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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): 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
3.
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
4.
Biomed Res Int ; 2019: 1425281, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31058184

RESUMO

Leishmania major, a protozoan parasite that diverged early from the main eukaryotic lineage, exhibits unusual mechanisms of gene expression. Little is known in this organism about the transcription factors involved in the synthesis of tRNA, 5S rRNA, and snRNAs, transcribed by RNA Polymerase III (Pol III). Here we identify and characterize the TFIIIB subunit Bdp1 in L. major (LmBdp1). Bdp1 plays key roles in Pol III transcription initiation in other organisms, as it participates in Pol III recruitment and promoter opening. In silico analysis showed that LmBdp1 contains the typical extended SANT domain as well as other Bdp1 conserved regions. Nevertheless, LmBdp1 also displays distinctive features, including the presence of only one aromatic residue in the N-linker region. We were not able to produce null mutants of LmBdp1 by homologous recombination, as the obtained double replacement cell line contained an extra copy of LmBdp1, indicating that LmBdp1 is essential for the viability of L. major promastigotes. Notably, the mutant cell line showed reduced levels of the LmBdp1 protein, and its growth was significantly decreased in relation to wild-type cells. Nuclear run-on assays demonstrated that Pol III transcription was affected in the mutant cell line, and ChIP experiments showed that LmBdp1 binds to 5S rRNA, tRNA, and snRNA genes. Thus, our results indicate that LmBdp1 is an essential protein required for Pol III transcription in L. major.


Assuntos
Leishmania major/genética , RNA Polimerase III/genética , Fator de Transcrição TFIIIB/genética , Transcrição Genética , Simulação por Computador , Sequência Conservada/genética , Regulação da Expressão Gênica/genética , Recombinação Homóloga/genética , Proteínas Mutantes/genética , Regiões Promotoras Genéticas , Domínios Proteicos/genética , Subunidades Proteicas/genética , RNA Ribossômico 5S/biossíntese , RNA Nuclear Pequeno/biossíntese , RNA de Transferência/biossíntese
5.
Arch Virol ; 164(8): 2049-2059, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31123965

RESUMO

Avipoxviruses (APVs) are large DNA viruses that are detected widely in many species of birds. Little information is available regarding genetic variations in these host-specific viruses. In the present study, nine canarypox virus and five pigeonpox virus isolates were collected from northeastern Iran and isolated via the chorioallantoic membrane of chicken embryos. Further investigations were conducted using analysis of virus growth in chicken embryo fibroblasts, histopathology, electron microscopy, and molecular techniques such as polymerase chain reaction (PCR) combined with sequencing and phylogenetic analysis to investigate variations in the highly conserved P4b gene of poxviruses. Virus replication and pock lesions were evident, and microscopic examination revealed eosinophilic intracytoplasmic inclusion bodies and biconcave enveloped virus particles with randomly arranged surface filaments, which are characteristic features of poxviruses. PCR results confirmed the presence of an APV-specific 578-bp fragment in all of the samples. Sequence analysis and phylogenetic analysis of 578-bp P4b fragments of eight isolates confirmed that our canary and pigeon isolates clustered with previously reported isolates. The similarity between the nucleotide sequences of most of our isolates and those isolated previously in other countries could be due to the high degree of conservation of these fragments. However, the FZRC6V isolate from a canary in this study did not have a canarypox virus origin according to the sequence analysis, and might have originated from cross-infection with different strains of avipoxviruses.


Assuntos
Avipoxvirus/genética , Vírus da Varíola dos Canários/genética , Infecções por Poxviridae/virologia , Animais , Doenças das Aves/virologia , Células Cultivadas , Galinhas/virologia , Sequência Conservada/genética , Infecção Hospitalar/virologia , Fibroblastos/virologia , Genes Virais/genética , Variação Genética/genética , Irã (Geográfico) , Filogenia , Doenças das Aves Domésticas/virologia , Poxviridae/genética
6.
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
7.
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
8.
BMC Plant Biol ; 19(1): 150, 2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-30995906

RESUMO

BACKGROUND: Powdery mildew (PM) is a widespread fungal disease of plants in temperate climates, causing significant economic losses in agricultural settings. Specific homologs of the MLO gene family are PM susceptibility factors, as their loss-of function results in durable PM resistance (mlo resistance) in several plant species. The role of MLO susceptibility genes in plant-pathogen interactions is still elusive, however it is known that they are strongly upregulated following PM infection. RESULTS: In this study, we investigated the structure of 414 Putative Promoter Regions (PPRs) of MLO genes and highlighted motif and regulatory element patterns related to genomic relationships among species and phylogenetic distance among homologs. A TC box-like motif and a thymine-rich motif were found to be overrepresented in MLO genes transcriptionally upregulated upon infection with PM fungi. As proof of concept, we showed that the expression of a melon (Cucumis melo L.) gene enriched for the motifs above mentioned was strongly upregulated upon infection with the PM fungus Podosphaera xanthii. CONCLUSION: While identifying a candidate MLO susceptibility gene in melon, this study provides insight on the transcriptional control of MLO genes and indicates diagnostic features useful to identify MLO susceptibility genes across species affected by the PM disease.


Assuntos
Sequência Conservada/genética , Evolução Molecular , Genes de Plantas , Regiões Promotoras Genéticas , Ascomicetos/fisiologia , Sequência de Bases , Biologia Computacional , Cucurbitaceae/genética , Cucurbitaceae/microbiologia , Regulação da Expressão Gênica de Plantas , Motivos de Nucleotídeos/genética , Filogenia , Doenças das Plantas/microbiologia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transcrição Genética , Regulação para Cima/genética
9.
BMC Evol Biol ; 19(1): 83, 2019 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-30917781

RESUMO

BACKGROUND: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae. RESULTS: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism. CONCLUSIONS: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.


Assuntos
Variação Antigênica/genética , Evolução Biológica , Transferência Genética Horizontal , Seleção Genética , Streptococcus/genética , Animais , Sequência Conservada/genética , DNA Intergênico , Fluxo Gênico , Ontologia Genética , Rearranjo Gênico/genética , Genes Bacterianos , Tamanho do Genoma , Humanos , Hidrolases/metabolismo , Nucleotídeos/genética , Filogenia , Deleção de Sequência , Especificidade da Espécie , Streptococcus pneumoniae/genética , Virulência/genética
10.
PLoS Biol ; 17(2): e3000094, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30742611

RESUMO

The repeatability or predictability of evolution is a central question in evolutionary biology and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage-compensation male-specific lethal (MSL) complex to study the mutational paths that have led to the acquisition of hundreds of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the D. melanica and D. robusta species groups by genome sequencing and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve hundreds of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element (TE) insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes and appears to be contingent on genomic properties of that species, such as simple repeat or TE density. This establishes the "genomic environment" as an important determinant in predicting the outcome of evolutionary adaptations.


Assuntos
Compensação de Dosagem (Genética) , Drosophila melanogaster/genética , Evolução Molecular , Redes Reguladoras de Genes , Animais , Sequência de Bases , Sítios de Ligação , Cromatina/metabolismo , Sequência Conservada/genética , Proteínas de Drosophila/metabolismo , Feminino , Masculino , Anotação de Sequência Molecular , Mutação/genética , Motivos de Nucleotídeos/genética , Filogenia , Cromossomos Sexuais/genética
11.
Biometals ; 32(2): 273-291, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30810877

RESUMO

Heme may represent a major iron-source for bacteria. In the symbiotic nitrogen-fixing bacterium Ensifer meliloti 1021, iron acquisition from heme depends on the outer-membrane heme-receptor ShmR. Expression of shmR gene is repressed by iron in a RirA dependent manner while under iron-limitation its expression requires the small protein HmuP. In this work, we identified highly conserved nucleotide motifs present upstream the shmR gene. These motifs are widely distributed among Alpha and Beta Proteobacteria, and correlate with the presence of HmuP coding sequences in bacterial genomes. According to data presented in this work, we named these new motifs as HmuP-responsive elements (HPREs). In the analyzed genomes, the HPREs were always present upstream of genes encoding putative heme-receptors. Moreover, in those Alpha and Beta Proteobacteria where transcriptional start sites for shmR homologs are known, HPREs were located in the 5'UTR region. In this work we show that in E. meliloti 1021, HPREs are involved in HmuP-dependent shmR expression. Moreover, we show that changes in sequence composition of the HPREs correlate with changes in a predicted RNA secondary structure element and affect shmR gene expression.


Assuntos
Regiões 5' não Traduzidas/genética , Proteínas da Membrana Bacteriana Externa/genética , Proteínas de Bactérias/genética , Sequência Conservada/genética , Motivos de Nucleotídeos/genética , Receptores de Superfície Celular/genética , Sinorhizobium meliloti/genética , Reação em Cadeia da Polimerase em Tempo Real , Sinorhizobium meliloti/crescimento & desenvolvimento
12.
Gene ; 696: 149-161, 2019 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-30753890

RESUMO

The distributions of secondary structural elements appear to differ between coding regions (CDS) of mRNAs compared to the untranslated regions (UTRs), presumably as a mechanism to fine-tune gene expression, including efficiency of translation. However, a systematic and comprehensive analysis of secondary structure avoidance because of potential bias in codon usage is difficult as some of the common secondary structures, such as, hairpins can be formed by numerous sequence combinations. Using G-quadruplex (GQ) as the model secondary structure we studied the impact of codon bias on GQs within the CDS. Because GQs can be predicted using specific consensus sequence motifs, they provide an excellent platform for investigation of the selectivity of such putative structures at the codon level. Using a bioinformatics approach, we calculated the frequencies of putative GQs within the CDS of a variety of species. Our results suggest that the most stable GQs appear to be significantly underrepresented within the CDS, through the use of specific synonymous codon combinations. Furthermore, we identified many peptide sequence motifs in which silent mutations can potentially alter translation via stable GQ formation. This work not only provides a comprehensive analysis on how stable secondary structures appear to be avoided within the CDS of mRNA, but also broadens the current understanding of synonymous codon usage as they relate to the structure-function relationship of RNA.


Assuntos
Códon/genética , Sequência Conservada/genética , Quadruplex G , RNA Mensageiro/genética , Sequência de Aminoácidos/genética , Biologia Computacional , Humanos , RNA Mensageiro/química , Mutação Silenciosa , Regiões não Traduzidas/genética
13.
Methods Mol Biol ; 1932: 41-50, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30701490

RESUMO

Plant microRNAs do not only perform important roles in development; they also have a fascinating evolutionary dynamics. Their genes appear to originate at quite a high rate during evolution, but most of them evolve initially in an almost neutral way and hence also get lost quite rapidly. Despite the high birth and death rate, a few miRNA-encoding genes got involved in the control of important target genes and thus have been conserved during evolution. This happened obviously at all times and taxonomic levels during land plant evolution. Consequently, the genomes of extant plant species contain a mix of miRNA-encoding genes of different ages, ranging from very young, often even species-specific loci to genes that had already been established in the stem group of extant land plants more than 400 million years ago. It could well be that the evolutionary dynamics of miRNA-encoding genes contributed substantially to the evolution of developmental plasticity in plants.


Assuntos
Sequência Conservada/genética , MicroRNAs/genética , RNA de Plantas/genética , Evolução Molecular , Genes de Plantas/genética , Genoma de Planta/genética , Humanos
14.
Mol Phylogenet Evol ; 135: 148-165, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30802595

RESUMO

Neotropical freshwaters host more than 6000 fish species, of which 983 are suckermouth armored catfishes of the family Loricariidae - the most-diverse catfish family and fifth most species-rich vertebrate family on Earth. Given their diversity and ubiquitous distribution across many habitat types, loricariids are an excellent system in which to investigate factors that create and maintain Neotropical fish diversity, yet robust phylogenies needed to support such ecological and evolutionary studies are lacking. We sought to buttress the systematic understanding of loricariid catfishes by generating a genome-scale data set (1041 loci, 328,330 bp) for 140 species spanning 75 genera and five of six previously proposed subfamilies. Both maximum likelihood and Bayesian analyses strongly supported the monophyly of Loricariidae. Our results also reinforced the established backbone of loricariid interrelationships: Delturinae as sister to all other analyzed loricariids, with subfamily Rhinelepinae diverging next, followed by Loricariinae sister to Hypostominae + Hypoptopomatinae. Previous DNA-based relationships within Hypostominae and Loricariinae were strongly supported. However, we evaluated for the first time DNA-based relationships among many Hypoptopomatinae genera and found significant differences with this subfamily's current genus-level classification, prompting several taxonomic changes. Finally, we placed our topological results within a fossil-calibrated temporal context indicating that early Loricariidae diversification occurred across the Cretaceous-Paleogene boundary ∼65 million years ago (Ma). Our study lays a strong foundation for future research to focus on relationships among species and the macroevolutionary processes affecting loricariid diversification rates and patterns.


Assuntos
Peixes-Gato/classificação , Peixes-Gato/genética , Sequência Conservada , Filogenia , Animais , Sequência de Bases , Teorema de Bayes , Calibragem , Sequência Conservada/genética , Ecossistema , Funções Verossimilhança , Análise de Sequência de DNA , Especificidade da Espécie , Fatores de Tempo
15.
BMC Evol Biol ; 19(1): 55, 2019 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-30764768

RESUMO

BACKGROUND: Micro RNAs (miRNAs), a class of small non-coding RNAs, have been implicated in various aspects of plant development. miR394 is required for shoot apical meristem organization, stem cell maintenance and abiotic stress responses in Arabidopsis, where it functions by negatively regulating the transcript level of target LEAF CURLING RESPONSIVENESS (LCR), which is an F-box protein-coding gene. The evolutionary conservation of stem cell regulatory miR394-LCR module among plants remains elusive. RESULTS: Our study has identified 79 miR394 and 43 target sequences across 40 plant species using various homology based search tools and databases, and analysed their co-evolution pattern. We customised an annotation workflow which computationally validates 20 novel miR394s from 14 plant species. Independent phylogenetic trees were reconstructed with precursor MIR394s, mature miR394s, and their target sequences along with complementary miR394 binding sites. The phylogeny revealed that mature sequences of miR394s as well as their targets belonging to the F-box protein encoding gene families, were highly conserved. Though, miR394-3p were complementary to miR394s/miR394-5p, they clustered separately. CONCLUSION: The existence and separate clustering of miR394-3p and miR394s/miR394-5p indicate their independent regulation. The phylogeny also suggests that miR394s had evolved at the beginning of gymnosperm-angiosperm divergence. Despite strong conservation, some level of sequence variation in miR394s and the complementary binding sites of their targets suggests possible functional diversification of miR394-LCR mediated stem cell regulation in plants.


Assuntos
Evolução Molecular , MicroRNAs/genética , Plantas/genética , RNA de Plantas/genética , Arabidopsis/genética , Sequência de Bases , Sequência Conservada/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , MicroRNAs/metabolismo , Anotação de Sequência Molecular , Família Multigênica , Filogenia , Precursores de RNA/genética , Precursores de RNA/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA de Plantas/metabolismo , Especificidade da Espécie , Estresse Fisiológico/genética
16.
PLoS One ; 14(1): e0209576, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30629625

RESUMO

Dengue being one of the deadliest diseases of tropical regions, enforces to put continuous efforts for the development of vaccine and effective therapeutics. Most of the antibodies generated during dengue infection are non-neutralizing and cause antibody dependent enhancement. Hence, making a potent neutralizing antibody against all four dengue serotypes could be very effective for the treatment. However, designing a single antibody for all serotypes is difficult due to variation in protein sequences. Therefore, the objective is to identify conserved region of dengue envelope protein and then develop an antibody against that conserved region. Before advancing to the development of such an antibody, it is desirable to validate the interactions between antibody and dengue envelope protein. In silico analysis of such interactions provides a good platform to find out a suitable region to design and construct an antibody against it by analyzing antigen-antibody interaction before synthesizing the antibody. In this study, two highly conserved regions of dengue envelope protein were identified and an scFv was constructed against it. Both scFv and FuBc proteins were expressed in bacterial expression system and binding efficiency was analyzed by SPR analysis with KD value 2.3 µM. In order to improve binding efficiency, an in silico scFv mutant library was created which was virtually screened for higher binding efficiency. Six mutants with high binding efficiency were selected for further analysis. The binding ability of these mutants were predicted using simulation analysis which shows these mutations were stabilizing scFv-FuBc complex.


Assuntos
Anticorpos Neutralizantes/imunologia , Vírus da Dengue/genética , Vírus da Dengue/imunologia , Animais , Anticorpos Neutralizantes/genética , Anticorpos Antivirais/imunologia , Sítios de Ligação de Anticorpos/genética , Simulação por Computador , Sequência Conservada/genética , Dengue/imunologia , Biblioteca Gênica , Humanos , Anticorpos de Cadeia Única/genética , Anticorpos de Cadeia Única/imunologia , Proteínas do Envelope Viral/genética , Proteínas do Envelope Viral/imunologia
17.
Nat Commun ; 10(1): 196, 2019 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-30643116

RESUMO

In response to viral infection, CD8+ T cells undergo expansion and differentiate into distinct classes of effector cells. After clearance of the virus, a small population of long-lived memory cells persists. Comprehensive studies have defined the protein-coding transcriptional changes associated with this process. Here we expand on this prior work by performing RNA-sequencing to identify changes in long noncoding RNA (lncRNA) expression in human and mouse CD8+ T cells responding to viral infection. We identify hundreds of unannotated lncRNAs and show that expression profiles of both known and novel lncRNAs are sufficient to define naive, effector, and memory CD8+ T cell subsets, implying that they may be involved in fate decisions during antigen-driven differentiation. Additionally, in comparing mouse and human lncRNA expression, we find that lncRNAs with conserved sequence undergo similar changes in expression in the two species, suggesting an evolutionarily conserved role for lncRNAs during CD8+ T cell differentiation.


Assuntos
Linfócitos T CD8-Positivos/imunologia , Diferenciação Celular/genética , Coriomeningite Linfocítica/imunologia , RNA Longo não Codificante/metabolismo , Subpopulações de Linfócitos T/imunologia , Animais , Linfócitos T CD8-Positivos/metabolismo , Diferenciação Celular/imunologia , Sequência Conservada/genética , Sequência Conservada/imunologia , Conjuntos de Dados como Assunto , Modelos Animais de Doenças , Perfilação da Expressão Gênica , Humanos , Memória Imunológica/genética , Ativação Linfocitária/genética , Coriomeningite Linfocítica/virologia , Vírus da Coriomeningite Linfocítica/imunologia , Camundongos , Camundongos Endogâmicos C57BL , RNA Longo não Codificante/imunologia , RNA Longo não Codificante/isolamento & purificação , Análise de Sequência de RNA , Sintenia/imunologia , Subpopulações de Linfócitos T/metabolismo , Transcriptoma/imunologia
18.
Plant Physiol Biochem ; 136: 204-214, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30690277

RESUMO

Magnesium (Mg2+) is an essential element for plant growth. Its transport and homeostasis in plants is mainly maintained by the MRS2/MGT of Mg2+ transporters. Little is known about the MRS2/MGT gene family in Brassica napus L. (B. napus), one of the most important oil grains. In our present study, we identified 36 putative MRS2/MGT genes (BnMGTs) from B. napus and investigated their phylogeny, expression pattern and function. These BnMGT genes were sorted into five distinguished groups by the phylogenetic analysis, and they were clearly homologous with the MRS2/MGT genes in Arabidopsis and rice. Complementation assays using the Salmonella typhimurium mutant MM281 demonstrated that the BnMGT genes were capable of mediating Mg2+ uptake and transport, with varied affinities to Mg2+. The expression pattern analysis showed that the expression of BnMGTs were tissue-specific and varied in different tissues. This work provides the molecular basis to discover the function of BnMGT gene family in plant growth and development.


Assuntos
Brassica napus/genética , Proteínas de Transporte de Cátions/genética , Genes de Plantas/genética , Mapeamento Cromossômico , Clonagem Molecular , Sequência Conservada/genética , Genes de Plantas/fisiologia , Magnésio/metabolismo , Filogenia , Reação em Cadeia da Polimerase em Tempo Real , Alinhamento de Sequência , Análise de Sequência de DNA
19.
Proc Natl Acad Sci U S A ; 116(5): 1639-1644, 2019 01 29.
Artigo em Inglês | MEDLINE | ID: mdl-30647110

RESUMO

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.


Assuntos
Homem de Neandertal/genética , Seleção Genética/genética , Alelos , Animais , Sequência Conservada/genética , DNA/genética , Europa (Continente) , Grupo com Ancestrais do Continente Europeu/genética , Evolução Molecular , Fluxo Gênico/genética , Humanos , RNA não Traduzido/genética
20.
Planta ; 249(4): 1133-1142, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30603789

RESUMO

MAIN CONCLUSION: Alternative splicing EVENTS were genome-wide identified for four legume species, and nitrogen fixation-related gene families and evolutionary analysis was also performed. Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. Investigation of the genome-wide conserved AS events across different species will help with the understanding of the evolution of the functional diversity in legumes, allowing for genetic improvement. Genome-wide identification and characterization of AS were performed using the publically available mRNA, EST, and RNA-Seq data for four important legume species. A total of 15,165 AS genes in Glycine max, 6077 in Cicer arietinum, 7240 in Medicago truncatula, and 7358 in Lotus japonicus were identified. Intron retention (IntronR) was the dominant AS type among the identified events, with IntronR occurring from 53.76% in M. truncatula to 43.91% in C. arietinum. We identified 1159 AS genes that were conserved among four species. Furthermore, nine nitrogen fixation-related gene families with 237 genes were identified, and 80 of them were AS, accounting for the 43.48% in G. max and 27.78% in C. arietinum. An evolutionary analysis showed that these AS genes tended to be located adjacent to each other in the evolutionary tree and are unbalanced in the distribution in the sub-family. This study provides a foundation for future studies on transcription complexity, evolution, and the role of AS on plant functional regulation.


Assuntos
Processamento Alternativo/genética , Cicer/genética , Lotus/genética , Medicago truncatula/genética , Soja/genética , Sequência Conservada/genética , Genes de Plantas/genética , Estudo de Associação Genômica Ampla , Fixação de Nitrogênio/genética , Alinhamento de Sequência
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