Molecular cloning and copy number variation of a ferritin subunit (Fth1) and its association with growth in freshwater pearl mussel Hyriopsis cumingii

Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cumingii) was isolated and characterized. The complete cDNA contained 822 bp, with an open reading frame (ORF) of 525 bp, a 153 bp 5' untranslated region (UTR) and a 144 bp 3' UTR. The complete genomic DNA was 4125 bp, containing four exons and three introns. The ORF encoded a protein of 174 amino acids without a signal sequence. The deduced ferritin contained a highly conserved motif for the ferroxidase center comprising seven residues of a typical vertebrate heavy-chain ferritin. It contained one conserved iron associated residue (Try27) and iron-binding region signature 1 residues. The mRNA contained a 27 bp iron-responsive element with a typical stem-loop structure in the 5'-UTR position. Copy number variants (CNVs) of Fth1 in two populations (PY and JH) were detected using quantitative real-time PCR. Associations between CNVs and growth were also analyzed. The results showed that the copy number of the ferritin gene of in the diploid genome ranged from two to 12 in PY, and from two to six in JH. The copy number variation in PY was higher than that in JH. In terms of shell length, mussels with four copies of the ferritin gene grew faster than those with three copies (P<0.05), suggesting that CNVs in the ferritin gene are associated with growth in shell length and might be a useful molecular marker in selective breeding of H. cumingii.     

西伯利亚蓼钙调蛋白基因的克隆及其在盐胁迫下的表达

已从西伯利亚蓼叶中cDNA文库中获得的钙调蛋白EST序列,采用cDNA末端快速扩增（RACE）技术克隆了具有完整编码区的钙调蛋白基因的cDNA序列（GenBank登录号GQ988382）,命名为PsCaM。该基因全长615bp,编码区为450bp,编码149个氨基酸,5＇非翻译区为63bp,3＇非翻译区为102bp。同源性分析表明,该蛋白与其他植物钙调蛋白高度保守,氨基酸同源性高达98%。用实时荧光定量PCR研究3%NaHCO3胁迫下西伯利亚蓼基因表达的结果显示,自然条件下,该基因在叶中表达量最高,地下茎次之,茎中最低;盐胁迫下CaM在西伯利亚蓼的地下茎、茎和叶中均有表达,表达模式不同。     

The 3' untranslated region of tobacco necrosis virus RNA contains a barley yellow dwarf virus-like cap-independent translation element

RNAs of many viruses are translated efficiently in the absence of a 5' cap structure. The tobacco necrosis virus (TNV) genome is an uncapped, nonpolyadenylated RNA whose translation mechanism has not been well investigated. Computational analysis predicted a cap-independent translation element (TE) within the 3' untranslated region (3' UTR) of TNV RNA that resembles the TE of barley yellow dwarf virus (BYDV), a luteovirus. Here we report that such a TE does indeed exist in the 3' UTR of TNV strain D. Like the BYDV TE, the TNV TE (i) functions both in vitro and in vivo, (ii) requires additional sequence for cap-independent translation in vivo, (iii) has a similar secondary structure and the conserved sequence CGGAUCCUGGGAAACAGG, (iv) is inactivated by a four-base duplication in this conserved sequence, (v) can function in the 5' UTR, and (vi) when located in its natural 3' location, may form long-distance base pairing with the viral 5' UTR that is conserved and probably required. The TNV TE differs from the BYDV TE by having only three helical domains instead of four. Similar structures were found in all members of the Necrovirus genus of the Tombusviridae family, except satellite tobacco necrosis virus, which harbors a different 3' cap-independent translation domain. The presence of the BYDV-like TE in select genera of different families indicates that phylogenetic distribution of TEs does not follow standard viral taxonomic relationships. We propose a new class of cap-independent TE called BYDV-like TE.     

MOLECULAR CLONING OF SOLUBLE TREHALASE FROM Chironomus riparius LARVAE, ITS HETEROLOGOUS EXPRESSION IN Escherichia coli AND BIOINFORMATIC ANALYSIS

Trehalase is involved in the control of trehalose concentration, the main blood sugar in insects. Here, we describe the molecular cloning of the cDNA encoding for the soluble form of the trehalase from the midge larvae of Chironomus riparius, a well-known bioindicator of the quality of freshwater environments. Molecular cloning was achieved through multiple alignment of Diptera trehalase sequences, allowing the synthesis of internal homology-based primers; the complete open reading frame(ORF) was subsequently obtained through RACE-PCR(where RACE is rapid amplification of cDNA ends). The cDNA contained the 5' untranslated region (UTR), the 3' UTR including a poly(A) tail and the ORF of 1,725 bp consisting of 574 amino acid residues with a predicted molecular mass of 65,778 Da. Recombinant trehalase was successfully expressed in Escherichia coli as a His-tagged protein and purified on Ni-NTA affinity chromatography. Primary structure analysis showed a series of characteristic features shared by all insect trehalases, while three-dimensional structure prediction yielded the typical glucosidase fold, the two key residues involved in the catalytic mechanism being conserved. Production of recombinant insect trehalases opens the way to structural characterizations of the catalytic site, which might represent, among others, an element for reconsidering the enzyme as a target in pest insects' control.     

Isolation and characterization of microsomal omega-6-desaturase gene (fad2-1) from soybean

A genomic DNA sequence (fad2-1) encoding seed specific microsomal 0-6 desaturase was isolated from soybean (Glycine max. L cv. Pusa-9702). A positive genomic clone of 1852 nucleotides containing a single uninterrupted 3' end exonic region with an ORF of 1140 bp encoding a peptide of 379 amino acids, a complete 3' UTR of 206 bp and 86 bp of 5' UTR interrupted by a single intron of 420 bp was obtained on screening the sub-genomic library of soybean. Southern blots revealed at least two copies of the gene per haploid genome. Analysis of the translated product showed the presence of three histidine boxes, with the general sequence HXXXH and five probable transmembrane segments reported to be involved in substrate specificity.     

草鱼CD81基因的克隆及功能分析

为研究白细胞表面分化抗原81(CD81)的功能, 对草鱼CD81进行了克隆, CD81全长共1376 bp, 其中5'非翻译区87 bp, 3'非翻译区581 bp, 开放阅读框为708 bp, 包括8个外显子, 7个内含子, 编码235个氨基酸。实验采用实时荧光定量PCR的方法检测了CD81在健康草鱼不同组织中的表达情况及草鱼出血病病毒(GCRV)攻毒前后的表达变化情况。结果显示草鱼CD81在所有被检测组织中均有表达, 在头肾中表达量最高。在GCRV攻毒前后草鱼鳃、脾、肝、肠及头肾5个组织中的CD81表达量均有明显变化。同时, 采用绿色荧光蛋白(GFP)来示踪CD81的亚细胞表达部位, 激光共聚焦显微镜显示, 同人类一样, 草鱼CD81定位于细胞膜上。       

Cloning of two different 5' untranslated exons of bovine acidic fibroblast growth factor by the single strand ligation to single-stranded cDNA methodology.

In an attempt to characterize the 5' UTR of the aFGF mRNAs we used the new anchored PCR methodology, single strand ligation to ss-cDNAs (SLIC). In bovine brain and retina, two kinds of aFGF cDNA clones were isolated. They contained two alternative exons located 34 bp upstream to the translation initiation codon ATG. Taking into account the number of clones specific for each exon, the two mRNAs are expressed with the same ratio in both tissues. One of these bovine 5' UTR exons (136 bp) showed 81% identity to a human 5' UTR exon, the second one (323 bp) was 70% identical to the second human 5' UTR exon with a central region of 90 nucleotides showing 41% identity. The conservation of the splicing positions for these 5' UTR alternate exons in both bovine and human species, suggests that the overall structure of the aFGF gene is conserved in mammals. Furthermore, the conservation of the nucleotide sequences and of the localization of these 5' UTR exons suggests that these non-coding regions may be involved in the control of aFGF gene expression.     

Isolation of cDNA from Jacaratia mexicana encoding a mexicain-like cysteine protease gene

Cysteine proteases (CPs) from the C1 family, which are similar to papain, can be found in animals and plants, as well as some viruses and prokaryotes. These enzymes have diverse physiological functions and are thus very attractive for science and industry. Jacaratia mexicana, a member of the Caricaceae plant family, contains several CPs, the principal being mexicain, found to favorably compete against papain for many industrial applications due to its high stability and specific activity. In this study, leaves of J. mexicana were used to isolate a CP-coding gene, similar to those that code for mexicain and chymomexicain. By using rapid amplification of cDNA ends (RACE) as well as oligonucleotide design from papain-like conserved amino acids (aa), a sequence of 1404 bp consisting of a 5' terminal untranslated region (UTR) of 153 bp, a 3' terminal UTR of 131 bp, with a polyadenylation (poly(A)) signal sequence and a poly(A) tail, and an open reading frame (ORF) of 1046 bp, was obtained by overlapping three partial sequences. Two full-length cDNA sequences that encode for mexicain-like proteases were cloned from mRNA (JmCP4 and JmCP5). JmCP4 is predicted to have an ORF of 1044 bp, which codifies for polypeptides that have a 26 aa signal peptide region, a 108 aa propeptide region and a mature enzyme of 214 aa. A 969 bp fragment (JmCP5) encodes for a partial sequence of a CP gene, without the signal peptide region but with a full-length propeptide region. The sequence analysis showed that this protease presented a high similarity to other plant CPs from J. mexicana, Vasconcellea cundinamarcensis, Vasconcellea stipulata, and Carica papaya, among others, mainly at the conserved catalytic site. Obtaining the sequence of this CP gene from J. mexicana provides an alternative for production in a standard system and could be an initial step towards the commercialization of this enzyme.     

口蹄疫病毒Asia1/YNBS/58株全基因组序列分析

口蹄疫是由口蹄疫病毒(Foot-and-mouth dis-ease virus,FMDV)感染引起的偶蹄动物(猪、牛、羊、骆驼等)共患的一种急性、烈性、接触性传染病。FMDV是小核糖核酸病毒科(Picornaviridae)口蹄疫病毒属(Aphthovirus)的成员,有7个血清型,分别为O、A、C、Asia1、SAT1、SAT2、SAT3,完整     

海参i型溶菌酶基因及其编码产物的结构特点

通过RT-PCR 和 RACE PCR技术,从海参(Stichopus japonicus)体壁中克隆得到一种溶菌酶基因(GenBank：EF036468).生物信息软件分析表明,其中全长cDNA为 713 bp,5′非编码区（UTR）246 bp,3′UTR 29 bp,开放阅读框438 bp,编码145个氨基酸,包括溶菌酶成熟肽124个氨基酸和信号肽21个氨基酸.对海参溶菌酶与多种无脊椎动物的c、g和i型溶菌酶进行分析比较,发现它与i型溶菌酶有较高的同源性,并具有i型溶菌酶高度保守的2个活性位点,即Glu34和Ser50.活性位点附近具有i型溶菌酶的一段特有的氨基酸保守序列MDVGSLSCG(P/Y)(Y/F)QIK,所以推断克隆的海参溶菌酶为i型.另外,通过搜索蛋白保守结构域数据库,发现海参溶菌酶与医用水蛭失稳酶相似性最高,并且这2个酶的三级结构模型也极其相似.因此推测,海参i型溶菌酶具有双功能特性,既能作用于细菌细胞壁的糖苷键使细胞裂解,又具有失稳酶的一些生化功能,能够水解纤维蛋白,这些特点在海参自溶过程中发挥重要的作用.     

衣藻质体分裂相关基因CrFtsZ2的克隆及其进化分析

ＦｔｓＺ(ｆｉｌａｍｅｎｔｉｎｇｔｅｍｐｅｒａｔｕｒｅｓｅｎｓｉｔｉｖｅ)是一类从大肠杆菌温度敏感型突变体中分离到的基因 .该基因与Ｅ .ｃｏｌｉ细胞分裂密切相关 .突变体由于细胞分裂受阻而呈现“长丝状”[1] .此类基因于 1980年首次被克隆[2 ] .随后的研究表明 ,ＦｔｓＺ蛋白在Ｅ .ｃｏｌｉ分裂细胞的凹陷处形成环状多聚体 ,Ｚ环 ,是Ｅ .ｃｏｌｉ细胞分裂的限制因子[3 ] .衣藻属于绿藻 ,在现存的所有单细胞真核藻类中 ,绿藻是与陆生植物亲缘关系最近的一支[4] .由于衣藻为单细胞真核生物 ,并且仅含有一个巨大的叶绿体 ,因而是研究…     

虾夷扇贝脂多糖诱导的肿瘤坏死因子LITAF基因的克隆及表达分析

脂多糖诱导的肿瘤坏死因子(Lipopolysaccharide-induced TNF-alpha factor,LITAF)是一类重要的炎症细胞因子,在先天性免疫系统中发挥重要的介质作用。文章根据虾夷扇贝LITAF基因EST序列,应用RACE技术克隆了虾夷扇贝LITAF全长cDNA,对序列及编码的氨基酸进行生物信息学分析。结果显示,该基因cDNA全长1 551 bp,其5′非编码区包含76 bp,3′非编码区包含1 001 bp;开放阅读框(ORF)为474 bp,编码157个氨基酸,氨基酸序列中存在一个保守的LITAF结构域;理论分子量16.99 kDa,等电点为6.24。LITAF基因序列为3 698 bp,由3个外显子和两个内含子组成。利用实时荧光定量PCR技术分析LITAF在虾夷扇贝不同组织、不同胚胎发育阶段以及鳗弧菌(Vibrio anguillarum)刺激后各时间段的表达情况。结果表明:LITAF基因在所检测的6个成体组织中均有表达,其中肾脏的表达量最高;胚胎发育的7个时期中,担轮幼体时期表达量最高;菌刺激36 h实验组与对照组的表达量差异大。LITAF基因是LITAF家族的一员,推测LITAF基因参与虾夷扇贝的先天性免疫反应。