Comparative sequence analysis and radiation hybrid mapping of the canine keratin 10 gene.

The type I keratin, K10, is expressed in epidermal keratinocytes undergoing terminal differentiation to form the stratum corneum, a barrier essential for life. In order to facilitate the study of keratinization disorders in the dog, the sequence and mapping of KRT10 is reported. The coding region of KRT10 is 1707 bp and is comprised of eight exons. Although the length of KRT10 has been reported to be polymorphic in humans, this was not observed in the eight domestic dog breeds studied, although one wild canid displayed a size difference. The structure and sequence of this gene is highly conserved across mammalian species. Canine K10 had an 86% amino acid identity with the human gene. KRT10 was localized to the on-going canine radiation hybrid map to chromosome 9 in the type I keratin gene cluster.     

Uncv无毛小鼠无毛基因的分子克隆及序列分析

目的 探讨Unev无毛小鼠的无毛性状与无毛基因(hairless gene,hr)的相关性.方法 参照Gen-Bank上公布的小鼠的hr序列,设计5对引物,用RT-PCR方法对本单位培育的Unev无毛小鼠hr的编码区序列进行了克隆与分析.结果 获得了Unev无毛小鼠及野生型hr的全部编码区序列(3546 bp).Unev无毛小鼠hr基因与野生型小鼠hr基因的长度及序列完全一致,同源性为100%.与GenBank上发表的国外小鼠hr基因序列(Z32675)相比,同源性为99.7%,共10个碱基发生了突变,其中2个碱基突变导致了相应的氨基酸突变;和昆明小鼠的hr(AY547391)相比,同源性为99.6%,共12个碱基发生了突变,其中3个碱基突变导致了相应的氨基酸突变;但这些突变是由种属差异造成的.结论 Uncv无毛小鼠的无毛性状产生与hr基因无关.     

幽门螺杆菌尿素酶B亚单位的克隆和序列分析

幽门螺杆菌是消化道疾病的主要致病菌。其有效抗原成份尿素酶B亚单位(UreB)可刺激机体产生保护性的免疫反应。用高保真PCR扩增系统扩增出UreB基因片段,将其克隆至质粒pUC19中,对其全序列进行了测定。克隆的UreB基因序列与报道的序列完全一致。这一研究获得了序列正确的UreB基因,为将来以UreB分子为抗原的疫苗研制工作打下了良好的基础。     

Cloning, mapping, and expression analysis of a gene encoding a novel mammalian EGF-related protein (SCUBE1)

The epidermal growth factor (EGF) superfamily comprises a diverse group of proteins that function as secreted signaling molecules, growth factors, and components of the extracellular matrix, many with a role in vertebrate development. We have isolated a novel mammalian gene encoding an EGF-related protein with a CUB (C1s-like) domain that defines a new mammalian gene family. The Scube1 (signal peptide-CUB domain-EGF-related 1) gene was isolated from a developing mouse urogenital ridge cDNA library and is expressed prominently in the developing gonad, nervous system, somites, surface ectoderm, and limb buds. We have mapped Scube1 to mouse chromosome 15 and show that it is orthologous to a human gene in the syntenic region of chromosome 22q13. We discuss the possible functions of this novel gene and its role in heritable disease in light of these data.     

黑线仓鼠及其白化突变系酪氨酸酶基因的克隆与序列分析

目的 对黑线仓鼠及其白化突变系酪氨酸酶基因进行比较研究,揭示黑线仓鼠白化突变系白化性状产生的分子机理.方法 根据小鼠与大鼠的酪氨酸酶基因保守区设计3对引物,利用RT-PCR方法,从黑线仓鼠及其白化系皮肤总RNA中扩增得到酪氨酸酶的cDNA基因,并对其二者进行克隆测序.结果 成功获得了黑线仓鼠及其白化突变系的酪氨酸酶基因,对二者的序列比较分析结果表明,二者的编码区没有差异.结论 黑线仓鼠白化突变系白化性状产生的原因与已知小鼠的白化性状产生原因不同,并不是由酪氨酸酶基因编码区突变造成的,其白化性状产生的机理有待进一步的研究.     

Radiation hybrid mapping of the canine type I and type IV collagen gene subfamilies

We are interested in the collagen gene superfamily and its involvement in hereditary diseases of the human and domestic dog. Presented here is radiation hybrid mapping of the type I and type IV collagen gene subfamilies on the most recent version of the canine map. The col1A1 gene was mapped to chromosome 9, col1A2 was mapped to chromosome 14, col4A1 and col4A2 were mapped to chromosome 22 and col4A3 and col4A4 were mapped to chromosome 25. The col4A5 and col4A6 genes, while linked to one another, are not linked in the present version of the canine map but likely are present on the X chromosome. These data provide an insight into the molecular evolution of these subfamilies and increase the number of mapped genes in discrete regions of the canine genome. J.K. Lowe and R. Guyon contributed equally to this work Sequences determined during the course of this work have been deposited in GenBank. Accession numbers are AF291995 (col1A1) and AF291996 (col1A2)     

Wide-cross whole-genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome

Whole-genome radiation hybrid mapping has been applied extensively to human and certain animal species, but little to plants. We recently demonstrated an alternative mapping approach in cotton (Gossypium hirsutum L.), based on segmentation by 5-krad γ-irradiation and derivation of wide-cross whole-genome radiation hybrids (WWRHs). However, limitations observed at the 5-krad level suggested that higher doses might be advantageous. Here, we describe the development of an improved second-generation WWRH panel after higher dose irradiation and compare the resulting map to the 5-krad map. The genome of G. hirsutum (n=26) was used to rescue the radiation-segmented genome of G. barbadense (n=26) introduced via 8- and 12-krad γ-irradiated pollen. Viable seedlings were not recovered after 12-krad irradiation, but 8-krad irradiation permitted plant recovery and construction of a 92-member WWRH mapping panel. Assessment of 31 SSR marker loci from four chromosomes revealed that the 8-krad panel has a marker retention frequency of ca. 76%, which is approximately equivalent to the rate of loss in a low-dose animal radiation hybrid panel. Retention frequencies of loci did not depart significantly from independence when compared between the A and D subgenomes, or according to positions along individual chromosomes. WWRH maps of chromosomes 10 and 17 were generated by the maximum likelihood RHMAP program and the general retention model. The resulting maps bolster evidence that WWRH mapping complements traditional linkage mapping and works in cotton, and that the 8-krad panel complements the 5-krad panel by offering higher rates of chromosome breakages, lower marker retention frequency, and more retention patterns. Electronic Supplementary Material Supplementary material is available for this article at     

Cloning and mapping of a testis-specific gene with sequence similarity to a sperm-coating glycoprotein gene

A testis-specific gene Tpx-1, located between Pgk-2 and Mep-1 on mouse chromosome 17, was isolated from a cosmid clone, and its cDNA sequences were determined. The predicted coding sequence of Tpx-1 isolated from BALB/c mice showed 64.2% nucleotide and 55.1% amino acid sequence similarity with that of a rat sperm-coating glycoprotein gene, the protein product of which is secreted by the epididymis. To examine the evolutionary relationship between Tpx-1 and a sperm-coating glycoprotein gene, the cDNA sequence of TPX1, the human counterpart of Tpx-1, was determined. The comparison of the predicted coding sequences of Tpx-1 and TPX1 showed 77.8% nucleotide and 70% amino acid sequence similarity. Since Tpx-1 (from mouse) is more similar to TPX1 (from man) than it is to a rat sperm-coating glycoprotein gene, we conclude that Tpx-1 (TPX1) and a sperm-coating glycoprotein gene are closely related, but distinct, genes belonging to the same gene family. The predicted Tpx-1 protein of a t mutant mouse CRO437 differs from that of BALB/c mice by one amino acid insertion in the putative signal peptide. TPX1 was mapped to 6p21-qter by Southern blot analysis of interspecies somatic hybrid cell lines.     

Cloning, sequence analysis and heterologous expression of a beta-mannanase gene from Bacillus subtilis Z-2

Mannanase, an extracellular enzyme catalyzes the hydrolysis of hemicelluloses to produce oligosaccharides, has a potential to be applied in food industries. In this study, a mannanase gene from B. subtilis Z-2 was isolated through PCR screening of a genomic DNA library. The nucleotide sequence of the mannanase gene, man, contained an open reading frame of 1.080 bp, which codes for a deduced 26 amino-acid signal peptide and a mature protein with the deduced molecular mass of 38 KDa. The man gene can both be expressed heterologously into the periplasm in plasmid pET22b(+) containing intact signal peptide (pET-NdeI18) and the pelB signal peptide of the pET22b(+)vector (pET-NcoI3). The Escherichia coli BL21 (DE3) containing pET-NcoI3 secreted about twice as much mannanase as that harboring pET-NdeI18. In E. coli DH5alpha, expression of man was under the control of the lac promoter in the pRK415 vector and was much more effective when the Shine-Dalgamo (SD) sequence was changed from GGGGAG to AAGGAG and the start codon was changed from TTG to ATG, respectively. These results suggest that genetic modification of the SD sequence and start codon is practical for high-level expression of mannanase in different bacterial strains.     

Cloning, sequence analysis and identification of a nonsense mutation-mediated mRNA decay of porcine GSTM2 gene

The glutathione S-transferase mu 2 gene （GSTM2） encodes a GST functioning in the elimination of electrophilic compounds and the regulation of cell growth. In this study, the sequence of porcine GSTM2 gene that contains the complete sequence encoding a protein of 218 amino acids was cloned. The deduced amino acid sequence shared 76%, 78% and 76% identity with that of human, mouse and rat, respectively, mRNA expression analysis showed that the porcine GSTM2 gene was expressed at a high level in liver and testis, at a medium level in longissimus dorsi muscle, adipose tissue, spleen and lung, at a low level in kidney, and at a very low level in heart and embryo. A nonsense mutation （CGA→TGA） resulted from C27T substitution in the fifth exon to produce a premature translation termination codon was identified, and it was discovered that nonsense-mediated mRNA decay might have an effect on the regulation of porcine GSTM2 gene expression. This polymorphism was analyzed in Large White, Landrace, Meishan and Qingping pig populations using the Taq I-polymerase chain reaction-restriction fragment length polymorphism method. The result showed that allele C had a higher frequency than allele T in each population.     

棉铃虫HaTO-like基因的克隆、序列分析和表达特征

【目的】克隆和分析了棉铃虫Helicoverpa armigera HaTO-like基因的编码框序列,检测了该基因的时空表达谱以及在棉铃虫感染核型多角体病毒HaSNPV后的转录变化,为深入研究该基因的功能提供理论依据。【方法】本研究利用RT-PCR的方法首次克隆获得HaTO-like基因的全长cDNA序列,通过几种生物信息学软件对该基因的核苷酸序列和氨基酸序列进行了分析,并利用荧光定量PCR技术检测了该基因在棉铃虫不同发育阶段、幼虫组织和成虫组织的表达情况,以及HaSNPV感染对HaTO-like基因表达的影响。【结果】棉铃虫HaTO-like基因cDNA全长为994 bp,开放阅读框为756 bp,编码251个氨基酸,其蛋白序列的N端含有23个氨基酸的信号肽。进一步的序列分析表明棉铃虫HaTO-like与其他昆虫同源蛋白的氨基酸序列一致性不是太高,大概在39%~61%之间,其中与家蚕和脐橙螟在系统进化上关系最近。荧光定量PCR结果表明该基因在棉铃虫的5龄0 h和成虫第1天的的表达量相对较高,在幼虫的头部和表皮内的表达量较其他幼虫组织较高,在成虫的头部和足的表达量也相对较高。而病毒感染则显著地诱导了该基因在棉铃虫幼虫头部和表皮内的表达。【讨论】本研究克隆了棉铃虫HaTO-like基因的全长cDNA序列,分析了该基因的序列特征和表达谱,为进一步阐释该基因的功能奠定理论基础。     

Cloning and sequence analysis ofglnB-like gene from nitrogen-fixingPaenibacillus polymyxa G2

A 240 bpglnB-like gene fragment was PCR amplified fromPaenibacillus polymyxa G2 using universal degenerate primers. These degenerate primers, based on all knownglnB-like genes including thenrgB ofBacillus subtilis at the time of design, were chosen from highly conserved amino acid sequences. The GlnB-like sequence ofP. polymyxa G2 had relatively high identities (more than 70%) to other bacteria GlnB, e.g.Escherichia coli (78%) andKlebsiella pneuomoniae (79%). However, the identity of theP. polymyxa GlnB-like sequence to a GlnK homologue (NrgB) of B.subtilis was low (46%). This is the first report of the sequence of theglnB-like gene from the genusPaenibacillus. Knowledge of theglnB-like gene sequence ofP. polymyxa will make us study deeply the function ofglnB in the genusPaenibacillus.     

Characterization and radiation hybrid mapping of expressed sequence tags from the canine brain

Abstract Maps of the canine genome are now developing rapidly. Most of the markers on the current integrated canine radiation hybrid/genetic linkage/cytogenetic map are highly polymorphic microsatellite (type II) markers that are very useful for mapping disease loci. However, there is still an urgent need for the mapping of gene-based (type I) markers that are required for comparative mapping, as well as identifying candidate genes for disease loci that have been genetically mapped. We constructed an adult brain cDNA library as a resource to increase the number of gene-based markers on the canine genome map. Eighty-one percent of the 2700 sequenced expressed sequence tags (ESTs) represented unique sequences. The canine brain ESTs were compared with sequences in public databases to identify putative canine orthologs of human genes. One hundred nine of the canine ESTs were mapped on the latest canine radiation hybrid (RH) panel to determine the location of the respective canine gene. The addition of these new gene-based markers revealed three conserved segments (CS) between human and canine genomes previously detected by fluorescence in situ hybridization (FISH), but not by RH mapping. In addition, five new CS between dog and human were identified that had not been detected previously by RH mapping or FISH. This work has increased the number of gene-based markers on the canine RH map by approximately 30% and indicates the benefit to be gained by increasing the gene content of the current canine comparative map.     

Cloning and expression analysis of a novel WD repeat gene, WDR3, mapping to 1p12-p13.

WD repeat proteins are components of multiprotein complexes that are involved in a wide spectrum of cellular activities, such as cell cycle progression, signal transduction, apoptosis, and gene regulation. These proteins are characterized by repeat units bracketed by Gly-His and Trp-Asp (GH-WD). We report here the isolation of a new member of the WD repeat gene family, WDR3, which encodes a putative 943-amino-acid nuclear protein consisting of 10 WD repeat modules. WDR3 is widely expressed in hematopoietic cell lines and in nonhematopoietic tissues. Fluorescence in situ hybridization mapped WDR3 to human chromosome 1p12-p13, a region that is affected by chromosomal rearrangements in a number of hematologic malignancies and solid tumors.     

Molecular Cloning, Mapping, and Polymorphism of the Porcine SCG2 gene

The secretogranin II (SCG2) gene is associated with the synthesis and secretion of follicle-stimulating hormone and luteinizing hormone. In the present study, we have determined the complete cDNA sequence of pig SCG2, which was submitted to GenBank with accession no. AY870646. Its complete open reading frame of 1,851 nucleotides encodes 616 amino acids. The predicted protein shares 80–87% identity with mouse, human, and bovine SCG2 proteins, and all four species share almost complete identity in the secretoneurin and EM66 domains. Pig SCG2 is a protein of 589 amino acids and 68,132 Da, preceded by a signal peptide of 27 residues. It contains nine pairs of dibasic residues, which are used as potential cleavage sites for generation of physiologically active peptides. Analysis of the SCG2 gene across the INRA-Minnesota porcine radiation hybrid panel indicates close linkage with microsatellite marker SW2608, located on Sus scrofa chromosome 15 (SSC15) q25, which harbors several QTL for ovulation rate and meat quality. Comparative sequencing and EST analysis revealed nine SNPs in porcine SCG2 cDNA, including seven SNPs in the coding region and two SNPs in the 3′ UTR. Four nonsynonymous SNPs (G622A, G1671T, C1718T, and A1790C) resulted in amino acid substitutions of Ala→Thr, Glu→Asp, Pro→Leu, and Asn→Thr, respectively.     

Cloning and sequence analysis of cDNAs encoding mammalian mitochondrial malate dehydrogenase

A cDNA clone, named ppmMDH-1 and covering a part of the porcine mitochondrial malate dehydrogenase (mMDH; L-malate:NAD+ oxidoreductase, EC 1.1.1.37) mRNA, was isolated from a porcine liver cDNA library with a mixture of 24 oligodeoxyribonucleotides as a probe. The sequences of the probe were deduced from the known sequence of porcine mMDH amino acid residues 288-293. ppmMDH-1 covered the coding region for porcine mMDH amino acid residues 17-314 and the 3' untranslated region. Subsequently, mouse mMDH cDNA clones were isolated from a mouse liver cDNA library with the ppmMDH-1 cDNA as a probe. One of the clones, named pmmMDH-1 and containing a cDNA insert of about 1350 base pairs, was selected for sequence analysis, and the primary structure of the mouse precursor form of mMDH (pre-mMDH) was deduced from its cDNA sequence. The sequenced coding regions for the porcine and mouse mMDH mRNAs showed about 85% homology. When the deduced amino acid sequence of the mouse pre-mMDH was compared with that of the porcine mMDH, they shared a 95% homology, and the mouse pre-mMDH yielded a leader sequence consisting of 24 amino acid residues and a mature mMDH, consisting of 314 amino acid residues. The leader sequence contained three basic amino acid residues, no acidic residues, and no hydrophobic amino acid stretch. The mouse mMDH leader sequence was compared with those of three other rodent mitochondrial matrix proteins.