DNA Sequence (DNA SEQUENCE)

Publications in this journal

• Article: Sequencing and Radiation Hybrid Mapping of Canine Uromodulin

  Melissa L. Cox, Pascale Quignon, Francis Galibert, George E. Lees, Keith E. Murphy
  [show abstract] [hide abstract]
  ABSTRACT: Our interest is in understanding the genetic bases for hereditary renal diseases of the domestic dog ( Canis familiaris ) and in characterizing gene loci for placement on the map of the canine genome. We report here on the cloning, sequencing and radiation hybrid mapping of the canine cDNA encoding uromodulin, a renal-specific glycoprotein. The cDNA is 2.3 kb in length and, as expected, comparisons of nucleotide sequences reveal that canine umod is quite similar to umod of other mammals. The predicted amino acid sequence of canine uromodulin has at least 70% identity with other mammalian uromodulin proteins. Canine umod has been mapped on the RHDF5000 radiation hybrid panel and positioned on the most recent canine genome map. Data indicate that umod is linked to the marker CZP2 (canine zona pellucida gene) on an RH group not yet assigned to a canine chromosome. The human umod and CZP2 genes are located on chromosome 16p13.
  DNA Sequence 07/2009; 14(1):61-69.
• Article: Cloning and characterization of human CAGLP gene encoding a novel EF-hand protein.

  Shuai Chen, Jin-Hu Guo, Hexige Saiyin, Li Chen, Guang-Jin Zhou, Chao-Qun Huang, Long Yu
  [show abstract] [hide abstract]
  ABSTRACT: The EF-hand proteins, containing conserved Ca2+ binding motifs, play important roles in many biological processes. Through data mining, a novel human gene, CAGLP (calglandulin-like protein) was predicted and subsequently isolated from human skeleton muscle. The open reading frame of CAGLP is 543 bp in length, coding a putative Ca2+ binding protein with four EF-hand motifs. The deduced amino acid sequence of CAGLP displays high similarity with Bothrops insularis snake protein calglandulin (80%). The results of PCR amplification using cDNA from 17 human tissues indicated that human CAGLP is expressed in prostate, thymus, heart, skeleton muscle, bone marrow and ovary. Functional CAGLP::EGFP (enhanced green fluorescent protein) fusion protein revealed that CAGLP accumulated through-out Hela cells. Western blot using anti-EGFP antibodies indicated that the CAGLP protein has a molecular weight of about 19 kD. A phylogenetic tree showed that CAGLP and calglandulin may be orthologous proteins representing a distinct group in the EF-hand proteins.
  DNA Sequence 07/2009; 15(5-6):365-8.
• Article: Isolation and characterization of a cDNA encoding a papain-like cysteine protease from alfalfa.

  Longfeng Yan, Jianguo Han, Qingchuan Yang, Yan Sun, Junmei Kang, Zhipeng Liu, Mingsheng Wu
  [show abstract] [hide abstract]
  ABSTRACT: Protein hydrolyzation is activated and involved in response to various stress signals. In the present study, a full-length cDNA, named MsCP1, encoding a papain-like cysteine protease was obtained by degenerated primers and 3'- and 5'-RACE from salt-tolerant alfalfa. The cDNA contained an open reading frame encoding a deduced protein of 350 amino acids with a putative N-terminal signal peptide, NPIR vacuole-sorting signal sequence and potential N-linked glycosylation sites. The deduced sequence showed a high similarity to deduced proteins from pea, tobacco, tomato and ryegrass. Fusion expression analysis in Escherichia coli showed that the putative eukaryotic signal peptide prevented its expression in prokaryotic system. The integration and transcript of the expression elements in transgenic tobacco plants were detected with Southern blot and RT-PCR analysis.
  DNA Sequence 07/2008; 19(3):274-81.
• Article: Nucleotide sequence of a G/11 family xylanase encoding gene in Scytalidium thermophilum.

  Sophon Boonlue, Tadanori Aimi, Yutaka Kitamoto, Tsutomu Morinaga
  [show abstract] [hide abstract]
  ABSTRACT: The nucleotide sequence of the xylanase encoding gene in Scytalidium thermophilum Af101-3 was determined. The gene encodes a family G/11 xylanase, and the coding region is interrupted by a 72 bp intron. Transcription of the gene was investigated by reverse transcription PCR (RT-PCR). Transcription of the gene was not affected by the presence of 2% glucose in the medium. Xylanase production in S. thermophilum Af101-3 was also affected by concentration of glucose in the medium (modified Czapek's supplemented with 2% corn cob powder and 0.1% glucose). Therefore, xylanase expression in this fungus may not be regulated by the carbon source in the medium.
  DNA Sequence 07/2008; 19(3):366-70.
• Article: Genome-wide analysis of SINA family in plants and their phylogenetic relationships.

  Meng Wang, Ying Jin, Junjie Fu, Yun Zhu, Jun Zheng, Jian Hu, Guoying Wang
  [show abstract] [hide abstract]
  ABSTRACT: SINA genes in plants are part of a multigene family with 5 members in Arabidopsis thaliana, 10 members in Populus trichocarpa, 6 members in Oryza sativa, at least 6 members in Zea mays and at least 1 member in Physcomitrella patens. Six members in maize were confirmed by RT-PCR. All SINAs have one RING domain and one SINA domain. These two domains are highly conserved in plants. According to the motif organization and phylogenetic tree, SINA family members were divided into 2 groups. In addition, through semi-quantitative RT-PCR analysis of maize members and Digital Northern analysis of Arabidopsis and rice members, we found that the tissue expression patterns are more diverse in monocot than in Arabidopsis.
  DNA Sequence 07/2008; 19(3):206-16.
• Article: Cloning and characterization of a novel PI-like MADS-box gene in Phalaenopsis orchid.

  Bin Guo, Tian Zhang, Jinlei Shi, Donghong Chen, Daleng Shen, Feng Ming
  [show abstract] [hide abstract]
  ABSTRACT: The specification of floral organ identity during development depends on the function of a limited number of homeotic genes, which are grouped into three classes. Most of these genes belong to the MADS-box gene family. The PISTILLATA (PI) family of MADS-box genes plays important roles in controlling the development of the petal and stamen of flowering plants. In an attempt to understand the molecular mechanisms behind floral development in the orchid, a MADS-box gene, PhPI10 was cloned from Phalaenopsis orchid. We provide phylogenetic evidence that PhPI10 is closely related to PI-like genes of angiosperms, which are required for establishing petal and stamen identity. In addition, there is a PI-motif in the C-terminal of the putative amino acid sequence of PhPI10. Southern analysis showed that a single copy of PhPI10 was present in the Phalaenopsis orchid genome. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that its transcription was only detectable in the top of the floral bud and undetectable in other vegetative organs. In the floral organs its expression was limited to the lip of the Phalaenopsis flower.
  DNA Sequence 07/2008; 19(3):332-9.
• Article: Cloning and characterization of farnesyl pyphosphate synthase gene from the ABA-producing fungi Botrytis cinerea.

  Hong-Yuan Deng, Xin-Rong Ma, Zhi-Dong Li, Hong Tan
  [show abstract] [hide abstract]
  ABSTRACT: Farnesyl pyphosphate synthase (FPPS) catalyzes the systhesis of farnesyl pyphosphate and appears to be a promising regulation site of Abscisic acid (ABA) biosynthesis pathway in fungi. Here we reported the isolation and characterization of Botrytis cinerea (FPPS) gene. The cloned FPPS gene carries an open reading frame of 1044-bp encoding a deduced protein of 347 amino acids with a molecular weight of 39.83 kDa, and the coding region is interrupted with a 63-bp intron. Comparison analysis showed that the deduced amino acids sequence share high similarity with other known FPPS gene. Southern blot revealed a single copy of FPPS gene in the genomic DNA. The result of transcription analysis indicated that the cloned FPPS gene expressed constitutively and was not induced in ABA accumulation phase.
  DNA Sequence 07/2008; 19(3):313-8.
• Article: Isolation and characterization of two distinct classes of DXS genes in Hevea brasiliensis.

  Yortyot Seetang-Nun, Thomas D Sharkey, Wallie Suvachittanont
  [show abstract] [hide abstract]
  ABSTRACT: Two cDNAs encoding two distinct classes of DXSs were cloned from leaves (HbDXS1) and latex (HbDXS2) of Hevea brasiliensis by RT-PCR based methods. HbDXS1 encodes a protein of 720 amino acids, with a high homology to the class I of plant DXS proteins, and HbDXS2 encodes a protein predicted to contain 711 amino acids and with a high homology to the plant DXS class II proteins. Several important motifs and amino acid positions characteristic of DXS proteins are strictly conserved in both new HbDXS proteins. The two HbDXS genes were differentially expressed in various tissues of H. brasiliensis. The transcriptional levels of HbDXS2 were similar in both a high-yielding rubber clone (RRIM 600) and the wild type. Ethephon increased the latex yield and caused a transient increase of expression of the HbDXS2 gene. The expression of HbDXS2 in latex indicates that it may have a primary function in carotenoid biosynthesis rather than for natural rubber.
  DNA Sequence 07/2008; 19(3):291-300.
• Article: Evolution and expression of gamma-aminobutyric acid type A receptor-associated protein from the amphioxus Branchiostoma belcheri.

  Jianxiao Tian, Shicui Zhang, Zhenhui Liu, Yongjun Wang
  [show abstract] [hide abstract]
  ABSTRACT: The cDNA encoding a gamma-aminobutyric acid type A (GABA(A)) receptor-associated protein (GABARAP) was identified from the gut cDNA library of amphioxus Branchiostoma belcheri. It consisted of 1246 bp with a 354 bp open reading frame coding for a 117 amino acids protein of 13.9 kDa. The phylogenetic tree analysis showed that amphioxus GABARAP clustered with GABARAPs, separating from GABARAP-like proteins including amphioxus GABARAPL2. Amphioxus GABARAP gene had an exon-intron organization similar to human, mouse, zebrafish and sea squirt GABARAP homologs in terms of both exon number and sequence homology of each exon, hinting at the clue that GABARAP gene transcription is regulated similarly in all the chordates. In situ hybridization histochemistry revealed a ubiquitous expression pattern of amphioxus GABARAP gene, although it was temporally expressed specifically in the primitive gut of 2- to 10-day larvae, suggesting a conserved role of GABARAP in amphioxus as well as in mammalian species.
  DNA Sequence 07/2008; 19(3):319-25.
• Article: Cloning and characterization of DGAT1 gene of Riverine buffalo.

  R T Venkatachalapathy, Arjava Sharma, Soumi Sukla, Tarun K Bhattacharya
  [show abstract] [hide abstract]
  ABSTRACT: The present study was carried out to characterize the DGAT1 gene of Riverine buffalo. Total RNA was extracted from the mammary tissue of buffalo and DGAT1cDNA were synthesized by RT-PCR, then cloned using pDRIVE cloning vector and sequenced. The sequencing revealed that the size of DGAT1 gene was 1470 bp with GC content of 62.30%. The gene encoded for 489 amino acid precursors and that it possessed 32 amino acids signal peptide. The similarity of buffalo DGAT1 mRNA sequence with that of cattle, pig, monkey, human, mice and rat were determined as 98.4, 90.7, 85.4, 85.0, 77.4 and 77.1%, respectively. Phylogenetic tree constructed from the derived DGAT1 protein sequences of 15 different species illustrated a unique branches for mammals, fly, nematode and plants. Among mammals, cattle and buffalo grouped together, whereas swine formed another group in the same branch. Four motifs were predicted in buffalo DGAT1 peptide sequence, one N-linked glycosylation site (246th position), two putative tyrosine phosphorylation site (316 and 261), one putative diacylglycerol binding site (382-392 amino acid position) and a conserved domain MBOAT (membrane bound acyl transferase from 150 to 474 amino acids) with a histidine as an active residue.
  DNA Sequence 07/2008; 19(3):177-84.
• Article: Mapping two genes in the purine metabolism pathway of soybean.

  J L Shultz, J D Ray, J R Smith
  [show abstract] [hide abstract]
  ABSTRACT: Mapping genes in biochemical pathways allow study of the genomic organization of pathways and geneic relationships within these pathways. Additionally, molecular markers located within the boundaries of a specific gene sequence represent important marker assisted selection resources. We report map locations of two geneic markers from the purine synthesis pathway in soybean (Glycine max (L. merr.)), utilizing a 90 plant F(2) population created from the cross of "DT97-4290" x "DS97-84-1". Primers were designed based on sequences from annotated soybean complimentary DNA. A polymorphic, co-dominant, sequence-characterized amplified region marker was created for hypoxanthine phosphoribosyl transferase (EC 2.4.2.8). Linkage analysis placed this gene on linkage group (LG) O. In addition, a single-nucleotide polymorphism (SNP) marker was developed for a urate oxidase gene (EC 1.7.3.3). Linkage analysis of the SNP placed the urate oxidase gene on LG I. For both genes, amplicon sequence data confirmed the identification of the respective gene. Mapping these genes represents the first step in understanding the genomic organization of the purine biochemical pathway in soybean.
  DNA Sequence 07/2008; 19(3):264-9.
• Article: Sequence and organization of the complete mitochondrial genomes of spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri).

  Chongbo He, Jiabo Han, Longli Ge, Zunchun Zhou, Xianggang Gao, Yunlei Mu, Weidong Liu, Jie Cao, Zhanjiang Liu
  [show abstract] [hide abstract]
  ABSTRACT: In this work, the mitochondrial genomes for spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri) were completely sequenced. The entire mitochondrial genome sequences of the spotted halibut and barfin flounder were 17,273 and 17,588 bp in length, respectively. The organization of the two mitochondrial genomes was similar to those reported from other fish mitochondrial genomes containing 37 genes (2 rRNAs, 22 tRNAs and 13 protein-coding genes) and two non-coding regions (control region (CR) and WANCY region). In the CR, the termination associated sequence (ETAS), six central conserved block (CSB-A,B,C,D,E,F), three conserved sequence blocks (CSB1-3) and a region of 61-bp tandem repeat cluster at the end of CSB-3 were identified by similarity comparison with fishes and other vertebrates. The tandem repeat sequences show polymorphism among the different individuals of the two species. The complete mitochondrial genomes of spotted halibut and barfin flounder should be useful for evolutionary studies of flatfishes and other vertebrate species.
  DNA Sequence 07/2008; 19(3):246-55.
• Article: Cloning, genomic organization and expression of two glycosyl hydrolase family 10 (GHF10) genes from golden apple snail (Pomacea canaliculata).

  Chanprapa Imjongjirak, Piti Amparyup, Siriporn Sittipraneed
  [show abstract] [hide abstract]
  ABSTRACT: Two cellulase cDNAs (GHF10-Pc1 and GHF10-Pc3) belonging to glycoside hydrolase family 10 (GHF10) were successfully isolated and characterized from stomach tissue of golden apple snail (Pomacea canaliculata), a kind of herbivorous mollusca. Sequencing analysis revealed full-length cDNAs of 1300 and 1277 bp in length, respectively. The open reading frame (ORF) of cellulase cDNA was 1188 and 1191 bp, encoding 395 and 396 amino acid, respectively. Sequence alignment revealed that GHF10-Pc1 and GHF10-Pc3 shared high identity with glycosyl hydrolase family 10 (GHF10) and had an overall similarity of 98 and 82% to those of Ampullaria crossean cellulase EGX. A neighbour-joining tree showed a clear differentiation between each species and also indicated that GHF10-Pc1 and GHF10-Pc3 from P. canaliculata and A. crossean EGX are closely related phylogenetically. The genomic organization of cellulase GHF10-Pc1 and GHF10-Pc3 genes was also investigated. The GHF10-Pc1 and GHF10-Pc3 genes spanned over 4937 and 4512 bp, respectively. Both genes contained 9 exons interrupted by eight introns. The result verified the endogenous origin of the GHF10-Pc1 and GHF10-Pc3 genes. Analysis of RNA by RT-PCR from several ages of P. canaliculata revealed that neither gene was expressed in eggs. GHF10-Pc1 was also expressed in 1- and 10-day-old juvenile snails whereas GHF10-Pc3 was expressed only in 1-day-old juvenile snails. The result showed that two GHF10-Pc transcripts were developmentally expressed.
  DNA Sequence 07/2008; 19(3):224-36.
• Article: The narQP genes for a two-component regulatory system from the deep-sea bacterium Shewanella violacea DSS12.

  Hideyuki Tamegai, Sayaka Chikuma, Masami Ishii, Kaoru Nakasone, Chiaki Kato
  [show abstract] [hide abstract]
  ABSTRACT: Shewanella violacea DSS12 is facultative piezophile isolated from the deep-sea. The expression of cydDC genes (required for d-type cytochrome maturation) of the organism is regulated by hydrostatic pressure. In this study, we analyzed the nucleotide sequence upstream of cydDC in detail and found that there are putative binding sites for the NarL protein which is part of a two-component regulatory system also containing the sensor protein NarX. Furthermore, we identified the narQP genes (homologues of narXL) from S. violacea DSS12 and demonstrated the heterologous expression of narP in Escherichia coli. These results will be helpful in examining pressure regulation of gene expression in S. violacea at the molecular level.
  DNA Sequence 07/2008; 19(3):308-12.
• Article: Cloning and comparative bioinformatic analysis of feline glucose-6-phosphatase catalytic subunit cDNA.

  Sara Lindbloom, Michelle Lecluyse, Thomas Schermerhorn
  [show abstract] [hide abstract]
  ABSTRACT: Glucose-6-phosphatase is a multicomponent enzyme composed of a transporter subunit and a catalytic subunit that is involved in hepatic glucose production. The objective of the present study was to determine the complete nucleotide sequence of feline hepatic glucose-6-phosphatase catalytic subunit (G6Pc) cDNA and to perform comparative analysis of the molecular features of the feline G6Pc cDNA and protein. Feline G6Pc cDNA contains 2261 bases and encodes a 357 aa protein. The feline cDNA and protein are highly conserved with overall identity ranging from 73-86% to 86-95%, respectively, among mammalian species. Membrane topology, phosphatase consensus sequence, ER retention sequence, N-glycosylation sites and active site residues are conserved in the feline protein. Analysis of the putative feline G6Pc protein did not reveal any species-specific features to explain the unusual in vivo regulation of G6Pase activity reported in feline liver.
  DNA Sequence 07/2008; 19(3):256-63.
• Article: Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes.

  Ashraf Hosseini, Suvidya H Ranade, Indira Ghosh, Pramod Khandekar
  [show abstract] [hide abstract]
  ABSTRACT: Simple sequence repeats (SSRs) are omnipresent in prokaryotes and eukaryotes, and are found anywhere in the genome in both protein encoding and noncoding regions. In present study the whole genome sequences of seven chromosomes (Shigella flexneri 2a str301 and 2457T, Shigella sonnei, Escherichia coli k12, Mycobacterium tuberculosis, Mycobacterium leprae and Staphylococcus saprophyticus) have downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs and also to determine difference between the tandem repeats in real genome and randomness genome (using sequence shuffling tool) of the organisms included in this study. The data obtained in the present study show that: (i) tandem repeats are widely distributed throughout the genomes; (ii) SSRs are differentially distributed among coding and noncoding regions in investigated Shigella genomes; (iii) total frequency of SSRs in noncoding regions are higher than coding regions; (iv) in all investigated chromosomes ratio of Trinucleotide SSRs in real genomes are much higher than randomness genomes and Di nucleotide SSRs are lower; (v) Ratio of total and mononucleotide SSRs in real genome is higher than randomness genomes in E. coli K12, S. flexneri str 301 and S. saprophyticus, while it is lower in S. flexneri str 2457T, S.sonnei and M. tuberculosis and it is approximately same in M. leprae; (vi) frequency of codon repetitions are vary considerably depending on the type of encoded amino acids.
  DNA Sequence 07/2008; 19(3):167-76.
• Article: Characterization of phosphatidylinositol-glycan biosynthesis protein class F gene in rice.

  Dong Hoon Lee, Sang Gu Kang
  [show abstract] [hide abstract]
  ABSTRACT: The glycosylphosphatidylinositol (GPI) anchors are linked to glycosylphosphatidylinositol-anchored proteins (GAPs) which are essential for the growth of mammalian, yeast and protozoan cells. The GPI anchor is covalently linked to GAP by amide bond formation between the carboxyl terminus and phosphoethanolamine attached at the third mannose and mediated by a transamidase complex. Mediation of GPI synthesis is by the sequential additions of GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex, the GlcN-PI de-N-acetylase, the GlcN-PI mannosyltransferases and the GPI lipid anchor phosphoethanolamine transferase complexes. We report a rice gene OsPIG-F that encodes a homolog to the human PIG-F protein, one of GPI lipid anchor phosphoethanolamine transferase complexes. The amino acid sequences of rice PIG-F consisted of six helix transmembrane domains, one glycosaminoglycan attachment site, one cGMP-dependent protein kinase phosphorylation site and a protein C phosphorylation site at the C-terminus. This unique structure of rice PIG-F indicates the typical membrane bound structure of a protein. Polyclonal antibody for rice PIG-F was found to be cross-reactive with a protein extracted from the leaves of rice. The levels of rice PIG-F transcripts were found to be abundant in leaves, moderately in the milky stage of seed development and less in the floral spikelet, indicating that the rice PIG-F gene was differentially regulated in specific tissues. Furthermore, the levels of rice PIG-F transcription were up-regulated by growth hormones including GA(3), NAA and kinetin. These results indicated that the rice PIG-F gene expression may medicated by these growth regulators.
  DNA Sequence 07/2008; 19(3):282-90.
• Article: Molecular characterization of cDNA encoding B. taurus cathelicidin-7 like antibiotic peptide from bone marrow cells of Bubalus bubalis.

  Hemen Das, Shahaj Uddin Ahmed, Tukaram More
  [show abstract] [hide abstract]
  ABSTRACT: Cathelicidins represent a diverse family of endogenous cationic antibiotic peptide present in all mammalian species. In the present study, a novel cathelicidin cDNA was identified and characterized from bone marrow cells of buffalo (Bubalus bubalis) using RT-PCR based approach. The cDNA encodes a propeptide of 1.18 kDa with net positive charge at neutral pH. The precursor peptide possesses a signal peptide of 29 amino acids and a biologically active peptide of 34 residues. Comparison of sequences indicates only 66.1 and 64.1% identity at nucleotides and amino acids level respectively, with the already reported cathelicidin congener from the same species. However, high degree of similarity (92.8% nucleotides and 81.9% amino acids) was noticed with cathelicidin 7 sequence of Bos taurus suggesting interspecies conservation of cathelicidin peptides rather than intra-species within bovidae family. Phylogenetic trees analyses also support these data. Our findings, further justify the cloned cDNA as a unique cathelicidin member of B. bubalis, and may reasonably considered to be another example of structural diversity exhibited by cathelicidin-derived peptides as reported from other mammals.
  DNA Sequence 07/2008; 19(3):347-56.