scholarly journals pgaA and pgaB encode two constitutively expressed endopolygalacturonases of Aspergillus niger

2000 ◽  
Vol 345 (3) ◽  
pp. 637-644 ◽  
Author(s):  
Lucie PAŘENICOVÁ ◽  
Jacques A. E. BENEN ◽  
Harry C. M. KESTER ◽  
Jaap VISSER
Keyword(s):  
Mode Of Action ◽  
Genomic Library ◽  
Degree Of Polymerization ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Ph Optimum ◽  
Protein Coding ◽  
Standard Assay ◽  
Genes Encoding ◽  
Specific Mrna

pgaA and pgaB, two genes encoding endopolygalacturonases (PGs, EC 3.2.1.15) A and B, were isolated from a phage genomic library of Aspergillusniger N400. The 1167 bp protein coding region of the pgaA gene is interrupted by one intron, whereas the 1234 bp coding region of the pgaB gene contains two introns. The corresponding proteins, PGA and PGB, consist of 370 and 362 amino acid residues respectively. Northern-blot analysis revealed that pgaA- and pgaB-specific mRNA accumulate in mycelia grown on sucrose. mRNAs are also present upon transfer to media containing D-galacturonic acid and pectin. Recombinant PGA and PGB were characterized with respect to pH optimum, activity on polygalacturonic acid, and mode of action and kinetics on oligogalacturonates of different chain length (n = 3-7). At their pH optimum the specific activities in a standard assay for PGA (pH 4.2) and PGB (pH 5.0) were 16.5 μkat·mg-1 and 8.3 μkat·mg-1 respectively. Product progression analysis, using polygalacturonate as a substrate, revealed a random cleavage pattern for both enzymes and indicated processive behaviour for PGA. This result was confirmed by analysis of the mode of action using oligogalacturonates. Processivity was observed when the degree of polymerization of the substrate exceeded 6. Using pectins of various degrees of methyl esterification, it was shown that PGA and PGB both preferred partially methylated substrates.

scholarly journals The cDNA and protein sequences of human lactate dehydrogenase B

1987 ◽  
Vol 248 (3) ◽  
pp. 933-936 ◽  
Author(s):  
I Sakai ◽  
F S Sharief ◽  
Y C Pan ◽  
S S Li
Keyword(s):  
Amino Acid ◽  
Lactate Dehydrogenase ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Amino Acid Sequences ◽  
British Library ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Cdna Insert ◽  
Protein Coding

Human lactate dehydrogenase B (LDH-B) cDNA was isolated and sequenced. The LDH-B cDNA insert consists of the protein-coding sequence (999 bp), the 5′ (54 bp) and 3′ (203 bp) non-coding regions, and the poly(A) tail (50 bp). The predicted sequence of 333 amino acid residues was confirmed by amino acid composition and/or sequence analyses of a total of 185 (56%) residues from tryptic peptides of human LDH-B protein. The nucleotide and amino acid sequences of the human LDH-B coding region show 68% and 75% homologies respectively with those of the human LDH-A. The peptide map and amino acid composition data have been deposited as Supplementary Publication SUP 50139 (7 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment [see Biochem. J. (1987) 241, 5].

scholarly journals Structure and expression of B-myc, a new member of the myc gene family

1988 ◽  
Vol 8 (8) ◽  
pp. 3168-3174
Author(s):  
S Ingvarsson ◽  
C Asker ◽  
H Axelson ◽  
G Klein ◽  
J Sümegi
Keyword(s):  
Southern Blotting ◽  
Cdna Libraries ◽  
Rat Tissues ◽  
Coding Region ◽  
Specific Expression ◽  
Protein Coding ◽  
Myc Gene ◽  
The Brain ◽  
Mouse Somatic Cell ◽  
Specific Mrna

The myc family of genes contains five functional members. We describe the cloning of a new member of the myc family from rat genomic and cDNA libraries, designated B-myc. A fragment of cloned B-myc was used to map the corresponding rat locus by Southern blotting of DNA prepared from rat X mouse somatic cell hybrids. B-myc mapped to rat chromosome 3. We have previously mapped the c-myc to rat chromosome 7 (J. Sümegi, J. Spira, H. Bazin, J. Szpirer, G. Levan, and G. Klein, Nature [London] 306:497-498, 1983) and N-myc and L-myc to rat chromosomes 6 and 5, respectively (S. Ingvarsson, C. Asker, Z. Wirschubsky, J. Szpirer, G. Levan, G. Klein, and J. Sümegi, Somat. Cell Mol. Genet. 13:335-339, 1987). A partial sequence of B-myc had extensive sequence homology to the c-myc protein-coding region, and the detection of intron homology further indicated that these two genes are closely related. The DNA regions conserved among the myc family members, designated myc boxes, were highly conserved between c-myc and B-myc. A lower degree of homology was detected in other parts of the coding region in c-myc and B-myc not present in N-myc and L-myc. A 1.3-kilobase B-myc-specific mRNA was detected in most rat tissues, with the highest expression in the brain. This resembled the expression pattern of c-myc, although at different relative levels, and was in contrast to the more tissue-specific expression of N-myc and L-myc. B-myc was expressed at uniformly high levels in all fetal tissues and during subsequent postnatal development, in contrast to the stage-specific expression of c-myc.

Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP7, a protein of the large subunit of the mitochondrial ribosome

1988 ◽  
Vol 8 (9) ◽  
pp. 3636-3646
Author(s):  
K Fearon ◽  
T L Mason
Keyword(s):  
Amino Acid ◽  
Catabolite Repression ◽  
Genomic Library ◽  
Large Subunit ◽  
Nuclear Gene ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Expression Library ◽  
Computer Data ◽  
Mitochondrial Ribosome

The gene for MRP7, a 40-kilodalton protein of the large subunit of the yeast mitochondrial ribosome, was identified in a lambda gt11 expression library by immunological screening with a monoclonal antibody to MRP7. An intact copy of MRP7 was then isolated from a yeast genomic library by colony hybridization. Gene disruption showed that MRP7 protein was essential for ribosomal function. Sequencing of MRP7 revealed a coding region for a basic (pI 10.6), 43.2-kilodalton protein containing 371 amino acid residues. Amino acid residues 28 to 112 of the deduced MRP7 sequence aligned with the 84 residues of the Escherichia coli ribosomal protein L27, but no significant similarity was detected between the carboxy-terminal 259 amino acids of MRP7 and other protein sequences in existing computer data bases. Within the aligned region, there was 49% amino acid identity between MRP7 and L27, compared with the 57% identity observed between L27 and its homolog in Bacillus stearothermophilus. The steady-state levels of the MRP7 protein and its mRNA were monitored in response to catabolite repression and to increased dosage of the MRP7 gene. The response to catabolite repression was characterized by a ninefold change in the level of the protein and little, if any, change in the level of the mRNA. In cells carrying the MRP7 gene on a high-copy-number plasmid, the mRNA was increased 20-fold, but there was no significant increase in MRP7 protein. Furthermore, MRP7 mRNA and protein accumulated at normal levels in [rho0] cells, which are devoid of 21S rRNA, indicating that the protein is relatively stable in the absence of ribosome assembly. Together, these results suggest that MRP7 is regulated posttranscriptionally, probably at the level of protein synthesis rather than protein turnover.

scholarly journals Structure of the human cyclo-oxygenase-2 gene

1994 ◽  
Vol 302 (3) ◽  
pp. 723-727 ◽  
Author(s):  
S B Appleby ◽  
A Ristimäki ◽  
K Neilson ◽  
K Narko ◽  
T Hla
Keyword(s):  
Genomic Library ◽  
Regulatory Sequences ◽  
Coding Region ◽  
Nf Kappa B ◽  
Protein Coding ◽  
Quiescent Cells ◽  
Cox 2 ◽  
Rate Limiting ◽  
Element Sequence ◽  
Cox 1

Cyclo-oxygenase (Cox), a rate-limiting enzyme in the synthesis of prostanoids, is encoded by two genes, Cox-1 and Cox-2, which are differentially expressed and regulated. Human Cox-1 and -2 polypeptides share 61% primary sequence identity. While the expression of Cox-1 is maximal in quiescent cells. Cox-2 expression is induced by growth factors and cytokines. We have screened a human genomic library with a probe from the 5′-untranslated region (UTR) of the human Cox-2 (hCox-2) cDNA and isolated two overlapping genomic clones. We have determined the DNA sequence of 0.8 kb upstream of the transcription start site, 6 kb of protein coding region, which includes 10 exons and 9 introns, as well as 2.5 kb of the 3′-UTR. The structures of the hCox-1 and hCox-2 and the murine TIS10 (Cox-2) genes are highly conserved, with a few exceptions. The 3′-UTRs of the Cox-1 and -2 genes are distinct; for example, the largest exon in the Cox-2 gene encodes the entire 3′-UTR, containing 22 copies of the ‘AUUUA’ RNA instability element. Sequence analysis of the 5′-flanking region has shown several potential transcription regulatory sequences, including a TATA box, a C/EBP motif, two AP-2 sites, three SP1 sites, two NF-kappa B sites, a CRE motif and an Ets-1 site. These efforts serve as a basis for future studies on transcriptional and post-transcriptional mechanisms of Cox-2 gene regulation.

scholarly journals Structure and expression of B-myc, a new member of the myc gene family.

1988 ◽  
Vol 8 (8) ◽  
pp. 3168-3174 ◽  
Author(s):  
S Ingvarsson ◽  
C Asker ◽  
H Axelson ◽  
G Klein ◽  
J Sümegi
Keyword(s):  
Southern Blotting ◽  
Cdna Libraries ◽  
Rat Tissues ◽  
Coding Region ◽  
Specific Expression ◽  
Protein Coding ◽  
Myc Gene ◽  
The Brain ◽  
Mouse Somatic Cell ◽  
Specific Mrna

The myc family of genes contains five functional members. We describe the cloning of a new member of the myc family from rat genomic and cDNA libraries, designated B-myc. A fragment of cloned B-myc was used to map the corresponding rat locus by Southern blotting of DNA prepared from rat X mouse somatic cell hybrids. B-myc mapped to rat chromosome 3. We have previously mapped the c-myc to rat chromosome 7 (J. Sümegi, J. Spira, H. Bazin, J. Szpirer, G. Levan, and G. Klein, Nature [London] 306:497-498, 1983) and N-myc and L-myc to rat chromosomes 6 and 5, respectively (S. Ingvarsson, C. Asker, Z. Wirschubsky, J. Szpirer, G. Levan, G. Klein, and J. Sümegi, Somat. Cell Mol. Genet. 13:335-339, 1987). A partial sequence of B-myc had extensive sequence homology to the c-myc protein-coding region, and the detection of intron homology further indicated that these two genes are closely related. The DNA regions conserved among the myc family members, designated myc boxes, were highly conserved between c-myc and B-myc. A lower degree of homology was detected in other parts of the coding region in c-myc and B-myc not present in N-myc and L-myc. A 1.3-kilobase B-myc-specific mRNA was detected in most rat tissues, with the highest expression in the brain. This resembled the expression pattern of c-myc, although at different relative levels, and was in contrast to the more tissue-specific expression of N-myc and L-myc. B-myc was expressed at uniformly high levels in all fetal tissues and during subsequent postnatal development, in contrast to the stage-specific expression of c-myc.

scholarly journals Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP7, a protein of the large subunit of the mitochondrial ribosome.

1988 ◽  
Vol 8 (9) ◽  
pp. 3636-3646 ◽  
Author(s):  
K Fearon ◽  
T L Mason
Keyword(s):  
Amino Acid ◽  
Catabolite Repression ◽  
Genomic Library ◽  
Large Subunit ◽  
Nuclear Gene ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Expression Library ◽  
Computer Data ◽  
Mitochondrial Ribosome

The gene for MRP7, a 40-kilodalton protein of the large subunit of the yeast mitochondrial ribosome, was identified in a lambda gt11 expression library by immunological screening with a monoclonal antibody to MRP7. An intact copy of MRP7 was then isolated from a yeast genomic library by colony hybridization. Gene disruption showed that MRP7 protein was essential for ribosomal function. Sequencing of MRP7 revealed a coding region for a basic (pI 10.6), 43.2-kilodalton protein containing 371 amino acid residues. Amino acid residues 28 to 112 of the deduced MRP7 sequence aligned with the 84 residues of the Escherichia coli ribosomal protein L27, but no significant similarity was detected between the carboxy-terminal 259 amino acids of MRP7 and other protein sequences in existing computer data bases. Within the aligned region, there was 49% amino acid identity between MRP7 and L27, compared with the 57% identity observed between L27 and its homolog in Bacillus stearothermophilus. The steady-state levels of the MRP7 protein and its mRNA were monitored in response to catabolite repression and to increased dosage of the MRP7 gene. The response to catabolite repression was characterized by a ninefold change in the level of the protein and little, if any, change in the level of the mRNA. In cells carrying the MRP7 gene on a high-copy-number plasmid, the mRNA was increased 20-fold, but there was no significant increase in MRP7 protein. Furthermore, MRP7 mRNA and protein accumulated at normal levels in [rho0] cells, which are devoid of 21S rRNA, indicating that the protein is relatively stable in the absence of ribosome assembly. Together, these results suggest that MRP7 is regulated posttranscriptionally, probably at the level of protein synthesis rather than protein turnover.

Selection on Rapidly Evolving Proteins in the Arabidopsis Genome

Genetics ◽  
2003 ◽  
Vol 163 (2) ◽  
pp. 723-733 ◽  
Author(s):  
Marianne Barrier ◽  
Carlos D Bustamante ◽  
Jiaye Yu ◽  
Michael D Purugganan
Keyword(s):  
Expressed Sequence Tag ◽  
Amino Acid Replacement ◽  
Adaptive Divergence ◽  
Coding Region ◽  
Protein Coding ◽  
Hierarchical Bayesian Analysis ◽  
Brassicaceae Species ◽  
Replacement Site ◽  
Orthologous Loci ◽  
Selection Intensities

Abstract Genes that have undergone positive or diversifying selection are likely to be associated with adaptive divergence between species. One indicator of adaptive selection at the molecular level is an excess of amino acid replacement fixed differences per replacement site relative to the number of synonymous fixed differences per synonymous site (ω = Ka/Ks). We used an evolutionary expressed sequence tag (EST) approach to estimate the distribution of ω among 304 orthologous loci between Arabidopsis thaliana and A. lyrata to identify genes potentially involved in the adaptive divergence between these two Brassicaceae species. We find that 14 of 304 genes (∼5%) have an estimated ω > 1 and are candidates for genes with increased selection intensities. Molecular population genetic analyses of 6 of these rapidly evolving protein loci indicate that, despite their high levels of between-species nonsynonymous divergence, these genes do not have elevated levels of intraspecific replacement polymorphisms compared to previously studied genes. A hierarchical Bayesian analysis of protein-coding region evolution within and between species also indicates that the selection intensities of these genes are elevated compared to previously studied A. thaliana nuclear loci.

Protease B of Saccharomyces cerevisiae: Isolation and Regulation of the PRB1 Structural Gene

Genetics ◽  
1987 ◽  
Vol 115 (2) ◽  
pp. 255-263 ◽  
Author(s):  
Charles M Moehle ◽  
Martha W Aynardi ◽  
Michael R Kolodny ◽  
Frances J Park ◽  
Elizabeth W Jones
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Molecular Weight ◽  
Structural Gene ◽  
Genomic Library ◽  
Time Lag ◽  
Proteolytic Processing ◽  
Coding Region ◽  
Protease B ◽  
Endonuclease Mapping ◽  
Protein Molecular Weight

ABSTRACT We have isolated the structural gene, PRB1, for the vacuolar protease B of Saccharomyces cerevisiae from a genomic library by complementation of the prb1-1122 mutation. Deletion analysis localized the complementing activity to a 3.2-kilobase pair XhoI-HindIII restriction enzyme fragment. The fragment was used to identify a 2.3-kilobase mRNA. S1 endonuclease mapping indicated that the mRNA and the gene were colinear. No introns were detected. The mRNA is of sufficient size to encode a protein of about 69,000 molecular weight, a number much larger than either the mature enzyme (≃30,000 protein molecular weight) or the sole reported precursor (≃39,000 protein molecular weight). These results suggest that proteolytic processing steps beyond that thought to be catalyzed by protease A may be required to convert the initial glycosylated translation product into mature protease B. The PRB1 mRNA is made in substantial amounts only when the cells have exhausted the glucose supply and enter the diauxic plateau. There is an extended time lag between PRB1 transcription and expression of protease B activity. A deletion that removes about 83% of the coding region was constructed as a diploid heterozygote. Spores bearing the deletion germinate, grow at normal rates into colonies, and have no obvious phenotype beyond protease B deficiency.

scholarly journals Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Catarina Leal ◽  
Florence Fontaine ◽  
Aziz Aziz ◽  
Conceiçao Egas ◽  
Christophe Clément ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Vitis Vinifera ◽  
Genome Sequence ◽  
Draft Genome ◽  
Rhizospheric Soil ◽  
Bioactive Substances ◽  
Protein Coding ◽  
Genes Encoding ◽  
Stimulate Plant Growth ◽  
Biocontrol Potential

Abstract Background Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity. Results The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes. Conclusions Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.

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