Artykuły w czasopismach na temat „Amino Acid Sequence Homology”
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1
Giorda, R., i H. L. Ennis. "Structure of two developmentally regulated Dictyostelium discoideum ubiquitin genes". Molecular and Cellular Biology 7, nr 6 (czerwiec 1987): 2097–103. http://dx.doi.org/10.1128/mcb.7.6.2097-2103.1987.
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A previously isolated cDNA clone, pLK229, that is specific for mRNA developmentally expressed during Dictyostelium discoideum spore germination and multicellular development, was used to screen two genomic libraries. Two genomic sequences homologous to pLK229 were isolated and sequenced. Genomic clone p229 is identical to the cDNA clone pLK229 and codes for a polypeptide of 381 amino acids. This polypeptide is composed of five tandem repeats of the same 76-amino-acid sequence. Clone lambda 229 codes for a protein of 229 amino acids, containing three tandem repeats of the identical 76-amino-acid sequence. A computer search for homology to known proteins revealed that the 76-amino-acid repeat was identical to human and bovine ubiquitin except for two amino acid differences.
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Giorda, R., i H. L. Ennis. "Structure of two developmentally regulated Dictyostelium discoideum ubiquitin genes." Molecular and Cellular Biology 7, nr 6 (czerwiec 1987): 2097–103. http://dx.doi.org/10.1128/mcb.7.6.2097.
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A previously isolated cDNA clone, pLK229, that is specific for mRNA developmentally expressed during Dictyostelium discoideum spore germination and multicellular development, was used to screen two genomic libraries. Two genomic sequences homologous to pLK229 were isolated and sequenced. Genomic clone p229 is identical to the cDNA clone pLK229 and codes for a polypeptide of 381 amino acids. This polypeptide is composed of five tandem repeats of the same 76-amino-acid sequence. Clone lambda 229 codes for a protein of 229 amino acids, containing three tandem repeats of the identical 76-amino-acid sequence. A computer search for homology to known proteins revealed that the 76-amino-acid repeat was identical to human and bovine ubiquitin except for two amino acid differences.
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Day, A. A., C. I. McQuillan, J. D. Termine i M. R. Young. "Molecular cloning and sequence analysis of the cDNA for small proteoglycan II of bovine bone". Biochemical Journal 248, nr 3 (15.12.1987): 801–5. http://dx.doi.org/10.1042/bj2480801.
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The cDNA for the full-length core protein of the small chondroitin sulphate proteoglycan II of bovine bone was cloned and sequenced. A 1.3 kb clone (lambda Pg28) was identified by plaque hybridization with a previously isolated 1.0 kb proteoglycan cDNA clone (lambda Pg20), positively identified previously by polyclonal and monoclonal antibody reactivity and by hybrid-selected translation in vitro [Day, Ramis, Fisher, Gehron Robey, Termine & Young (1986) Nucleic Acids Res. 14, 9861-9876]. The cDNA sequences of both clones were identical in areas of overlap. The 360-amino-acid-residue protein contains a 30-residue propeptide of which the first 15 residues are highly hydrophobic. The mature protein consists of 330 amino acid residues corresponding to an Mr of 36,383. The core protein contains three potential glycosaminoglycan-attachment sites (Ser-Gly), only one of which is within a ten-amino-acid-residue homologous sequence seen at the known attachment sites of related small proteoglycans. Comparisons of the published 24-residue N-terminal protein sequence of bovine skin proteoglycan II core protein with the corresponding region in the deduced sequence of the bovine core protein reveals complete homology. Comparison of the cDNA-derived sequences of bovine bone and human embryonic fibroblast proteoglycans shows a hypervariable region near the N-terminus. Nucleotide homology between bone and fibroblast core proteins was 87% and amino acid homology was 90%.
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Qaisar, U., M. Irfan, A. Meqbool, M. Zahoor, M. Y. Khan, B. Rashid, S. Riazuddin i T. Husnain. "Identification, sequencing and characterization of a stress induced homologue of fructose bisphosphate aldolase from cotton". Canadian Journal of Plant Science 90, nr 1 (1.01.2010): 41–48. http://dx.doi.org/10.4141/cjps08056.
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A drought-induced homologue of fructose-1, 6 bisphosphate aldolase full length cDNA (GaAldp) was isolated and sequenced by gene homology and rapid amplification of cDNA ends (RACE) from cotton variety FDH-786 (Gossypium arboretum). Quantitative polymerase chain reaction (PCR) analysis showed that drought stress, salinity and exogenous treatment with abscisic acid (ABA) enhanced the accumulation of GaAldp transcripts in the leaf and stem tissues of the plant. An alignment of the 1413 bp cDNA and 1937 bp genomic DNA sequences revealed that GaAldp has an open reading frame (ORF) encoding 394 amino acids and contains five introns. The predicted amino acid sequence is homologous to a heat-induced isoform of oat chlorplastic fructose bisphosphate aldolase (FBP) (AF216582) and NPALDP1 from Nicotiana paniculata. The GaAldp sequence includes a novel stroma targeting N-terminal transit peptide (TP) of 45 amino acids, which is 63-76% similar to other chloroplastic TPs.Key words: Fructose-1, 6 bisphosphate aldolase, Gossypium arboreum, drought, abscisic acid, transit peptide, salt stress
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Gotschlich, E. C., M. Seiff i M. S. Blake. "The DNA sequence of the structural gene of gonococcal protein III and the flanking region containing a repetitive sequence. Homology of protein III with enterobacterial OmpA proteins." Journal of Experimental Medicine 165, nr 2 (1.02.1987): 471–82. http://dx.doi.org/10.1084/jem.165.2.471.
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The insert of a lambda gt11 clone expressing gonococcal protein III was sequenced. The deduced amino acid sequence showed a coding frame of 236 amino acids with a typical 22-amino-acid signal peptide, followed by the known NH2-terminal sequence of PIII. The mature protein has a molecular weight of 23,298. It was found that PIII had extensive and very striking homology to the carboxy-terminal portion of enterobacterial OmpA proteins. The homology encompasses the OmpA domain that is believed to be located in the periplasmic space. If the disposition of PIII across the OM is analogous, then the surface-exposed domain consists of less than 40 amino acids. These include a potential 15-amino-acid disulfide loop, a feature not found in OmpA proteins. Hybridization studies with the sequenced insert indicated that it contained a repetitive sequence that occurred at least 20 times in the genome. By additional hybridization studies the area containing the repetitive sequence was narrowed to a region of 43 bp. This region contained an exact copy of the consensus sequence of a 26-bp repetitive sequence recently described. An analogous sequence recurs in an inverted orientation 53 bp downstream.
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Xia-Yun, Jiang, Zou Shu-Ming i Zhou Pei-Gen. "Cloning and sequence analysis of complete cDNA of chitin deacetylase from Mucor racemosus". Chinese Journal of Agricultural Biotechnology 4, nr 2 (sierpień 2007): 167–72. http://dx.doi.org/10.1017/s1479236207001489.
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AbstractA complete chitin deacetylase (CDA) complementary DNA (cDNA) from Mucor racemosus was cloned and sequenced by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification cDNA end (RACE) with gene special conserved primers. The cDNA sequence was submitted to GenBank (DQ538514). The complete cDNA with full-length of 1506 bp contained a 67 bp 5′-untranslated region, an open reading frame of 1344 bp and 95 bp 3′-untranslated region including tailing site AATAAA. The gene encoded a sequence of 448 amino acid residues and consisted of core nucleotides encoding a polysaccharide deacetylase domain covering 32% of the entire sequence. The CDA gene shared sequence homology with those of several fungi. The corresponding homology of the deduced amino acid sequences varied from 21 to 69%. Phylogenetic analysis according to the deduced amino acid sequences matched the classical fungi taxonomy. The three-dimensional structure of this protein was predicted. The protein had a whole CDA functional domain and a polysaccharide deacetylase domain.
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Reenan, R. A., i R. D. Kolodner. "Isolation and characterization of two Saccharomyces cerevisiae genes encoding homologs of the bacterial HexA and MutS mismatch repair proteins." Genetics 132, nr 4 (1.12.1992): 963–73. http://dx.doi.org/10.1093/genetics/132.4.963.
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Abstract Homologs of the Escherichia coli (mutL, S and uvrD) and Streptococcus pneumoniae (hexA, B) genes involved in mismatch repair are known in several distantly related organisms. Degenerate oligonucleotide primers based on conserved regions of E. coli MutS protein and its homologs from Salmonella typhimurium, S. pneumoniae and human were used in the polymerase chain reaction (PCR) to amplify and clone mutS/hexA homologs from Saccharomyces cerevisiae. Two DNA sequences were amplified whose deduced amino acid sequences both shared a high degree of homology with MutS. These sequences were then used to clone the full-length genes from a yeast genomic library. Sequence analysis of the two MSH genes (MSH = mutS homolog), MSH1 and MSH2, revealed open reading frames of 2877 bp and 2898 bp. The deduced amino acid sequences predict polypeptides of 109.3 kD and 109.1 kD, respectively. The overall amino acid sequence identity with the E. coli MutS protein is 28.6% for MSH1 and 25.2% for MSH2. Features previously found to be shared by MutS homologs, such as the nucleotide binding site and the helix-turn-helix DNA binding motif as well as other highly conserved regions whose function remain unknown, were also found in the two yeast homologs. Evidence presented in this and a companion study suggest that MSH1 is involved in repair of mitochondrial DNA and that MSH2 is involved in nuclear DNA repair.
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Mcintyre, CL, AL Rae, MD Curtis i JM Manners. "Sequence and Expression of a Caffeic Acid O-Methyl Transferase Cdna Homologue in the Tropical Forage Legume Stylosanthes Humilis." Functional Plant Biology 22, nr 3 (1995): 471. http://dx.doi.org/10.1071/pp9950471.
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The isolation and characterisation of a cDNA encoding a caffeic acid 0-methyl transferase cDNA homologue (COMT) from Stylosanthes humilis are described. The clone is 1391 nucleotides in length, with an open reading frame encoding a predicted protein of 366 amino acids. Cluster analysis of the deduced amino acid sequence revealed extensive homology to other published O-methyl transferase sequences. Maximum levels of homology were seen with COMTs from alfalfa (87%) and aspen (84%). Southern analysis suggested that this enzyme is encoded by two genes in S. humilis. The mRNA is most strongly expressed in stem tissue, with intermediate levels of expression in young leaves and roots, and does not appear to be induced upon fungal infection or wounding.
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Saxena, A., R. Padmanabha i C. V. Glover. "Isolation and sequencing of cDNA clones encoding alpha and beta subunits of Drosophila melanogaster casein kinase II". Molecular and Cellular Biology 7, nr 10 (październik 1987): 3409–17. http://dx.doi.org/10.1128/mcb.7.10.3409-3417.1987.
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Cloned cDNAs encoding both subunits of Drosophila melanogaster casein kinase II have been isolated by immunological screening of lambda gt11 expression libraries, and the complete amino acid sequence of both polypeptides has been deduced by DNA sequencing. The alpha cDNA contained an open reading frame of 336 amino acid residues, yielding a predicted molecular weight for the alpha polypeptide of 39,833. The alpha sequence contained the expected semi-invariant residues present in the catalytic domain of previously sequenced protein kinases, confirming that it is the catalytic subunit of the enzyme. Pairwise homology comparisons between the alpha sequence and the sequences of a variety of vertebrate protein kinase suggested that casein kinase II is a distantly related member of the protein kinase family. The beta subunit was derived from an open reading frame of 215 amino acid residues and was predicted to have a molecular weight of 24,700. The beta subunit exhibited no extensive homology to other proteins whose sequences are currently known.
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Saxena, A., R. Padmanabha i C. V. Glover. "Isolation and sequencing of cDNA clones encoding alpha and beta subunits of Drosophila melanogaster casein kinase II." Molecular and Cellular Biology 7, nr 10 (październik 1987): 3409–17. http://dx.doi.org/10.1128/mcb.7.10.3409.
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Cloned cDNAs encoding both subunits of Drosophila melanogaster casein kinase II have been isolated by immunological screening of lambda gt11 expression libraries, and the complete amino acid sequence of both polypeptides has been deduced by DNA sequencing. The alpha cDNA contained an open reading frame of 336 amino acid residues, yielding a predicted molecular weight for the alpha polypeptide of 39,833. The alpha sequence contained the expected semi-invariant residues present in the catalytic domain of previously sequenced protein kinases, confirming that it is the catalytic subunit of the enzyme. Pairwise homology comparisons between the alpha sequence and the sequences of a variety of vertebrate protein kinase suggested that casein kinase II is a distantly related member of the protein kinase family. The beta subunit was derived from an open reading frame of 215 amino acid residues and was predicted to have a molecular weight of 24,700. The beta subunit exhibited no extensive homology to other proteins whose sequences are currently known.
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Lawler, J., i R. O. Hynes. "The structure of human thrombospondin, an adhesive glycoprotein with multiple calcium-binding sites and homologies with several different proteins." Journal of Cell Biology 103, nr 5 (1.11.1986): 1635–48. http://dx.doi.org/10.1083/jcb.103.5.1635.
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Thrombospondin is one of a class of adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. We have used two monoclonal antibodies to isolate cDNA clones of thrombospondin from a human endothelial cell cDNA library and have determined the complete nucleotide sequence of the coding region. Three regions of known amino acid sequence of human platelet thrombospondin confirm that the clones are authentic. Three types of repeating amino acid sequence are present in thrombospondin. The first is 57 amino acids long and shows homology with circumsporozoite protein from Plasmodium falciparum. The second is 50-60 amino acids long and shows homology with epidermal growth factor precursor. The third occurs as a continuous eightfold repeat of a 38-residue sequence; structural homology with parvalbumin and calmodulin indicates that these repeats constitute the multiple calcium-binding sites of thrombospondin. The amino acid sequence arg-gly-asp-ala is included in the last type 3 repeat. This sequence is probably the site for the association of thrombospondin with cells. In addition, localized homologies with procollagen, fibronectin, and von Willebrand factor are present in one region of the thrombospondin molecule.
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Wypijewski, K., T. Malinowski, W. Musiał i J. Augustyniak. "Nucleotide sequence of the coat protein gene of the Skierniewice isolate of plum pox virus (PPV)." Acta Biochimica Polonica 41, nr 1 (31.03.1994): 87–95. http://dx.doi.org/10.18388/abp.1994_4778.
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The coat protein (CP) gene of the Skierniewice isolate of plum pox virus (PPV-S) has been amplified using the reverse transcription--polymerase chain reaction (RT-PCR), cloned and sequenced. The nucleotide sequence of the gene and the deduced amino-acid sequence of PPV-S CP were compared with those of other PPV strains. The nucleotide sequence showed very high homology to most of the published sequences. The motif: Asp-Ala-Gly (DAG), important for the aphid transmissibility, was present in the amino-acid sequence. Our isolate did not react in ELISA with monoclonal antibodies MAb06 supposed to be specific for PPV-D.
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Tsuge, Kenji, Takanori Akiyama i Makoto Shoda. "Cloning, Sequencing, and Characterization of the Iturin A Operon". Journal of Bacteriology 183, nr 21 (1.11.2001): 6265–73. http://dx.doi.org/10.1128/jb.183.21.6265-6273.2001.
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ABSTRACT Bacillus subtilis RB14 is a producer of the antifungal lipopeptide iturin A. Using a transposon, we identified and cloned the iturin A synthetase operon of RB14, and the sequence of this operon was also determined. The iturin A operon spans a region that is more than 38 kb long and is composed of four open reading frames, ituD, ituA, ituB, and ituC. The ituD gene encodes a putative malonyl coenzyme A transacylase, whose disruption results in a specific deficiency in iturin A production. The second gene, ituA, encodes a 449-kDa protein that has three functional modules homologous to fatty acid synthetase, amino acid transferase, and peptide synthetase. The third gene, ituB, and the fourth gene, ituC, encode 609- and 297-kDa peptide synthetases that harbor four and two amino acid modules, respectively. Mycosubtilin, which is produced by B. subtilis ATCC 6633, has almost the same structure as iturin A, but the amino acids at positions 6 and 7 in the mycosubtilin sequence ared-Ser→l-Asn, while in iturin A these amino acids are inverted (i.e., d-Asn→l-Ser). Comparison of the amino acid sequences encoded by the iturin A operon and the mycosubtilin operon revealed that ituD, ituA, andituB have high levels of homology to the counterpart genesfenF (79%), mycA (79%), and mycB(79%), respectively. Although the overall level of homology of the amino acid sequences encoded by ituC andmycC, the counterpart of ituC, is relatively low (64%), which indicates that there is a difference in the amino acid sequences of the two lipopeptides, the levels of homology between the putative serine adenylation domains and between the asparagine adenylation domains in the two synthetases are high (79 and 80%, respectively), implying that there is an intragenic domain change in the synthetases. The fact that the flanking sequence of the iturin A synthetase coding region was highly homologous to the flanking sequence that of xynD of B. subtilis 168 and the fact that the promoter of the iturin A operon which we identified was also conserved in an upstream sequence of xynD imply that horizontal transfer of this operon occurred. When the promoter was replaced by the repU promoter of the plasmid pUB110 replication protein, production of iturin A increased threefold.
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Choi, Sunju, Shinya Ohta i Eiichi Ohtsubo. "A Novel IS Element, IS621, of the IS110/IS492 Family Transposes to a Specific Site in Repetitive Extragenic Palindromic Sequences in Escherichia coli". Journal of Bacteriology 185, nr 16 (15.08.2003): 4891–900. http://dx.doi.org/10.1128/jb.185.16.4891-4900.2003.
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ABSTRACT An Escherichia coli strain, ECOR28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. This insertion sequence (named IS621) has one large open reading frame encoding a putative protein that is 326 amino acids in length. A computer-aided homology search using the DNA sequence as the query revealed that IS621 was homologous to the piv genes, encoding pilin gene invertase (PIV). A homology search using the amino acid sequence of the putative protein encoded by IS621 as the query revealed that the protein also has partial homology to transposases encoded by the IS110/IS492 family elements, which were known to have partial homology to PIV. This indicates that IS621 belongs to the IS110/IS492 family but is most closely related to the piv genes. In fact, a phylogenetic tree constructed on the basis of amino acid sequences of PIV proteins and transposases revealed that IS621 belongs to the piv gene group, which is distinct from the IS110/IS492 family elements, which form several groups. PIV proteins and transposases encoded by the IS110/IS492 family elements, including IS621, have four acidic amino acid residues, which are conserved at positions in their N-terminal regions. These residues may constitute a tetrad D-E(or D)-D-D motif as the catalytic center. Interestingly, IS621 was inserted at specific sites within repetitive extragenic palindromic (REP) sequences at 10 loci in the ECOR28 genome. IS621 may not recognize the entire REP sequence in transposition, but it recognizes a 15-bp sequence conserved in the REP sequences around the target site. There are several elements belonging to the IS110/IS492 family that also transpose to specific sites in the repeated sequences, as does IS621. IS621 does not have terminal inverted repeats like most of the IS110/IS492 family elements. The terminal sequences of IS621 have homology with the 26-bp inverted repeat sequences of pilin gene inversion sites that are recognized and used for inversion of pilin genes by PIV. This suggests that IS621 initiates transposition through recognition of their terminal regions and cleavage at the ends by a mechanism similar to that used for PIV to promote inversion at the pilin gene inversion sites.
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Marcus, Frank, Brigitte Gontero, Peter B. Harrsch i Judith Rittenhouse. "Amino acid sequence homology among fructose-1,6-bisphosphatases". Biochemical and Biophysical Research Communications 135, nr 2 (marzec 1986): 374–81. http://dx.doi.org/10.1016/0006-291x(86)90005-7.
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Oldberg, Å., P. Antonsson i D. Heinegård. "The partial amino acid sequence of bovine cartilage proteoglycan, deduced from a cDNA clone, contains numerous Ser-Gly sequences arranged in homologous repeats". Biochemical Journal 243, nr 1 (1.04.1987): 255–59. http://dx.doi.org/10.1042/bj2430255.
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We have determined the sequence of a partial cDNA clone encoding the C-terminal region of bovine cartilage aggregating proteoglycan core protein. The deduced amino acid sequence contains a cysteine-rich region which is homologous with chicken hepatic lectin. This lectin-homologous region has previously been identified in rat and chicken cartilage proteoglycan. The bovine sequence presented here is highly homologous with the rat and chicken amino acid sequences in this apparently globular region. A region containing clusters of Ser-Gly sequences is located N-terminal to the lectin homology domain. These Ser-Gly-rich segments are arranged in tandemly repeated, approx. 100-residue-long, homology domains. Each homology domain consists of an approx. 75-residue-long Ser-Gly-rich region separated by an approx. 25-residue-long segment lacking Ser-Gly dipeptides. These dipeptides are arranged in 10-residue-long segments in the 100-residue-long homology domains. The shorter homologous segments are tandemly repeated some six times in each 100-residue-long homology domain. Serine residues in these repeats are potential attachment sites for chondroitin sulphate chains.
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Bradac, J. A., C. E. Gruber, S. Forry-Schaudies i S. H. Hughes. "Isolation and characterization of related cDNA clones encoding skeletal muscle beta-tropomyosin and a low-molecular-weight nonmuscle tropomyosin isoform". Molecular and Cellular Biology 9, nr 1 (styczeń 1989): 185–92. http://dx.doi.org/10.1128/mcb.9.1.185-192.1989.
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We have isolated and characterized cDNA clones from chicken cDNA libraries derived from skeletal muscle, body wall, and cultured fibroblasts. A clone isolated from a skeletal muscle cDNA library contains the complete protein-coding sequence of the 284-amino-acid skeletal muscle beta-tropomyosin together with 72 bases of 5' untranslated sequence and nearly the entire 3' untranslated region (about 660 bases), lacking only the last 4 bases and the poly(A) tail. A second clone, isolated from the fibroblast cDNA library, contains the complete protein-coding sequence of a 248-amino-acid fibroblast tropomyosin together with 77 bases of 5' untranslated sequence and 235 bases of 3' untranslated sequence through the poly(A) tract. The derived amino acid sequence from this clone exhibits only 82% homology with rat fibroblast tropomyosin 4 and 80% homology with human fibroblast tropomyosin TM30nm, indicating that this clone encodes a third 248-amino-acid tropomyosin isoform class. The protein product of this mRNA is fibroblast tropomyosin 3b, one of two low-molecular-weight isoforms expressed in chicken fibroblast cultures. Comparing the sequences of the skeletal muscle and fibroblast cDNAs with a previously characterized clone which encodes the smooth muscle alpha-tropomyosin reveals two regions of absolute homology, suggesting that these three clones were derived from the same gene by alternative RNA splicing.
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Bradac, J. A., C. E. Gruber, S. Forry-Schaudies i S. H. Hughes. "Isolation and characterization of related cDNA clones encoding skeletal muscle beta-tropomyosin and a low-molecular-weight nonmuscle tropomyosin isoform." Molecular and Cellular Biology 9, nr 1 (styczeń 1989): 185–92. http://dx.doi.org/10.1128/mcb.9.1.185.
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We have isolated and characterized cDNA clones from chicken cDNA libraries derived from skeletal muscle, body wall, and cultured fibroblasts. A clone isolated from a skeletal muscle cDNA library contains the complete protein-coding sequence of the 284-amino-acid skeletal muscle beta-tropomyosin together with 72 bases of 5' untranslated sequence and nearly the entire 3' untranslated region (about 660 bases), lacking only the last 4 bases and the poly(A) tail. A second clone, isolated from the fibroblast cDNA library, contains the complete protein-coding sequence of a 248-amino-acid fibroblast tropomyosin together with 77 bases of 5' untranslated sequence and 235 bases of 3' untranslated sequence through the poly(A) tract. The derived amino acid sequence from this clone exhibits only 82% homology with rat fibroblast tropomyosin 4 and 80% homology with human fibroblast tropomyosin TM30nm, indicating that this clone encodes a third 248-amino-acid tropomyosin isoform class. The protein product of this mRNA is fibroblast tropomyosin 3b, one of two low-molecular-weight isoforms expressed in chicken fibroblast cultures. Comparing the sequences of the skeletal muscle and fibroblast cDNAs with a previously characterized clone which encodes the smooth muscle alpha-tropomyosin reveals two regions of absolute homology, suggesting that these three clones were derived from the same gene by alternative RNA splicing.
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Li, Bing, Yan Hong Wang, Ju Mei Wang i Wei De Shen. "Full Length cDNA Cloning and Expression Characteristics of Ace Gene from Wild Silkworm, Bombyx mandarina". Advanced Materials Research 175-176 (styczeń 2011): 51–55. http://dx.doi.org/10.4028/www.scientific.net/amr.175-176.51.
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Acetylcholinesterase (AChE), which contains two subfamilies, ace1 and ace2 in insects, was identified to be the target of organophosphorous and carbamate insecticides. To research the sequences and tissues expressions of two aces, full length cDNAs encoding two ace genes were cloned, designated as Bmm-ace1 and Bmm-ace2 from larvae of the Bombyx mandarina. The amino acid sequence of Bmm-ace1 shared 99.71 % homology with its homolog, Bm-ace1, in silkworm, Bombyx mori, with two mutations (G664S and S307P), and the amino acid sequence of Bmm-ace2 shared 99.37 % homology with Bm-ace2, in B. mori , with four mutations (M18I, N233S, I310V and G621S). Tissue expression analysis showed that ace1 gene expressed only in the brains and fat bodies of B. mandarina, while ace2 genes expressed in all the tissues tested. ace1 and ace2 expressed highly in brains and fat bodies. The present results are significant to the study of resistance evolution of Lepidorptera as well as the understanding of the mechanism of pesticide resistance of insects.
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Nelapati, Anand Kumar, i JagadeeshBabu PonnanEttiyappan. "Computational Analysis of Therapeutic Enzyme Uricase from Different Source Organisms". Current Proteomics 17, nr 1 (6.01.2020): 59–77. http://dx.doi.org/10.2174/1570164616666190617165107.
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Background:Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi, yeast, plants and animals.Objective:The present study is aimed at elucidating the structure and physiochemical properties of uricase by insilico analysis.Methods:A total number of sixty amino acid sequences of uricase belongs to different sources were obtained from NCBI and different analysis like Multiple Sequence Alignment (MSA), homology search, phylogenetic relation, motif search, domain architecture and physiochemical properties including pI, EC, Ai, Ii, and were performed.Results:Multiple sequence alignment of all the selected protein sequences has exhibited distinct difference between bacterial, fungal, plant and animal sources based on the position-specific existence of conserved amino acid residues. The maximum homology of all the selected protein sequences is between 51-388. In singular category, homology is between 16-337 for bacterial uricase, 14-339 for fungal uricase, 12-317 for plants uricase, and 37-361 for animals uricase. The phylogenetic tree constructed based on the amino acid sequences disclosed clusters indicating that uricase is from different source. The physiochemical features revealed that the uricase amino acid residues are in between 300- 338 with a molecular weight as 33-39kDa and theoretical pI ranging from 4.95-8.88. The amino acid composition results showed that valine amino acid has a high average frequency of 8.79 percentage compared to different amino acids in all analyzed species.Conclusion:In the area of bioinformatics field, this work might be informative and a stepping-stone to other researchers to get an idea about the physicochemical features, evolutionary history and structural motifs of uricase that can be widely used in biotechnological and pharmaceutical industries. Therefore, the proposed in silico analysis can be considered for protein engineering work, as well as for gout therapy.
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Takada, Y., i M. E. Hemler. "The primary structure of the VLA-2/collagen receptor alpha 2 subunit (platelet GPIa): homology to other integrins and the presence of a possible collagen-binding domain." Journal of Cell Biology 109, nr 1 (1.07.1989): 397–407. http://dx.doi.org/10.1083/jcb.109.1.397.
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VLA-2 (also called gpIa/IIa on platelets) is a collagen receptor with a unique alpha subunit and a beta subunit common to other adhesion receptors in the VLA/integrin family. Multiple cDNA clones for the human VLA-2 alpha 2 subunit have been selected from a lambda gtll library by specific antibody screening. The 5,374-bp nucleotide sequence encoded for 1,181 amino acids, including a signal peptide of 29 amino acids followed by a long extracellular domain (1,103 amino acids), a transmembrane domain, and a short cytoplasmic segment (22 amino acids). Direct sequencing of purified alpha 2 protein confirmed the identity of the 15 NH2-terminal amino acids. Overall, the alpha 2 amino acid sequence was 18-25% similar to the sequences known for other integrin alpha subunits. In particular, the alpha 2 sequence matched other integrin alpha chains in (a) the positions of 17 of its 20 cysteine residues; (b) the presence of three metal-binding domains of the general structure DXDXDGXXD; and (c) the transmembrane domain sequence. In addition, the alpha 2 sequence has a 191-amino acid insert (called the I-domain), previously found only in leukocyte integrins of the beta 2 integrin family. The alpha 2 I-domain was 23-41% similar to domains in cartilage matrix protein and von Willebrand factor, which are perhaps associated with collagen binding. The NH2-terminal sequence reported here for alpha 2 does not match the previously reported alpha 2 NH2-terminal sequence (Takada, Y., J. L. Strominger, and M. E. Hemler. 1987. Proc. Natl. Acad. Sci. USA. 84:3239-3243). Resolution of this discrepancy suggests that there may be another VLA heterodimer that resembles VLA-2 in size but has a different amino acid sequence.
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Kristensen, T., R. A. Wetsel i B. F. Tack. "Structural analysis of human complement protein H: homology with C4b binding protein, beta 2-glycoprotein I, and the Ba fragment of B2." Journal of Immunology 136, nr 9 (1.05.1986): 3407–11. http://dx.doi.org/10.4049/jimmunol.136.9.3407.
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Abstract We report here a partial primary structure for human complement protein H. Tryptic peptides comprising 27% of the H molecule were isolated by conventional techniques and were sequenced (333 amino acid residues). Several mixed-sequence oligonucleotide probes were constructed, based on the peptide sequence data, and were used to screen a human liver cDNA library. The largest recombinant plasmid (pH1050), which hybridized with two probes, was further characterized. The cDNA insert of this plasmid contained coding sequence (672 bp) for 224 amino acids of H. The 3' end of this clone had a polyadenylated tail preceded by a polyadenylation recognition site (ATTAAA) and a 3'-untranslated region (229 bp). Four regions of internal homology, each about 60 amino acids in length, were observed in the derived protein sequence from this cDNA clone, and a further seven from the tryptic peptide sequences. The consensus sequence for each of the repetitive units of H was four cysteines, two prolines, three glycines, one tryptophan, and two tyrosines/phenylalanines. Based on the mole percent values for each of these amino acids, it is likely that H is composed of about 20 repetitive units of this nature. Furthermore, the repetitive unit of H shows pronounced homology with the Ba fragment of B, the C4b binding protein, and beta 2-glycoprotein I. Therefore, it seems that at least portions of these proteins have evolved from a common ancestral DNA element.
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Collyear, K., S. I. Girgis, G. Saunders, I. MacIntyre i G. Holt. "Predicted structure of the bovine calcitonin gene-related peptide and the carboxy-terminal flanking peptide of bovine calcitonin precursor". Journal of Molecular Endocrinology 6, nr 2 (kwiecień 1991): 147–52. http://dx.doi.org/10.1677/jme.0.0060147.
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ABSTRACT We have isolated from a bovine genomic library a clone which contains the calcitonin (CT) and CT gene-related peptide (CGRP) sequences, using probes representing the human CT and CGRP sequences. Sequence analysis has identified the nucleotide sequence coding for bovine CT, its C-terminal flanking peptide and bovine CGRP. The deduced amino acid sequence of bovine CGRP revealed a significant homology with other CGRPs so far reported. It differs by only one amino acid from rat CGRPα and porcine CGRP, and by three and four amino acids from human CGRPβ and α respectively. Bovine CT has, however, only 14 out of 32 residues in common with human CT. As in the human CT precursor, the C-terminal flanking peptide of bovine CT precursor is a 21 amino acid peptide. It shares only 11 residues in common with its human counterpart. This study thus provides further evidence that CGRP, in contrast to CT and its C-terminal flanking peptide, is a highly conserved molecule.
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Kim, Keonhee, Chae-Hong Park i Soon-Jin Hwang. "Analyzing the Akinete Protein of the Harmful Freshwater Cyanobacterium, Dolichospermum circinale". Water 15, nr 15 (29.07.2023): 2746. http://dx.doi.org/10.3390/w15152746.
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Akinete is a survival structure in cyanobacteria that has overcome unfavorable environmental conditions and influences their perennial blooms in the freshwater system. However, the akinete cellular and biochemical properties are insufficiently explored. We analyzed the akinete structure, as well as akinete-specific proteins and their amino acid sequence. Akinetes of Dolichospermum circinale were produced from their vegetative cells isolated from the North Han River, Korea. The akinete protein was obtained using electrophoresis, and utilizing its amino acid sequences, its antibody-binding reaction potential (ig-score) was quantified. Akinete protein masses were 17 kDa–180 kDa, and the akinete protein mass was 110 kDa. The ig score was high (average 5.0121 points) in the first half of the amino acid sequence, indicating a β-turn form. The amino acid sequence, having over 50% homology with the D. circinale akinete protein, was not present in GenBank. The homology of the D. circinale akinete-specific protein was very low (9.8%) compared to that of Anabaena variabilis, indicating that its composition was substantially different, even among phylogenetically close taxa. To the best of our knowledge, this is the first report on the D. circinale akinete protein and its amino acid sequence, with preliminary information for their practical application for detecting akinetes in freshwater systems.
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Dang, Tu Thi My, Thao Thi Tran, Tien My Van, Quang Trung Le i Bich Tran Ngoc. "First molecular report of Feline panleukopenia virus infection in diarrheic cats at Can Tho City, Vietnam". Veterinary Integrative Sciences 22, nr 2 (19.10.2023): 631–43. http://dx.doi.org/10.12982/vis.2024.043.
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Feline panleukopenia virus (FPV) belongs to the family Parvoviridae and causes an acute viral infection in cats worldwide. Information on the circulation of FPV among cats is currently limited in Vietnam. Herein, the full–length VP2 gene and molecular characteristics of FPV isolated in diarrhea cats in Can Tho City were first exhibited. Phylogenetic analysis based on seven obtained nucleotide sequences revealed that the isolated sequences were clustered into a narrow group with FPV sequences in the neighboring countries such as China, Thailand, and Japan, and distantly grouped with the vaccine strains. Regarding nucleotide and amino acid sequence analysis, the nucleotide and amino acid homology of 99.98–100% and 99.99–100% among obtained sequences, and showed high homology with reference sequences, accounting for 97.38–98.51% and 98.96–99.27%, respectively. Besides, the nucleotide and amino acid sequences were a homology of 98.51% and 99.26% with two vaccine strains in GenBank. Regarding amino acid translation, seven obtained sequences were closely related to FPV strains, meanwhile, they were different from CPV–2 strains in GenBank at amino acid substitutions of K80, K93 and V103. Overall, this is the first detection of FPV in diarrhea cats and illustrated the molecular characteristics of FPV in the cat population in Can Tho City of Vietnam.
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Steiner, Bret, Sandra Romero-Steiner, Donna Cruce i Robert George. "Cloning and sequencing of the hyaluronate lyase gene fromPropionibacterium acnes". Canadian Journal of Microbiology 43, nr 4 (1.04.1997): 315–21. http://dx.doi.org/10.1139/m97-044.
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The hyaluronate lyase (hyaluronidase) gene from Propionibacterium acnes was cloned and sequenced. The gene was isolated on an EcoRI-generated 3-kb piece of DNA. Expression was less in Escherichia coli than in P. acnes; in E. coli, active enzyme was only cell associated and not secreted. The gene is 2256-bp long and codes for a protein of 82 kDa. Amino terminal sequencing of the protein of the partially purified gene indicated the presence of a 32-amino-acid leader sequence. The leader sequence showed a membrane-spanning domain and all of the features usually associated with the leader for a secreted protein. The amino acid sequence is predicted to share homology with the hyaluronidase enzymes from Streptococcus pneumoniae, Streptococcus agalactiae, and Staphylococcus aureus. A potential hyaluronate-binding domain was identified and antibody against this domain was inhibitory to the enzyme.Key words: Propionibacterium acnes, hyaluronidase, leader sequence, hyaluronate binding domain, sequence homology among hyaluronidases.
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Shoemaker, C. B., i L. D. Mitsock. "Murine erythropoietin gene: cloning, expression, and human gene homology". Molecular and Cellular Biology 6, nr 3 (marzec 1986): 849–58. http://dx.doi.org/10.1128/mcb.6.3.849-858.1986.
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The gene for murine erythropoietin (EPO) was isolated from a mouse genomic library with a human EPO cDNA probe. Nucleotide sequence analysis permitted the identification of the murine EPO coding sequence and the prediction of the encoded amino acid sequence based on sequence conservation between the mouse and human EPO genes. Both the coding DNA and the amino acid sequences were 80% conserved between the two species. Transformation of COS-1 cells with a mammalian cell expression vector containing the murine EPO coding region resulted in secretion of murine EPO with biological activity on both murine and human erythroid progenitor cells. The transcription start site for the murine EPO gene in kidneys was determined. This permitted tentative identification of the transcription control region. The region included 140 base pairs upstream of the cap site which was over 90% conserved between the murine and human genes. Surprisingly, the first intron and much of the 5'- and 3'-untranslated sequences were also substantially conserved between the genes of the two species.
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Shoemaker, C. B., i L. D. Mitsock. "Murine erythropoietin gene: cloning, expression, and human gene homology." Molecular and Cellular Biology 6, nr 3 (marzec 1986): 849–58. http://dx.doi.org/10.1128/mcb.6.3.849.
Pełny tekst źródłaStreszczenie:
The gene for murine erythropoietin (EPO) was isolated from a mouse genomic library with a human EPO cDNA probe. Nucleotide sequence analysis permitted the identification of the murine EPO coding sequence and the prediction of the encoded amino acid sequence based on sequence conservation between the mouse and human EPO genes. Both the coding DNA and the amino acid sequences were 80% conserved between the two species. Transformation of COS-1 cells with a mammalian cell expression vector containing the murine EPO coding region resulted in secretion of murine EPO with biological activity on both murine and human erythroid progenitor cells. The transcription start site for the murine EPO gene in kidneys was determined. This permitted tentative identification of the transcription control region. The region included 140 base pairs upstream of the cap site which was over 90% conserved between the murine and human genes. Surprisingly, the first intron and much of the 5'- and 3'-untranslated sequences were also substantially conserved between the genes of the two species.
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Cerretti, D. P., K. McKereghan, A. Larsen, D. Cosman, S. Gillis i P. E. Baker. "Cloning, sequence, and expression of bovine interferon-gamma." Journal of Immunology 136, nr 12 (15.06.1986): 4561–64. http://dx.doi.org/10.4049/jimmunol.136.12.4561.
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Abstract Bovine interferon-gamma (IFN-gamma) sequences have been isolated by screening a cDNA library with a human IFN-gamma cDNA probe. The cDNA library was constructed from RNA isolated from concanavalin A-stimulated bovine lymph node cells. The open reading frame predicts that the bovine IFN-gamma precursor is composed of 166 amino acids with a predicted m.w. of 19,393. Alignment of the amino acid sequence with human IFN-gamma indicates that mature bovine IFN-gamma is composed of 143 amino acids with a predicted m.w. of 16,858. It has an amino acid homology of 63% with human IFN-gamma, and 47% with murine IFN-gamma. Biologically active bovine IFN-gamma was synthesized in an Escherichia coli expression system.
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Binnie, Craig, Linda Liao, Eva Walczyk i Lawrence T. Malek. "Isolation and characterization of a gene encoding a chymotrypsin-like serine protease fromStreptomyces lividans66". Canadian Journal of Microbiology 42, nr 3 (1.03.1996): 284–88. http://dx.doi.org/10.1139/m96-041.
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A gene encoding a Streptomyces lividans homologue of the chymotrypsin-like serine protease (SAM-P20) of Streptomyces albogriseolus was isolated using the Streptomyces griseus prtB gene as a hybridization probe. Nucleotide sequence analysis of a representative clone uncovered the possible presence of a sequence of 900 nucleotides encoding 300 amino acids, including a putative "prepro" region of 115 amino acids. Alignment of the predicted amino acid sequence of this putative gene with other members of the family of Streptomyces extracellular chymotrypsin-like proteases indicated a high degree of homology in all cases, especially with the SAM-P20 protease. This gene product has been identified as the second member of a potentially larger family of SAL (SAM-P20-like) proteases in S. lividans 66. Keywords: Streptomyces, protease, chymotrypsin.
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Jenne, D., C. Rey, D. Masson, K. K. Stanley, J. Herz, G. Plaetinck i J. Tschopp. "cDNA cloning of granzyme C, a granule-associated serine protease of cytolytic T lymphocytes." Journal of Immunology 140, nr 1 (1.01.1988): 318–23. http://dx.doi.org/10.4049/jimmunol.140.1.318.
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Abstract A cDNA clone corresponding to the complete amino acid sequence of a putative protease CCP2 of murine cytotoxic T lymphocytes was isolated and sequenced. The clone encodes a 248-residue long serine esterase. The deduced N-terminal amino acid sequence is identical over 40 residues to that of granzyme C, a protease of unknown function present in granules of cytotoxic lymphocytes. Analysis of the sequence of granzyme C/CCP2 reveals high homology to other granzyme proteases, i.e. granzyme A (40%) and granzyme B (67%) and to rat mast cell protease II (46%). The amino acids lining the specificity pocket are well conserved between granzyme B, C, and rat mast cell protease II, but not granzyme A, suggesting a similar general specificity of these three proteases.
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Purwantini, Endang, i Lacy Daniels. "Molecular Analysis of the Gene Encoding F420-Dependent Glucose-6-Phosphate Dehydrogenase fromMycobacterium smegmatis". Journal of Bacteriology 180, nr 8 (15.04.1998): 2212–19. http://dx.doi.org/10.1128/jb.180.8.2212-2219.1998.
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ABSTRACT The gene fgd, which codes for F420-dependent glucose-6-phosphate dehydrogenase (FGD), was cloned from Mycobacterium smegmatis, and its sequence was determined and analyzed. A homolog of FGD which has a very high similarity to the M. smegmatis FGD-derived amino acid sequence was identified in Mycobacterium tuberculosis. FGD showed significant homology with F420-dependentN 5,N 10-methylene-tetrahydromethanopterin reductase (MER) from methanogenic archaea and with several hypothetical proteins from M. tuberculosis andArchaeoglobus fulgidus, but FGD showed no significant homology with NADP-dependent glucose-6-phosphate dehydrogenases. Multiple alignment of FGD and MER proteins revealed four conserved consensus sequences. Multiple alignment of FGD with the hypothetical proteins also revealed portions of the same conserved sequences. Moderately high levels of FGD were expressed inEscherichia coli BL21(DE3) carrying fgd in pBluescript.
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Gilchrist, Angus, James A. Fisher i John Smit. "Nucleotide sequence analysis of the gene encoding the Caulobacter crescentus paracrystalline surface layer protein". Canadian Journal of Microbiology 38, nr 3 (1.03.1992): 193–202. http://dx.doi.org/10.1139/m92-033.
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The entire nucleotide sequence of the rsaA gene, encoding the paracrystalline surface (S) layer protein (RsaA) of Caulobacter crescentus CB15A, was determined. The rsaA gene encoded a protein of 1026 amino acids, with a predicted molecular weight of 98 132. Protease cleavage of mature RsaA protein and amino acid sequencing of retrievable peptides yielded two peptides: one aligned with a region approximately two-thirds the way into the predicted amino acid sequence and the second peptide corresponded to the predicted carboxy terminus. Thus, no cleavage processing of the carboxy portion of the RsaA protein occurred during export, and with the exception of the removal of the initial methionine residue, the protein was not processed by cleavage to produce the mature protein. The predicted RsaA amino acid profile was unusual, with small neutral residues predominating. Excepting aspartate, charged amino acids were in relatively low proportion, resulting in an especially acidic protein, with a predicted pI of 3.46. As with most other sequenced S-layer proteins, RsaA contained no cysteine residues. A homology scan of the Swiss Protein Bank 17 produced no close matches to the predicted RsaA sequence. However, RsaA protein shared measurable homology with some exported proteins of other bacteria, including the hemolysins. Of particular interest was a specific region of the RsaA protein that was homologous to the repeat regions of glycine and aspartate residues found in several proteases and hemolysins. These repeats are implicated in the binding of calcium for proper structure and biological activity of these proteins. Those present in the RsaA protein may perform a similar function, since S-layer assembly and surface attachment requires calcium. RsaA protein also shared some homology with 10 other S-layer proteins, with the Campylobacter fetus S-layer protein scoring highest. Key words: Caulobacter crescentus, surface layer, nucleotide sequence, rsaA, calcium.
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Takeshita, S., R. Kikuno, K. Tezuka i E. Amann. "Osteoblast-specific factor 2: cloning of a putative bone adhesion protein with homology with the insect protein fasciclin I". Biochemical Journal 294, nr 1 (15.08.1993): 271–78. http://dx.doi.org/10.1042/bj2940271.
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A cDNA library prepared from the mouse osteoblastic cell line MC3T3-E1 was screened for the presence of specifically expressed genes by employing a combined subtraction hybridization/differential screening approach. A cDNA was identified and sequenced which encodes a protein designated osteoblast-specific factor 2 (OSF-2) comprising 811 amino acids. OSF-2 has a typical signal sequence, followed by a cysteine-rich domain, a fourfold repeated domain and a C-terminal domain. The protein lacks a typical transmembrane region. The fourfold repeated domain of OSF-2 shows homology with the insect protein fasciclin I. RNA analyses revealed that OSF-2 is expressed in bone and to a lesser extent in lung, but not in other tissues. Mouse OSF-2 cDNA was subsequently used as a probe to clone the human counterpart. Mouse and human OSF-2 show a high amino acid sequence conservation except for the signal sequence and two regions in the C-terminal domain in which ‘in-frame’ insertions or deletions are observed, implying alternative splicing events. On the basis of the amino acid sequence homology with fasciclin I, we suggest that OSF-2 functions as a homophilic adhesion molecule in bone formation.
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Kusano, A., M. Iwama, A. Sanda, K. Suwa, E. Nakaizumi, Y. Nakatani, H. Ohkawa, K. Ohgi i M. Irie. "Primary structure of porcine spleen ribonuclease: sequence homology." Acta Biochimica Polonica 44, nr 4 (31.12.1997): 689–99. http://dx.doi.org/10.18388/abp.1997_4371.
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The primary structure of porcine spleen RNase (RNase Psp1) was investigated as a mean of assessing the structure-function relationship of base non-specific ribonucleases of animal origin. N-terminal analysis of RNase Psp1 yielded three N-terminal sequences. These peptides were separated by gel-filtration on Superdex 75HR, after reduction and S-carboxymethylation of RNase Psp1. Determination of the amino-acid sequence of these peptides indicated that the RNase Psp1 preparation consisted of three peptides having 20 (RCM RNase Psp1 pep1), 15 (RCM RNase Psp1 pep2), and 164 (RCM RNase Psp1 pro) amino-acid residues, respectively. It possessed two unique segments containing most of the active site amino-acid residues of the RNases of the RNase T2 family. The alignment of these three peptides in RNase Psp1 was determined by comparison with the other enzymes in the RNase T2 family. The overall results showed that RCM RNase Psp1 pep1 and RCM RNase Psp1 pep2 are derived from the N-terminal and C-terminal regions of RNase Psp1, respectively, probably by processing by some protease. The molecular mass of the protein moiety of RNase Psp1 was 23235 Da.
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Szopa, J. "Expression analysis of a Cucurbita cDNA encoding endonuclease." Acta Biochimica Polonica 42, nr 2 (30.06.1995): 183–89. http://dx.doi.org/10.18388/abp.1995_4643.
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The nuclear matrices of plant cell nuclei display intrinsic nuclease activity which consists in nicking supercoiled DNA. A cDNA encoding a 32 kDa endonuclease has been cloned and sequenced. The nucleotide and deduced amino-acid sequences show high homology to known 14-3-3 protein sequences from other sources. The amino-acid sequence shows agreement with consensus sequences for potential phosphorylation by protein kinase A and C and for calcium, lipid and membrane-binding sites. The nucleotide-binding site is also present within the conserved part of the sequence. By Northern blot analysis, the differential expression of the corresponding mRNA was detected; it was the strongest in sink tissues. The endonuclease activity found on DNA-polyacrylamide gel electrophoresis coincided with mRNA content and was the highest in tuber.
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Kato, Naoki, Sachie Suyama, Masao Shirokane, Masashi Kato, Tetsuo Kobayashi i Norihiro Tsukagoshi. "Novel α-Glucosidase from Aspergillus nidulans with Strong Transglycosylation Activity". Applied and Environmental Microbiology 68, nr 3 (marzec 2002): 1250–56. http://dx.doi.org/10.1128/aem.68.3.1250-1256.2002.
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ABSTRACT Aspergillus nidulans possessed an α-glucosidase with strong transglycosylation activity. The enzyme, designated α-glucosidase B (AgdB), was purified and characterized. AgdB was a heterodimeric protein comprising 74- and 55-kDa subunits and catalyzed hydrolysis of maltose along with formation of isomaltose and panose. Approximately 50% of maltose was converted to isomaltose, panose, and other minor transglycosylation products by AgdB, even at low maltose concentrations. The agdB gene was cloned and sequenced. The gene comprised 3,055 bp, interrupted by three short introns, and encoded a polypeptide of 955 amino acids. The deduced amino acid sequence contained the chemically determined N-terminal and internal amino acid sequences of the 74- and 55-kDa subunits. This implies that AgdB is synthesized as a single polypeptide precursor. AgdB showed low but overall sequence homology to α-glucosidases of glycosyl hydrolase family 31. However, AgdB was phylogenetically distinct from any other α-glucosidases. We propose here that AgdB is a novel α-glucosidase with unusually strong transglycosylation activity.
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Kirana, Maha, Rahaju Ernawati, Jola Rahmahani i Fedik Abdul Rantam. "Characterization of Gene Coding Fusion Protein of Newcastle Disease Virus Infected in Native Chicken in Surabaya". Jurnal Medik Veteriner 5, nr 1 (22.04.2022): 103–8. http://dx.doi.org/10.20473/jmv.vol5.iss1.2022.103-108.
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This study aimed to discover the homology of nucleotide sequence, homology percentage, and those relations phylogenetic of protein Fusion (F) gene coding of Newcastle disease in domestic chicken (Gallus gallus domesticus) in Surabaya using some comparison isolate from GenBank. Samples were scoured of digestive organs from native chicken, that was collected from a traditional market in Wonokromo, Surabaya. Samples were tested using RT-PCR with primer forward and reverse with target 976bp, a positive sample which is continued with sequencing then homology and nucleotide analysis which is done and which is translated into amino acid. The result of homology chc/SBY/2018 sample has a similarity of 88% with references sequence, while with Lasota vaccine has a similarity of 87%, and the highest result of homology showed by the comparison with various isolates in Indonesia 90-95%. Translation results from nucleotide alignment into amino acid showed shifts in amino acid structure, which is amino acid shifts could be affected by many things like nutrition, wheater, environment, etc. The conclusion was chc/SBY/2018 sample has a quite high similarity with Indonesian isolates and undergoes mutation on nucleotide structure on amino acid and phylogenetic analysis. This study related to some isolates of vaccine and some isolates in Indonesia.
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Upton, C., i G. McFadden. "DNA sequence homology between the terminal inverted repeats of Shope fibroma virus and an endogenous cellular plasmid species". Molecular and Cellular Biology 6, nr 1 (styczeń 1986): 265–76. http://dx.doi.org/10.1128/mcb.6.1.265-276.1986.
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DNA hybridization experiments indicate that the genome of a tumorigenic poxvirus. Shope fibroma virus (SFV), possesses sequence homology with DNA isolated from uninfected rabbit cells. Southern blotting experiments, either with high-complexity rabbit DNA as probe and SFV restriction fragments as targets or with high-specific activity, 32P-labeled, cloned SFV sequences as probes and rabbit DNA as target, indicate that the homologous sequences map at two locations within the viral genome, one in each copy of the terminal inverted repeat sequences. Unexpectedly, Southern blots revealed that the homologous host sequences reside in a rabbit extrachromosomal DNA element. This autonomous low-molecular-weight DNA species could be specifically amplified by cycloheximide treatment and was shown by isopycnic centrifugation in cesium chloride-ethidium bromide to consist predominantly of covalently closed circular DNA molecules. DNA sequencing of pSIC-9, a cloned 1.9-kilobase fragment of the rabbit plasmid species, indicated extensive homology at the nucleotide level over a 1.5-kilobase stretch of the viral terminal inverted repeat. Analysis of open reading frames in both the plasmid and SFV DNA revealed that (i) the N-terminal 157-amino acid sequence of a potential 514-amino acid SFV polypeptide is identical to the N-terminal 157 amino acids of one pSIC-9 open reading frame, and (ii) a second long pSIC-9 open reading frame of 361 amino acids, although significantly diverged from the comparable nucleotide sequence in the virus, possessed considerable homology to a family of cellular protease inhibitors, including alpha 1-antichymotrypsin, alpha 1-antitrypsin, and antithrombin III. The potential role of such cellular plasmid-like DNA species as a mediator in the exchange of genetic information between the host cell and a cytoplasmically replicating poxvirus is discussed.
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Upton, C., i G. McFadden. "DNA sequence homology between the terminal inverted repeats of Shope fibroma virus and an endogenous cellular plasmid species." Molecular and Cellular Biology 6, nr 1 (styczeń 1986): 265–76. http://dx.doi.org/10.1128/mcb.6.1.265.
Pełny tekst źródłaStreszczenie:
DNA hybridization experiments indicate that the genome of a tumorigenic poxvirus. Shope fibroma virus (SFV), possesses sequence homology with DNA isolated from uninfected rabbit cells. Southern blotting experiments, either with high-complexity rabbit DNA as probe and SFV restriction fragments as targets or with high-specific activity, 32P-labeled, cloned SFV sequences as probes and rabbit DNA as target, indicate that the homologous sequences map at two locations within the viral genome, one in each copy of the terminal inverted repeat sequences. Unexpectedly, Southern blots revealed that the homologous host sequences reside in a rabbit extrachromosomal DNA element. This autonomous low-molecular-weight DNA species could be specifically amplified by cycloheximide treatment and was shown by isopycnic centrifugation in cesium chloride-ethidium bromide to consist predominantly of covalently closed circular DNA molecules. DNA sequencing of pSIC-9, a cloned 1.9-kilobase fragment of the rabbit plasmid species, indicated extensive homology at the nucleotide level over a 1.5-kilobase stretch of the viral terminal inverted repeat. Analysis of open reading frames in both the plasmid and SFV DNA revealed that (i) the N-terminal 157-amino acid sequence of a potential 514-amino acid SFV polypeptide is identical to the N-terminal 157 amino acids of one pSIC-9 open reading frame, and (ii) a second long pSIC-9 open reading frame of 361 amino acids, although significantly diverged from the comparable nucleotide sequence in the virus, possessed considerable homology to a family of cellular protease inhibitors, including alpha 1-antichymotrypsin, alpha 1-antitrypsin, and antithrombin III. The potential role of such cellular plasmid-like DNA species as a mediator in the exchange of genetic information between the host cell and a cytoplasmically replicating poxvirus is discussed.
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Kalmokoff, M. L., D. Lu, M. F. Whitford i R. M. Teather. "Evidence for Production of a New Lantibiotic (Butyrivibriocin OR79A) by the Ruminal Anaerobe Butyrivibrio fibrisolvensOR79: Characterization of the Structural Gene Encoding Butyrivibriocin OR79A". Applied and Environmental Microbiology 65, nr 5 (1.05.1999): 2128–35. http://dx.doi.org/10.1128/aem.65.5.2128-2135.1999.
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ABSTRACT The ruminal anaerobe Butyrivibrio fibrisolvens OR79 produces a bacteriocin-like activity demonstrating a very broad spectrum of activity. An inhibitor was isolated from spent culture fluid by a combination of ammonium sulfate and acidic precipitations, reverse-phase chromatography, and high-resolution gel filtration. N-terminal analysis of the isolated inhibitor yielded a 15-amino-acid sequence (G-N/Q-G/P-V-I-L-X-I-X-H-E-X-S-M-N). Two different amino acid residues were detected in the second and third positions from the N terminus, indicating the presence of two distinct peptides. A gene with significant homology to one combination of the determined N-terminal sequence was cloned, and expression of the gene was confirmed by Northern blotting. The gene (bvi79A) encoded a prepeptide of 47 amino acids and a mature peptide, butyrivibriocin OR79A, of 25 amino acids. Significant sequence homology was found between this peptide and previously reported lantibiotics containing the double-glycine leader peptidase processing site. Immediately downstream of bvi79Awas a second, partial open reading frame encoding a peptide with significant homology to proteins which are believed to be involved in the synthesis of lanthionine residues. These findings indicate that the isolated inhibitory peptides represent new lantibiotics. Results from both total and N-terminal amino acid sequencing indicated that the second peptide was identical to butyrivibriocin OR79A except for amino acid substitutions in positions 2 and 3 of the mature lantibiotic. Only a single coding region was detected when restriction enzyme digests of total DNA were probed either with an oligonucleotide based on the 5′ region of bvi79A or with degenerate oligonucleotides based on the predicted sequence of the second peptide.
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Nakagomi, K., Y. Kohwi, L. A. Dickinson i T. Kohwi-Shigematsu. "A novel DNA-binding motif in the nuclear matrix attachment DNA-binding protein SATB1". Molecular and Cellular Biology 14, nr 3 (marzec 1994): 1852–60. http://dx.doi.org/10.1128/mcb.14.3.1852-1860.1994.
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The nuclear matrix attachment DNA (MAR) binding protein SATB1 is a sequence context-specific binding protein that binds in the minor groove, making virtually no contact with the DNA bases. The SATB1 binding sites consist of a special AT-rich sequence context in which one strand is well-mixed A's, T's, and C's, excluding G's (ATC sequences), which is typically found in clusters within different MARs. To determine the extent of conservation of the SATB1 gene among different species, we cloned a mouse homolog of the human STAB1 cDNA from a cDNA expression library of the mouse thymus, the tissue in which this protein is predominantly expressed. This mouse cDNA encodes a 764-amino-acid protein with a 98% homology in amino acid sequence to the human SATB1 originally cloned from testis. To characterize the DNA binding domain of this novel class of protein, we used the mouse SATB1 cDNA and delineated a 150-amino-acid polypeptide as the binding domain. This region confers full DNA binding activity, recognizes the specific sequence context, and makes direct contact with DNA at the same nucleotides as the whole protein. This DNA binding domain contains a novel DNA binding motif: when no more than 21 amino acids at either the N- or C-terminal end of the binding domain are deleted, the majority of the DNA binding activity is lost. The concomitant presence of both terminal sequences is mandatory for binding. These two terminal regions consist of hydrophilic amino acids and share homologous sequences that are different from those of any known DNA binding motifs. We propose that the DNA binding region of SATB1 extends its two terminal regions toward DNA to make direct contact with DNA.
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Nakagomi, K., Y. Kohwi, L. A. Dickinson i T. Kohwi-Shigematsu. "A novel DNA-binding motif in the nuclear matrix attachment DNA-binding protein SATB1." Molecular and Cellular Biology 14, nr 3 (marzec 1994): 1852–60. http://dx.doi.org/10.1128/mcb.14.3.1852.
Pełny tekst źródłaStreszczenie:
The nuclear matrix attachment DNA (MAR) binding protein SATB1 is a sequence context-specific binding protein that binds in the minor groove, making virtually no contact with the DNA bases. The SATB1 binding sites consist of a special AT-rich sequence context in which one strand is well-mixed A's, T's, and C's, excluding G's (ATC sequences), which is typically found in clusters within different MARs. To determine the extent of conservation of the SATB1 gene among different species, we cloned a mouse homolog of the human STAB1 cDNA from a cDNA expression library of the mouse thymus, the tissue in which this protein is predominantly expressed. This mouse cDNA encodes a 764-amino-acid protein with a 98% homology in amino acid sequence to the human SATB1 originally cloned from testis. To characterize the DNA binding domain of this novel class of protein, we used the mouse SATB1 cDNA and delineated a 150-amino-acid polypeptide as the binding domain. This region confers full DNA binding activity, recognizes the specific sequence context, and makes direct contact with DNA at the same nucleotides as the whole protein. This DNA binding domain contains a novel DNA binding motif: when no more than 21 amino acids at either the N- or C-terminal end of the binding domain are deleted, the majority of the DNA binding activity is lost. The concomitant presence of both terminal sequences is mandatory for binding. These two terminal regions consist of hydrophilic amino acids and share homologous sequences that are different from those of any known DNA binding motifs. We propose that the DNA binding region of SATB1 extends its two terminal regions toward DNA to make direct contact with DNA.
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Wu, C. T., M. Budding, M. S. Griffin i J. M. Croop. "Isolation and characterization of Drosophila multidrug resistance gene homologs". Molecular and Cellular Biology 11, nr 8 (sierpień 1991): 3940–48. http://dx.doi.org/10.1128/mcb.11.8.3940-3948.1991.
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Mammalian multidrug-resistant cell lines, selected for resistance to a single cytotoxic agent, display cross-resistance to a broad spectrum of structurally and functionally unrelated compounds. These cell lines overproduce a membrane protein, the P-glycoprotein, which is encoded by a member(s) of a multigene family, termed mdr or pgp. The amino acid sequence of the P-glycoprotein predicts an energy-dependent transport protein with homology to a large superfamily of proteins which transport a wide variety of substances. This report describes the isolation and characterization of two Drosophila homologs of the mammalian mdr gene. These homologs, located in chromosomal sections 49EF and 65A, encode proteins that share over 40% amino acid identity to the human and murine mdr P-glycoproteins. Fly strains bearing disruptions in the homolog in section 49EF have been constructed and implicate this gene in conferring colchicine resistance to the organism. This work sets the foundation for the molecular and genetic analysis of mdr homologs in Drosophila melanogaster.
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Wu, C. T., M. Budding, M. S. Griffin i J. M. Croop. "Isolation and characterization of Drosophila multidrug resistance gene homologs." Molecular and Cellular Biology 11, nr 8 (sierpień 1991): 3940–48. http://dx.doi.org/10.1128/mcb.11.8.3940.
Pełny tekst źródłaStreszczenie:
Mammalian multidrug-resistant cell lines, selected for resistance to a single cytotoxic agent, display cross-resistance to a broad spectrum of structurally and functionally unrelated compounds. These cell lines overproduce a membrane protein, the P-glycoprotein, which is encoded by a member(s) of a multigene family, termed mdr or pgp. The amino acid sequence of the P-glycoprotein predicts an energy-dependent transport protein with homology to a large superfamily of proteins which transport a wide variety of substances. This report describes the isolation and characterization of two Drosophila homologs of the mammalian mdr gene. These homologs, located in chromosomal sections 49EF and 65A, encode proteins that share over 40% amino acid identity to the human and murine mdr P-glycoproteins. Fly strains bearing disruptions in the homolog in section 49EF have been constructed and implicate this gene in conferring colchicine resistance to the organism. This work sets the foundation for the molecular and genetic analysis of mdr homologs in Drosophila melanogaster.
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Kiiskinen, Laura-Leena, i Markku Saloheimo. "Molecular Cloning and Expression in Saccharomyces cerevisiae of a Laccase Gene from the Ascomycete Melanocarpus albomyces". Applied and Environmental Microbiology 70, nr 1 (styczeń 2004): 137–44. http://dx.doi.org/10.1128/aem.70.1.137-144.2004.
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ABSTRACT The lac1 gene encoding an extracellular laccase was isolated from the thermophilic fungus Melanocarpus albomyces. This gene has five introns, and it encodes a protein consisting of 623 amino acids. The deduced amino acid sequence of the laccase was shown to have high homology with laccases from other ascomycetes. In addition to removal of a putative 22-amino-acid signal sequence and a 28-residue propeptide, maturation of the translation product of lac1 was shown to involve cleavage of a C-terminal 14-amino-acid extension. M. albomyces lac1 cDNA was expressed in Saccharomyces cerevisiae under the inducible GAL1 promoter. Extremely low production was obtained with the expression construct containing laccase cDNA with its own signal and propeptide sequences. The activity levels were significantly improved by replacing these sequences with the prepro sequence of the S. cerevisiae α-factor gene. The role of the C-terminal extension in laccase production in S. cerevisiae was also studied. Laccase production was increased sixfold with the modified cDNA that had a stop codon after the native processing site at the C terminus.
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Kita, T., C. E. Smith, K. F. Fok, K. L. Duffin, W. M. Moore, P. J. Karabatsos, J. F. Kachur i in. "Characterization of human uroguanylin: a member of the guanylin peptide family". American Journal of Physiology-Renal Physiology 266, nr 2 (1.02.1994): F342—F348. http://dx.doi.org/10.1152/ajprenal.1994.266.2.f342.
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Guanylin, a peptide homologue of the bacterial heat-stable enterotoxins (ST), is an endogenous activator of guanylate cyclase C (GC-C). We have initiated a search for other members of the guanylin peptide family and in the current study describe a "guanylin-like peptide" from human urine. Bioactivity was monitored by determining the effect of urine extracts on T84 cell guanosine 3',5'-cyclic monophosphate (cGMP) levels. Purification yielded two bioactive peaks of peptides that, when sequenced by NH2-terminal analysis, possessed 15 and 16 amino acids. The sequence of the smaller peptide represented an NH2-terminal truncation of the larger peptide. We have termed the larger peptide human uroguanylin; it has the following amino acid sequence: NDDCELCVNVACTGCL. Human uroguanylin shares amino acid sequence homology with guanylin and ST. Synthetic uroguanylin increased cGMP levels in T84 cells, competed with 125I-labeled ST for receptors, and stimulated Cl- secretion as reflected by an increased short-circuit current. Thus we report the isolation from human urine of a unique peptide, uroguanylin, that behaves in a manner similar to guanylin and appears to be a new member of this peptide family.
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Watson, D. C., M. Yaguchi, J. G. Bisaillon, R. Beaudet i R. Morosoli. "The amino acid sequence of a gonococcal growth inhibitor from Staphylococcus haemolyticus". Biochemical Journal 252, nr 1 (15.05.1988): 87–93. http://dx.doi.org/10.1042/bj2520087.
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A gonococcal inhibitor produced by Staphylococcus haemolyticus was separated into three components by reverse-phase h.p.l.c. The amino acid composition analysis of each of the three components indicated extensive similarities. N-Terminal sequence analysis of all three components allowed the identification of the first 27-30 residues of each. The complete primary structure of each component was determined from the sequence analysis of trypic peptides and peptides generated by mild acid hydrolysis. Each component is composed of 44 amino acid residues, with evidence suggesting the presence of an N-terminal formylmethionine residue in each. The components I, II and III have respectively 33, 29 and 33 identical amino acid residues in their sequences, which represents 75%, 65.9% and 75% homology. These components contain a high proportion of hydrophobic amino acids, and their hydrophobicity profiles are closely related. Also, each of the three components contains a positively charged residue (lysine) as the third residue, followed by a core of hydrophobic residues. These results suggest that the three components are possible signal sequences of one or more secreted or membrane-associated proteins.
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Palfree, R. G., S. Sirlin, F. J. Dumont i U. Hämmerling. "N-terminal and cDNA characterization of murine lymphocyte antigen Ly-6C.2." Journal of Immunology 140, nr 1 (1.01.1988): 305–10. http://dx.doi.org/10.4049/jimmunol.140.1.305.
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Abstract The Ly-6C.2 molecule was purified from K36 tumor cells by affinity chromatography and gel filtration. The electrophoretically homogeneous preparation, with m.w. 15,000, was tested with a panel of antibodies that confirmed the presence of the LY-6C.2 epitope. An N-terminal sequence of 39 amino acids was obtained showing 59% homology with the corresponding portion of the Ly-6A.2 polypeptide. Based on the least homologous (29%) 14 amino acid segment, an oligonucleotide probe was constructed, and Ly-6C.2 cDNA was cloned from a BW5147 cDNA library. A 794-base pair cDNA containing the entire coding region had 82% homology with Ly-6A.2 cDNA. The encoded polypeptide sequence of 131 amino acids containing a perfect correlation with the N-terminal sequence data was 63% homologous with that of Ly-6A.2. The greatest homology was in the leader, first 16 N-terminal and last 39 C-terminal amino acids. The latter are likely to be important in determining the attachment of glycophosphatidylinositol. Despite results indicating fewer disulfide constraints in the Ly-6C molecule, the predicted sequence contains 10 cysteine residues nearly perfectly matched with those predicted in Ly-6A.
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Hellman, U., G. Eggertsen, A. Engström i J. Sjöquist. "Amino acid sequence of the trypsin-generated C3d fragment from human complement factor C3". Biochemical Journal 230, nr 2 (1.09.1985): 353–61. http://dx.doi.org/10.1042/bj2300353.
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Human C3d (try-C3d), prepared from trypsin-digested C3, was fragmented by cleavage with CNBr. Eight peptides were defined and separated by h.p.l.c. on reversed-phase columns. By automatic Edman degradation the complete sequences of five peptides and partial sequences of three peptides were determined. To obtain overlapping peptides the latter three fragments were digested with trypsin, chymotrypsin or Staphylococcus aureus V8 proteinase, after which the fragments were separated on reversed-phase columns. Two of the CNBr-cleavage peptides were completely sequenced, and 70% of the sequence of the remaining CNBr-cleavage peptide was determined. The non-sequenced part represents a very hydrophobic segment of try-C3d. The sequence data obtained represent 90% of the primary structure of try-C3d. Alignment of the CNBr-cleavage fragments was made easier by comparison with the cDNA sequence of mouse pro-C3 [Wetsel, Lundwall, Davidson, Gibson, Tack & Fey (1984) J. Biol. Chem. 259, 13857-13862]. Comparison of try-C3d with the equivalent part of human C4B revealed an extensive sequence homology in the N-terminal half of the molecules.