Cloning and morphological properties of Nicgl;CYCD3;1 gene in genetic tumors from interspecific hybrid of N. langsdorffii and N. glauca

Plant genetic tumors represent neoplastic growths, which arise spontaneously in hybrid plants without apparent external induction. To understand the molecular nature of unregulated cell proliferation, a cyclin D cDNA clone encoding a cyclin D of 1104bp was isolated from a genetic tumor and designated Nicgl;CYCD3;1 gene. DNA gel blot analysis suggested that there are two copies of Nicgl;CYCD3;1 in the genetic tumors. Northern analysis showed that this gene had the highest expression level in genetic tumor compared to Nicotiana glauca, N. langsdorffii and hybrid plants. Plant morphology of hybrid plant was an intermediate between N. glauca and N. langsdorffii and was altered in the genetic tumors. The cell cycle distribution in N. glauca was G0/G1, 90.59; S, 0.60; G2/M, 8.81; in N. langsdorffii it was G 0/G1, 86.22; S, 6.90; G2/M, 6.88; in hybrid plants it was G 0/G1, 96.40; S, 1.79; G2/M, 1.81; and in genetic tumors G 0/G1, 74.70; S, 2.35; G2/M, 22.94. These data provide new insights into the molecular mechanisms underlying genetic tumor formation from interspecific hybrid between N. langsdorffii and N. glauca.     

森林草莓SUN基因家族的鉴定及其对逆境的响应

SUN基因是调控植物生长发育的关键基因。本研究鉴定了二倍体森林草莓(Fragaria vesca)的SUN基因家族,并对各成员的理化性质、基因结构、系统进化以及基因表达进行了分析。结果表明,森林草莓有31个FvSUN基因,其编码蛋白可聚类为7个组,同一组内成员具有高度相似的基因结构与编码蛋白保守域;FvSUNs蛋白的亚细胞定位主要在细胞核中。共线性分析表明森林草莓FvSUNs基因家族主要通过染色体片段复制产生,拟南芥与森林草莓存在23对直系同源基因。利用森林草莓的转录组数据,对FvSUNs基因的组织表达特征进行分析,发现主要可归为3类：各组织均表达、组织中几乎不表达、组织特异性表达,并通过实时荧光定量PCR (quantitative real-time polymerase chain reaction, qRT-PCR)进一步验证结果。此外,还对森林草莓进行不同的逆境胁迫处理,qRT-PCR分析了31个FvSUNs基因的表达情况,发现大部分基因均在不同程度上受低温、高盐或干旱胁迫的诱导表达。这些研究结果为深入揭示草莓SUN基因的生物学功能及其分子机制奠定了基础。     

The Mycobacterium tuberculosis mysB gene product is a functional equivalent of the Escherichia coli sigma factor, KatF

Mycobacterium tuberculosis, the causative agent of tuberculosis, may remain dormant within its host for many years. The nature of this dormant or latent state is not known, but it may be a specialized form of the stationary growth phase. In Escherichia coli, KatF (or RpoS) is the major stationary phase sigma factor regulating an array of genes expressed in this phase of growth. A potential M. tuberculosis katF homologue was cloned using a fragment of the E. coli katF gene as a probe. DNA sequence analysis of a resultant clone showed 100% identity to a fragment of DNA encoding the M. tuberculosis mysA and mysB genes. Overexpression of mysB in M. bovis BCG resulted in an increase in katG mRNA and catalase and peroxidase activity, and an increase in sensitivity of the cells to isoniazid. An increase in katG promoter activity from a reporter vector was demonstrated when mysB was overexpressed from the same plasmid, indicating a direct relationship between MysB and katG expression.     

卡氏德巴利酵母植酸酶在毕赤酵母中的异源表达及优化

【背景】植酸是一种能螯合金属离子和蛋白质的有机磷类化合物,广泛存在于植物组织中,影响动物对营养元素的吸收。在饲料中加入植酸酶可有效降解植酸。【目的】构建毕赤酵母异源表达卡氏德巴利酵母(Debaryomyces castellii,D. castellii)植酸酶的菌株,促进卡氏德巴利酵母植酸酶的研究及工业应用。【方法】将卡氏德巴利酵母植酸酶基因进行密码子优化后转入毕赤酵母GS115中,通过筛选多拷贝、敲除蛋白酶、过表达分子伴侣及转运蛋白的方法获取优势菌株。【结果】所得重组菌株GS115/DCphy(ΔPep4)(BFR2)的产酶酶活是低拷贝菌株的7倍。【结论】研究结果为卡氏德巴利酵母植酸酶的异源表达及潜在工业应用提供了一定的指导。     

Molecular cloning and characterization of the dpy-20 gene of Caenorhabditis elegans

We describe the molecular analysis of the dpy20 gene in Caenorhabditis elegans. Isolation of genomic sequences was facilitated by the availability of a mutation that resulted from insertion of a Tc1 transposable element into the dpy-20 gene. The Tc1 insertion site in the m474:: Tc1 allele was identified and was found to lie within the coding region of dpy-20. Three revertants (two wild-type and one partial revertant) resulted from the excision of this Tc1 element. Genomic dpy-20 clones were isolated from a library of wild-type DNA and were found to lie just to the left of the unc-22 locus on the physical map, compatible with the position of dpy-20 on the genetic map. Cosmid DNA containing the dpy-20 gene was successfully used to rescue the mutant phenotype of animals homozygous for another dpy-20 allele, e1282ts. Sequence analysis of the putative dpy-20 homologue in Caenorhabditis briggsae was performed to confirm identification of the coding regions of the C. elegans gene and to identify conserved regulatory regions. Sequence analysis of dpy-20 revealed that it was not similar to other genes encoding known cuticle components such as collagen or cuticulin. The dpy-20 gene product, therefore, identifies a previously unknown type of protein that may be directly or indirectly involved in cuticle function. Northern blot analysis showed that dpy-20 is expressed predominantly in the second larval stage and that the mRNA is not at all abundant. Data from temperature shift studies using the temperature-sensitive allele e1282ts showed that the sensitive period also occurs at approximately the second larval stage. Therefore, expression of dpy-20 mRNA and function of the DPY-20 protein are closely linked temporally.     

Sequence of the E. coli O104 antigen gene cluster and identification of O104 specific genes

The Escherichia coli O104 polysaccharide is an important antigen, which contains sialic acid and is often associated with EHEC clones. Sialic acid is a component of many animal tissues, and its presence in bacterial polysaccharides may contribute to bacterial pathogenicity. We sequenced the genes responsible for O104 antigen synthesis and have found genes which from their sequences are identified as an O antigen polymerase gene, an O antigen flippase gene, three CMP-sialic acid synthesis genes, and three potential glycosyl transferase genes. The E. coli K9 group IB capsular antigen has the same structure as the O104 O antigen, and we find using gene by gene PCR that the K9 gene cluster is essentially the same as that for O104. It appears that the distinction between presence as group IB capsule or O antigen for this structure does not involve any difference in genes present in the O antigen gene cluster. By PCR testing against representative strains for the 166 E. coli O antigens and some randomly selected Gram-negative bacteria, we identified three O antigen genes which are highly specific to O104/K9. This work provides the basis for a sensitive test for rapid detection of O104 E. coli. This is important both for decisions on patient care as early treatment may reduce the risk of life-threatening complications and for a faster response in control of food borne outbreaks.     

龙眼UGD6基因克隆及其表达特性分析

该试验采用RT-PCR和RACE技术,对龙眼多糖合成的关键基因尿苷二磷酸-葡萄糖6-脱氢酶基因(DlUGD6)进行分离克隆、生物信息学分析和亚细胞定位研究,并采用qRT-PCR技术,对其在龙眼体细胞胚胎发生、合子胚发育及不同组织器官中的表达模式进行分析。结果表明:(1)DlUGD6基因的cDNA序列全长1 860bp,包含开放阅读框1 443bp,编码480个氨基酸(GenBank登录号KU198438);生物信息学分析显示,DlUGD6属于稳定的酸性亲水蛋白,不含信号肽,具有跨膜结构和3个典型的保守结构域,属于UDP-葡萄糖/GDP-甘露糖脱氢酶家族;进化树分析表明,DlUGD6与柑橘亲缘关系较近。(2)洋葱内表皮GFP荧光定位观察发现,DlUGD6定位于细胞质;qRT-PCR结果显示,DlUGD6在龙眼非胚性愈伤组织中表达量相对较高,且在其他体胚发育阶段也均有稳定表达;在合子胚发育中子叶胚形成后第8天(S3)和第24天(S7)时表达量最高,整体呈"W"型;在不同组织器官中,DlUGD6在花药和茎中的表达量最高,且整体上生殖器官中的表达水平高于营养器官。研究认为,DlUGD6基因可能参与龙眼生长发育各个阶段中细胞壁多糖合成。     

Identification and expression of the GTcyc cDNA clone from genetic tumors formed on a Nicotiana glauca-N. langsdorffii hybrid

Cell division is one of the fundamental processes in all eukaryotes and plays a crucial role in growth and development of multicellular organisms. A 192-bp predicted DNA product was amplified from the genetic tumors of Nicotiana glauca-Nicotiana langsdorffii hybrid using degenerate primers specific for cyclin genes. A full-length cyclin cDNA clone was subsequently identified from the genetic tumors using a cDNA library screening strategy. In situ hybridization analysis showed that the GTcyc was detected in numerous, small spots in the whole range of genetic tumor.     

Role in tumorigenesis of silent mutations in the TP53 gene

Over 10,000 mutations in the TP53 suppressor gene have been recorded in the International Agency for Research on Cancer (IARC) tumor data base. About 4% of these mutations are silent. It is a question whether these mutations play a role in tumor development. In order to approach this question, we asked whether the reported silent mutations are randomly distributed throughout the TP53 gene. The p53 data base was searched exon by exon. From the frequency of codons with no silent mutations, the average number of silent mutations per codon for each exon was calculated using the Poisson distribution. The results indicate the distribution to be non-random. About one-third of all silent mutations occur in “hot-spots” and after subtraction of these hot-spots, the remaining silent mutations are randomly distributed. In addition, the percentage of silent mutations among the total in the silent mutation hot-spots is close to that expected for random mutation. We conclude that most of the silent mutations recorded in tumors play no role in tumor development and that the percentage of silent mutation is an indication of the amount of random mutation during tumorigenesis. Silent mutations occur to a significantly different extent in different tumor types. Tumors of the esophagus and colon have a low frequency of silent mutations, tumors of the prostate have a high frequency.     

芥菜WOX基因家族的全基因组鉴定与分析

WUSCHEL相关-同源盒(WUSCHEL related-homeobox, WOX)基因家族是一类植物特有的转录因子基因家族,在植物的生长发育过程中发挥重要作用。本研究利用芥菜(Brassica juncea)基因组数据,通过HUMMER、Smart等软件进行检索筛选,共鉴定出51个WOX基因家族成员。利用Expasy在线软件对这些家族成员的蛋白质分子量、氨基酸序列长度、等电点等进行分析,并利用生物信息学软件对芥菜WOX基因家族进化关系、保守区域、基因结构等进行系统性分析,将芥菜WOX基因家族分为古老支、中间支和WUS支/现代支3个亚家族。结构分析表明,同一亚家族内的WOX转录因子家族成员的保守结构域的种类、组织形式以及基因结构具有高度的一致性,而不同亚家族之间呈现一定的多样性。51个WOX基因不均匀分布于芥菜18条染色体上,这些基因的启动子大多含有响应光、激素和非生物逆境胁迫相关的顺式作用元件。利用转录组数据和实时荧光定量PCR (real-time fluorescence quantitative PCR, qRT-PCR)分析发现,芥菜WOX基因的表达具有时空特异性,其中B...     

Phylogenetic investigations of Sordariaceae based on multiple gene sequences and morphology

The family Sordariaceae incorporates a number of fungi that are excellent model organisms for various biological, biochemical, ecological, genetic and evolutionary studies. To determine the evolutionary relationships within this group and their respective phylogenetic placements, multiple-gene sequences (partial nuclear 28S ribosomal DNA, nuclear ITS ribosomal DNA and partial nuclear β-tubulin) were analysed using maximum parsimony and Bayesian analyses. Analyses of different gene datasets were performed individually and then combined to generate phylogenies. We report that Sordariaceae, with the exclusion Apodus and Diplogelasinospora, is a monophyletic group. Apodus and Diplogelasinospora are related to Lasiosphaeriaceae. Multiple gene analyses suggest that the spore sheath is not a phylogenetically significant character to segregate Asordaria from Sordaria. Smooth-spored Sordaria species (including so-called Asordaria species) constitute a natural group. Asordaria is therefore congeneric with Sordaria. Anixiella species nested among Gelasinospora species, providing further evidence that non-ostiolate ascomata have evolved from ostiolate ascomata on several independent occasions. This study agrees with previous studies that show heterothallic Neurospora species to be monophyletic, but that homothallic ones may have a multiple origins. Although Gelasinospora and Neurospora are closely related and not resolved as monophyletic groups, there is insufficient evidence to place currently accepted Gelasinospora and Neurospora species into the same genus.     

The C. elegans sex determination gene laf-1 encodes a putative DEAD-box RNA helicase

The Caenorhabditis elegans gene laf-1 is critical for both embryonic development and sex determination. Laf-1 is thought to promote male cell fates by negatively regulating expression of tra-2 in both hermaphrodites and males. We cloned laf-1 and established that it encodes a putative DEAD-box RNA helicase related to Saccharomyces cerevisiae Ded1p and Drosophila Vasa. Three sequenced laf-1 mutations are missense alleles affecting a small region of the protein in or near helicase motif III. We demonstrate that the phenotypes resulting from laf-1 mutations are due to loss or reduction of laf-1 function, and that both laf-1 and a related helicase vbh-1 function in germline sex determination. Laf-1 mRNA is expressed in both males and hermaphrodites and in both the germline and soma of hermaphrodites. It is expressed at all developmental stages and is most abundant in embryos. LAF-1 is predominantly, if not exclusively, cytoplasmic and colocalizes with PGL-1 in P granules of germline precursor cells. Previous results suggest that laf-1 functions to negatively regulate expression of the sex determination protein TRA-2, and we find that the abundance of TRA-2 is modestly elevated in laf-1/+ females. We discuss potential functions of LAF-1 as a helicase and its roles in sex determination.     

银杏bHLH91转录因子基因的克隆及表达分析

bHLH转录因子在植物的生长发育、胁迫应答和次生代谢中具有重要的调控作用。该研究通过PCR技术从银杏(Ginkgo biloba)叶中分离得到了一个bHLH基因的cDNA序列,并将其命名为GbbHLH91。序列分析结果显示扩增的GbbHLH91基因cDNA序列长度为1 425 bp,开放阅读框是1 065 bp,编码354个氨基酸,分子量为40.1 kDa,等电点为8.20。系统进化分析结果显示,从用于进化树构建的bHLH蛋白质聚类情况来看,银杏GbbHLH91蛋白与裸子植物油松(Pinus tabuliformis)bHLH蛋白亲缘关系最近,且与被子植物无油樟(Amborella trichopoda)bHLH蛋白相似性达到60%,表明该基因在进化过程中相对比较保守。实时荧光定量PCR分析发现银杏bHLH91基因在银杏的各个组织中均有表达,其中在银杏叶中表达量最高,在根和茎中基因的表达量次之,在银杏雌花和果中表达量较少,在雄花中的表达水平最低;GbbHLH91基因在不同发育时期的银杏叶片中,表达量也存在一定的差异,其中在4月中旬该基因的表达水平达到最高,而后随着叶片的生长发育,该基因的表达水平呈现下降趋势。该研究结果为进一步验证GbbHLH91基因的功能奠定了前期基础。     

The mechanism of sex-specific splicing at the doublesex gene is different between Drosophila melanogaster and Bombyx mori

We have previously reported that Bmdsx, a homologue of the sex-determining gene, doublesex (dsx), was found to be sex-specifically expressed in various tissues at larval, pupal, and adult stages in the silkworm, Bombyx mori, and was alternatively spliced to yield male- and female-specific mRNAs. To reveal sex-specific differences in splicing patterns of Bmdsx pre-mRNA, the genomic sequence was determined and compared with male- and female-specific Bmdsx cDNA sequences. The open reading frame (ORF) consisted of five exons. Exons 3 and 4 were specifically incorporated into the female type of Bmdsx mRNA. On the other hand, exon 2 was spliced to exon 5 to produce the male type mRNA of Bmdsx. As in the case of Drosophila dsx, the OD2 domain was separated by a female-specific intron into sex-independent and sex-dependent regions. Sex-specific splicing occurred in equivalent positions in the Drosophila dsx gene. However, unlike Drosophila dsx, the female-specific introns showed no weak 3′ splice sites, and the TRA/TRA-2 binding site related sequences were not found in the female-specific exon, nor even in any other regions of the Bmdsx gene. Moreover, an in vitro splicing reaction consisting of HeLa cell nuclear extracts showed that the female-type of Bmdsx mRNA represented the default splicing. These findings suggest that the structural features of the sex-specific splicing patterns of Bmdsx pre-mRNA are similar to those of Drosophila dsx but the regulation of sex-specific alternative splicing of Bmdsx pre-mRNA is different.     

Regulation of Krüppel expression in the anlage of the Malpighian tubules in the Drosophila embryo

The expression of most Drosophila segmentation genes is not limited to the early blastoderm stage, when the segmental anlagen are determined. Rather, these genes are often expressed in a variety of organs and tissues at later stages of development. In contrast to the early expression, little is known about the regulatory interactions that govern the later expression patterns. Among other tissues, the central gap gene Krüppel is expressed and required in the anlage of the Malpighian tubules at the posterior terminus of the embryo. We have studied the interaction of Krüppel with other terminal genes. The gap genes tailles and huckebein, which repress Krüppel in the central segmentation domain, activate Krüppel expression in the posterior Malpighian tubule domain. The opposite effect on the posterior Krüppel expression is achieved by the interposition of another factor, the homeotic gene fork head, which is not involved in the control of the central domain. In addition, Krüppel activates different genes in the Malpighian tubules than in the central domain. Thus, both the regulation and the function of Krüppel in the Malpighian tubules differ strikingly from its role in segmentation.     

An allelic exchange system for compliant genetic manipulation of the select agents Burkholderia pseudomallei and Burkholderia mallei

Burkholderia pseudomallei and B. mallei are Gram-negative bacterial pathogens that cause melioidosis in humans and glanders in horses, respectively. Both bacteria are classified as category B select agents in the United States. Due to strict select-agent regulations, the number of antibiotic selection markers approved for use in these bacteria is greatly limited. Approved markers for B. pseudomallei include genes encoding resistance to kanamycin (Km), gentamicin (Gm), and zeocin (Zeo); however, wild type B. pseudomallei is intrinsically resistant to these antibiotics. Selection markers for B. mallei are limited to Km and Zeo resistance genes. Additionally, there are few well developed counter-selection markers for use in Burkholderia. The use of SacB as a counter-selection method has been of limited success due to the presence of endogenous sacBC genes in the genomes of B. pseudomallei and B. mallei. These impediments have greatly hampered the genetic manipulation of B. pseudomallei and B. mallei and currently few reliable tools for the genetic manipulation of Burkholderia exist. To expand the repertoire of genetic tools for use in Burkholderia, we developed the suicide plasmid pMo130, which allows for the compliant genetic manipulation of the select agents B. pseudomallei and B. mallei using allelic exchange. pMo130 harbors an aphA gene which allows for Km selection, the reporter gene xylE, which allows for reliable visual detection of Burkholderia transformants, and carries a modified sacB gene that allows for the resolution of co-integrants. We employed this system to generate multiple unmarked and in-frame mutants in B. pseudomallei, and one mutant in B. mallei. This vector significantly expands the number of available tools that are select-agent compliant for the genetic manipulation of B. pseudomallei and B. mallei.