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IDENTIFICATION AND PHYSICAL CHARACTERIZATION OF YEAST MALTASE STRUCTURAL GENES

MOLECULAR AND GENERAL GENETICS 1983年第3期191卷 366-371页

作者： CHOW, T GOLDENTHAL, MJ COHEN, JD HEGDE, M MARMUR, J YESHIVA UNIV ALBERT EINSTEIN COLL MED DEPT BIOCHEM BRONX NY 10461 USA

Each of at least 5 unlinked MAL loci (MAL1 through MAL4 and MAL6) on the yeast genome controls the ability to synthesize an inducible .alpha.-D-glucosidase (maltase). A subcloned fragment of the coding sequence of the MAL6 maltase structural gene was used as a hybridization probe to investigate the physical structure of the family of MAL structural genes in the genomes of different Saccharomyces strains. Mal+ strains, each carrying a genetically defined MAL locus, were crossed with a Mal strain, and the segregation behavior of the functional locus and of sequences complementary to the maltase structural gene at that locus was analyzed. The maltase structural gene sequences of each MAL locus were detected by Southern blot hybridization using BamH1 digests of genomic DNA of the meiotic products. This restriction enzyme was previously shown to cleave outside the confines of the MAL6 locus. Each MAL locus apparently encompasses at least 1 maltase structural gene sequence homologous to that of MAL6;yeast strains that lack functional MAL loci may or may not contain the corresponding maltase structural gene sequence. The MAL1 maltase structural gene sequence or one of its alleles can be detected in all laboratory yeast strains examined, and each MAL locus can be identified as a characteristic BamH1 fragment of genomic DNA which includes a maltase structural gene. Yeast strains vary in the number of maltase structural gene sequences that they carry. By using the approach described here, the ones corresponding to the different functional MAL loci and residing within a BamH1 generated restriction fragment can be identified.

关键词： Genome genomic DNA structural genes Confined DNA Restriction Enzymes Loci coding sequence Southern blot hybridization Yeast hybridisation alpha-Glucosidases

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Cloning of a mammalian elk potassium channel gene and EAG:: mRNA distribution in rat sympathetic ganglia

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JOURNAL OF PHYSIOLOGY-LONDON 1998年第3期511卷 675-682页

作者： Shi, WM Wang, HS Pan, ZM Wymore, RS Cohen, IS McKinnon, D Dixon, JE SUNY Stony Brook Dept Neurobiol & Behav Stony Brook NY 11794 USA SUNY Stony Brook Dept Physiol & Biophys Stony Brook NY 11794 USA

1. Three new members of the EAG potassium channel gene family were identified in rat and the complete coding sequence of one of these genes (elk1) was determined by cDNA cloning. 2. The elk1 gene, when expressed in Xenopus oocytes, encodes a slowly activating and slowly deactivating potassium channel. 3. The elk1 gene is expressed in sympathetic ganglia and is also expressed in sciatic nerve. 4. Six of the seven known EAG genes were found to be expressed in rat sympathetic ganglia, suggesting an important functional role for these channels in the sympathetic nervous system.

关键词： Ganglia Sympathetic Potassium Channels eag protein elk1-protein DNA Complementary 神经节交感钾通道 Potassium Channels DNA Rats Ganglia sympathetic ganglion Complementary coding sequence Cloning

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Genetic variation of FUT3 gene in the Han population from Northern China

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TRANSFUSION MEDICINE 2024年第5期34卷 437-444页

作者： Zhou, Shihang Zheng, Ziwei Wang, Liying Song, Wenqian Xia, Yuexin Shao, Linnan Liang, Xiaohua Dalian Blood Ctr Dept Blood Grp Dalian Peoples R China Dalian Med Univ Coll Lab Med Dalian Peoples R China

Background and Objectives: The FUT3 gene encodes alpha(1,3/1,4)-fucosyltransferase, which is a crucial enzyme in the synthesis of Lewis antigens. FUT3 gene variants show race-specific differences. In this study, we conducted a systematic sequence analysis of the FUT3 coding sequence. The objective was to explore genetic variations of the FUT3 gene within the Han population of Northern China. Materials and MethodsA cohort of 313 blood donors was recruited for the study. The coding sequence of the FUT3 gene was amplified using polymerase chain reaction, followed by sequencing and haplotype construction. Results: Twelve single nucleotide variations (SNVs) were identified within the coding sequence of the FUT3 gene. Notably, the c.59 T > G site exhibited the highest mutation frequency of 43.13%, followed by the c.508G > A and c.1067 T > A sites with mutation frequencies of 27.48% and 16.93%, respectively. Le was the most common haplotype, accounting for 67.57% of the cases, and Le/Le was the most common diplotype, accounting for 46.33% of the cases. The study also highlighted a significant difference in mutation frequencies of FUT3 gene between the Han Chinese of Northern China and the Dai of Xishuangbanna, China, but not the Han Chinese in Beijing in the North and the Southern Han Chinese, emphasising that Han Chinese in Northern China are genetically most distant from Europeans and closest to East Asians. Conclusions: Our study characterises FUT3 gene variations in Han Chinese from Northern China, and provides basic genetic data for genetics, forensic medicine, and genotyping of Lewis blood groups.

关键词： Chinese coding sequence FUT3 genetic variation

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The role of components of recombination signal sequences in immunoglobulin gene segment usage: a V81x model

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NUCLEIC ACIDS RESEARCH 1999年第11期27卷 2304-2309页

作者： Larijani, M Yu, CCK Golub, R Lam, QLK Wu, GE Univ Toronto Dept Immunol Toronto ON M5G 2M9 Canada Univ Toronto Ontario Canc Inst Toronto ON M5G 2M9 Canada

It has long been appreciated that some immunoglobulin (and T-cell receptor) gene segments are used much more frequently than others. The V-H Segment V81x is a particularly striking case of overusage, Its usage varies with the stage of B-cell development and with the strain of mice, but it is always high in B cell progenitors. We have found that the coding sequence and the recombination signal sequences (RSS) are identical in five mouse strains, including CAST/Ei, a strain derived from the species Mus castaneus, Thus, the strain differences cannot be attributed to sequences within V81x itself. V81x RSS mediated recombination at rates significantly higher than another V-H RSS, Although the V81x nonamer differs at one base pair from the consensus sequence, an RSS with this nonamer and a consensus heptamer recombines as well as the consensus RSS. When the V81x spacer is replaced by that of VA1, the frequency of recombination decreases by similar to 5-fold;thus, the contribution of variation in natural spacers to variability in V-H usage in vivo is likely to be more than has been previously appreciated, Furthermore, the contribution of the heptamer and nonamer to differential V-H usage in our assay is correlated inversely with their conservation throughout the V-H locus.

关键词： .contribute spacer coding sequence functional analysis RSS recombination signal Gene Segment Nonamer heptamer role of components sequences in immunoglobulin overusage

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THE TRANSCRIPTION TERMINATION SITE AT THE END OF THE EARLY REGION OF BACTERIOPHAGE-T7 DNA

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NUCLEIC ACIDS RESEARCH 1980年第10期8卷 2119-2132页

作者： DUNN, JJ STUDIER, FW Biology Department Brookhaven National LaboratoryUpton NY 11973 USA

The nucleotide sequence through the transcription termination site for Escherichia coli RNA polymerase at the end of the early region of T7 DNA has been determined. RNA chains terminate at adjacent residues in the DNA sequence: about 2/3 of the chains end in C and 1/3 in G. A potential stem and loop structure, containing a stem of eight uninterrupted base pairs and a four-base loop, is centered 17-18 bases ahead of the chain termini. Transcription by E. coli RNA polymerase terminates efficiently at this site in vivo and in vitro, but transcription by T7 RNA polymerase is essentially unaffected. There are no primary cleavage sites for RNase III near the transcription termination site. The site of termination lies within HpaI fragment Q of T7 DNA, whose entire 446-nucleotide long sequence was determined. Cleavage sites for other restriction endonucleases are located conveniently for manipulating the DNA sequence around the termination site. The coding sequence for the last 82 amino acids of the T7 DNA ligase protein was identified, as was the beginning of a coding sequence for a possible late T7 protein from beyond the termination site.

关键词： Ribonuclease III stopping DNA Restriction Enzymes coding sequence Anatomic Site Base sequence Bacteriophage T7 Early region DNA sequence bacteriophage T7 RNA polymerase Transcription Termination Chains

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The promoter of a lysosomal membrane transporter gene, CTNS, binds Sp-1, shares sequences with the promoter of an adjacent gene, carkl, and causes cystinosis if mutated in a critical region

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AMERICAN JOURNAL OF HUMAN GENETICS 2001年第4期69卷 712-721页

作者： Phornphutkul, C Anikster, Y Huizing, M Braun, P Brodie, C Chou, JY Gahl, WA NICHHD Sect Human Biochem Genet Heritable Disorders Branch NIH Bethesda MD 20892 USA Bar Ilan Univ Ramat Gan Israel

Although >55 CTNS mutations occur in patients with the lysosomal storage disorder cystinosis, no regulatory mutations have been reported, because the promoter has not been defined. Using CAT reporter constructs of sequences 5' to the CTNS coding sequence, we identified the CTNS promoter as the region encompassing nucleotides -316 to +1 with respect to the transcription start site. This region contains an Sp-1 regulatory element (GGCGGCG) at positions -299 to -293, which binds authentic Sp-1, as shown by electrophoretic-mobility-shift assays. Three patients exhibited mutations in the CTNS promoter. One patient with nephropathic cystinosis carried a -295 G -->C substitution disrupting the Sp-1 motif, whereas two patients with ocular cystinosis displayed a -303 G -->T substitution in one case and a -303 T insertion in the other case. Each mutation drastically reduced CAT activity when inserted into a reporter construct. Moreover, each failed either to cause a mobility shift when exposed to nuclear extract or to compete with the normal oligonucleotide's mobility shift. The CTNS promoter region shares 41 nucleotides with the promoter region of an adjacent gene of unknown function, CARKL, whose start site is 501 bp from the CTNS start site. However, the patients' CTNS promoter mutations have no effect on CARKL promoter activity. These findings suggest that the CTNS promoter region should be examined in patients with cystinosis who have fewer than two coding-sequence mutations.

关键词： .authentic constructs Transporter insertion Binds nucleotides mutated coding sequence CAT reporter Nephropathic CAT activity GrT Lysosomal Membrane Adjacent Gene CARKL Cystinosis Gene CTNS CTNS promoter

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Identification, sequencing and expression of selenium-dependent glutathione peroxidase transcript in the freshwater bivalve Unio tumidus exposed to Aroclor 1254

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COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY 2006年第2期144卷 122-129页

作者： Doyen, Perine Vasseur, Paule Rodius, Francois Univ Metz CNRS Lab ESE Ecotox UMR 7146 F-57070 Metz France

Glutathione peroxidases (GPx) and glutathione S-transferases (GST) are essential enzymes of the cellular defense system. The aim of this work was the identification of GPx transcript in a freshwater bivalve, Unio tumidus, and the effects of Aroclor 1254 on GPx and pi-class GST (pi-GST) expression pattern. The GPx full-length coding sequence was obtained by reverse transcription PCR using degenerated primers followed by 5' and 3' rapid amplification of cDNA ends. The GPx cDNA encodes a protein of 232 amino acids. The 72nd amino acid corresponds to a selenocysteine encoded by a TGA codon. Residues essential to the enzymatic function are conserved in GPx of U. tumidus. Specific amplifications of the Se-GPx mRNA from U. tumidus were performed on the digestive gland, the excretory system and the gills. Se-GPx expression level is highest in the digestive gland. No induction of the Se-GPx was observed at the transcriptional level in the digestive gland and the excretory system of Aroclor-treated mussels, while an increase of the pi-GST mRNA level was observed in the excretory system. (c) 2006 Elsevier Inc. All rights reserved.

关键词： freshwater bivalve Unio tumidus Se-GPx Pi-GST coding sequence expression level RT-PCR RACE-PCR Aroclor

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A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis

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ARCHIVES OF VIROLOGY 2018年第7期163卷 1921-1926页

作者： Nibert, Max L. Manny, Austin R. Debat, Humberto J. Firth, Andrew E. Bertini, Laura Caruso, Carla Harvard Med Sch Dept Microbiol & Immunobiol Boston MA 02115 USA Harvard Univ PhD Program Virol Cambridge MA 02138 USA Inst Nacl Tecnol Agr IPAVE CIAP INTA Inst Patol Vegetal Ctr Invest Agr X5020ICA Cordoba Argentina Univ Cambridge Dept Pathol Div Virol Cambridge CB2 1QP England Univ Tuscia Dept Ecol & Biol Sci I-01100 Viterbo Italy

Because so few viruses in the family Barnaviridae have been reported, we searched for more of them in public sequence databases. Here, we report the complete coding sequence of Colobanthus quitensis associated barnavirus 1, mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis. The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on - 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. The possible derivation of this virus from a fungus associated with C. quitensis is discussed.

关键词： Transcriptome Open Reading Frames sequential data base Capsid Proteins coding sequence Antarctic Ribosomal frameshifting Colobanthus quitensis viruses

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The translational signal database, TransTerm, is now a relational database

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NUCLEIC ACIDS RESEARCH 1998年第1期26卷 335-337页

作者： Dalphin, ME Brown, CM Stockwell, PA Tate, WP Univ Otago Dept Biochem Dunedin New Zealand Univ Otago Ctr Gene Res Dunedin New Zealand

TransTerm-97 contains more than 97500 non-redundant coding-sequence initiation and termination contexts compiled from GenBank, release 101 (15-June-1997). In addition, several coding sequence parameters are available: coding sequence length, Nc, GC3, and, when it is computable, codon adaptation index (CAI), Codon usage tables and summaries of start and stop codon contexts are also included, The information covers more than 325 species and organelles, including seven complete bacterial genomes and one complete eukaryotic genome, To promote research in translational control of protein synthesis, TransTerm has been converted into a relational database to ease the process of making queries, The relational database manager, Postgresql, gives access to the database using SQL (Structured Query Language), A World Wide Web interface using forms is being completed to allow the casual user access to the database, Extensions are planned to include the full 5'-UTR, full coding sequence and 3'-UTR, TransTerm-97 is available on the World Wide Web at: http://***:800/Transterm/***.

关键词： Codon Initiator Terminator Databases Factual Translation Genetic 密码子起始终止数据库事实型翻译遗传 Codons Translation Process bacterial genome Relational databases translational control Initiators Terminator Device Component coding sequence SQL Database

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Codon usage of Botryococcus braunii (Trebouxiophyceae, Chlorophyta): implications for genetic engineering applications

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PHYCOLOGIA 2013年第4期52卷 352-356页

作者： Ioki, Motohide Baba, Masato Nakajima, Nobuyoshi Shiraiwa, Yoshihiro Watanabe, Makoto M. Univ Tsukuba Grad Sch Life & Environm Sci Tsukuba Ibaraki Japan Natl Inst Environm Studies Ctr Environm Biol & Ecosyst Studies Tsukuba Ibaraki 3058506 Japan

The colonial unicellular freshwater green alga Botryococcus braunii has recently attracted attention from the biofuel industry because of its unique traits to biosynthesize extraordinarily large amounts of hydrocarbon oils resembling petroleum constituents and to accumulate the oils within the colony. The purpose of this study was to evaluate B. braunii in terms of codon compatibility with other organisms in view of genetic engineering applications. Here, GC contents and codon usage were compared among three strains of B. braunii (BOT-88-2, BOT-22, and BOT-70), three other species of Chlorophyta (green algae), five species of the Streptophyta (land plants), and eight species of other phyla including bacteria, archaea, fungi, and mammals. Interestingly, B. braunii exhibited GC contents remarkably lower than the other Chlorophyta species and it also had an unbiased codon usage unlike other green microalgae. Codon usage of B. braunii rather resembled bacteria, animals, and land plants. Our results indicated that genes derived from various nonmicroalgal species could readily be expressed in B. braunii with relatively minor codon usage optimization, and vice versa.

关键词： coding sequence Codon GC content

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