Identification and analysis of the TALE transcription factor family in radish / 生物工程学报

Three-amino acid loop extension (TALE) transcription factors play important roles in plant growth and cell differentiation. There are plenty of studies on TALE transcription factors in several model plants, but not in radish (Raphanus sativas). A genome-wide bioinformatics analysis identified 33 TALE family genes in the Xiang-Ya-Bai (XYB) radish, These genes, are distributed on nine chromosomes and all contain 4-6 exons. The 33 TALE genes in radish showed a co-linearity relationship with the 17 homologous genes in Arabidopsis thaliana. Moreover, a large number of stress response cis-elements were found in the promoter regions of these genes. Expression analysis showed that four genes in the BELL subfamily were highly expressed in roots, and two genes in the KNOX subfamily were highly expressed in shoots of bolting plants and callus. All radish TALE genes contain sequences encoding the conserved HOX domain, except for the gene RSA10037940, which is homologous to Arabidopsis KNATM. The deduced 3D structures of the TALE proteins irrespective of subtypes are highly similar. All the encoded proteins were weakly acidic and hydrophilic. The radish TALE gene family is relatively evolutionarily conserved, which was consistent with results from Arabidopsis, but quite different from that of rice. This study provides important clues for studying the biological functions of TALE transcription factors in radish.

Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L)

BACKGROUND: Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet. METHODS: We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively. RESULTS: In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress. CONCLUSION: We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.

Insights into the evolution of extracellular leucine-rich repeats in metazoans with special reference to Toll-like receptor 4

The importance of the widely spread leucine-rich repeat (LRR) motif was studied considering TLRs, the LRR-containingprotein involved in animal immune response. The protein connects intracellular signalling with a chain of molecularinteractions through the presence of LRRs in the ectodomain and TIR in the endodomain. Domain analyses with humanTLR1-9 reported ectodomain with tandem repeats, transmembrane domain and TIR domain. The repeat number variedacross members of TLR and remained characteristic to a particular member. Analysis of gene structure revealed absence ofcodon interruption with TLR3 and TLR4 as exceptions. Extensive study with TLR4 from metazoans confirmed thepresence of 23 LRRs in tandem. Distinct clade formation using coding and amino acid sequence of individual repeatsillustrated independent evolution. Although ectodomain and endodomain exhibited differential selection pressure, withinthe ectodomain, however, the individual repeats displayed positive, negative and neutral selection pressure depending ontheir structural and functional significance.

Type Ⅶ secretion system in Mycobacteria / 中华微生物学和免疫学杂志

Type Ⅶ secretion system(T7SS) is a novel and specialized secretion system discovered in recent years. It was first found in Mycobacterium tuberculosis. Type Ⅶ secretion system is involved in the secretion of virulence-associated proteins, the interaction between pathogens and hosts and the balance of zinc/iron ions. Moreover,it plays a critical role in the growth and pathogenesis of Mycobacteria. This review summarizes the components,substrates and translocation mechanisms of the type Ⅶ secretion system and its relation to the virulence of Mycobacteria aiming to provide references for developing novel strategies for disea-ses diagnosis,treatment and prevention.

Construction of pMSV-Slfn5-GFP plasmid and analysis of gene structure in mice / 重庆医学

Objective To perform mouse pMSV-Slfn5-GFP gene recombinant expression plasmid construction and gene structure analysis.Methods Total RNA was extracted from mouse liver and turned into cDNA by reverse transcription.Mouse Slfn5 coding sequence (CDS) fragment was amplified by PCR and connected with the pGEM-T Easy vector.The connected product was transferred the E.coli DH5a.The positive clones were selected for extracting plasmid,which was identified by double enzyme of restriction endonuclease Hpa Ⅰ and Xho Ⅰ.Then correct plasmid identified by enzyme digestion was sequenced by Macrogen USA.Then correct plasmid by sequencing was connected with pMSV-GFP by HindⅢ and Xbo Ⅰ,which was named as pMSV-Slfn5-GF.UCSC (http://genome.ucsc.Edu/) was used to analyze mouse Slfn5 and its family genomic structure.Slfn5 protein structural domain was determined by NCBI.Results Slfn5 full-length gene sequence was cloned into the expression vector pMSV-GFP,the fragment size was about 2.65 kb by enzyme digestion identification.The conservatism of AAA_4 protein domain in Slfn5 protein family was determined by phylogeny.fr.Conclusion Mouse full-length gene pMSV-Slfn5-GFP expression vector is successfully constructed.

Arginine kinase in Toxocara canis: Exon–intron organization, functional analysis of site-directed mutants and evaluation of putative enzyme inhibitors

Objectives To determine exon/intron organization of the Toxocara canis (T. canis) AK (TCAK) and to test green and black tea and several other chemicals against the activity of recombinant TCAK in the guanidino-specific region by site-directed mutants. Methods Amplification of genomic DNA fragments containing introns was carried out by PCRs. The open-reading frame (1 200 bp) of TCAK (wild type) was cloned into the BamH1/SalI site of pMAL-c2X. The maltose-binding protein-TCAK fusion protein was expressed in Escherichia coli TB1 cells. The purity of the expressed enzyme was verified by SDS-PAGE. Mutations were introduced into the guanidino-specific region and other areas of pMAL/TCAK by PCR. Enzyme activity was measured with an NADH-linked assay at 25 °C for the forward reaction (phosphagen synthesis). Results Arginine kinase in T. canis has a seven-exon/six-intron gene structure. The lengths of the introns ranged from 542 bp to 2 500 bp. All introns begin with gt and end with ag. Furthermore, we measured the enzyme activity of site-directed mutants of the recombinant TCAK. The K

Arginine kinase in Toxocara canis: Exon-intron organization, functional analysis of site-directed mutants and evaluation of putative enzyme inhibitors

OBJECTIVES@#To determine exon/intron organization of the Toxocara canis (T. canis) AK (TCAK) and to test green and black tea and several other chemicals against the activity of recombinant TCAK in the guanidino-specific region by site-directed mutants.@*METHODS@#Amplification of genomic DNA fragments containing introns was carried out by PCRs. The open-reading frame (1200 bp) of TCAK (wild type) was cloned into the BamH1/SalI site of pMAL-c2X. The maltose-binding protein-TCAK fusion protein was expressed in Escherichia coli TB1 cells. The purity of the expressed enzyme was verified by SDS-PAGE. Mutations were introduced into the guanidino-specific region and other areas of pMAL/TCAK by PCR. Enzyme activity was measured with an NADH-linked assay at 25 °C for the forward reaction (phosphagen synthesis).@*RESULTS@#Arginine kinase in T. canis has a seven-exon/six-intron gene structure. The lengths of the introns ranged from 542 bp to 2 500 bp. All introns begin with gt and end with ag. Furthermore, we measured the enzyme activity of site-directed mutants of the recombinant TCAK. The K value of the mutant (Alanine to Serine) decreased indicating a higher affinity for substrate arginine than the wild-type. The K value of the mutant (Serine to Glycine) increased to 0.19 mM. The K value (0.19 mM) of the double mutant (Alanine-Serine to Serine-Glycine) was slightly greater than in the wild-type (0.12 mM). In addition, several other chemicals were tested; including plant extract Azadiracta indica (A. indica), an aminoglycoside antibiotic (aminosidine), a citrus flavonoid glycoside (rutin) and a commercially available catechin mixture against TCAK. Green and black tea (1:10 dilution) produced 15% and 25% inhibition of TCAK, respectively. The extract of A. indica produced 5% inhibition of TCAK. Moreover, green and black tea produced a non-competitive type of inhibition and A. indica produced a mixed-type of inhibition on TCAK.@*CONCLUSIONS@#Arginine kinase in T. canis has a seven-exon/six-intron gene structure. However, further studies are needed to identify a specific compound within the extract causing the inhibitory effect and also to determine the molecular mechanisms behind inhibition of arginine kinase in T. canis.

Molecular cloning of chitinase 33 (chit33) gene from Trichoderma atroviride / Clonagem molecular do gene quitinase 33 (chit33) em Trichoderma atroviride

In this study Trichoderma atroviride was selected as over producer of chitinase enzyme among 30 different isolates of Trichoderma sp. on the basis of chitinase specific activity. From this isolate the genomic and cDNA clones encoding chit33 have been isolated and sequenced. Comparison of genomic and cDNA sequences for defining gene structure indicates that this gene contains three short introns and also an open reading frame coding for a protein of 321 amino acids. The deduced amino acid sequence includes a 19 aa putative signal peptide. Homology between this sequence and other reported Trichoderma Chit33 proteins are discussed. The coding sequence of chit33 gene was cloned in pEt26b(+) expression vector and expressed in E. coli.

Neste estudo Trichoderma atroviride foi escolhido como superprodutor da enzima quitinase dentre 30 isolados de Trichoderma sp. com base na atividade específica de quitinase. Clones de cDNA e genômico codificando chit33 foram obtidos deste isolado e seqüenciados. A comparação das seqüências genômica e de cDNA para definir a estrutura do gene indicou que este contém três pequenos introns e uma fase aberta de leitura codificando uma proteína de 321 aminoácidos. A seqüência de aminoácidos deduzida inclui um possível peptídio sinal de 19 aminoácidos. Homologia entre esta seqüência e outras proteínas Chit33 descritas de Trichoderma é discutida. A seqüência codificadora do gene chit33 foi clonada no vetor de expressão pET26b(+) e expressa em E. coli.

Partial molecular characterization of the Nile tilapia (Oreochromis niloticus) alpha-cardiac muscle actin gene and its relationship to actin isoforms of other fish species

An alpha actin gene segment, isolated from Nile tilapia (Oreochromis niloticus), was characterized by nucleotide sequencing, predicted amino acid sequence and Southern blot hybridization. Genomic DNA amplification resulted in a 1063-bp fragment corresponding to a partial alpha-cardiac muscle actin gene containing exons 3 to 6. Southern blot analysis of the restriction-digested DNA revealed that the Nile tilapia genome contains multiple muscle actin isoforms. Although comparison of the nucleotide sequence, amino acid residues and exon-intron organization of the isolated actin gene with those of other vertebrates showed a high level of identity, diagnostic amino acid residues can still be correlated to distinct actin genes in fish species.

Radish Phospholipid Hydroperoxide Glutathione Peroxidase Gene Structure and Upstream Regulatory Sequence Analysis / 生物化学与生物物理进展

A novel radish RsPHGPx cDNA, which encodes a functional phospholipid hydroperoxide glutathioneperoxidase (PHGPx) protein, was identified in the previous work. In the study genomic organization and the upstream regulatory sequence analysis of this gene was presented. Southern blot analysis showed that RsPHGPx gene existed in radish genome in manner of single copy. Moreover, a 3.3 kb genomic DNA fragment of RsPHGPx gene was isolated by combination of common PCR and genome-walking method. Sequence analysis on this genomic fragment demonstrated that RsPHGPx gene consists of seven exons separated by six introns, and suggested that a short 5'-flanking sequence immediately before the exon 1 should be the putative RsPHGPx promoter region, which is proceeded by the upstream neighboring biotin synthase gene. Cis-acting elements search showed that the putative promoter contains elements responsive to hormones (eg. E-Box and W-Box), abiotic stresses (eg. MYB and MYC binding sites), and light (Box Ⅱ and Ⅰ-Box), etc. Northern blot analysis indicated that the expression of RsPHGPx was subjected to up-regulation of chilling and down-regulation of ABA and successive illumination (in etiolated seedlings), implying the regulatory roles of some predicted elements. However the up-regulation effect of herbicide paraquat, which can induce oxidative stress, suggested the presence of some unknown elements in the promoter region. This is the first report on gene structure and upstream regulatory sequence analysis in reported plant PHGPx genes, which will be a prerequisite to understand regulatory mechanism of PHGPx gene expression in plants.

Structure,Function and Evolution of Baculoviral Inhibitor of Apoptosis Protein Gene / 微生物学通报

Baculoviral IAP(inhibitor of apoptosis protein) gene was identified firstly in IAP gene family.The structurcal feature of baculoviral IAP genes are characterized BIR and RING domain;Despite similar to P35 in antiapoptotic function,baculovrial IAP and P35 differ in structure and mechnism of action.Phylogenetic analysis of IAP genes and lots of evidence sppport the origin of this viral gene by capture of a host gene early in the evolution of Lepidoptera.

Research Advances Baculovirus DNA polymerase gene / 微生物学通报

Baculovirus DNA polymerase gene belongs to an early gene of baculovirus. It is a necessary gene required for replication of virus in insect cells. It can encode DNA polymerase induced by virus. In the process of replication, DNA polymerase can bind to homologous regions and non-homologous regions, which are believed to act as the origins of virus DNA replication with other replication factors. In addition, DNA polymerase has advantages over occlusion protein and egt gene for resolving deep branching taxonomic relationships of baculovirus phylogenies.

RESEARCH ADVANCES ON STRUCTURES AND FUNCTIONS OF BACULOVIRUS CHITINASE GENES / 微生物学通报

The chitinase gene of baculovirus is an unnecessary and high conservative gene Chitinase is expressed in the late phase virus replication in insect cells There are signal peptide in its N termini, chitinases active motifs in its central section and ER attaching motifs of chitinase in its C termini Baculoviral chitinase possesses both endo and exo chitinase activities, which can hydrolyze inherent chitin in insects body Chitinase is necessary for liquefaction of the virus infected host insect, and it may also serve as a molecular chaperone for pro V Cath Perhaps Baculoviral chitinase has same ancestors with bacteriums chitinase