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1.
BMC Plant Biol ; 19(1): 336, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31370790

RESUMO

BACKGROUND: APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformation and flower organ development in many plants. However, the roles of miR172 and its target AP2 genes remain largely unknown in Brassica napus (B. napus). RESULTS: In this study, 19 euAP2 and four miR172 genes were identified in the B. napus genome. A sequence analysis suggested that 17 euAP2 genes were targeted by Bna-miR172 in the 3' coding region. EuAP2s were classified into five major groups in B.napus. This classification was consistent with the exon-intron structure and motif organization. An analysis of the nonsynonymous and synonymous substitution rates revealed that the euAP2 genes had gone through purifying selection. Whole genome duplication (WGD) or segmental duplication events played a major role in the expansion of the euAP2 gene family. A cis-regulatory element (CRE) analysis suggested that the euAP2s were involved in the response to light, hormones, stress, and developmental processes including circadian control, endosperm and meristem expression. Expression analysis of the miR172-targeted euAP2s in nine different tissues showed diverse spatiotemporal expression patterns. Most euAP2 genes were highly expressed in the floral organs, suggesting their specific functions in flower development. BnaAP2-1, BnaAP2-5 and BnaTOE1-2 had higher expression levels in late-flowering material than early-flowering material based on RNA-seq and qRT-PCR, indicating that they may act as floral suppressors. CONCLUSIONS: Overall, analyses of the evolution, structure, tissue specificity and expression of the euAP2 genes were peformed in B.napus. Based on the RNA-seq and experimental data, euAP2 may be involved in flower development. Three euAP2 genes (BnaAP2-1, BnaAP2-5 and BnaTOE1-2) might be regarded as floral suppressors. The results of this study provide insights for further functional characterization of the miR172 /euAP2 module in B.napus.


Assuntos
Brassica napus/genética , Flores/crescimento & desenvolvimento , Genes de Plantas/genética , MicroRNAs/genética , Brassica napus/crescimento & desenvolvimento , Mapeamento Cromossômico , Sequência Conservada/genética , Genes de Plantas/fisiologia , Estudo de Associação Genômica Ampla , MicroRNAs/fisiologia , Filogenia , Alinhamento de Sequência
2.
BMC Plant Biol ; 19(1): 339, 2019 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382883

RESUMO

BACKGROUND: Tartary buckwheat (Fagopyrum tataricum) is an edible cereal crop whose sprouts have been marketed and commercialized for their higher levels of anti-oxidants, including rutin and anthocyanin. UDP-glucose flavonoid glycosyltransferases (UFGTs) play an important role in the biosynthesis of flavonoids in plants. So far, few studies are available on UFGT genes that may play a role in tartary buckwheat flavonoids biosynthesis. Here, we report on the identification and functional characterization of seven UFGTs from tartary buckwheat that are potentially involved in flavonoid biosynthesis (and have varying effects on plant growth and development when overexpressed in Arabidopsis thaliana.) RESULTS: Phylogenetic analysis indicated that the potential function of the seven FtUFGT proteins, FtUFGT6, FtUFGT7, FtUFGT8, FtUFGT9, FtUFGT15, FtUFGT40, and FtUFGT41, could be divided into three Arabidopsis thaliana functional subgroups that are involved in flavonoid biosynthesis of and anthocyanin accumulation. A significant positive correlation between FtUFGT8 and FtUFGT15 expression and anthocyanin accumulation capacity was observed in the tartary buckwheat seedlings after cold stress. Overexpression in Arabidopsis thaliana showed that FtUFGT8, FtUFGT15, and FtUFGT41 significantly increased the anthocyanin content in transgenic plants. Unexpectedly, overexpression of FtUFGT6, while not leading to enhanced anthocyanin accumulation, significantly enhanced the growth yield of transgenic plants. When wild-type plants have only cotyledons, most of the transgenic plants of FtUFGT6 had grown true leaves. Moreover, the growth speed of the oxFtUFGT6 transgenic plant root was also significantly faster than that of the wild type. At later growth, FtUFGT6 transgenic plants showed larger leaves, earlier twitching times and more tillers than wild type, whereas FtUFGT15 showed opposite results. CONCLUSIONS: Seven FtUFGTs were isolated from tartary buckwheat. FtUFGT8, FtUFGT15, and FtUFGT41 can significantly increase the accumulation of total anthocyanins in transgenic plants. Furthermore, overexpression of FtUFGT6 increased the overall yield of Arabidopsis transgenic plants at all growth stages. However, FtUFGT15 shows the opposite trend at later growth stage and delays the growth speed of plants. These results suggested that the biological function of FtUFGT genes in tartary buckwheat is diverse.


Assuntos
Fagopyrum/genética , Genes de Plantas/genética , Glicosiltransferases/genética , Proteínas de Plantas/genética , Antocianinas/metabolismo , Arabidopsis/genética , Sequência Conservada , Fagopyrum/enzimologia , Flavonoides/metabolismo , Genes de Plantas/fisiologia , Glicosiltransferases/fisiologia , Filogenia , Proteínas de Plantas/fisiologia , Plantas Geneticamente Modificadas , Análise de Sequência de DNA
3.
BMC Plant Biol ; 19(1): 370, 2019 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-31438851

RESUMO

BACKGROUND: Accumulating evidences show that SPLs are crucial regulators of plant abiotic stress tolerance and the highly conserved module miR156/SPL appears to balance plant growth and stress responses. The halophyte Tamarix chinensis is highly resistant to salt tress. SPLs of T. chinensis (TcSPLs) and theirs roles in salt stress responses remain elusive. RESULTS: In this study, we conducted a systematic analysis of the TcSPLs gene family including 12 members belonging to 7 groups. The physicochemical properties and conserved motifs showed divergence among groups and similarity in each group. The microRNA response elements (MREs) are conserved in location and sequence, with the exception of first MRE within TcSPL5. The miR156-targeted SPLs are identified by dual-luciferase reporter assay of MRE-miR156 interaction. The digital expression gene profiles cluster suggested potential different functions of miR156-targeted SPLs vs non-targeted SPLs in response to salt stress. The expression patterns analysis of miR156-targeted SPLs with a reverse expression trend to TcmiR156 suggested 1 h (salt stress time) could be a critical time point of post-transcription regulation in salt stress responses. CONCLUSIONS: Our work demonstrated the post-transcription regulation of miR156-targeted TcSPLs and transcription regulation of non-targeted TcSPLs in salt stress responses, and would be helpful to expound the miR156/SPL-mediated molecular mechanisms underlying T. chinensis salt stress tolerance.


Assuntos
MicroRNAs/fisiologia , Proteínas de Plantas/fisiologia , RNA de Plantas/fisiologia , Estresse Salino/genética , Tamaricaceae/genética , Fatores de Transcrição/fisiologia , Motivos de Aminoácidos , Sequência Conservada , Genes de Plantas , Família Multigênica , Filogenia , Transcriptoma
4.
BMC Plant Biol ; 19(1): 329, 2019 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-31337346

RESUMO

BACKGROUND: Zinc finger proteins (ZFPs) containing only a single zinc finger domain play important roles in the regulation of plant growth and development, as well as in biotic and abiotic stress responses. To date, the evolutionary history and functions of the ZFP gene family have not been identified in cotton. RESULTS: In this paper, we identified 29 ZFP genes in Gossypium hirsutum. This gene family was divided into seven subfamilies, 22 of which were distributed over 17 chromosomes. Bioinformatic analysis revealed that 20 GhZFP genes originated from whole genome duplications and two originated from dispersed duplication events, indicating that whole genome duplication is the main force in the expansion of the GhZFP gene family. Most GhZFP8 subfamily genes, except for GhZFP8-3, were highly expressed during fiber cell growth, and were induced by brassinosteroids in vitro. Furthermore, we found that a large number of GhZFP genes contained gibberellic acid responsive elements, auxin responsive elements, and E-box elements in their promoter regions. Exogenous application of these hormones significantly stimulated the expression of these genes. CONCLUSIONS: Our findings reveal that GhZFP8 genes are involved in cotton fiber development and widely induced by auxin, gibberellin and BR, which provides a foundation for the identification of more downstream genes with potential roles in phytohormone stimuli, and a basis for breeding better cotton varieties in the future.


Assuntos
Gossypium/genética , Reguladores de Crescimento de Planta/fisiologia , Proteínas de Plantas/genética , Dedos de Zinco/genética , Brassinosteroides/metabolismo , Mapeamento Cromossômico , Sequência Conservada/genética , Giberelinas/fisiologia , Gossypium/fisiologia , Ácidos Indolacéticos/metabolismo , Filogenia , Proteínas de Plantas/fisiologia , Reação em Cadeia da Polimerase , Alinhamento de Sequência , Transcriptoma , Dedos de Zinco/fisiologia
5.
DNA Cell Biol ; 38(8): 824-839, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31295023

RESUMO

Tea plant is an important economic crop on a global scale. Its yield and quality are affected by abiotic stress. The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) family genes play irreplaceable roles in plant development and stress resistance. More and more CBL-CIPK genes have been identified, but a few CBL-CIPK genes have been cloned and characterized in tea plants. In this study, 7 CsCBLs and 18 CsCIPKs were identified based on the tea plant genome. Physicochemical properties, phylogenetic, conserved motifs, gene structure, homologous gene network, and promoter upstream elements of these 25 genes were analyzed. Conserved motifs of these genes varied with phylogenetic tree node. From the genetic structure, members of the tea plant CIPK gene family can be divided into two types: intron rich and no intron. Many stress-related elements were found in the 2000 bp upstream of the promoter, and PlantCARE predicted that CsCBL4 contained 30 stress-related elements. PlantPAN2 shows that CsCIPK6 contains 48 ABRELATERD1; CsCIPK17 contains 37 GT1CONSENSUS; CsCIPK3 contains 64 MYBCOREATCYCB1; CsCBL3 contains 52 SORLIP1AT; CsCBL5 contains 65 SURECOREATSULTR11; and CsCIPK11 contains 83 WBOXATNPR1. In addition, eight genes were selected for quantitative real-time PCR (RT-qPCR) to detect their expression profiles under high-temperature, low-temperature, salt, and drought treatments. These genes were found to be responsive to one or more abiotic stress treatments. The expression levels of CsCBL4, CsCIPK2, and CsCIPK14 were similar, and they were homologous to AtSOS3 and AtSIP3 and AtSIP4 in Arabidopsis, which were involved in the SOS pathway. This study provides insight into the potential functions of the CsCBL and CsCIPK of tea plant.


Assuntos
Camellia sinensis/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas Serina-Treonina Quinases/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Arabidopsis/genética , Proteínas de Ligação ao Cálcio/genética , Camellia sinensis/fisiologia , Sequência Conservada , Secas , Evolução Molecular , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Anotação de Sequência Molecular , Filogenia , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética
6.
BMC Evol Biol ; 19(1): 143, 2019 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-31299890

RESUMO

BACKGROUND: Our laboratory identified ADGRL4/ELTD1, an orphan GPCR belonging to the adhesion GPCR (aGPCR) family, as a novel regulator of angiogenesis and a potential anti-cancer therapeutic target. Little is known about how ADGRL4/ELTD1 (and aGPCRs in general) function, a problem compounded by a lack of known ligands or means of activation. With this in mind, we turned to computational evolutionary biology with the aim of better understanding ADGRL4/ELTD1. RESULTS: We identified ADGRL4/ELTD1 as a highly conserved early angiogenic gene which emerged in the first true vertebrates (bony fish) approximately 435 million years ago (mya), evolving alongside key angiogenic genes VEGFR2 and DLL4. We identified 3 evolutionary ADGRL4/ELTD1 variants based on EGF domain deletions with variant 2 first emerging 101 mya (95% CI 96-105) in Afrotheria and 82 mya (95% CI 76-89) in Primates. Additionally, conservation mapping across all orthologues reveals highest level conservation in EGF Ca binding domain 1, suggesting that this motif plays an essential role, as well as specific regions of the GAIN domain, GPS motif and 7TM domain, suggesting possible activation mechanisms and ligand binding positions. Additionally, we found that ADGRL4/ELTD1 (a member aGPCR family 1) is possibly ancestral to members of aGPCR family 2. CONCLUSION: This work establishes ADGRL4/ELTD1's evolution, sheds light on its possible activation and ligand binding zones, and establishes the first temporal references for the emergence of ADGRL4/ELTD1 variants during vertebrate evolution. Our approach is applicable to the greater aGPCR family and opens up new avenues for future experimental work.


Assuntos
Sequência Conservada , Evolução Molecular , Neovascularização Fisiológica , Receptores Acoplados a Proteínas-G/genética , Vertebrados/genética , Animais , Adesão Celular , Sistemas de Liberação de Medicamentos , Peixes/genética , Humanos , Neovascularização Fisiológica/genética , Filogenia , Domínios Proteicos , Receptores Acoplados a Proteínas-G/química , Deleção de Sequência , Fatores de Tempo
7.
Cytogenet Genome Res ; 158(2): 88-97, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31220833

RESUMO

Human chromosome 7 has been the focus of many behavioral, genetic, and medical studies because it carries genes related to cancer and neurodevelopment. We examined the evolution of the chromosome 7 homologs, and the 7q31 region in particular, using chromosome painting analyses and 3 paint probes derived from (i) the whole of chimpanzee chromosome VII (wcVII), (ii) human 7q31 (h7q31), and (iii) the chimpanzee homolog VIIq31 (cVIIq31). The wcVII probe was used instead of the whole human chromosome 7 because the chimpanzee contains additional C-bands and revealed large areas of synteny conservation as well as fragmentation across 20 primate species. Analyses focusing specifically on the 7q31 homolog and vicinity revealed considerable conservation across lineages with 2 exceptions. First, the probes verified an insertion of repetitive sequence at VIIq22 in chimpanzees and bonobos and also detected the sequence in most subtelomeres of the African apes. Second, a paracentric inversion with a breakpoint in the cVIIq31 block was found in the common marmoset, confirming earlier studies. Subsequent in silico comparative genome analysis of 17 primate species revealed that VIIq31.1 is more significantly conserved at the sequence level than other regions of chromosome VII, which indicates that its components are likely responsible for critical shared traits across the order, including conditions necessary for proper human development and wellbeing.


Assuntos
Coloração Cromossômica/métodos , Cromossomos Humanos Par 7/genética , Cromossomos de Mamíferos/genética , Animais , Simulação por Computador , Sequência Conservada , Evolução Molecular , Humanos , Hibridização in Situ Fluorescente , Pan paniscus/genética , Pan troglodytes/genética , Primatas/genética , Homologia de Sequência do Ácido Nucleico
8.
BMC Plant Biol ; 19(1): 272, 2019 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-31226952

RESUMO

BACKGROUND: Cyclophilins (CYPs), belonging to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily, play important roles during plant responses to biotic and abiotic stresses. RESULTS: Here, a total of 79 CYPs were identified in the genome of Gossypium hirsutum. Of which, 65 GhCYPs only contained one cyclophilin type PPIase domain, others 14 GhCYPs contain additional domains. A number of cis-acting elements related to phytohormone signaling were predicated in the upstream of GhCYPs ORF. The expression analysis revealed that GhCYPs were induced in response to cold, hot, salt, PEG and Verticillium dahliae infection. In addition, the functional importance of GhCYP-3 in Verticillium wilt resistance was also presented in this study. GhCYP-3 showed both cytoplasmic and nuclear localization. Overexpression of GhCYP-3 in Arabidopsis significantly improved Verticillium wilt resistance of the plants. Recombinant GhCYP-3 displayed PPIase activity and evident inhibitory effects on V. dahliae in vitro. Moreover, the extracts from GhCYP-3 transgenic Arabidopsis displayed significantly inhibit activity to conidia germinating and hyphal growth of V. dahliae. CONCLUSIONS: Our study identified the family members of cotton CYP genes using bioinformatics tools. Differential expression patterns of GhCYPs under various abiotic stress and V. dahliae infection conditions provide a comprehensive understanding of the biological functions of candidate genes. Moreover, GhCYP-3 involved in the resistance of cotton to V. dahliae infection presumably through antifungal activity.


Assuntos
Ciclofilinas/genética , Resistência à Doença/genética , Gossypium/genética , Doenças das Plantas/microbiologia , Verticillium , Sequência de Aminoácidos , Arabidopsis/genética , Clonagem Molecular , Sequência Conservada , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Humanos , Doenças das Plantas/genética , Reguladores de Crescimento de Planta/metabolismo , Alinhamento de Sequência , Estresse Fisiológico , Transcriptoma
9.
BMC Plant Biol ; 19(1): 276, 2019 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-31234799

RESUMO

BACKGROUND: Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined. RESULTS: A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAPpromoter::GUS techniques, the activities of PtAP66 promoters were observed only in fiber cells, not in the vessels of stems as the xylem and leaf veins developed in the transgenic Populus tree, and strong GUS signals were detected in interfascicular fiber cells, roots, anthers and sepals of PtAP17promoter::GUS transgenic plants. Intensive GUS activities in various secondary tissues implied that PtAP66 and PtAP17 could function in wood formation. In addition, most of the PtAP proteins were predicted to contain N- and (or) O-glycosylation sites, and the integration of PNGase F digestion and western blotting revealed that the PtAP17 and PtAP66 proteins were N-glycosylated in Populus. CONCLUSIONS: Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.


Assuntos
Ácido Aspártico Proteases/genética , Genes de Plantas , Família Multigênica , Proteínas de Plantas/genética , Populus/genética , Madeira/crescimento & desenvolvimento , Parede Celular/genética , Sequência Conservada , Duplicação Gênica , Perfilação da Expressão Gênica , Glicosilação , Filogenia , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Populus/enzimologia , Populus/crescimento & desenvolvimento , Regiões Promotoras Genéticas
10.
Gene ; 711: 143925, 2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31212048

RESUMO

More than 2300 genes have been reported to be involved in spermatogenesis but the functional roles of most genes in male fertility remain to be elucidated. In this study, we explored the function of dipeptidase 3 (Dpep3), a gene predicted to be testis-specific, in male fertility of mice. We showed that Dpep3 is evolutionarily conserved in human and mouse along with other eutherians. Its mRNA was exclusively detected in testicular tissue and expressed in testes from 7 days postpartum. To further explore its role in male fertility, we generated Dpep3 knockout mice (Dpep3-/-) using the CRISPR/Cas9 technology and found that the male Dpep3-/- mice are fertile despite a significant reduction in sperm count. Histology of testis and progression of meiotic prophase I showed no obvious difference between wild-type and Dpep3-/- mice. All these findings indicate that Dpep3 is not essential for male fertility in mice. These findings will help other researchers to avoid research duplication, save their time and resources to focus on the genes that are indispensable for male fertility.


Assuntos
Dipeptidases/genética , Dipeptidases/metabolismo , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Espermatogênese , Testículo/metabolismo , Animais , Sequência Conservada , Técnicas de Inativação de Genes , Humanos , Infertilidade Masculina/genética , Infertilidade Masculina/metabolismo , Masculino , Camundongos , Especificidade de Órgãos , Filogenia , Contagem de Espermatozoides , Motilidade Espermática
11.
Gene ; 711: 143934, 2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31228540

RESUMO

Phytopathogenic fungi secrete a wide range of enzymes to penetrate and colonize host tissues. Of them protease activity is reported to increase disease aggressiveness in the plant. With the aim to explore the reason of the higher infection potential of proteases, we have compared several genomic and proteomic attributes among different hydrolytic enzymes coded by five pathogenic fungal species which are the potent infectious agents of plant. Categorizing the enzymes into four major groups, namely protease, lipase, amylase and cell-wall degraders, we observed that proteases are evolutionary more conserved, have higher expression levels, contain more hydrophobic buried residues, short linear motifs and post-translational modified (PTM) sites than the other three groups of enzymes. Again, comparing these features of protease between pathogenic and non-pathogenic Aspergillus sps, we have hypothesized that protein structural properties could play significant roles in imposing infection potency to the fungal proteases.


Assuntos
Aspergillus/patogenicidade , Biologia Computacional/métodos , Peptídeo Hidrolases/química , Peptídeo Hidrolases/genética , Aspergillus/classificação , Aspergillus/genética , Simulação por Computador , Sequência Conservada , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica , Interações Hidrofóbicas e Hidrofílicas , Filogenia , Conformação Proteica , Processamento de Proteína Pós-Traducional , Proteômica/métodos
12.
Nat Commun ; 10(1): 2682, 2019 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-31213602

RESUMO

RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence.


Assuntos
Evolução Molecular , Proteômica/métodos , Motivos de Ligação ao RNA/genética , Proteínas de Ligação a RNA/genética , RNA/metabolismo , Sequência de Aminoácidos/genética , Animais , Linhagem Celular , Sequência Conservada/genética , Reagentes para Ligações Cruzadas/química , Drosophila , Humanos , Peptídeos/química , Peptídeos/genética , Ligação Proteica/genética , Proteoma/genética , RNA/química , Proteínas de Ligação a RNA/química
13.
Arch Virol ; 164(9): 2309-2314, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31172288

RESUMO

The surface (SU) and transmembrane (TM) glycoproteins of many retroviruses are linked by disulphide bonds, and the interaction of SU with a cellular receptor results in disulphide bond isomerisation triggered by the CXXC motif in SU. This reaction leads to the fusion of viral and host cell membranes. In this work, we show that the cysteine at amino acid position 212 in the CAIC motif of the SU glycoprotein of bovine leukaemia virus has a free thiol group. A C-to-A mutation at position 212, either individually or in combination with a C-to-A mutation at position 215, was found to inhibit the maturation process, suggesting its involvement in the formation of the covalent bond with TM.


Assuntos
Cisteína/metabolismo , Leucose Enzoótica Bovina/virologia , Vírus da Leucemia Bovina/genética , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/metabolismo , Internalização do Vírus , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Bovinos , Sequência Conservada , Cisteína/genética , Vírus da Leucemia Bovina/química , Vírus da Leucemia Bovina/isolamento & purificação , Vírus da Leucemia Bovina/fisiologia , Glicoproteínas de Membrana/genética , Mutação
14.
Pol J Microbiol ; 68(2): 233-246, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31250594

RESUMO

The aim of this study was to identify the potential vaccine antigens in Corynebacterium diphtheriae strains by in silico analysis of the amino acid variation in the 67-72p surface protein that is involved in the colonization and induction of epithelial cell apoptosis in the early stages of infection. The analysis of pili structural proteins involved in bacterial adherence to host cells and related to various types of infections was also performed. A polymerase chain reaction (PCR) was carried out to amplify the genes encoding the 67-72p protein and three pili structural proteins (SpaC, SpaI, SapD) and the products obtained were sequenced. The nucleotide sequences of the particular genes were translated into amino acid sequences, which were then matched among all the tested strains using bioinformatics tools. In the last step, the affinity of the tested proteins to major histocompatibility complex (MHC) classes I and II, and linear B-cell epitopes was analyzed. The variations in the nucleotide sequence of the 67-72p protein and pili structural proteins among C. diphtheriae strains isolated from various infections were noted. A transposition of the insertion sequence within the gene encoding the SpaC pili structural proteins was also detected. In addition, the bioinformatics analyses enabled the identification of epitopes for B-cells and T-cells in the conserved regions of the proteins, thus, demonstrating that these proteins could be used as antigens in the potential vaccine development. The results identified the most conserved regions in all tested proteins that are exposed on the surface of C. diphtheriae cells.The aim of this study was to identify the potential vaccine antigens in Corynebacterium diphtheriae strains by in silico analysis of the amino acid variation in the 67­72p surface protein that is involved in the colonization and induction of epithelial cell apoptosis in the early stages of infection. The analysis of pili structural proteins involved in bacterial adherence to host cells and related to various types of infections was also performed. A polymerase chain reaction (PCR) was carried out to amplify the genes encoding the 67­72p protein and three pili structural proteins (SpaC, SpaI, SapD) and the products obtained were sequenced. The nucleotide sequences of the particular genes were translated into amino acid sequences, which were then matched among all the tested strains using bioinformatics tools. In the last step, the affinity of the tested proteins to major histocompatibility complex (MHC) classes I and II, and linear B-cell epitopes was analyzed. The variations in the nucleotide sequence of the 67­72p protein and pili structural proteins among C. diphtheriae strains isolated from various infections were noted. A transposition of the insertion sequence within the gene encoding the SpaC pili structural proteins was also detected. In addition, the bioinformatics analyses enabled the identification of epitopes for B-cells and T-cells in the conserved regions of the proteins, thus, demonstrating that these proteins could be used as antigens in the potential vaccine development. The results identified the most conserved regions in all tested proteins that are exposed on the surface of C. diphtheriae cells.


Assuntos
Adesinas Bacterianas/genética , Antígenos de Bactérias/genética , Corynebacterium diphtheriae/genética , Toxoide Diftérico/genética , Difteria/prevenção & controle , Variação Genética , Proteínas de Membrana/genética , Adesinas Bacterianas/imunologia , Antígenos de Bactérias/imunologia , Biologia Computacional , Sequência Conservada , Corynebacterium diphtheriae/imunologia , Toxoide Diftérico/imunologia , Epitopos de Linfócito B/genética , Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/genética , Epitopos de Linfócito T/imunologia , Antígenos de Histocompatibilidade Classe I/imunologia , Antígenos de Histocompatibilidade Classe II/imunologia , Proteínas de Membrana/imunologia , Reação em Cadeia da Polimerase , Ligação Proteica , Análise de Sequência de DNA
15.
BMC Plant Biol ; 19(1): 257, 2019 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-31200645

RESUMO

BACKGROUND: Proliferating cell nuclear antigen (PCNA), a conserved trimeric ring complex, is loaded onto replication fork through a hetero-pentameric AAA+ ATPase complex termed replication factor C (RFC) to maintain genome stability. Although architectures of PCNA-RFC complex in yeast have been revealed, the functions of PCNA and protein-protein interactions of PCNA-RFC complex in higher plants are not very clear. Here, essential regions mediating interactions between PCNA and RFC subunits in Arabidopsis and rice were investigated via yeast-two-hybrid method and bimolecular fluorescence complementation techniques. RESULTS: We observed that OsPCNA could interact with all OsRFC subunits, while protein-protein interactions only exist between Arabidopsis RFC2/3/4/5 and AtPCNA1/2. The truncated analyses indicated that the C-terminal of Arabidopsis RFC2/3/4/5 and rice RFC1/2 is essential for binding PCNA while the region of rice RFC3/4/5 mediating interaction with PCNA distributed both at the N- and C-terminal. On the other hand, we found that the C- and N-terminal of Arabidopsis and rice PCNA contribute equally to PCNA-PCNA interaction, and the interdomain connecting loop (IDCL) domain and C-terminal of PCNAs are indispensable for interacting RFC subunits. CONCLUSIONS: These results indicated that Arabidopsis and rice PCNAs are highly conserved in sequence, structure and pattern of interacting with other PCNA monomer. Nevertheless, there are also significant differences between the Arabidopsis and rice RFC subunits in binding PCNA. Taken together, our results could be helpful for revealing the biological functions of plant RFC-PCNA complex.


Assuntos
Arabidopsis/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Antígeno Nuclear de Célula em Proliferação/metabolismo , Proteína de Replicação C/metabolismo , Arabidopsis/genética , Sequência Conservada , Oryza/genética , Proteínas de Plantas/genética , Antígeno Nuclear de Célula em Proliferação/genética
16.
Gene ; 710: 291-306, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31185283

RESUMO

The WD40 transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. To our knowledge, to date, WD40 superfamily genes have been identified and characterized in several plant species, but little information is available on the WD40 superfamily genes in peach. In this study, we identified 220 members of the WD40 superfamily in the peach genome, and these members were further classified into five subfamilies based on phylogenetic comparison with those in Arabidopsis. The members within each subfamily had conserved motifs and gene structures. The WD40 genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. Additionally, 58 pairs of paralog WD40 members were found on eight chromosomes in peach, and 242 pairs of orthologous WD40 genes in peach and Arabidopsis were matched. The 54 selected putative WD40 genes in peach had diverse expression patterns in red-fleshed and white-fleshed peach fruits at five developmental stages. Prupe.6G211800.1 was located only on the cytomembrane, while Prupe.1G428200.1 and Prupe.I003200.1 were located on both the cytomembrane and in the nucleus; Prupe.1G558700.1 was densely localized around the nuclear rim but relatively faintly localized in the nucleoplasm; Prupe.5G116300.1 was located in the nucleus and cytomembrane with strong signals but showed weak signals in the cytoplasm; and Prupe.8G212400.1 and Prupe.1G053600.1 were located mainly in the nuclear envelope and cytomembrane but relatively faintly in the nucleoplasm. This study provides a foundation for the further functional verification of WD40 genes in peach.


Assuntos
Mapeamento Cromossômico/métodos , Família Multigênica , Proteínas de Plantas/genética , Prunus persica/genética , Núcleo Celular/genética , Núcleo Celular/metabolismo , Cromossomos de Plantas/genética , Sequência Conservada , Citoplasma/genética , Citoplasma/metabolismo , Regulação da Expressão Gênica de Plantas , Filogenia , Proteínas de Plantas/metabolismo , Prunus persica/metabolismo , Repetições WD40
17.
BMC Plant Biol ; 19(1): 191, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072335

RESUMO

BACKGROUND: BRASSINAZOLE-RESISTANT (BZR) family genes encode plant-specific transcription factors (TFs) that participate in brassinosteroid signal transduction. BZR TFs have vital roles in plant growth, including cell elongation. However, little is known about BZR genes in sugar beet (Beta vulgaris L.). RESULTS: Therefore, we performed a genome-wide investigation of BvBZR genes in sugar beet. Through an analysis of the BES1_N conserved domain, six BvBZR gene family members were identified in the sugar beet genome, which clustered into three subgroups according to a phylogenetic analysis. Each clade was well defined by the conserved motifs, implying that close genetic relationships could be identified among the members of each subfamily. According to chromosomal distribution mapping, 2, 1, 1, 1, and 1 genes were located on chromosomes 1, 4, 5, 6, and 8, respectively. The cis-acting elements related to taproot growth were randomly distributed in the promoter sequences of the BvBZR genes. Tissue-specific expression analyses indicated that all BvBZR genes were expressed in all three major tissue types (roots, stems, and leaves), with significantly higher expression in leaves. Subcellular localization analysis revealed that Bv1_fxre and Bv6_nyuw are localized in the nuclei, consistent with the prediction of Wolf PSORT. CONCLUSION: These findings offer a basis to predict the functions of BZR genes in sugar beet, and lay a foundation for further research of the biological functions of BZR genes in sugar beet.


Assuntos
Beta vulgaris/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Fatores de Transcrição/genética , Motivos de Aminoácidos , Beta vulgaris/efeitos dos fármacos , Cromossomos de Plantas/genética , Sequência Conservada/genética , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genes de Plantas , Proteínas de Fluorescência Verde/metabolismo , Motivos de Nucleotídeos/genética , Filogenia , Reguladores de Crescimento de Planta/farmacologia , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Regiões Promotoras Genéticas , Fatores de Transcrição/metabolismo
18.
BMC Plant Biol ; 19(1): 192, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072362

RESUMO

BACKGROUND: The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (the first, fifth and ninth days of the late bloom stage), with 50 mg/L GA3 (calyx persistence treatment, C_1, C_5, C_9) or 500 mg/L PP333 (calyx abscission treatment, T_1, T_5, T_9), were collected and simultaneously conducted transcriptome and small RNA sequencing. RESULTS: Through association analysis of transcriptome and small RNA sequencing, mRNA-miRNA network was conducted. Compared calyx persistence groups with calyx abscission groups during the same stage, 145, 56 and 150 mRNA-miRNA pairs were obtained in C_1 vs T_1, C_5 vs T_5 and C_9 vs T_9, respectively; When C_1 compared with C_5 and C_9, 90 and 506 mRNA-miRNA pairs were screened respectively, and 255 mRNA-miRNA pairs were obtained from the comparison between C_5 and C_9; When T_1 compared with the T_5 and T_9, respectively, 206 and 796 mRNA-miRNA pairs were obtained, and 383 mRNA-miRNA pairs were obtained from the comparison between T_5 and T_9. These mRNAs in miRNA-mRNA pairs were significantly enriched into the terpenoid backbone biosynthesis, photosynthesis - antenna proteins, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, zeatin biosynthesis and plant hormone signal transduction. In addition, we obtained some key genes from miRNA-mRNA pairs that may be associated with calyx abscission, including protein phosphatase 2C (psi-miR394a-HAB1), receptor-like protein kinase (psi-miR396a-5p-HERK1), cellulose synthase-like protein D3 (psi-miR827-CSLD3), beta-galactosidase (psi-miR858b-ß-galactosidase), SPL-psi-miR156j/157d, abscisic acid 8'-hydroxylase 1 (psi-miR396a-5p-CYP707A1) and auxin response factor (psi-miR160a-3p-ARF6, psi-miR167d-ARF18, psi-miR167a-5p-ARF25), etc. CONCLUSION: By integrated analysis mRNA and miRNA, our study gives a better understanding of the important genes and regulation pathway related to calyx abscission in Korla fragrant pear. We have also established the network of miRNA-mRNA pairs to learn about precise regulation of miRNA on calyx abscission.


Assuntos
Flores/genética , MicroRNAs/genética , Pyrus/genética , Análise de Sequência de RNA , Sequência Conservada/genética , Ontologia Genética , Genes de Plantas , MicroRNAs/metabolismo , Anotação de Sequência Molecular , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reprodutibilidade dos Testes , Transcriptoma/genética
19.
BMC Vet Res ; 15(1): 143, 2019 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-31077188

RESUMO

BACKGROUND: Novel Muscovy duck reovirus (N-MDRV), emerged in southeast China in 2002, which can infect a wide range of waterfowl and induces clinical signs and cytopathic effects that are distinct from those of classical MDRV, and continues to cause high morbidity and 5-50% mortality in ducklings. The present study aimed to investigate the characteristics of two novel reoviruses isolated from Muscovy ducklings in Guangdong, China. RESULTS: Two novel MDRV strains, designated as MDRV-SH12 and MDRV-DH13, were isolated from two diseased Muscovy ducklings in Guangdong province, China in June 2012 and September 2013, respectively. Sequencing of the complete genomes of these two viruses showed that they consisted of 23,418 bp and were divided into 10 segments, ranging from 1191 bp (S4) to 3959 bp (L1) in length, and all segments contained conserved sequences in the 5' non-coding region (GCUUUU) and 3' non-coding region (UCAUC). Pairwise sequence comparisons demonstrated that MDRV-SH12 and MDRV-DH13 showed the highest similarity with novel MDRVs. Phylogenetic analyses of the nucleotide sequences of all 10 segments revealed that MDRV-SH12 and MDRV-DH13 were clustered together with other novel waterfowl-origin reoviruses and were distinct from classical waterfowl-origin and chicken-origin reoviruses. The analyses also showed possible genetic re-assortment events in segment M2 between waterfowl-origin and chicken-origin reoviruses and the segments encoding λA, µA, µNS, σA, and σNS between classical and novel waterfowl-origin reoviruses. Potential recombination events detection in segment S2 suggests that MDRV-SH12 and MDRV-DH13 may be recombinants of classical and novel WRVs. CONCLUSIONS: The results presented in this study, the full genomic data for two novel MDRV strains, will improve our understanding of the evolutionary relationships among the waterfowl-origin reoviruses circulating in China, and may aid in the development of more effective vaccines against various waterfowl-origin reoviruses.


Assuntos
Doenças das Aves/virologia , Orthoreovirus Aviário/classificação , Orthoreovirus Aviário/genética , Filogenia , Infecções por Reoviridae/veterinária , Animais , China , Sequência Conservada , Patos , Genoma Viral/genética , Infecções por Reoviridae/virologia , Análise de Sequência de DNA
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