkage to genes conferring race-specific resistance to rice blast (Pi-k, Pi-f and Pi-1) and bacterial blight disease (Xa-1, Xa-3 and Xa-4), in barley to powdery mildew (Mla) and the rust fungus (Rpg1). In rice four mixed clusters were detected, each harboring at least two highly dissimilar NBS-LRR genes. A YAC-contig was established for one of these mixed clusters. YAC fragmentation experiments revealed the presence of at least five NBS-LRR genes within 200 kb in head-to-tail orientation.

Characterization of a prolidase from Lactobacillus delbrueckii subsp. bulgaricus CNRZ 397 with an unusual regulation of biosynthesis.

Lactobacillus delbrueckii subsp. bulgaricus CNRZ 397 (Lb. bulgaricus) is characterized by a high level of peptidase activities specific to proline-containing peptides. A prolidase (PepQ, EC 3.4.13.9) was purified to homogeneity and characterized as a strict dipeptidase active on X-Pro dipeptides, except Gly-Pro and Pro-Pro. The values for Km and Vmax were, respectively, 2.2 mM and 0.33 mmol min(-1) mg(-1), with Leu-Pro as the substrate. The enzyme exhibited optimal activity at 50 degrees C and pH 6.0, and required the presence of Zn2+. Size exclusion chromatographies and SDS-PAGE analysis led to the conclusion that this prolidase was a homodimer. Antibodies raised against the purified protein allowed the detection of PepQ among several Lactobacillus species but not lactococci. The pepQ gene and the upstream region were isolated and sequenced. The deduced peptide sequence showed that PepQ belongs to the M24 family of metallopeptidases. The pepR1 gene is located immediately upstream of pepQ and its product is homologous to the transcription factor CcpA, which is involved in catabolite repression of catabolic operons from Gram-positive bacteria. The pepR1-pepQ intergenic region contains a consensus catabolite-responsive element (CRE) which could be a target for PepR1 protein. Moreover, in contrast to other proline-specific enzymes from Lb. bulgaricus, PepQ biosynthesis was shown to be dependent on the composition of the culture medium, but not on the peptide concentration. A possible regulation mechanism is discussed.

A polymorphism in the major immediate-early gene delineates groups among cytomegalovirus clinical isolates

Major immediate-early gene exon 4 sequences were determined at codons 161–241 and 254–397 in 25 cytomegalovirus clinical strains and compared with those of reference strains AD169 and Towne. The nucleotide sequences at codon 161–241 segregated into three groups which could be determined by restriction mapping of a 247-nucleotide amplified target. AD169 and Towne belonged to the same group. Clustered variations and group-specific amino-acid motifs found in the deduced peptide sequence of the two immediate-early (IE) exon 4 regions raised a question as to the effects of polymorphism on IE1 function and/or immunogenicity. On the basis of restriction analysis of polymerase chain reaction (PCR) products, virus isolates were also classified into four glycoprotein B (gB) genotypes. Strain distribution in IE1 and gB genotypes showed a lack of concordance of the two grouping methods, and no preferential association was observed between the clinical context or kind of specimen and IE1 or gB groups. These data lead up to further prospective studies which could provide important information on the implication of the MIE gene region in virus pathogenesis and indicate whether linkage unbalance exists in particular clinical contexts between IE1 and gB loci.

An extended-spectrum AmpC-type beta-lactamase obtained by in vitro antibiotic selection.

A predictive approach was assayed to evaluate the possibility of mutant Amp-C beta-lactamase emergence with increased substrate spectrum (including new C-3' quaternary ammonium cephems). The ampC gene encoding the AmpC beta-lactamase from Enterobacter cloacae was cloned and expressed in an AmpC-defective strain of E. coli. After the AmpC containing strain was challenged with cefpirome, an ampC variant encoding an enzyme with increased resistance to cefpirome and cefepime was selected. In addition, this variant conferred increased resistance to penicillins and third generation cephalosporins. The complete nucleotide sequence of the gene was determined. The deduced peptide sequence showed a single change with respect to the wild-type gene: valine to glutamic acid at position 318 of the native protein (298 of the mature enzyme). The potential emergence and spread of this type of AmpC variants among pathogens should be considered.

An extended-spectrum AmpC-type β-lactamase obtained by in vitro antibiotic selection

A predictive approach was assayed to evaluate the possibility of mutant Amp-C β-lactamase emergence with increased substrate spectrum (including new C-3′ quaternary ammonium cephems). The ampC gene encoding the AmpC β-lactamase from Enterobacter cloacae was cloned and expressed in an AmpC-defective strain of E. coli. After the AmpC containing strain was challenged with cefpirome, an ampC variant encoding an enzyme with increased resistance to cefpirome and cefepime was selected. In addition, this variant conferred increased resistance to penicillins and third generation cephalosporins. The complete nucleotide sequence of the gene was determined. The deduced peptide sequence showed a single change with respect to the wild-type gene: valine to glutamic acid at position 318 of the native protein (298 of the mature enzyme). The potential emergence and spread of this type of AmpC variants among pathogens should be considered.

Molecular cloning, expression and characterization of cDNA encoding a mouse alpha1a-adrenoceptor.

1. In this study, we have cloned, expressed, and characterized an alpha1a-adrenoceptor gene from the mouse. We designed oligonucleotide PCR primers complementary to regions of the rat alpha1a-adrenoceptor sequence and amplified cDNA fragments from total RNA of mouse cerebral cortex, liver and kidney by reverse transcription-polymerase chain reaction (RT PCR). 2. Both the nucleotide and deduced peptide sequences of the cDNA showed high sequence identity with those of cloned alpha1a-adrenoceptors from other species. The cDNA clone had an open reading frame of 1398 nucleotides encoding a 466 amino acid peptide which had 97%, 92% and 90% identity with the deduced amino acid sequences of the rat, human and bovine alpha1a-adrenoceptor, respectively. 3. The amplified mouse cDNA was inserted into a mammalian expression vector pcDNA3.1(+) and expressed in COS-1 cells. The pharmacological properties of the mouse cDNA clone were examined in radioligand binding studies and functional assays. The expressed mouse protein had a high affinity for [3H]-prazosin (Kd = 0.48 nM) and pattern of affinity for antagonists in competition studies that is similar to that of the rat alpha1a-adrenoceptor. Chloroethylclonidine (CEC) could slowly alkylate the expressed protein, with a rate similar to that of the rat alpha1a-adrenoceptor. 4. The expressed receptors were able to mediate noradrenaline (NA) stimulation of the production of inositol phosphates in COS-1 cells, consistent with coupling to phospholipase C. This response to NA could be reversed by pretreatment of the transfected cells with prazosin. 5. Based on the above evidence, we concluded that the cloned cDNA is that of the mouse alpha1a-adrenoceptor.

Functional characteristics and the complete primary structure of ascidian gelsolin

The body wall of the ascidian is composed of unusual multi-nucleated smooth muscle cells enriched with thin actin filaments containing troponin–tropomyosin which run along the longitudinal cell axis without being organized into striated structures. We purified an actin-binding protein of 80 kDa, tentatively termed 80K protein, from the body wall muscle of ascidian, Halocynthia roretzi, and characterized the functional properties and molecular structures. In the presence of Ca 2+, the 80K protein accelerated the initial phase of actin polymerization, namely the nucleation process, decreased the level of polymerization at the steady state, caused marked reduction in viscosity of an F-actin solution, and fragmented F-actin filaments, while in the absence of Ca 2+, it remained associated with F-actin without severing the filaments. The interaction of the 80K protein with actin was inhibited by phosphatidylinositol 4,5-bisphosphate (PIP 2). When actin was polymerized in the presence of acrosome actin bundles from horseshoe crab sperm, the 80K protein inhibited the growth of actin filaments at the barbed end but not at the pointed end, indicating that the 80K protein functions as a barbed-end capping protein. In order to characterize the molecular structure of the 80K protein, cDNAs encoding this protein were isolated from the λgt11 cDNA library of the ascidian muscle by using a monoclonal antibody (AS23) specific for this protein and the entire sequence was determined. The deduced peptide sequence showed about 44% homology in amino acid residues with the human gelsolin sequence, and in addition, 6 repeating segments were observed in the sequence of the 80K protein as has been described in the gelsolin sequence. These results indicate strongly that the 80K protein belongs to the gelsolin family.

CYP86A1 fromArabidopsis thalianaEncodes a Cytochrome P450-Dependent Fatty Acid Omega-Hydroxylase

TheA. thalianaEST database was screened using consensus motifs derived from P450 families CYP52 and CYP4 catalyzing the omega-hydroxylation of fatty acids and alkanes inCandidaand in mammals. One EST cDNA fragment was detected in this way and the corresponding full-length cDNA was cloned from a cDNA library ofA. thaliana.This cDNA coded the first member of a new plant P450 family and was termed CYP86A1. The deduced peptide sequence showed highest homology with P450s from families 4 and 52. To confirm the catalytic function, CYP86A1 was expressed in a yeast overexpressing its own NADPH-P450 reductase. Efficient expression was evidenced by spectrophotometry, SDS-PAGE and catalytic activity. CYP86A1 was found to catalyze the ω-hydroxylation of saturated and unsaturated fatty acids with chain lengths from C12 to C18 but not of hexadecane. Genomic organization analyzed by Southern blot suggested a single gene encoding CYP86A1 inA. thaliana.

Characterization of border species among Pythiaceae: several Pythium isolates produce elicitins, typical proteins from Phytophthora spp.

Elicitins, holoproteins which act as inducers of hypersensitivity on tobacco, were considered as a characteristic of Phytophthora. They are also produced, along with glycosylated isoforms, by three species belonging to the related genus Pythium, Py. vexans, Py. oedochilum and Py. marsipium, while other Pythium species do not possess such proteins. Various elicitin-like sequences were determined, bringing novel features to the elicitin family, such as an histidine residue and C-terminal extensions on the deduced peptide sequences. As the unique elicitin content of these species supports a distinct location among Pythiaceae, we suggest the separation of vexans, Py. oedochilum and Py. marsipium from Pythium and consider them as linking species between Phytophthora and Pythium.

Identification and sequence analysis of the genes encoding a polyketide synthase required for pyoluteorin biosynthesis in Pseudomonas fluorescens Pf-5.

Pyoluteorin is a chlorinated antifungal metabolite of mixed polyketide/amino-acid origin produced by certain strains of Pseudomonas spp., including the soil bacterium Pseudomonas fluorescens Pf-5. Sequence analysis of a gene cluster required for pyoluteorin biosynthesis by Pf-5 (Kraus, J., Loper, J., 1995. Appl. Environ. Microbiol. 61, 849-854) has identified two genes whose deduced peptide sequences exhibit characteristics of both fungal and bacterial Type I polyketide synthases (PKSs). The pyoluteorin PKS does not contain a loading domain that is typically present in bacterial Type I PKSs. Furthermore, this PKS possesses an acyltransferase domain that does not contain the conserved residues surrounding the active-site motif typically found in domains of similar function. Based on the organization of the functional domains within the pyoluteorin PKS, we propose a biosynthetic pathway analogous to non-aromatic polyketide biosynthesis within the Actinomycete bacteria that is responsible for the formation of the resorcinol moiety of pyoluteorin.

Differentiation-dependent expression of laminin-8 (alpha 4 beta 1 gamma 1) mRNAs in mouse 3T3-L1 adipocytes.

We report that laminin-8 (alpha 4 beta 1 gamma 1) is the specific isoform of laminin synthesized in adipocytes. Reverse transcription-polymerase chain reaction (RT-PCR) of mRNA from mouse 3T3-L1 cells with paired primers for alpha 1, alpha 2, alpha 3, alpha 4, alpha 5, beta 1, beta 2, beta 3, gamma 1 and gamma 2 laminins yielded amplified fragments only for alpha 4, beta 1 and gamma 1. A polyclonal antibody against mouse laminin-1 (alpha 1 beta 1 gamma 1) precipitated alpha 4 in addition to beta 1 and gamma 1, while the antibody against a deduced peptide sequence of mouse alpha 4 in addition to beta 1 and gamma 1 in addition to alpha 4. Thus, laminin-8 (alpha 4 beta 1 gamma 1) is the only isoform expressed in 3T3-L1 cells. Northern blots showed that the levels of alpha 4, beta 1 and gamma 1 mRNAs increased 2.5-fold during adipose conversion of 3T3-L1 cells. A 1062 bp cDNA fragment cloned by RT-PCR demonstrated a polymorphism in the mouse alpha 4 gene which would lead to five amino acid changes in the domain G.

Subcellular localization and purification of a p-hydroxyphenylpyruvate dioxygenase from cultured carrot cells and characterization of the corresponding cDNA.

p-Hydroxyphenylpyruvate dioxygenase catalyses the transformation of p-hydroxyphenylpyruvate into homogentisate. In plants this enzyme has a crucial role because homogentisate is the aromatic precursor of all prenylquinones. Furthermore this enzyme was recently identified as the molecular target for new families of potent herbicides. In this study we examine precisely the localization of p-hydroxyphenylpyruvate dioxygenase activity within carrot cells. Our results provide evidence that, in cultured carrot cells, p-hydroxyphenylpyruvate dioxygenase is associated with the cytosol. Purification and SDS/PAGE analysis of this enzyme revealed that its activity is associated with a polypeptide of 45-46 kDa. This protein specifically cross-reacts with an antiserum raised against the p-hydroxyphenylpyruvate dioxygenase of Pseudomonas fluorescens. Gel-filtration chromatography indicates that the enzyme behaves as a homodimer. We also report the isolation and nucleotide sequence of a cDNA encoding a carrot p-hydroxyphenylpyruvate dioxygenase. The nucleotide sequence (1684 bp) encodes a protein of 442 amino acid residues with a molecular mass of 48094 Da and shows specific C-terminal regions of similarity with other p-hydroxyphenylpyruvate dioxygenases. This cDNA encodes a functional p-hydroxyphenylpyruvate dioxygenase, as evidenced by expression studies with transformed Escherichia coli cells. Comparison of the N-terminal sequence of the 45-46 kDa polypeptide purified from carrot cells with the deduced peptide sequence of the cDNA confirms that this polypeptide supports p-hydroxyphenylpyruvate dioxygenase activity. Immunodetection studies of the native enzyme in carrot cellular extracts reveal that N-terminal proteolysis occurs during the process of purification. This proteolysis explains the difference in molecular masses between the purified protein and the deduced polypeptide.

Evidence for numerous omp1 alleles of porcine Chlamydia trachomatis and novel chlamydial species obtained by PCR.

A nested PCR for genus-specific amplification of the Chlamydia omp1 locus was established. This PCR detected single template molecules in 200-microl specimen aliquots. Amplified chlamydial omp1 alleles were typed by heminested species PCRs and allele PCRs. We applied this method to 407 specimens from several host animals with various clinical conditions, and we detected prevalences of chlamydiae from 6 to 50%. Amplicons from peacock enteritis and equine infertility specimens were not typeable according to present omp1 allelic criteria for the chlamydial species. DNA sequencing revealed novel omp1 alleles which were 29.9 and 47.6% divergent in the deduced peptide sequences from the most closely related chlamydiae. Phylogenetic reconstruction indicated segregation of these alleles from the current four chlamydial species (90 and 97% bootstrap support), thus strongly suggesting the existence of additional chlamydial species. Allele typing of amplicons from swine with intestinal, urogenital, and respiratory infections demonstrated several unique omp1 allelic variants of Chlamydia trachomatis. These novel alleles had deduced peptide sequences which were 11.6 to 19% divergent from porcine C. trachomatis S45. Mutations were clustered in the C-terminal region of variable segment IV of the omp1 locus encoding subspecies and serovar determinants of the chlamydial major outer membrane protein, thus implying that there are numerous serovars of porcine C. trachomatis. These results demonstrate the need for routine application of sensitive genus-specific detection of chlamydiae in animal specimens and suggest a more prominent role than anticipated for chlamydiae in animal diseases.

Masc2, a C5-DNA-methyltransferase from Ascobolus immersus with similarity to methyltransferases of higher organisms.

The filamentous fungus Ascobolus immersus represents an eukaryotic model organism to study genetic phenomena linked to DNA methylation. Following our previous characterization of a gene, masc1 from A. immersus, encoding the 'de novo' C5-DNA-methyltransferase (MTase), we report here the identification of a second MTase gene, masc2. The deduced peptide sequence of Masc2 is similar to previously identified eukaryotic MTases and distinct from Masc1 by having a large N-terminal domain in addition to the ubiquitous C-terminal catalytic domain. Following cloning of the gene, Masc2 was overexpressed and purified. Masc2 shows MTase activity with double stranded DNAs. Structural and biochemical properties of Masc2 suggest that it may function as a 'maintenance' MTase. With this finding, A. immersus represents so far the only eukaryotic organism in which two possibly synergistically operating MTases have been identified.

Characterization of a cDNA Encoding an α Thyroid Hormone Receptor in Muscovy Duckling

A complementary deoxyribonucleic acid (cDNA) clone encoding an α thyroid hormone receptor (TRα) from muscovy duckling liver was isolated and sequenced. Comparison with the chicken TRα sequence showed a high degree of homology. Despite 45 nucleotide substitutions, the deduced peptide sequence was similar. This cDNA was used as a probe to characterize the TRα mRNA transcripts expressed in muscovy duckling liver and skeletal muscle.

Myelin/oligodendrocyte glycoprotein is alternatively spliced in humans but not mice.

Myelin/oligodendrocyte glycoprotein (MOG) is an integral membrane protein expressed on the oligodendrocyte cell surface and the outermost surface of myelin sheaths. Due to this localization, MOG is a primary target antigen involved in immune-mediated demyelination. We previously reported that MOG is a unique member of the immunoglobulin (Ig) superfamily in that it possesses two large hydrophobic domains. MOG is highly conserved between deduced peptide sequences of rodent and human MOG (approximately 89% identity). We have completed an investigation of alternative splicing within the human and mouse MOG genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of total cellular RNA isolated from both fetal and adult human central nervous system (CNS) tissues reveals a complex array of alternatively spliced MOG-specific variants and the presence of two novel exons. Exon 3 encodes a short hydrophilic domain containing multiple in-frame termination codons that would result in truncation of MOG prior to translation of its transmembrane domain. Exon 7 encodes an additional hydrophilic domain that replaces MOG's second hydrophobic domain in one splice variant. We also observed that five of our eight MOG variants exhibited an alternative internal 3' splice acceptor within MOG's terminal exon. Surprisingly, no splicing was observed in a developmental study using mouse brainstem RNA.

Molecular characterization of carrier rabies isolates

We compared the genomes of nine dog rabies virus isolates using two molecular methods. The viruses used in the comparison included three Ethiopian rabies strains from carrier dogs, a street strain from a rabid dog from the same geographic area, two saliva isolates made from an experimentally infected carrier dog, the virus isolated from the tonsil of this carrier dog at necropsy, and two laboratory strains. We produced overlapping polymerase chain reaction (PCR) segments spanning 97% of the genome. Restriction analysis of these PCR products with AvaII, Bc1I, and BamHI detected 39 variable sites representing 668 nucleotides (nt) or 5.5% of the genome. We also compared the DNA and the deduced peptide sequences of a 200-nt segment of the 3′ end of the rabies nucleoprotein gene. Previous work with these Ethiopian carrier viruses and the endemic street strain had failed to show any differences among them. Both restriction mapping and sequence analysis of 200 nt of the nucleoprotein gene allowed us to individually identify these isolates. Phylogenetic analyses of these data sets showed only the two saliva isolates of the experimentally infected carrier dog to be identical. Each of the viruses in this study, including the one isolated from the tonsil of the experimentally infected carrier dog, could be distinguished by these techniques.