In vitro and in vivo characterization of the minimal promoter region of the human thiamin transporter SLC19A2

The molecular mechanisms involved in the regulation of thiamin transport in mammalian cells are poorly understood. Previous studies established that a human thiamin transporter, SLC19A2, plays a role in thiamin uptake in human tissues. We cloned the 5' regulatory region of the SLC19A2 gene, identified the minimal promoter required for basal activity, and located multiple putative cis elements. To further characterize the SLC19A2 promoter, we investigated, in the present study, the role of the putative cis elements in regulating the activity of the SLC19A2 promoter in vitro and confirmed the activity of the SLC19A2 promoter in vivo. In vitro studies demonstrated that mutation of specific cis elements in the SLC19A2 minimal promoter [Gut-enriched Krupple-like factor (GKLF), nuclear factor-1 (NF-1), and stimulating protein-1 (SP-1)] led to a decrease in activity. Using electrophoretic mobility shift assays, four specific DNA/protein complexes were identified. The interacting factors were determined by oligonucleotide competition and antibody supershift analysis and shown to be GKLF, NF-1, and SP-1. Cotransfection studies of the SLC19A2 promoter with an SP-1 containing vector in Drosophila SL2 cells further confirmed a role for SP-1 in regulating SLC19A2 promoter activity. In vivo studies using transgenic mice established the functionality of the full-length and minimal SLC19A2 promoters. Furthermore, our studies revealed that the pattern of expression of the SLC19A2 promoter-Luciferase constructs in transgenic mice was similar to the reported SLC19A2 RNA expression pattern in native human tissues. The results demonstrate the importance of GKLF, NF-1, and SP-1 in regulating the activity of the SLC19A2 promoter and provide direct in vivo confirmation of promoter activity. promoter analysis in vitro and in vivo; thiamin transport; transgenic mice     

Cloning and Characterization of New Repetitive Sequences in Field Bean (Vicia fabaL.)

Five new repetitive sequences have been isolated from theViciafabagenome, by cloning bands visible on agarose gel electrophoresisafter digestion of genomic DNA with various restriction enzymes.The sequences were 109 to 584 bp long, their abundance rangingfrom 5x10⁴to 5x10⁵copies per haploid genome. Southern blot andinsituhybridization revealed that four of five newly isolatedrepeats were dispersed in theV. fabagenome. One of the repeats(TIII15) showed tandem organization with several major hybridizationspots on mitotic chromosomesin situ.These sites were distributedin euchromatic as well as in heterochromatic chromosomal regions,and in several loci they were simultaneously localized withpreviously describedFokI repeated elements. The sequence ofTIII15 comprises four 26–27 bp subrepeats, but sharesno homology toFokI elements which have similar sequence organization.All newly described sequences were highly specific forV. faba,withlittle or no hybridization to DNA of otherViciaspecies, andno hybridization to DNA of other legumes tested.Copyright 1999Annals of Botany Company Vicia faba, field bean, repeated DNA sequences, FISH, PRINS, genome organization, copy number.     

Isolation and Characterization of a Water Stress-Specific Genomic Gene, pwsi 18, from Rice

One of the water stress-specific cDNA clones of rice characterisedpreviously, wsi18, was selected for further study. The wsi18gene can be induced by water stress conditions such as mannitol,NaCl, and dryness, but not by ABA, cold, or heat. A genomicclone for wsi18, pwsi18, contained about 1.7 kbp of the 5' upstreamsequence, two introns, and the full coding sequence. The 5'-upstreamsequence of pwsi18 contained putative cis-acting elements, namelyan ABA-responsive element (ABRE), three G-boxes, three E-boxes,a MEF-2 sequence, four direct and two inverted repeats, andfour sequences similar to DRE, which is involved in the dehydrationresponse of Arabi-dopsis genes. The gusA reporter gene underthe control of the pwsi18 promoter showed transient expressionin response to water stress. Deletion of the downstream DRE-likesequence between the distal G-boxes-2 and -3 resulted in ratherlow GUS expression. (Received March 27, 1997; Accepted November 5, 1997)     

昆虫细胞色素P450基因的多样性、进化及表达调控

细胞色素P450单加氧酶（cytochrome P450 monooxygenases, P450s）是由多个功能相关的亚铁血红素 硫醇盐蛋白基因组成的一个基因超家族, 在各种内源和外源物质的代谢中起着主要作用。目前GenBank中注册的昆虫P450基因序列已超过1 000个, 其中双翅目占序列总数的74%, 鳞翅目占序列总数的16%。而昆虫P450基因序列已克隆的全长序列中大部分属于CYP4和CYP6家族, 两个家族成员分别占总数的20%和45%。利用GenBank中现已注册的昆虫P450基因的cDNA全长序列进行比对并绘制进化树, 揭示不同种类昆虫P450的亲缘关系。结果显示基于P450基因的昆虫部分目的进化关系与大部分先前依据其他分子数据或形态分类学得到的昆虫系统进化关系基本吻合。现有研究表明, 细胞色素P450基因的表达可能受顺式作用元件(cis-acting element)、反式作用因子(trans-acting factor)或两者共同调控, 调控可能涉及转录增强的转录机制或mRNA稳定性增加的转录后机制。     

Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843

The nucleotide sequence of the complete genome of a cyanobacterium,Microcystis aeruginosa NIES-843, was determined. The genomeof M. aeruginosa is a single, circular chromosome of 5 842 795base pairs (bp) in length, with an average GC content of 42.3%.The chromosome comprises 6312 putative protein-encoding genes,two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species,and genes for tmRNA, the B subunit of RNase P, SRP RNA, and6Sa RNA. Forty-five percent of the putative protein-encodingsequences showed sequence similarity to genes of known function,32% were similar to hypothetical genes, and the remaining 23%had no apparent similarity to reported genes. A total of 688kb of the genome, equivalent to 11.8% of the entire genome,were composed of both insertion sequences and miniature inverted-repeattransposable elements. This is indicative of a plasticity ofthe M. aeruginosa genome, through a mechanism that involveshomologous recombination mediated by repetitive DNA elements.In addition to known gene clusters related to the synthesisof microcystin and cyanopeptolin, novel gene clusters that maybe involved in the synthesis and modification of toxic smallpolypeptides were identified. Compared with other cyanobacteria,a relatively small number of genes for two component systemsand a large number of genes for restriction-modification systemswere notable characteristics of the M. aeruginosa genome.     

Developmental Features of Cell Wall Formation in Sieve Elements of the Grass Aegilops comosa var. thessalica

In differentiating sieve elements of Aegilops comosa var. thessalicadictyosomes are abundant and they produce numerous smooth vesicles.Coated vesicles seem to bud from smooth ones. Since both kindsof vesicles appear both in the cytoplasm and in associationwith the plasmalemma, it is proposed that they move to and fusewith the plasmalemma transferring products for cell wall synthesis.During differentiation sub-plasmalemmal microtubules are initiallyscarce and randomly oriented but soon afterwards they becomenumerous and transversely oriented to the long axis. Cellulosemicrofibrils in the cell wall appear to run parallel to themicrotubules and the latter may regulate microfibril orientation. Root protophloem sieve elements develop wave-like wall thickenings,which are, during development, overlaid by microtubules perpendicularto the long axis. Just after maturation these thickenings progressivelybecome smooth and finally the walls appear uniform in thickness.The wave-like wall thickenings may function as stored wall material,utilized in later stages of development when wall material willbe needed and its synthesis will be impossible because of theabsence of a synthesizing mechanism in the highly degraded protoplastsof mature sieve elements. It is suggested that in this way thethickenings may enable root protophloem sieve elements to growand keep pace with the active clongation of the surroundingcells. Aegilops comosa var. thessalica, sieve elements. cell wall, microtubules, dictyosomes, coated vesicles, wave-like thickenings     

家蚕G蛋白α亚基基因BmGα73B的克隆与表达

异三元G蛋白是真核细胞感知外界信号后将信号传递到胞内的重要分子,在生物中参与了广泛的信号转导途径,如光、神经递质和激素等。为了研究G蛋白在家蚕Bombyx mori中的生理功能及其作用机理,我们运用生物信息学方法在已有的家蚕基因组数据库中找到了一段与G蛋白alpha亚基（Gα）同源性很高的序列。通过设计特异性引物,运用PCR和RACE技术,成功地克隆了一个家蚕Gα基因的全长cDNA序列。该基因全长1 509 bp (GenBank登录号：EU914850),开放阅读框（ORF）为1 158 bp,编码385个氨基酸。Blast和DNAstar等软件分析发现该基因编编码的蛋白质与其他物种已知的Gα具有一定的保守性,将它命名为BmGα73B。RT-PCR扩增检测该基因在家蚕不同组织器官和不同发育时期的转录表达活性,结果表明它在不同发育时期的家蚕各组织器官中都有表达。从组织水平上看,BmGα73B在中肠中表达量最高,在马氏管、头部和神经索等组织中也有适量表达。在家蚕的不同发育时期中,转录水平峰值出现在幼虫期,在蛹早期也有适量的表达,而在预蛹期、蛹后期和成虫期几乎没有表达。结果说明BmGα73B可能参与了家蚕生长前期的中肠发育过程,为进一步研究G蛋白在家蚕发育过程的作用奠定了一定的基础。     

Ethylene-Induced Gene Expression of Osmotin-Like Protein, a Neutral Isoform of Tobacco PR-5, is Mediated by the AGCCGCC eft-Sequence

Osmotin-like protein (OLP) is a neutral isoform in the group5 pathogenesis-related (PR) tobacco proteins. The OLP gene,like the basic PR protein genes, is constitutively expressedin tobacco roots and cultured cells. OLP is not naturally presentin intact healthy leaves, but ethylene treatment induces a highaccumulation there. To study the mechanism of OLP gene expressionas induced by ethylene, we cloned the gene from Nicotiana sylvestris,an ancestor of N. tabacum. Sequence analysis showed that ithas no intron and that its promoter region contains two AGCCGCCsequences that are conserved in most basic PR-protein genes.The function of the AGCCGCC sequences in transgenic tobaccoplants that harbor the wild and mutated OLP promoter::GUS fusiongenes was analyzed. Mutation in the AGCCGCC sequences clearlyinhibited the GUS expression induced by ethylene, indicativethat the AGCCGCC sequence(s) is a DNA element(s) responsiveto ethylene. An EREBP2 protein, isolated as one of the proteinsbinding the AGCCGCC sequence of the tobacco rß-1,3-glucanasegene, also was found to bind to the AGCCGCC sequence(s) of OLPgene. These results suggest that the ethylene-induced expressionof OLP is regulated by trans-acting factor(s) common to basicPR-proteins. (Received November 13, 1995; Accepted January 17, 1996)     

Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection

Motivation: Although the outbreak of the severe acute respiratorysyndrome (SARS) is currently over, it is expected that it willreturn to attack human beings. A critical challenge to scientistsfrom various disciplines worldwide is to study the specificityof cleavage activity of SARS-related coronavirus (SARS-CoV)and use the knowledge obtained from the study for effectiveinhibitor design to fight the disease. The most commonly usedinductive programming methods for knowledge discovery from dataassume that the elements of input patterns are orthogonal toeach other. Suppose a sub-sequence is denoted as P₂P₁P_1'P_2',the conventional inductive programming method may result ina rule like ‘if P₁ = Q, then the sub-sequence is cleaved,otherwise non-cleaved’. If the site P₁ is not orthogonalto the others (for instance, P₂, P_1' and P_2'), the predictionpower of these kind of rules may be limited. Therefore thisstudy is aimed at developing a novel method for constructingnon-orthogonal decision trees for mining protease data. Result: Eighteen sequences of coronavirus polyprotein were downloadedfrom NCBI (http://www.ncbi.nlm.nih.gov). Among these sequences,252 cleavage sites were experimentally determined. These sequenceswere scanned using a sliding window with size k to generateabout 50 000 k-mer sub-sequences (for short, k-mers). The valueof k varies from 4 to 12 with a gap of two. The bio-basis functionproposed by Thomson et al. is used to transform the k-mers toa high-dimensional numerical space on which an inductive programmingmethod is applied for the purpose of deriving a decision treefor decision-making. The process of this transform is referredto as a bio-mapping. The constructed decision trees select about10 out of 50 000 k-mers. This small set of selected k-mers isregarded as a set of decisive templates. By doing so, non-orthogonaldecision trees are constructed using the selected templatesand the prediction accuracy is significantly improved. Availability: The program for bio-mapping can be obtained byrequest to the author. Contact: z.r.yang{at}exeter.ac.uk     

Analysis of Organ Specificity of a Low Temperature Responsive Gene Family in Rye (Secale cereale L.)

The barley (Hordeum vulgare L.) low temperature responsive geneblt14 was used as a probe, to isolate two different cognateclones (rlt1412; rlt1421) from a rye (Secale cereale L.) cDNAlibrary prepared from low temperature-treated (6°C day/2°C night) shoot meristems of the cultivar, Puma. Northernblot analysis revealed that low temperature expression of rlt1412is highest in root tissues whereas, rlt1421 shows greatest mRNAaccumulation in mature leaf tissues. There is a relationshipbetween the steady-state levels of these mRNA species and thefrost hardiness of Puma (North American cultivar) and Rhayader(UK cultivar) such that the expression ofboth genes is higherin the more frost hardy cultivar, Puma, compared with Rhayader. DNA and predicted amino acid sequence analysis indicated thatthe rye and barley clones encode small proteins with consensusN-terminal signal sequences whose biological function is atpresent unknown. The relevant sequences are lodged in the EMBL data base. Key words: Rye, cold, cDNA, organ specificity, low temperature genes     

The Promoter of the Gene for Plastidic Glutamine Synthetase (GS2) fromRice Is Developmentally Regulated and Exhibits Substrate-Induced Expression in Transgenic Tobacco Plants

A 1.3-kb fragment from the 5'-flanking region of the RGS-38gene, which encodes the plastidic glutamine synthetase in Oryzasativa L., was fused to a ß-glucuronidase (GUS) reportergene and introduced into Nicotiana tabacum by Agrobacterium-mediatedtransformation. The promoter directed GUS expression, both inleaves and in roots, and the expression of GUS was regulatedby light. The GUS activity was high in the mature leaves ofthe transgenic tobacco plants, in marked contrast to the activityof the GS1 promoter. The GS2 promoter also responded to externallyapplied ammonia, as is the case for the GS1 promoter. Theseresults suggest that the cis-acting regulatory elements thatcontrol the response to ammonia, a substrate for glutamine synthetase,are located within a 1.3-kb region of the promoter. (Received October 1, 1991; Accepted January 20, 1992)     

Rapid analysis of an osmotic stress responsive promoter by transient expression in intact wheat embryos

Expression of the wheat ‘Em’ genes in embryos isstrongly induced both by abscisic acid and by subjection toosmotic stress. We have examined the basis of this inductionin an homologous system by con structing fusions between thepromoter sequences of a cloned ‘Em’ gene and theGUS reporter gene. The ABA-and stress-mediated expression ofthese constructs has been assayed following delivery to intactwheat embryos by particle bombardment. Staining of bombardedembryos with the chromogenic substrate X-gluc enabled a simpleand rapid visual identification of promoter activity by scoringthe numbers of stained spots. Although not rigorously quantitative,a general correspondence between number of expression events(spots) and promoter activity could be inferred when the resultsobtained with bombarded embryos were compared with those obtainedby the fluorlmetnc measurement of GUS activity in cereal aleuroneprotoplasts transfected with the same constructs. Analysis ofa series of 5'-deletions of the ‘Em’ promoters indicatedthat the stress-responsive cis-acting regulatory elements comprisethe same sequences as those responsible for ABA-mediated geneexpression. Key words: Abscisic acid, osmotic stress, Em genes, wheat embryos, transient expression