Complete Sequence of pABTJ2, A Plasmid from Acinetobacter baumannii MDR-TJ,Carrying Many Phage-like Elements

Acinetobacter baumannii is an important opportunistic pathogeq in hospital, and tile multidrug-resistant isolates of A. haumannii have been increasingly reported i,a recent years. A num- ber of different mechanisms of resistance have been reported, some of which are associated with plasmid-mediated acquisition of genes. Therefore, studies on plasmids in A. haumannii have been a hot issue lately. We have performed complete genome sequencing of A. haumannii MDR-TJ, which is a multidrug-resistant isolate. Finalizing the remaining large scaffold of the previous assem- bly, we found a new plasmid pABTJ2, which carries many phage-like elements. The plasmid pAB- TJ2 is a circular double-stranded DNA molecule, which is 110,967 bp in length. We annotated 125 CDSs from pABTJ2 using IMG ER and ZCURVE_V, accounting lbr 88.28% of the whole plasmid sequence. Many phage-like elements and a tRNA-coding gene were detected in pABTJ2, which is rarely reported among A. haumannii. The tRNA gene is specific for asparagine codon GTT, which may be a small chromosomal sequence picked up through incorrect excision during plasmid forma- tion. The phage-like elements may have been acquired during the integration process, as the GC content of the region carrying phage-like elements was higher than that of the adjacent regions. The finding of phage-like elements and tRNA-coding gene in pABTJ2 may provide a novel insight into the study of A. haumannii pan-plasmidome.     

Construction of a rice immature seeds cDNA library and molecular cloning of oryzacystatin cDNA

Total RNA was extracted from rice immature seeds harvested 2 weeks after flowering; then mRNA was purified. cDNA with NotI and SaiI cohesive ends was synthesized and inserted into λgt22A. After packaged in vitno, the cDNA library was constructed with 1.5×106pfu. A 21-mer oligodeoxynucleotide was synthesized according to the 5'-end conserved coding sequence of oryzacystatin (a thiol proteinase inhibitor) and labeled as a probe. From 2.1 × 104 pfu, 9 positive dones have been isolated, 8 of which contain the entire coding region of oryzacystatin. λOC1 has the longest cDNA insert, which contains an open reading frame of 309 bp coding sequence, 84 bp 5'-end non-coding region and a poly(A) signal AATAAA at the 3'-end followed by 31 Nt of poly(A). The coding sequence is the same compared with oryzacystatin genomic DNA sequence, while there are some obvious differences such as insertion and variation in the non-coding region, especially lots of nonsucoessive insertion in the 3' region after poly(A) signal.     

苹果一个锌指蛋白基因的cDNA克隆及其表达特性分析(英文)

A cDNA library was created from stem apex tissue from Jonathan apples (Malus domestica Borkh.), harvested in June to August, during which the plant transitions from vegetative growth to reproductive growth. From this library, we isolated an expressed sequence tag (EST) sequence containing a zinc finger motif, using this sequence, a 779 bp cDNA fragment was obtained by using 5‘ RACE, and a final full-length cDNA encoding an apple zinc finger protein (named MdZF1; GenBank accession number AB116545) was obtained by further PCR. This zinc finger motif of MdZF1 has high homology with INOETERMINATE1 (ID1) gene from maize which seemed to be involved in the transition to flowering. Northern blot and RT-PCR analyses showed that the MdZF1 expressed in the root, stem, leaves, shoot apex and floral organs of the apple, with expression levels higher in root, stem, leaves and floral shoot apex than that in floral organs (sepals, petals, stamens and pistils). Genomic Southern analysis showed that there was a single copy gene in apple genome.     

Interactions between HMG proteins and the core sequence of DNaseI hypersensitive site 2 in the locus control region (LCR) of the human β-Mike globin gene cluster

HMG proteins are abundant chromosomal non-histone proteins. It has been suggested that the HMG proteins may play an important role in the structure and function of chromatin. In the present study, the binding of HMG proteins (HMG1/2 and HMG14/17) to the core DNA sequence of DNasel hypersensitive site 2 (HS2core DNA sequence, -10681-10970 bp) in the locus control region (LCR) of the human β-like globin gene cluster has been examined by using both the in vitro nucleosome reconstitution and the gel mobility shift assays. Here we show that HMG1/2 can bind to the naked HS2core DNA sequence, however, HMG 14/17 cannot. Using the in vitro nucleosome reconstitution we demonstrate that HMG14/17 can bind to the HS2core DNA sequence which is assembled into nucleosomes with the core histone octamer transferred from chicken erythrocytes. In contrast, HMG 1/2 cannot bind to the nucleosomes reconstituted in vitro with the HS2core DNA sequence. These results indicate that the binding patterns between HMG proteins and t     

Quality control system of the endoplasmic reticulum and related diseases

The quality control (QC) system of the endoplasmic reticulum (ER) is an important monitoringmechanism in the protein maturation process,which ensures export of properly folded proteins from the ER.Incorrectly or incompletely folded proteins are retained in the ER for refolding or degradation by the ER-residing proteasome.The calnexin/calreticulin cycle and ER-associated degradation are the key elements inQC.These two mechanisms work together to allow incorrectly folded proteins have additional opportunitiesto achieve their native conformations.The QC dysfunction is involved in many diseases caused by mutantproteins,many of which are causes of neurodegenerative disorders.A better understanding of molecularregulation in the QC system will uncover the molecular pathogenic mechanisms of many diseases caused byprotein misfolding and help discover novel strategies for preventing or treating these diseases.     

The complete mitochondrial genome and phylogenetic analysis of Nyctereutes procyonoides

The complete mitochondrial genome sequence of the raccoon dog (Nyctereutes procyonoides) was determined by using the long and accurate polymerase chain reaction. The entire mitochondrial genome sequence is 16,713 bp in length contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 control region. Most mitochondrial genes are encoded on the H strand, except for the ND6 gene and 8 tRNA genes. The base compositions of mitochondrial genomes present clearly A–T skew. All the transfer RNA genes can be folded into the typical cloverleaf-shaped structure except tRNA-Ser (AGY), which lacks the dihydrouridine arm. Protein-coding genes mainly initiate with ATG and terminate with TAA. Some reading frame intervals and overlaps are found in the mitochondrial genome. The control region can be divided into three domains: the extended termination associated sequences (ETASs) domain, the central conserved domain and the conserved sequence blocks (CSBs) domain. Three conserved sequence blocks (CSBs) and one extended termination associated sequences (ETAS-1) is found in the control region. The phylogenetic analysis based on the concatenated data set of 14 genes in the mitochondrial genome of Canidae shows that the raccoon dog has close phylogenetic position with the red fox (Vulpes vulpes) and they constitute a clade which has an equil evolutionary position with the clade formed by the genera Canis and Cuon.     

Ozone- and ethylene-induced regulation of a grapevine resveratrol synthase promoter in transgenic tobacco

Stilbene synthases (STSs) are enzymes that play a critical role in the biosynthesis of stilbene, phytoalexins in a small number of unrelated plant species, and are induced by various biotic and abiotic stressors like pathogen attack, UV-irradiation or ozone exposure. To investigate the molecular basis for ozone-induced plant stress responses, we have examined the promoter of the grapevine resveratrol synthase (Vst1). In this report we summarize the influence of ozone on gene regulation. In transgenic tobacco a chimeric gene construct, containing the Vst1 promoter combined with the β-glucuronidase (GUS) reporter gene, is rapidly induced by ozone (0.1 μl·l⁻¹, 12 h). The same construct is also strongly induced by ethylene (20 μl·l⁻¹, 12 h). Promoter deletion analysis of the 5′ flanking sequence identified a positive regulatory element between −430 bp and −280 bp. This region contains ethylene-responsive enhancer elements, as well as an elicitor-responsive sequence in inverse orientation.     

CS3 fimbriae of enterotoxigenic Escherichia coli as chimeric expression carriers of heterologous antigenic determinants

CS3 fimbriae, which are the strong immunogen, are produced by human enterotoxigenic Escherichia coli (ETEC). The possibility of using CS3 as a carrier of foreign antigenic determinants was investigated. A SacII site sequence was inserted into the structural gene of CS3 subunit by site-specific mutagenesis based on analyzing and predicting the properties of the proteins. A recombinant strain expressing CS3/CTP3 hybrid fimbriae was constructed by inserting the sequence encoding CTP3 into the SacII site created by directed mutagenesis in the structural gene of CS3 subunit and transforming the recombinant plasmid into the host of DH5α. The result of SDS-PAGE showed that the hybrid CS3/CTP3 molecules were the fusion proteins with molecular, masses of about 18.5 ku. Inoculating mice orally and intraperitoneally showed that both antibodies against CS3 and CTP3 were elicited. These results indicate that CS3 pill could be an exposure vector for heterologous antigenic determinants and become a powerful tool for     

Molecular cloning of pheromone biosynthesis activating neuropeptide in silkworm, Bombyx mori

Pheromone biosynthesis activating neuropeptide (PBAN) is a suboesophageal ganglion secretory polypeptide of insect, which activates the pheromone gland to produce sex pheromone biosynthesis in female silkworm, Bombyx mori. A Bombyx genomic library was screened by the method of plaque hybridization using the 32P-labeled BomDH cDNA as a probe. The genomic sequence encoding PBAN has been cloned and its structure is analyzed. The PBAN gene comprises two exons interspersed by a single intron 697 bp in length. Preceding the PBAN amino acid sequence is a 32-amino acid sequence containing two FXPRL amide peptides, which are α-SGNP (Ile-Ile-Phe-Thr-Pro-Lys-Leu) and β-SGNP (Ser-Val-Ala-Asn-Pro-Arg-Thr-His-Glu-Ser-Leu-Glu-Phe-Ile-Pro-Arg-Leu), which is followed by a Gly-Arg processing site. Immediately, after the PBAN amino acid sequence is a Gly-Arg processing site and a FXPRL amide peptide γ-SGNP (Thr-Met-Ser-Phe-Ser-Pro-Arg-Leu). It is suggested that besides PBAN, 7-, 8-, and 17-residue amidated peptides wer     

Molecular Characterization of Two Silenced y-type Genes for Glu-B1 in Triticum aestivum ssp. yunnanese and ssp. tibetanum

The high molecular weight glutenin subunits （HMW-GSs） are a major class of common wheat storage proteins. The breadmaking quality of common wheat flour is influenced by the composition of HMW-GSs. In the present study, two unexpressed 1 By genes from Triticum aesitvum L.ssp.yunnanese AS332 and T. aesitvum ssp.tibetanurn AS908 were respectively cloned and characterized. The results indicated that both of the silenced 1By genes in AS332 and AS908 were 1Byg. In contrast to previously reported mechanisms for silenced genes lAx and lay, which was due to the insertion of transposon elements or the presence of premature stop codon via base substitution of C→T transition in trinucleotides CAA or CAG, the silence of 1By9 genes was caused by premature stop codons via the deletion of base A in trinucleotide CA.A, which lead to frameshift mutation and indirectly produced several premature stop codons （TAG） downstream of the coding sequence.     

CS3 fimbriae of enterotoxigenic Escherichia coli as chimeric expression carriers of heterologous antigenic determinants

CS3 fimbriae, which are the strong immunogen, are produced by human enterotoxigenic Escherichia coli (ETEC). The possibility of using CS3 as a carrier of foreign antigenic determinants was investigated. A SacⅡ site sequence was inserted into the structural gene of CS3 subunit by site-specific mutagenesis based on analyzing and predicting the properties of the proteins. A recombinant strain expressing CS3/CTP3 hybrid fimbriae was constructed by inserting the sequence encoding CTP3 into the SacII site created by directed mutagenesis in the structural gene of CS3 subunit and transforming the recombinant plasmid into the host of DH5α. The result of SDS-PAGE showed that the hybrid CS3/CTP3 molecules were the fusion proteins with molecular masses of about 18.5 ku. Inoculating mice orally and intraperitoneally showed that both antibodies against CS3 and CTP3 were elicited. These results indicate that CS3 pili could be an exposure vector for heterologous antigenic determinants and become a powerful tool for the development of oral vaccines directed against mucosal pathogens.     

Structural feature of sorghum chloroplast psbA gene and regulation effects of its 5'-noncoding region*

Comparative analysis reveals remarkable homology between the sequences of both psbA gene nucleotides and the inferred amino acids of sorghum, a C_4 plant, and those of rice, a C_3 plant. The 5'-noncoding region of sorghum psbA gene contains the conservative promoter elements, "-35" element and "-10" element, like the prokaryote and the promoter element, TATA box, like the eukaryote. As compared with that of the rice, an extra sequence of 7 bp is found in the leader sequence of the mRNA in the former. Using an in vitro system, it has been demonstrated that protein factor exists in sorghum chloroplast protein extract which specifically binds to the 5'-noncoding region of psbA gene. Measurement of the expression of luciferase shows a 2—5 time greater reaction of the expression plasmids pALqs which contain leader region of sorghum psbA gene than that of the expression plasmids pALqr which contain leader region of rice psbA gene in E. coli.     

基因组常用术语解释(中)

精确序列 (Finished sequence) :序列中碱基鉴定的误差不超过万分之一 ,碱基排序和方向定位正确 ,碱基在染色体上排列几乎不存在间隙 (Sequence in which bases are identified to an accuracy of no morethan 1 error in 1 0 ,0 0 0 and are placed in the rightorder and orientation along a chromosome with almostno gaps)。原位荧光杂交 (FISH,Fluorescence in situ hybridization) :在染色体上精确定位一段 DNA序列的方法(a method for pinpointing the location of a piece of DNA sequence on a chromosome)。功能基因组学 (…     

A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases

Transposons are sequence elements widely distributed among genomes of all three kingdoms of life,providing genomic changes and playing significant roles in genome evolution.Trichomonas vaginalis is an excellent model system for transposon study since its genome(～160 Mb) has been sequenced and is composed of～65%transposons and other repetitive elements.In this study,we primarily report the identification of Kolobok-type transposons(termed tvBac) in T.vaginalis and the results of transposase sequence analy...     

伪狂犬病病毒湖北株糖蛋白gD基因的克隆及序列测定

According to the sequence of gD gene of PRV Rice strain, the primers of 22bp were designed.Using PRV genomic DNA of Hubei and Shuangcheng virus strains which infected BHK 21 cell separately as template, the gD gene of PRV was amplified sucessfully by PCR and cloned into pGEM T vector. Restriction enzyme analysis showed that the cloned gD gene at SmaⅠ,SalⅠ,KpnⅠ,PvuⅡ sites was the same as that of PRV Rice strain. The gD gene consisted of 1,263 nucleotides including an open reading frame spanning 1,197 nucleotieds which could encode a protein of 398 amino acids. The ORF didn′t include an amino acid sequence directing N linked glycosylation (NXT or NXS). Comparison of our complete Hubei strain gD gene sequence with the Rice strain gD gene sequence showed that the nucleotide and deduced amino acid homology were about 97% and there was an 12 basepair deletion in 835 846 nucleotide sites that coded Arg Pro Arg Pro. A region of the amino acid sequence and the positions of the cysteine residues of PRV HB gD were homologous to HSV I glycoprotein D. This work laid foundation for PRV gene immunization and studying PRV sub unit vaccine.     

Comparison of the Δ~(12) fatty acid desaturase gene between high-oleic and normal-oleic peanut genotypes

Δ12 fatty acid desaturase gene has been targeted as a logical candidate controlling the high oleate trait in peanut seeds.By RT-PCR method,the full-length cDNAs of Δ12 fatty acid desaturase gene were isolated from peanut(Arachis hypogaea L.) genotypes with normal and high ratio of oleic to linoleic acid,which were designated AhFAD2B and AhFAD2B',respectively.Sequence alignment of their coding regions revealed that an extra A was inserted at the position +442 bp of AhFAD2B' sequence of high oleic acid genoty...     

耐辐射奇球菌超氧化物歧化酶基因的克隆与序列分析

By using a 453 bp length gene fragment of superoxide dismutase(SOD)as a probe,which was firstly amplified from Deinococcus radiodurans genomic DNA by PCR with degenerate oligonucleotide primers corresponding to the conservative regions of known SODs,a putative SOD gene was identified from the database of D.radiodurans whole genome.Its 636 bp length open reading frame and 5′ and 3′ flanking sequence was determined.The conventional E.coli ribosomal and RNA polymerase binding sites were found upstream from SOD encoding region and an inverted repeat sequence downstream of the termination codon.The deduced 211 amino acid sequence of the structural gene showed a high similarity to other manganese and iron containing SODs in normally conserve regions.