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PubMed2004

Structural analysis of the eukaryotic initiation factor 4E gene controlling potyvirus resistance in pepper: exploitation of a BAC library.

The pvr2 locus in pepper codes for a eukaryotic translation initiation factor 4E (eIF4E) gene that confers resistance to viruses belonging to the potyvirus genus. In this work, we describe the isolation and characterisation of the genomic sequence carrying the pvr2 locus. A Bacterial Artificial Chromosome (BAC) library that consisted of 239,232 clones with an average insert size of 123 kilobases (kb) was constructed from a Capsicum annuum line with the pvr2(+) allele for susceptibility to potato virus Y (PVY) and tobacco etch virus (TEV). Based on a polymerase chain reaction (PCR) screen with single-copy markers, three to seven positive BAC clones per markers were identified, indicating that the BAC library is suitable for pepper genome analysis. To determine the genomic organization of the pepper eIF4E gene, the library was screened with primers designed from the cDNA sequence and four positive BAC clones carrying the pvr2 locus were identified. A 7-kb DNA fragment containing the complete eIF4E gene was sub-cloned from the positive BAC clones and analysed. The eIF4E gene is organised into five exons and four introns and showed a strictly conserved exon/intron structure with eIF4E genes from Arabidopsis thaliana and rice. Moreover, the splice sites between plant exons 1/2 and 2/3 are conserved among eukaryotes including human, Drosophila and yeast. Several potential binding sites for MADS box transcription factors within the 5' flanking region of eIF4E genes from the three plant species were also predicted.

Amino Acid Sequence↗

PubMed1990

Nucleotide sequence of the fosB gene conferring fosfomycin resistance in Staphylococcus epidermidis.

We have determined the nucleotide sequence of gene fosB of plasmid pIP1842, which confers resistant to fosfomycin in Staphylococcus epidermidis BM2641. The resistance gene was identified as a coding sequence of 417 bases pairs corresponding to a protein with a calculated Mw of 16,345 daltons. This value is in good agreement with that of 15,000, estimated by SDS-polyacrylamide gel electrophoresis of a bacterial cell-free coupled transcription-translation system. The fosB gene product exhibits 48% sequence homology with the fosfomycin resistance protein FOSA of Enterobacteriaceae. The substitutions are scattered throughout indicating that the two corresponding genes have diverged from a common ancestor. Downstream from fosB is located an open reading frame that was partially sequenced. The deduced amino-acid sequence was 50% homologous to REP alpha 1, a protein involved in the replication of the Enterococcus faecalis plasmid pAM alpha 1.

Amino Acid Sequence↗

PubMed2001

Identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in Shewanella oneidensis strain MR1.

Two abundant, low-redox-potential cytochromes c were purified from the facultative anaerobe Shewanella oneidensis strain MR1 grown anaerobically with fumarate. The small cytochrome was completely sequenced, and the genes coding for both proteins were cloned and sequenced. The small cytochrome c contains 91 residues and four heme binding sites. It is most similar to the cytochromes c from Shewanella frigidimarina (formerly Shewanella putrefaciens) NCIMB400 and the unclassified bacterial strain H1R (64 and 55% identity, respectively). The amount of the small tetraheme cytochrome is regulated by anaerobiosis, but not by fumarate. The larger of the two low-potential cytochromes contains tetraheme and flavin domains and is regulated by anaerobiosis and by fumarate and thus most nearly corresponds to the flavocytochrome c-fumarate reductase previously characterized from S. frigidimarina to which it is 59% identical. However, the genetic context of the cytochrome genes is not the same for the two Shewanella species, and they are not located in multicistronic operons. The small cytochrome c and the cytochrome domain of the flavocytochrome c are also homologous, showing 34% identity. Structural comparison shows that the Shewanella tetraheme cytochromes are not related to the Desulfovibrio cytochromes c(3) but define a new folding motif for small multiheme cytochromes c.

Amino Acid Sequence↗

PubMed1996

Heterologous growth phase- and temperature-dependent expression and H2O2 toxicity protection of a superoxide-inducible monofunctional catalase gene from Xanthomonas oryzae pv. oryzae.

Catalase is an important protective enzyme against H2O2 toxicity. Here, we report the characterization of a Xanthomonas oryzae pv. oryzae catalase gene (katX). The gene was localized and its nucleotide sequence was determined. The gene codes for a 77-kDa polypeptide. The deduced katX amino acid sequence shares regions of high identity with other monofunctional catalases in a range of organisms from bacteria to eukaryotes. The transcriptional regulation of katX was atypical of bacterial monofunctional kat genes. Northern (RNA) analysis showed that katX transcription was highly induced by treatments with low concentrations of menadione, a superoxide generator, and methyl methanesulfonate, a mutagen. It was only weakly induced by H2O2. Unlike in other bacteria, a high level of catalase in Xanthomonas spp. provided protection from the growth-inhibitory and killing effects of H2O2 but not from those of organic peroxides and superoxide generators. Unexpectedly, heterologous expression of katX in Escherichia coli was both growth phase and temperature dependent. Catalase activity in E. coli kat mutants harboring katX on an expression vector was detectable only when the cells entered the stationary phase of growth and at 28 degrees C. The patterns of transcription regulation, heterologous expression, and physiological function of katX are different from previously studied bacterial kat genes.

Amino Acid Sequence↗

PubMed1998

In vivo retargeting of T cell effector function by recombinant bispecific single chain Fv (anti-CD3 x anti-idiotype) induces long-term survival in the murine BCL1 lymphoma model.

As demonstrated in several preclinical models, bispecific Abs are attractive immunotherapeutic agents for tumor treatment. We have previously reported that a bacterially produced anti-CD3 x antitumor bispecific single chain variable fragment of Ab fragment (BsscFv), which is capable of retargeting CTLs toward BCL1 tumor cells, exhibits antitumor activity in vitro. To further facilitate BsscFv production, the coding sequence was subcloned in a eukaryotic expression vector and introduced into Chinese hamster ovary cells for large-scale production. In this report, we have determined the serum stability and the clearance rate from the circulation of BsscFv. Most important, we prove here the therapeutic value of BsscFv in the treatment of BCL1 lymphoma, a murine model for human non-Hodgkin's lymphoma. Tumor-bearing mice that were treated with rscFv in combination with staphylococcal enterotoxin B superantigen, human rIL-2, or murine rIL-12 showed long-term survival, whereas untreated mice all died. This is the first report of the successful in vivo use of BsscFv as an immunotherapeutic agent. Furthermore, long-term survival was the result of complete tumor removal and was not due to the induction of dormancy.

Animals↗

PubMed1995

Detection of new genes in a bacterial genome using Markov models for three gene classes.

We further investigated the statistical features of the three classes of Escherichia coli genes that have been previously delineated by factorial correspondence analysis and dynamic clustering methods. A phased Markov model for a nucleotide sequence of each gene class was developed and employed for gene prediction using the GeneMark program. The protein-coding region prediction accuracy was determined for class-specific Markov models of different orders when the programs implementing these models were applied to gene sequences from the same or other classes. It is shown that at least two training sets and two program versions derived for different classes of E. coli genes are necessary in order to achieve a high accuracy of coding region prediction for uncharacterized sequences. Some annotated E. coli genes from Class I and Class III are shown to be spurious, whereas many open reading frames (ORFs) that have not been annotated in GenBank as genes are predicted to encode proteins. The amino acid sequences of the putative products of these ORFs initially did not show similarity to already known proteins. However, conserved regions have been identified in several of them by screening the latest entries in protein sequence databases and applying methods for motif search, while some other of these new genes have been identified in independent experiments.

Algorithms↗

PubMed1992

Isolation and characterization of kikA, a region on IncN group plasmids that determines killing of Klebsiella oxytoca.

Transfer of the IncN group plasmid pCU1 from Escherichia coli to Klebsiella oxytoca by conjugation kills a large proportion (90 to 95%) of the recipients of plasmid DNA, whereas transfer to E. coli or even to the closely related Enterobacter aerogenes does not. Two regions, kikA and kikB, have been identified on pCU1 that contribute to the Kik (killing in klebsiellas) phenotype. We have localized the kikA region to 500 bp by deletion analysis and show by DNA-DNA hybridization that kikA is highly conserved among the plasmids of incompatibility group N. The expression in K. oxytoca of kikA under the control of the strong inducible E. coli tac promoter results in loss of cell viability. The nucleotide sequence showed two overlapping open reading frames (ORFs) within the kikA region. The first ORF codes for a putative polypeptide of 104 amino acids (ORF104). The second ORF codes for a 70-amino-acid polypeptide (ORF70). The properties of the putative protein encoded by ORF104 and gene fusions of kikA to alkaline phosphatase by using TnphoA suggest that killing may involve an association with the bacterial membrane; however, we could not rule out the possibility that ORF70 plays a role in the Kik phenotype.

Amino Acid Sequence↗

PubMed1995

Genetic and molecular characterization of a gene encoding a wide specificity purine permease of Aspergillus nidulans reveals a novel family of transporters conserved in prokaryotes and eukaryotes.

In Aspergillus nidulans, loss-of-function mutations in the uapA and azgA genes, encoding the major uric acid-xanthine and hypoxanthine-adenine-guanine permeases, respectively, result in impaired utilization of these purines as sole nitrogen sources. The residual growth of the mutant strains is due to the activity of a broad specificity purine permease. We have identified uapC, the gene coding for this third permease through the isolation of both gain-of-function and loss-of-function mutations. Uptake studies with wild-type and mutant strains confirmed the genetic analysis and showed that the UapC protein contributes 30% and 8-10% to uric acid and hypoxanthine transport rates, respectively. The uapC gene was cloned, its expression studied, its sequence and transcript map established, and the sequence of its putative product analyzed. uapC message accumulation is: (i) weakly induced by 2-thiouric acid; (ii) repressed by ammonium; (iii) dependent on functional uaY and areA regulatory gene products (mediating uric acid induction and nitrogen metabolite repression, respectively); (iv) increased by uapC gain-of-function mutations which specifically, but partially, suppress a leucine to valine mutation in the zinc finger of the protein coded by the areA gene. The putative uapC gene product is a highly hydrophobic protein of 580 amino acids (M(r) = 61,251) including 12-14 putative transmembrane segments. The UapC protein is highly similar (58% identity) to the UapA permease and significantly similar (23-34% identity) to a number of bacterial transporters. Comparisons of the sequences and hydropathy profiles of members of this novel family of transporters yield insights into their structure, functionally important residues, and possible evolutionary relationships.

Amino Acid Sequence↗

PubMed2006

The relation between mRNA folding and protein structure.

About 200 mRNA sequences of Escherichia coli and human with matching protein secondary structure data were studied. The mRNA folding for each native sequence and for corresponding randomized sequences was calculated through free energy minimization. We have found that the folding energy of mRNA segments in different protein secondary structures is significantly different. The average Z score is more negative for regular secondary structure (alpha-helix and beta-strand) than that for coil. This suggests that the codon choice in native mRNA sequence coding for protein regular structure contributes more to the mRNA folding stability.

Escherichia coli Proteins↗

PubMed1985

Tn3 as the molecular basis of ampicillin resistance in E. coli--an epidemiological survey.

Plasmids of 31 E. coli strains coding for the TEM-1 beta-lactamase were analysed for the molecular basis of this enzyme. In transposition experiments we could demonstrate that only 50% of the plasmids were able to transpose their ampicillin-resistance gene. Two of the non-transposing structures were further examined. The 8.1 kb plasmid pBP738 contained Tn3 having suffered a point mutation within the transposase gene that could be complemented by an intact transposase. The 79 kb plasmid pBP749 carried a TEM-1 coding sequence, but the homology with Tn3 was limited to 1.18 kb.

Ampicillin↗

PubMed1990

Primary structure of a DNA (N6-adenine)-methyltransferase from Escherichia coli virus T1. DNA sequence, genomic organization, and comparative analysis.

Escherichia coli virus T1 encodes a DNA (N6-adenine)-methyltransferase (M.T1) with the same sequence specificity as the E. coli DNA (N6-adenine)-methyltransferase (M.Eco dam). This enzyme was purified to homogeneity and a partial amino acid sequence determined. Oligonucleotides were constructed and used not only as probes to map the gene on the T1 genome, but also as primers in sequencing reactions to establish the nucleotide sequence of the M.T1 locus by primer extension. These data represent the first analysis of the genomic organization of bacterial virus T1 on a molecular level. Significant homology to E. coli consensus transcription and translation-initiation signals suggest that the gene for M.T1 is most probably under control of its own promoter. It may be transcribed as a polycistronic mRNA, together with a downstream open reading frame which codes for a polypeptide containing 83 amino acids (HP 83). Both the deduced primary and the secondary structure of the M.T1 were compared to those of other known DNA methyltransferases, especially those recognizing the sequence, GATC; there is little similarity of the T1 enzyme to the other members of this family.

Amino Acid Sequence↗

PubMed1995

Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis.

The gene encoding D-lactate dehydrogenase was isolated on a 2.9-kb insert from a library of Pediococcus acidilactici DNA by complementation for growth under anaerobiosis of an Escherichia coli lactate dehydrogenase and pyruvate-formate lyase double mutant. The nucleotide sequence of ldhD encodes a protein of 331 amino acids (predicted molecular mass of 37,210 Da) which shows similarity to the family of D-2-hydroxyacid dehydrogenases. The enzyme encoded by the cloned fragment is equally active on pyruvate and hydroxypyruvate, indicating that the enzyme has both D-lactate and D-glycerate dehydrogenase activities. Three other open reading frames were found in the 2.9-kb insert, one of which (rpsB) is highly similar to bacterial genes coding for ribosomal protein S2. Northern (RNA) blotting analyses indicated the presence of a 2-kb dicistronic transcript of ldhD (a metabolic gene) and rpsB (a putative ribosomal protein gene) together with a 1-kb monocistronic rpsB mRNA. These transcripts are abundant in the early phase of exponential growth but steadily fade away to disappear in the stationary phase. Primer extension analysis identified two distinct promoters driving either cotranscription of ldhD and rpsB or transcription of rpsB alone.

Amino Acid Sequence↗

PubMed2006

Molecular characterization of a novel translocation t(5;14)(q21;q32) in a patient with congenital abnormalities.

Chromosomal translocations are frequently found to be associated with various malignant disorders as well as congenital abnormalities. We report the characterization of a novel reciprocal translocation t(5;14)(q21;q32) in a patient with congenital abnormalities manifested by severe mental retardation, athetotic tetraplegia, microcephaly, peculiar facies (upward slanting of palpebral fissures), clinodactyly of the fifth fingers, and overlapping toes. Using a JHGP24 lymphoblast cell line derived from this patient, metaphase fluorescence in situ hybridization with bacterial artificial chromosome and cosmid probes and subsequent molecular analysis mapped the translocation breakpoint to the nucleotide level. Sequence analysis of the breakpoint junctions revealed the presence of a homologous sequence, GTGGC, along with a single nucleotide substitution and an insertion in der(14), and a single nucleotide deletion in the der(5) chromosome. We also attempted to identify and characterize the transcripts near the breakpoint by 5' and 3' rapid amplification of cDNA ends. Although we found several transcripts near the breakpoint of chromosome 14, the lack of significant ORFs within these transcripts suggests they are likely to be non-coding RNAs. These transcripts may have an important role in the neurogenesis or differentiation.

Adult↗

PubMed1997

Direct expression of PCR products in a cell-free transcription/translation system: synthesis of antibacterial peptide cecropin.

A simple and effective methodology is proposed for direct expression of PCR-generated linear DNAs in cell-free transcription/translation systems without cloning DNA fragments in plasmids. This methodology is realized for the synthesis of the active antibacterial peptide cecropin using the synthetic coding sequence. Possible scientific applications and perspectives of the proposed approach are discussed.

Amino Acid Sequence↗

PubMed1987

Construction and use of signal sequence selection vectors in Escherichia coli and Bacillus subtilis.

To study the diversity and efficiency of signal peptides for secreted proteins in gram-positive bacteria, two plasmid vectors were constructed which were used to probe for export signal-coding regions in Bacillus subtilis. The vectors contained genes coding for extracellular proteins (the alpha-amylase gene from Bacillus licheniformis and the beta-lactamase gene from Escherichia coli) which lacked a functional signal sequence. By shotgun cloning of restriction fragments from B. subtilis chromosomal DNA, a great variety of different export-coding regions were selected. These regions were functional both in B. subtilis and in E. coli. In a number of cases where protein export had been restored, intracellular precursor proteins of increased size could be detected, which upon translocation across the cellular membrane were processed to mature products. The high frequency with which export signal-coding regions were obtained suggests that, in addition to natural signal sequences, many randomly cloned sequences can function as export signal.

Bacillus subtilis↗

PubMed1986

[Nucleotide sequence and physical map of kanamycin-resistant plasmid pUB110 from Staphylococcus aureus].

The complete nucleotide sequence of Staphylococcus aureus plasmid pUB10 was determined. The sequence consists of 4545 b.p. and contains 64% A-T and 36% G-C pairs. pUB110 was found to contain four open reading frames, capable of coding for polypeptides having more than 80 amino acids. All the putative polypeptides are coded for by one DNA strand. The molecular weights of four putative polypeptides are (in kilodaltons): A-49.5; B-38.8; C-28.8 and D-9.5. Polypeptide C is involved in kanamycin resistance. Polypeptide B is, possibly, involved in pUB110 replication. No role has yet been established for polypeptides A and D, since deletions in their coding sequences have no detectable effect on any properties of pUB110 plasmid.

Base Sequence↗

PubMed1987

Purification and characterization of the CheZ protein of bacterial chemotaxis.

The cheZ gene is the most distal of five genes that comprise the Meche operon of the Salmonella typhimurium chemotaxis system. We have determined the sequence of the cheZ gene along with an 800-nucleotide flanking region at its 3' end. The flanking sequence contains an open reading frame that probably corresponds to the 5' end of flaM. The cheZ coding sequence predicts an extremely acidic, hydrophilic protein with a molecular weight of 23,900. We have purified and characterized this protein. N-terminal analysis of pure CheZ yields an amino acid sequence identical to that predicted by the nucleotide sequence except that the amino-terminal methionine residue is modified by N methylation. The purified CheZ protein exhibits a native molecular weight of 115,000, but in cell extracts the majority of CheZ exists as a much larger aggregate (Mr greater than 500,000). Under these conditions, CheZ appears to be a homopolymer composed of at least 20 monomeric subunits.

Amino Acid Sequence↗

PubMed1988

Unexpected translation initiation within the coding region of eukaryotic genes expressed in Escherichia coli.

When expressing several eukaryotic genes in Escherichia coli, we observed N-terminally truncated proteins which were attributed to translation initiation at downstream AUG codons. These AUG codons are located between 4 and 20 nucleotides 3' from sequences resembling bacterial SD elements. Although the presence of such downstream SD sequences is not sufficient for downstream initiation to occur, in two cases their removal abolishes synthesis of the truncated proteins. In one construct, a potential hairpin-loop structure is likely to inhibit translation initiation at the correct site and favor downstream initiation.

Base Sequence↗