The Sulfur Oxidation Operon Repressor Function is Influenced by the Product of its Adjacent Upstream ORF in <Emphasis Type="Italic">Pseudaminobacter salicylatoxidans</Emphasis> KCT001

The repressor of sulfur-oxidizing (sox) operon regulates expression of genes encoding a multienzyme complex that governs the chemolithotrophic sulfur oxidation in Pseudaminobacter salycylatoxidans KCT001. The inducer of sox operon viz., thiosulfate and other sulfur anions had no impact on in vitro repressor–operator interaction which indicates an atypical derepression mechanism. The reduced repressor has higher affinity for its operator DNA. The sulfur oxidation repressor binds with operator regions and led to efficient repression in trans, however, increased repressor concentration resulted in higher gene expression. Using a reporter system in E. coli, the present study established that the thioredoxin-like protein, encoded in immediate upstream ORF, could nullify the observed reversal of the repression at higher repressor concentration. In this context, the involvement of the upstream gene product in the regulation of the sulfur oxidation gene expression has been reported.     

Annotation and analysis of expressed sequence tags (ESTs) from Chinese sturgeon (Acipenser sinensis) pituitary cDNA library

Chinese sturgeon Acipenser sinensis belongs to the family Acipenseridae, an ancient species of actinopterygian fishes. In order to advance molecular research on its reproduction, ontogenetic development, we were seeking for genomic information in the NCBI expressed sequence tag (EST database). We found 3384 indentified cDNA sequences which were assembled into 861 unigenes. Blast analysis revealed 301 unigenes shared high similarity with genes in the public databases, and these were classified into three groups: 202 known genes, 81 putative genes and 8 unknown genes. The remainder (560 genes) had no significant match to any protein sequence. Further, 255 unigenes and 333 unmatched unigenes were annotated with Gene Ontology (GO), which could be classified into cellular component, molecular function, and biological process. Among the known genes, the hormone genes pomc A (proopiomelanocortin), pomc B, GtH alpha I subunit (gonadotropin hormone), GtH alpha II subunit and GH (growth hormone) were present in this library. Comparison of the Chinese sturgeon proteins (GH, GtH alpha subunit and POMC) to proteins of other species showed higher levels of homology among sturgeon species. We performed five hormone related genes including GnRHRI (gonadotropin-releasing hormone receptor I), cpH (carboxypeptidase H), ppiB (peptidylprolyl isomerase B), stmn3 (stathmin-like 3), 7B2 (neuroendocrine protein 7B2), and four novel genes (contig 192, 177, 170 and 168) a semi-quantitative RT-PCR on different tissues from Chinese sturgeon.     

sox30: a novel zebrafish sox gene expressed in a restricted manner at the midbrain-hindbrain boundary during neurogenesis

 The Sox family of proteins is thought to act to regulate gene expression in a wide variety of developmental processes. Here we describe the cloning of sox30, a novel sox gene from the zebrafish (Danio rerio). In situ hybridization shows that sox30 is expressed in a restricted manner at the boundary between the midbrain and hindbrain during nervous system development. This expression pattern is in direct contrast to that of most other neuronally expressed Sox genes which are expressed throughout the nervous system. Received: 30 October 1998 / Accepted: 1 February 1999     

Conservation and divergence of ADAM family proteins in the <Emphasis Type="Italic">Xenopus</Emphasis> genome

Background  

Members of the disintegrin metalloproteinase (ADAM) family play important roles in cellular and developmental processes through their functions as proteases and/or binding partners for other proteins. The amphibian Xenopus has long been used as a model for early vertebrate development, but genome-wide analyses for large gene families were not possible until the recent completion of the X. tropicalis genome sequence and the availability of large scale expression sequence tag (EST) databases. In this study we carried out a systematic analysis of the X. tropicalis genome and uncovered several interesting features of ADAM genes in this species.     

烟草TCP家族成员鉴定及表达分析

TCP家族作为植物特有的转录因子,在植物发育的不同方面发挥着重要作用。为筛选烟草中TCP家族成员,本研究通过全基因组同源比对,鉴定烟草与拟南芥TCP家族同源序列。利用生物信息学的方法分析其理化性质、系统进化关系、顺式作用元件等;筛选AtTCP3/AtTCP4的同源基因,并利用RT-qPCR检测在20% PEG6000处理下的基因表达量变化。结果表明烟草中含有TCP家族成员63个,其氨基酸序列长度范围为89−596 aa,蛋白亲水性(grand average of hydropathicity, GRAVY)范围为−1.147−0.125,等电点(isoelectric point, pI)范围为4.42−9.94,内含子个数为0−3,亚细胞定位均位于细胞核。保守结构域和系统进化关系分析结果表明,烟草TCP家族可分为PCF、CIN和CYC/TB1这3个亚家族且每个亚家族具有稳定序列。基因启动子区顺式作用元件结果表明,TCP家族基因含有低温顺式作用元件(LTR)及多种胁迫及代谢调控相关的元件(MYB、MYC)等顺式作用元件。基因表达模式分析表明,AtTCP3/AtTCP4同源基因(NtTCP6、NtTCP28、NtTCP30、NtTCP33、NtTCP42、NtTCP57和NtTCP63)在20% PEG6000处理下表达量显著上调表达/下调表达,并发现NtTCP30和NtTCP57基因对干旱胁迫响应较为明显。研究结果剖析了烟草基因组中的TCP家族,为烟草抗旱基因功能研究及品种培育提供了候选基因。     

Molecular characterization of inorganic sulfur‐compound metabolism in the deep‐sea epsilonproteobacterium Sulfurovum sp. NBC37‐1

The molecular components involved in energy metabolism of deep‐sea Epsilonproteobacteria were characterized in the mesophilic hydrogen‐ and sulfur‐oxidizing chemolithoautotroph Sulfurovum sp. NBC37‐1. Previous whole‐genome analysis of strain NBC37‐1 identified key genes likely to be associated with both sulfur reduction (psr gene families) and oxidation (two sox gene clusters). However, the sox gene clusters showed unique organizations and low homologies to those in other bacteria. Therefore, the biochemical mechanism of inorganic sulfur metabolism has been uncertain. Enzymatic activity measurements and partial protein purification indicated that the Sox enzyme system was constitutively expressed, whereas the expression of sulfur‐reduction enzymes varied depending on the culture conditions. The operative Sox system in strain NBC37‐1 required membrane components. The molecular basis of energy metabolism reported in this study provides important insight into how deep‐sea Epsilonproteobacteria change their energy metabolism in response to variable physical and chemical conditions in mixing zones between hydrothermal fluid and ambient seawater.     

Genomics and expression analysis of DHHC-cysteine-rich domain S-acyl transferase protein family in apple

S-acylation is one of a group of lipid modifications that occurs on eukaryotic proteins, mediated by DHHC-CRD-containing proteins, which plays an important role in regulating the membrane association, trafficking and function of target proteins. Although genome-wide identification of PAT family has been carried out in yeast, mice, humans and Arabidopsis, little is known about apple PAT genes. In this study, a total of 33 putative apple PAT proteins, containing DHHC-CRD by domain analysis, have been identified, and were classified into three groups according to the phylogenetic analysis of PAT proteins in apple and Arabidopsis. More complex TMDs in the most MdPATs revealed the PM location of the gene family. Gene structure, gene chromosomal location and paralogs analysis of MdPAT genes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of the PAT gene family in apple. According to the microarray and expressed sequence tag (ESTs) analysis, the different expression patterns indicate that they may play different roles during fruit development and rootstock-scion interactions process. Moreover, PATs were performed expression profile analyses in different tissues, indicating that the PATs are involved in various aspects of physiological and developmental processes of apple. To our knowledge, this is the first report of a genome-wide analysis of the apple PAT gene family, and this genomic analysis of apple DHHC-CRD PAT genes provides the first step towards a functional study of this gene family in apple.     

Genome scans and gene expression microarrays converge to identify gene regulatory loci relevant in schizophrenia

Multiple linkage regions have been reported in schizophrenia, and some appear to harbor susceptibility genes that are differentially expressed in postmortem brain tissue derived from unrelated individuals. We combined traditional genome-wide linkage analysis in a multiplex family with lymphocytic genome-wide expression analysis. A genome scan suggested linkage to a chromosome 4q marker (D4S1530, LOD 2.17, θ=0) using a dominant model. Haplotype analysis using flanking microsatellite markers delineated a 14 Mb region that cosegregated with all those affected. Subsequent genome-wide scan with SNP genotypes supported the evidence of linkage to 4q33–35.1 (LOD=2.39) using a dominant model. Genome-wide microarray analysis of five affected and five unaffected family members identified two differentially expressed genes within the haplotype AGA and GALNT7 (aspartylglucosaminidase and UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7) with nominal significance; however, these genes did not remain significant following analysis of covariance. We carried out genome-wide linkage analyses between the quantitative expression phenotype and genetic markers. AGA expression levels showed suggestive linkage to multiple markers in the haplotype (maximum LOD=2.37) but to no other genomic region. GALNT7 expression levels showed linkage to regulatory loci at 4q28.1 (maximum LOD=3.15) and in the haplotype region at 4q33–35.1 (maximum LOD=2.37). ADH1B (alcohol dehydrogenase IB) was linked to loci at 4q21–q23 (maximum LOD=3.08) and haplotype region at 4q33–35.1 (maximum LOD=2.27). Seven differentially expressed genes were validated with RT-PCR. Three genes in the 4q33–35.1 haplotype region were also differentially expressed in schizophrenia in postmortem dorsolateral prefrontal cortex: AGA, HMGB2, and SCRG1. These results indicate that combining differential gene expression with linkage analysis may help in identifying candidate genes and potential regulatory sites. Moreover, they also replicate recent findings of complex trans- and cis- regulation of genes.     

Ataxia and pancytopenia caused by a mutation in TINF2

Disseminated superficial actinic porokeratosis (DSAP) is a chronic autosomal dominant cutaneous disorder with high genetic heterogeneity. Two genetic loci for DSAP were identified, but no specific genes were reported to date. The pathogenic mechanism of this disorder remains to be elucidated. In this study, a large, five-generation Chinese family with DSAP was genetically characterized. Two known DSAP loci, DSAP1 and DSAP2, two DSAP candidate genes (SART3 and SSH1), one DSP-linked locus and one PPPD-linked locus were first excluded in the family. The family was then characterized by genome-wide linkage analysis and a new DSAP locus was identified on chromosome 1p31.3–p31.1 with a maximum two-point LOD score of 5.09 with marker D1S2897 (θ = 0). Fine mapping showed that the disease gene was located within an 8.2 cM or 11.9 Mb region between markers D1S438 and D1S464. This is the third locus identified for DSAP (DSAP3). Eight candidate genes including GNG12, IL12RB2, ITGB3BP, DNAJ6, PIN1L, GADD45A, RPE65 and NEGR1 were sequenced, but found to be negative for functional sequence variants. Further mutational analysis of the candidate genes in the region will identify the specific gene for DSAP, which will provide insights into the pathogenesis of DSAP.     

Genetics of Clubroot Resistance in <Emphasis Type="Italic">Brassica</Emphasis> Species

Clubroot disease, caused by the obligate plant pathogen Plasmodiophora brassicae Wor., is one of the most economically important diseases affecting Brassica crops in the world. The genetic basis of clubroot resistance (CR) has been well studied in three economically important Brassica species: B. rapa, B. oleracea, and B. napus. In B. rapa, mainly in Chinese cabbage, one minor and seven major CR genes introduced from European fodder turnips have been identified. Mapping of these CR genes localized Crr1 on R8, Crr2 on R1, CRc on R2, and Crr4 on R6 linkage groups of Chinese cabbage. Genes Crr3, CRa, CRb, and CRk mapped to R3, but at two separate loci, CRa and CRb are independent of Crr3 and CRk, which are closely linked. Further analysis suggested that Crr1, Crr2, and CRb have similar origins in the ancestral genome as in chromosome 4 of Arabidopsis thaliana. Genetic analysis of clubroot resistance genes in B. oleracea suggests that they are quantitative traits. Twenty-two quantitative trait loci (QTLs) were mapped in different linkage groups of B. oleracea. In B. napus, genetic analysis of clubroot resistance was found to be governed by one or two dominant genes, whereas resistance conferred by two recessive genes is reported. The quantitative analysis approach, however, proved that they are polygenic. In total, at least 16 QTLs have been detected on eight chromosomes of B. napus, N02, N03, N08, N09, N13, N15, N16, and N19. The chromosomal location of the other six QTLs is not clear. Cloning of any of these QTLs or resistance loci was not, however, possible until recently. Progress in genomics, particularly the techniques of comparative mapping and genome sequencing, supplements cloning and allows improved characterization of CR genes. Further development of DNA markers linked to CR genes will in turn hasten the breeding of clubroot-resistant Brassica cultivars.     

EST dataset of pituitary and identification of somatolactin and novel genes in Chinese sturgeon, <Emphasis Type="Italic">Acipenser sinensis</Emphasis>

Chinese sturgeon (Acipenser sinensis) is a rare and endangered species and also an important resource for the sturgeon aquaculture industry, however, a few genes have been identified in this species. We report here construction of a pituitary cDNA library from a 24 years old female Chinese sturgeon just after its spawning, and obtained 2,025 ESTs from the library. 885 unique sequences were identified, which were categorized into 12 functional groups. More than half of the unique sequences (57%) do not match with annotated sequences in the public databases. Three of these novel genes were further identified. Notably, a full-length of cDNA (1,143 bp) encoding somatolactin of 232 amino acids was identified. Phylogenetic analysis showed 97% amino acid identity with White sturgeon somatolactin. RT-PCR analysis indicated that the somatolactin mRNA was only detected in pituitary. Pituitary-specific expression of the somatolactin suggested that the protein may play important physiological functions in pituitary-endocrine system of the Chinese sturgeon.