DNA sequence : the journal of DNA sequencing and mapping最新文献

Interferon regulatory factor-1 (IRF-1) plays important roles in host immunity, cell proliferation and apoptosis. The current GenBank sequence for human IRF-1 (accession number: L05072) was derived from a human placenta DNA library and reported in 1992. In one recent population-based sequence study, we observed consistent discrepancies between our IRF-1 sequence data and GenBank reference sequences suggesting that, current IRF-1 reference sequence was not representative for all populations. By complete gene sequencing, we obtained a representative full-length IRF-1 sequence from a single subject. Compared to submission L05072, our population-based data contains: 35 nucleotide additions, 8 nucleotide removals and another 12 nucleotide replacements. A single nucleotide difference was observed in the IRF-1 promoter sequence compared to GenBank sequence (X53095). These changes were confirmed in 350 Kenyans and 28 non-African donors. The accuracy of a reference sequence is crucial for downstream genetic and functional studies and this study provides more complete and accurate data on the sequence of the human IRF-1 gene and its immediate promoter region.

SINA genes in plants are part of a multigene family with 5 members in Arabidopsis thaliana, 10 members in Populus trichocarpa, 6 members in Oryza sativa, at least 6 members in Zea mays and at least 1 member in Physcomitrella patens. Six members in maize were confirmed by RT-PCR. All SINAs have one RING domain and one SINA domain. These two domains are highly conserved in plants. According to the motif organization and phylogenetic tree, SINA family members were divided into 2 groups. In addition, through semi-quantitative RT-PCR analysis of maize members and Digital Northern analysis of Arabidopsis and rice members, we found that the tissue expression patterns are more diverse in monocot than in Arabidopsis.

Myostatin is a negative regulator of skeletal muscle growth and has a potential application in aquaculture. The black seabream myostatin gene was cloned and sequenced. It had three exons encoding a protein of 382 amino acids. A 90 bp 5'-untranslated region (UTR) and a 536 bp 3'-UTR were obtained by RACE. Four microsatellite sequences, a (CAG)9, a (TC)12, a (CA)16 repeat and an "imperfect" (CA)25 microsatellite, were found in the myostatin. Two introns were 329 and 742 bp in length, respectively. The deduced amino acid sequence of the myostatin had a putative amino terminal signal sequence, a TGF-beta propeptide domain, a RXXR proteolytic processing site, a TGF-beta domain, and 12 conserved cysteine residues. The myostatin gene was expressed in four of the examined ten tissues and organs. The expression of myostatin was the strongest in the skeletal muscle and brain, intermediate in the eye, and low in the heart.

The specification of floral organ identity during development depends on the function of a limited number of homeotic genes, which are grouped into three classes. Most of these genes belong to the MADS-box gene family. The PISTILLATA (PI) family of MADS-box genes plays important roles in controlling the development of the petal and stamen of flowering plants. In an attempt to understand the molecular mechanisms behind floral development in the orchid, a MADS-box gene, PhPI10 was cloned from Phalaenopsis orchid. We provide phylogenetic evidence that PhPI10 is closely related to PI-like genes of angiosperms, which are required for establishing petal and stamen identity. In addition, there is a PI-motif in the C-terminal of the putative amino acid sequence of PhPI10. Southern analysis showed that a single copy of PhPI10 was present in the Phalaenopsis orchid genome. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that its transcription was only detectable in the top of the floral bud and undetectable in other vegetative organs. In the floral organs its expression was limited to the lip of the Phalaenopsis flower.

Mapping genes in biochemical pathways allow study of the genomic organization of pathways and geneic relationships within these pathways. Additionally, molecular markers located within the boundaries of a specific gene sequence represent important marker assisted selection resources. We report map locations of two geneic markers from the purine synthesis pathway in soybean (Glycine max (L. merr.)), utilizing a 90 plant F(2) population created from the cross of "DT97-4290" x "DS97-84-1". Primers were designed based on sequences from annotated soybean complimentary DNA. A polymorphic, co-dominant, sequence-characterized amplified region marker was created for hypoxanthine phosphoribosyl transferase (EC 2.4.2.8). Linkage analysis placed this gene on linkage group (LG) O. In addition, a single-nucleotide polymorphism (SNP) marker was developed for a urate oxidase gene (EC 1.7.3.3). Linkage analysis of the SNP placed the urate oxidase gene on LG I. For both genes, amplicon sequence data confirmed the identification of the respective gene. Mapping these genes represents the first step in understanding the genomic organization of the purine biochemical pathway in soybean.

In this report we describe the complete sequence of the mtDNA genome of Ammotragus lervia (Barbary sheep or aoudad) as obtained by PCR and sequencing with primer walking using flanking sequences. The molecule is 16,530 base pairs in length, resulting similar to those of goat and sheep. The genome organization matches to those of other mammalian mitochondrial genomes. The phylogenetic position of the Ammotragus relative to twelve other mammalian species was assessed based on protein-coding sequences. A goat-aoudad split of 9.9-8.9 MYBP has been estimated, whereas the divergence ancestor/caprines was dated at 12.1-10.8 MYBP.

In this work, the mitochondrial genomes for spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri) were completely sequenced. The entire mitochondrial genome sequences of the spotted halibut and barfin flounder were 17,273 and 17,588 bp in length, respectively. The organization of the two mitochondrial genomes was similar to those reported from other fish mitochondrial genomes containing 37 genes (2 rRNAs, 22 tRNAs and 13 protein-coding genes) and two non-coding regions (control region (CR) and WANCY region). In the CR, the termination associated sequence (ETAS), six central conserved block (CSB-A,B,C,D,E,F), three conserved sequence blocks (CSB1-3) and a region of 61-bp tandem repeat cluster at the end of CSB-3 were identified by similarity comparison with fishes and other vertebrates. The tandem repeat sequences show polymorphism among the different individuals of the two species. The complete mitochondrial genomes of spotted halibut and barfin flounder should be useful for evolutionary studies of flatfishes and other vertebrate species.

Protein hydrolyzation is activated and involved in response to various stress signals. In the present study, a full-length cDNA, named MsCP1, encoding a papain-like cysteine protease was obtained by degenerated primers and 3'- and 5'-RACE from salt-tolerant alfalfa. The cDNA contained an open reading frame encoding a deduced protein of 350 amino acids with a putative N-terminal signal peptide, NPIR vacuole-sorting signal sequence and potential N-linked glycosylation sites. The deduced sequence showed a high similarity to deduced proteins from pea, tobacco, tomato and ryegrass. Fusion expression analysis in Escherichia coli showed that the putative eukaryotic signal peptide prevented its expression in prokaryotic system. The integration and transcript of the expression elements in transgenic tobacco plants were detected with Southern blot and RT-PCR analysis.

Shewanella violacea DSS12 is facultative piezophile isolated from the deep-sea. The expression of cydDC genes (required for d-type cytochrome maturation) of the organism is regulated by hydrostatic pressure. In this study, we analyzed the nucleotide sequence upstream of cydDC in detail and found that there are putative binding sites for the NarL protein which is part of a two-component regulatory system also containing the sensor protein NarX. Furthermore, we identified the narQP genes (homologues of narXL) from S. violacea DSS12 and demonstrated the heterologous expression of narP in Escherichia coli. These results will be helpful in examining pressure regulation of gene expression in S. violacea at the molecular level.

Two cDNAs encoding two distinct classes of DXSs were cloned from leaves (HbDXS1) and latex (HbDXS2) of Hevea brasiliensis by RT-PCR based methods. HbDXS1 encodes a protein of 720 amino acids, with a high homology to the class I of plant DXS proteins, and HbDXS2 encodes a protein predicted to contain 711 amino acids and with a high homology to the plant DXS class II proteins. Several important motifs and amino acid positions characteristic of DXS proteins are strictly conserved in both new HbDXS proteins. The two HbDXS genes were differentially expressed in various tissues of H. brasiliensis. The transcriptional levels of HbDXS2 were similar in both a high-yielding rubber clone (RRIM 600) and the wild type. Ethephon increased the latex yield and caused a transient increase of expression of the HbDXS2 gene. The expression of HbDXS2 in latex indicates that it may have a primary function in carotenoid biosynthesis rather than for natural rubber.