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1.
Genes Dev ; 33(23-24): 1688-1701, 2019 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-31727772

RESUMEN

Human nucleolar organizer regions (NORs), containing ribosomal gene (rDNA) arrays, are located on the p-arms of acrocentric chromosomes (HSA13-15, 21, and 22). Absence of these p-arms from genome references has hampered research on nucleolar formation. Previously, we assembled a distal junction (DJ) DNA sequence contig that abuts rDNA arrays on their telomeric side, revealing that it is shared among the acrocentrics and impacts nucleolar organization. To facilitate inclusion into genome references, we describe sequencing the DJ from all acrocentrics, including three versions of HSA21, ∼3 Mb of novel sequence. This was achieved by exploiting monochromosomal somatic cell hybrids containing single human acrocentric chromosomes with NORs that retain functional potential. Analyses revealed remarkable DJ sequence and functional conservation among human acrocentrics. Exploring chimpanzee acrocentrics, we show that "DJ-like" sequences and abutting rDNA arrays are inverted as a unit in comparison to humans. Thus, rDNA arrays and linked DJs represent a conserved functional locus. We provide direct evidence for exchanges between heterologous human acrocentric p-arms, and uncover extensive structural variation between chromosomes and among individuals. These findings lead us to revaluate the molecular definition of NORs, identify novel genomic structural variation, and provide a rationale for the distinctive chromosomal organization of NORs.


Asunto(s)
Cromosomas/química , Cromosomas/genética , ADN Ribosómico/química , ADN Ribosómico/genética , Región Organizadora del Nucléolo/química , Región Organizadora del Nucléolo/genética , Animales , Secuencia de Bases , Línea Celular , Secuencia Conservada/genética , Estructuras Genéticas/genética , Variación Genética , Humanos , Células Híbridas , Ratones , Pan troglodytes/genética
2.
PLoS Comput Biol ; 15(9): e1007345, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31545786

RESUMEN

HIV-1 replicates via a low-fidelity polymerase with a high mutation rate; strong conservation of individual nucleotides is highly indicative of the presence of critical structural or functional properties. Identifying such conservation can reveal novel insights into viral behaviour. We analysed 3651 publicly available sequences for the presence of nucleic acid conservation beyond that required by amino acid constraints, using a novel scale-free method that identifies regions of outlying score together with a codon scoring algorithm. Sequences with outlying score were further analysed using an algorithm for producing local RNA folds whilst accounting for alignment properties. 11 different conserved regions were identified, some corresponding to well-known cis-acting functions of the HIV-1 genome but also others whose conservation has not previously been noted. We identify rational causes for many of these, including cis functions, possible additional reading frame usage, a plausible mechanism by which the central polypurine tract primes second-strand DNA synthesis and a conformational stabilising function of a region at the 5' end of env.


Asunto(s)
Secuencia Conservada/genética , Genoma Viral/genética , VIH-1/genética , Algoritmos , Codón/genética , Biología Computacional , VIH-1/química , VIH-1/ultraestructura , Modelos Genéticos , Conformación de Ácido Nucleico , ARN Viral/química , ARN Viral/genética , ARN Viral/ultraestructura
3.
Genome Biol ; 20(1): 184, 2019 09 02.
Artículo en Inglés | MEDLINE | ID: mdl-31477167

RESUMEN

BACKGROUND: Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing patterns of disease caused by these two pathogens is based on studies with limited timeframes that provide few insights into their population dynamics or the dynamics in AMR elements that they can carry. RESULTS: We investigate the population dynamics of two priority AMR pathogens over 7 years between 2007 and 2012 in a major UK hospital, spanning changes made to UK national antimicrobial prescribing policy in 2007. Between 2006 and 2012, K. pneumoniae showed epidemiological cycles of multi-drug-resistant (MDR) lineages being replaced approximately every 2 years. This contrasted E. cloacae where there was no temporally changing pattern, but a continuous presence of the mixed population. CONCLUSIONS: The differing patterns of clonal replacement and acquisition of mobile elements shows that the flux in the K. pneumoniae population was linked to the introduction of globally recognized MDR clones carrying drug resistance markers on mobile elements. However, E. cloacae carries a chromosomally encoded ampC conferring resistance to front-line treatments and shows that MDR plasmid acquisition in E. cloacae was not indicative of success in the hospital. This led to markedly different dynamics in the AMR populations of these two pathogens and shows that the mechanism of the resistance and its location in the genome or mobile elements is crucial to predict population dynamics of opportunistic pathogens in clinical settings.


Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana/genética , Enterobacter cloacae/genética , Klebsiella pneumoniae/genética , Secuencia Conservada/genética , Farmacorresistencia Bacteriana/efectos de los fármacos , Enterobacter cloacae/efectos de los fármacos , Variación Genética , Genoma Bacteriano , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/aislamiento & purificación , Dinámica Poblacional , Análisis de Secuencia de ADN
4.
BMC Plant Biol ; 19(1): 336, 2019 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-31370790

RESUMEN

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.


Asunto(s)
Brassica napus/genética , Flores/crecimiento & desarrollo , Genes de Plantas/genética , MicroARNs/genética , Brassica napus/crecimiento & desarrollo , Mapeo Cromosómico , Secuencia Conservada/genética , Genes de Plantas/fisiología , Estudio de Asociación del Genoma Completo , MicroARNs/fisiología , Filogenia , Alineación de Secuencia
5.
BMC Genomics ; 20(1): 635, 2019 Aug 06.
Artículo en Inglés | MEDLINE | ID: mdl-31387534

RESUMEN

BACKGROUND: As one of the most important transcription factor families, GRAS proteins are involved in numerous regulatory processes, especially plant growth and development. However, they have not been systematically analyzed in Brachypodium distachyon, a new model grass. RESULTS: In this study, 48 BdGRAS genes were identified. Duplicated genes account for 41.7% of them and contribute to the expansion of this gene family. 33, 39, 35 and 35 BdGRAS genes were identified by synteny with their orthologs in rice, sorghum, maize and wheat genome, respectively, indicating close relationships among these species. Based on their phylogenic relationships to GRAS genes in rice and maize, BdGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar protein sequences, conserved motifs and gene structures, suggesting possible conserved functions. Although expression variation is high, some BdGRAS genes are tissue-specific, phytohormones- or abiotic stresses-responsive, and they may play key roles in development, signal transduction pathways and stress responses. In addition, DELLA genes BdSLR1 and BdSLRL1 were functionally characterized to play a role in plant growth via the GA signal pathway, consistent with GO annotations and KEGG pathway analyses. CONCLUSIONS: Systematic analyses of BdGRAS genes indicated that members of the same subfamily may play similar roles. This was supported by the conserved functions of BdSLR1 and BdSLRL1 in GA pathway. These results laid a foundation for further functional elucidation of BdGRAS genes, especially, BdSLR1 and BdSLRL1.


Asunto(s)
Brachypodium/genética , Genómica , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Secuencia de Aminoácidos , Brachypodium/crecimiento & desarrollo , Brachypodium/metabolismo , Secuencia Conservada/genética , Duplicación de Gen , Regulación de la Expresión Génica de las Plantas , Genoma de Planta/genética , Motivos de Nucleótidos , Filogenia , Proteínas de Plantas/química , Sintenía , Factores de Transcripción/química
6.
Biochim Biophys Acta Gene Regul Mech ; 1862(9): 194408, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31382053

RESUMEN

In Saccharomyces cerevisiae, Core Factor (CF) is a key evolutionarily conserved transcription initiation factor that helps recruit RNA polymerase I (Pol I) to the ribosomal DNA (rDNA) promoter. Upregulated Pol I transcription has been linked to many cancers, and targeting Pol I is an attractive and emerging anti-cancer strategy. Using yeast as a model system, we characterized how CF binds to the Pol I promoter by electrophoretic mobility shift assays (EMSA). Synthetic DNA competitors along with anti-tumor drugs and nucleic acid stains that act as DNA groove blockers were used to discover the binding preference of yeast CF. Our results show that CF employs a unique binding mechanism where it prefers the GC-rich minor groove within the rDNA promoter. In addition, we show that yeast CF is able to bind to the human rDNA promoter sequence that is divergent in DNA sequence and demonstrate CF sensitivity to the human specific Pol I inhibitor, CX-5461. Finally, we show that the human Core Promoter Element (CPE) can functionally replace the yeast Core Element (CE) in vivo when aligned by conserved DNA structural features rather than DNA sequence. Together, these findings suggest that the yeast CF and the human ortholog Selectivity Factor 1 (SL1) use an evolutionarily conserved, structure-based mechanism to target DNA. Their shared mechanism may offer a new avenue in using yeast to explore current and future Pol I anti-cancer compounds.


Asunto(s)
ADN Ribosómico/genética , ARN Polimerasa I/genética , Factores de Transcripción/genética , Transcripción Genética , Benzotiazoles/farmacología , Secuencia Conservada/genética , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/genética , Ensayo de Cambio de Movilidad Electroforética , Humanos , Naftiridinas/farmacología , Conformación de Ácido Nucleico/efectos de los fármacos , Regiones Promotoras Genéticas/genética , ARN Polimerasa I/química , Saccharomyces cerevisiae/genética , Factores de Transcripción/química
7.
BMC Plant Biol ; 19(1): 329, 2019 Jul 23.
Artículo en Inglés | MEDLINE | ID: mdl-31337346

RESUMEN

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.


Asunto(s)
Gossypium/genética , Reguladores del Crecimiento de las Plantas/fisiología , Proteínas de Plantas/genética , Dedos de Zinc/genética , Brasinoesteroides/metabolismo , Mapeo Cromosómico , Secuencia Conservada/genética , Giberelinas/fisiología , Gossypium/fisiología , Ácidos Indolacéticos/metabolismo , Filogenia , Proteínas de Plantas/fisiología , Reacción en Cadena de la Polimerasa , Alineación de Secuencia , Transcriptoma , Dedos de Zinc/fisiología
8.
BMC Genomics ; 20(1): 575, 2019 Jul 11.
Artículo en Inglés | MEDLINE | ID: mdl-31296158

RESUMEN

BACKGROUND: Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regulatory Component of ABA Receptor (RCAR) (hereafter referred to as PYLs) has been identified as the ABA receptors. The PYL family members have been well studied in many plants. However, the members of PYL family have not been systematically identified at genome level in cultivated tobacco (Nicotiana tabacum) and its two ancestors. In this study, the phylogenic relationships, chromosomal distribution, gene structures, conserved motifs/regions, and expression profiles of NtPYLs were analyzed. RESULTS: We identified 29, 11, 16 PYLs in the genomes of allotetraploid N. tabacum, and its two diploid ancestors N. tomentosiformis and N. sylvestris, respectively. The phylogenetic analysis revealed that NtPYLs can be divided into three subfamilies, and each NtPYL has one counterpart in N. sylvestris or N. tomentosiformis. Based on microarray analysis of NtPYL transcripts, four NtPYLs (from subfamily II, III), and five NtPYLs (from subfamily I) are highlighted as potential candidates for further functional characterization in N. tabacum seed development, response to ABA, and germination, and resistance to abiotic stresses, respectively. Interestingly, the expression profiles of members in the same NtPYL subfamily showed somehow similar patterns in tissues at different developmental stages and in leaves of seedlings under drought stress, suggesting particular NtPYLs might have multiple functions in both plant development and drought stress response. CONCLUSIONS: NtPYLs are highlighted for important functions in seed development, germination and response to ABA, and particular in drought tolerance. This work will not only shed light on the PYL family in tobacco, but also provides some valuable information for functional characterization of ABA receptors in N. tabacum.


Asunto(s)
Ácido Abscísico/metabolismo , Sequías , Evolución Molecular , Genómica , Proteínas de Plantas/genética , Estrés Fisiológico/genética , Tabaco/fisiología , Arabidopsis/genética , Secuencia de Bases , Cromosomas de las Plantas/genética , Secuencia Conservada/genética , Regulación de la Expresión Génica de las Plantas , Filogenia , Proteínas de Plantas/metabolismo , Soja/genética , Tabaco/genética , Tabaco/crecimiento & desarrollo
9.
Mar Drugs ; 17(8)2019 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-31344776

RESUMEN

Conus ateralbus is a cone snail endemic to the west side of the island of Sal, in the Cabo Verde Archipelago off West Africa. We describe the isolation and characterization of the first bioactive peptide from the venom of this species. This 30AA venom peptide is named conotoxin AtVIA (δ-conotoxin-like). An excitatory activity was manifested by the peptide on a majority of mouse lumbar dorsal root ganglion neurons. An analog of AtVIA with conservative changes on three amino acid residues at the C-terminal region was synthesized and this analog produced an identical effect on the mouse neurons. AtVIA has homology with δ-conotoxins from other worm-hunters, which include conserved sequence elements that are shared with δ-conotoxins from fish-hunting Conus. In contrast, there is no comparable sequence similarity with δ-conotoxins from the venoms of molluscivorous Conus species. A rationale for the potential presence of δ-conotoxins, that are potent in vertebrate systems in two different lineages of worm-hunting cone snails, is discussed.


Asunto(s)
Conotoxinas/química , Caracol Conus/química , Aminoácidos/genética , Animales , Cabo Verde , Conotoxinas/farmacocinética , Secuencia Conservada/genética , Femenino , Ganglios Espinales/efectos de los fármacos , Masculino , Ratones , Ratones Endogámicos C57BL , Neuronas/efectos de los fármacos , Péptidos/química , Péptidos/genética , Péptidos/farmacocinética , Filogenia
10.
Eur J Med Res ; 24(1): 22, 2019 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-31269974

RESUMEN

BACKGROUND: This study focuses on the identification of conserved genes involved in myocardial infarction (MI), and then analyzed the differentially expressed genes (DEGs) between the incident and recurrent events to identify MI-recurrent biomarkers. METHODS: Gene expression data of MI peripheral blood were downloaded from GSE97320 and GSE66360 datasets. We identified the common DEGs in these two datasets by functional enrichment analysis and protein-protein interaction (PPI) network analysis. GSE48060 was further analyzed to validate the conserved genes in MI and to compare the DEGs between the incident and recurrent MI. RESULTS: A total of 477 conserved genes were identified in the comparison between MI and control. Protein-protein interaction (PPI) network showed hub genes, such as MAPK14, STAT3, and MAPKAPK2. Part of those conserved genes was validated in the analysis of GSE48060. The DEGs in the incident and recurrent MI showed significant differences, including RNASE2 and A2M-AS1 as the potential biomarkers of MI recurrence. CONCLUSIONS: The conserved genes in the pathogenesis of MI were identified, benefit for target therapy. Meanwhile, some specific genes may be used as markers for the prediction of recurrent MI.


Asunto(s)
Predisposición Genética a la Enfermedad , Infarto del Miocardio/genética , Estudios de Casos y Controles , Secuencia Conservada/genética , Bases de Datos Genéticas , Perfilación de la Expresión Génica , Ontología de Genes , Redes Reguladoras de Genes , Humanos , Mapeo de Interacción de Proteínas , Reproducibilidad de los Resultados
11.
Genes (Basel) ; 10(7)2019 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-31261747

RESUMEN

The class Hematozoa encompasses several clinically important genera, including Plasmodium, whose members cause the major life-threating disease malaria. Hence, a good understanding of the interrelationships of organisms from this class and reliable means for distinguishing them are of much importance. This study reports comprehensive phylogenetic and comparative analyses on protein sequences on the genomes of 28 hematozoa species to understand their interrelationships. In addition to phylogenetic trees based on two large datasets of protein sequences, detailed comparative analyses were carried out on the genomes of hematozoa species to identify novel molecular synapomorphies consisting of conserved signature indels (CSIs) in protein sequences. These studies have identified 79 CSIs that are exclusively present in specific groups of Hematozoa/Plasmodium species, also supported by phylogenetic analysis, providing reliable means for the identification of these species groups and understanding their interrelationships. Of these CSIs, six CSIs are specifically shared by all hematozoa species, two CSIs serve to distinguish members of the order Piroplasmida, five CSIs are uniquely found in all Piroplasmida species except B. microti and two CSIs are specific for the genus Theileria. Additionally, we also describe 23 CSIs that are exclusively present in all genome-sequenced Plasmodium species and two, nine, ten and eight CSIs which are specific for members of the Plasmodium subgenera Haemamoeba, Laverania, Vinckeia and Plasmodium (excluding P. ovale and P. malariae), respectively. Additionally, our work has identified several CSIs that support species relationships which are not evident from phylogenetic analysis. Of these CSIs, one CSI supports the ancestral nature of the avian-Plasmodium species in comparison to the mammalian-infecting groups of Plasmodium species, four CSIs strongly support a specific relationship of species between the subgenera Plasmodium and Vinckeia and three CSIs each that reliably group P. malariae with members of the subgenus Plasmodium and P. ovale within the subgenus Vinckeia, respectively. These results provide a reliable framework for understanding the evolutionary relationships among the Plasmodium/Piroplasmida species. Further, in view of the exclusivity of the described molecular markers for the indicated groups of hematozoa species, particularly large numbers of unique characteristics that are specific for all Plasmodium species, they provide important molecular tools for biochemical/genetic studies and for developing novel diagnostics and therapeutics for these organisms.


Asunto(s)
Piroplasmida/clasificación , Plasmodium/clasificación , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Evolución Biológica , Secuencia Conservada/genética , Mutación INDEL , Filogenia , Piroplasmida/genética , Plasmodium/genética , Plasmodium malariae/genética , Plasmodium ovale/genética , Theileria/genética
12.
Acta Crystallogr F Struct Biol Commun ; 75(Pt 7): 507-514, 2019 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-31282871

RESUMEN

The crystal structure is reported of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida, a possible drug target to combat tetracycline resistance, in complex with flavin adenine dinucleotide (FAD). The structure was refined at 2.2 Šresolution with four polypeptide chains in the asymmetric unit. Based on the results of pairwise structure alignments, PobA from P. putida is structurally very similar to PobA from P. fluorescens and from P. aeruginosa. Key residues in the FAD-binding and substrate-binding sites of PobA are highly conserved spatially across the proteins from all three species. Additionally, the structure was compared with two enzymes from the broader class of oxygenases: 2-hydroxybiphenyl 3-monooxygenase (HbpA) from P. nitroreducens and 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) from Mesorhizobium japonicum. Despite having only 14% similarity in their primary sequences, pairwise structure alignments of PobA from P. putida with HbpA from P. nitroreducens and MHPCO from M. japonicum revealed local similarities between these structures. Key secondary-structure elements important for catalysis, such as the ßαß fold, ß-sheet wall and α12 helix, are conserved across this expanded class of oxygenases.


Asunto(s)
4-Hidroxibenzoato-3-Monooxigenasa/química , Proteínas Bacterianas/química , Pseudomonas putida/enzimología , Homología Estructural de Proteína , Secuencia de Aminoácidos , Sitios de Unión , Secuencia Conservada/genética , Cristalización , Dominios Proteicos
13.
BMC Genomics ; 20(1): 615, 2019 Jul 29.
Artículo en Inglés | MEDLINE | ID: mdl-31357934

RESUMEN

BACKGROUND: Heavy metal ATPases (HMAs) are responsible for Cd translocation and play a primary role in Cd detoxification in various plant species. However, the characteristics of HMAs and the regulatory mechanisms between HMAs and microRNAs in wheat (Triticum aestivum L) remain unknown. RESULTS: By comparative microRNA and transcriptome analysis, a total three known and 19 novel differentially expressed microRNAs (DEMs) and 1561 differentially expressed genes (DEGs) were found in L17 after Cd treatment. In H17, by contrast, 12 known and 57 novel DEMs, and only 297 Cd-induced DEGs were found. Functional enrichments of DEMs and DEGs indicate how genotype-specific biological processes responded to Cd stress. Processes found to be involved in microRNAs-associated Cd response include: ubiquitin mediated proteolysis, tyrosine metabolism, and carbon fixation pathways and thiamine metabolism. For the mRNA response, categories including terpenoid backbone biosynthesis and phenylalanine metabolism, and photosynthesis - antenna proteins and ABC transporters were enriched. Moreover, we identified 32 TaHMA genes in wheat. Phylogenetic trees, chromosomal locations, conserved motifs and expression levels in different tissues and roots under Cd stress are presented. Finally, we infer a microRNA-TaHMAs expression network, indicating that miRNAs can regulate TaHMAs. CONCLUSION: Our findings suggest that microRNAs play important role in wheat under Cd stress through regulation of targets such as TaHMA2;1. Identification of these targets will be useful for screening and breeding low-Cd accumulation wheat lines.


Asunto(s)
Cadmio/toxicidad , Genómica , Genotipo , MicroARNs/genética , Transcriptoma/efectos de los fármacos , Triticum/efectos de los fármacos , Triticum/genética , Secuencia Conservada/genética , Motivos de Nucleótidos/genética , Especificidad de Órganos , ARN Mensajero/genética , Contaminantes del Suelo/toxicidad , Estrés Fisiológico/efectos de los fármacos , Transcripción Genética/efectos de los fármacos , Triticum/fisiología
14.
PLoS Comput Biol ; 15(6): e1007056, 2019 06.
Artículo en Inglés | MEDLINE | ID: mdl-31170145

RESUMEN

Developing HIV-1 vaccines that trigger broadly neutralizing antibodies (bnAbs) is a priority as bnAbs are considered key to elicitation of a protective immune response. To investigate whether the breadth of a neutralizing antibody (nAb) depended on the conservation of its epitope among circulating viruses, we examined Antibody:Envelope (Ab:Env) interactions and worldwide Env diversity. We found that sites corresponding to bnAb epitopes were as variable as other accessible, non-hypervariable Env sites (p = 0.50, Mann-Whitney U-test) with no significant relationship between epitope conservation and neutralization breadth (Spearman's ρ = -0.44, adjusted p = 0.079). However, when accounting for key sites in the Ab:Env interaction, we showed that the broadest bnAbs targeted more conserved epitopes (Spearman's ρ = -0.70, adjusted p = 5.0e-5). Neutralization breadth did not stem from the overall conservation of Ab epitopes but depended instead on the conservation of key sites of the Ab:Env interaction, revealing a mechanistic basis for neutralization breadth that could be exploited for vaccine design.


Asunto(s)
Anticuerpos Neutralizantes , Secuencia Conservada , Anticuerpos Anti-VIH , Vacunas contra el SIDA , Anticuerpos Neutralizantes/genética , Anticuerpos Neutralizantes/inmunología , Biología Computacional , Secuencia Conservada/genética , Secuencia Conservada/inmunología , Epítopos/genética , Epítopos/inmunología , Anticuerpos Anti-VIH/genética , Anticuerpos Anti-VIH/inmunología , Simulación de Dinámica Molecular , Productos del Gen env del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen env del Virus de la Inmunodeficiencia Humana/inmunología
15.
Cells ; 8(6)2019 05 29.
Artículo en Inglés | MEDLINE | ID: mdl-31146469

RESUMEN

: The accumulation of lignin in fruit has a significant negative impact on the quality of fruit-producing trees, and in particular the lignin formation stimulates the development of stone cells in pear fruit. Reactive oxygen species (ROS) are essential for lignin polymerization. However, knowledge of the RBOH family, a key enzyme in ROS metabolism, remains unknown in most fruit trees. In this study, a total of 40 RBOHs were identified from five fruit-producing trees (Pyrus bretschneideri, Prunus persica, Citrus sinensis, Vitis vinifera, and Prunus mume), and 10 of these sequences came from Pyrus bretschneideri. Multiple sequence alignments revealed that all 10 PbRBOHs contained the NADPH_Ox domain and the six alpha-helical transmembrane domains (TM-I to TM-VI). Chromosome localization and interspecies phylogenetic tree analysis showed that 10 PbRBOHs irregularly distributed on 8 chromosomes and 3 PbRBOHs (PbRBOHA, PbRBOHB, and PbRBOHD) are closely related to known lignification-related RBOHs. Furthermore, hormone response pattern analysis showed that the transcription of PbRBOHs is regulated by SA, ABA and MeJA. Reverse transcription-quantitative real-time polymerase chain reaction (qRT-PCR) and transcriptome sequencing analysis showed that PbRBOHA, PbRBOHB, and PbRBOHD accumulated high transcript abundance in pear fruit, and the transcriptional trends of PbRBOHA and PbRBOHD was consistent with the change of stone cell content during fruit development. In addition, subcellular localization revealed that PbRBOHA and PbRBOHD are distributed on the plasma membrane. Combining the changes of apoplastic superoxide (O2.-) content and spatio-temporal expression analysis, these results indicate that PbRBOHA and PbRBOHD, which are candidate genes, may play an important role in ROS metabolism during the lignification of pear stone cells. This study not only provided insight into the molecular characteristics of the RBOH family in fruit-producing trees, but also lays the foundation for studying the role of ROS in plant lignification.


Asunto(s)
Simulación por Computador , Frutas/genética , Genes de Plantas , Lignina/metabolismo , Familia de Multigenes , NADPH Oxidasas/genética , Pyrus/enzimología , Pyrus/genética , Secuencia de Aminoácidos , Cromosomas de las Plantas/genética , Secuencia Conservada/genética , Exones/genética , Frutas/efectos de los fármacos , Duplicación de Gen , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Tamaño del Genoma , Intrones/genética , NADPH Oxidasas/química , NADPH Oxidasas/metabolismo , Motivos de Nucleótidos/genética , Especificidad de Órganos/efectos de los fármacos , Especificidad de Órganos/genética , Filogenia , Reguladores del Crecimiento de las Plantas/farmacología , Regiones Promotoras Genéticas/genética , Pyrus/efectos de los fármacos , Sintenía/genética , Árboles/enzimología , Árboles/genética
16.
Cells ; 8(6)2019 06 21.
Artículo en Inglés | MEDLINE | ID: mdl-31234415

RESUMEN

Single nucleotide polymorphisms located in 5' untranslated regions (5'UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5'UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5'UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5'UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5'UTRs, such as GC content variation, hairpin structure conservation or 5'UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.


Asunto(s)
Regiones no Traducidas 5'/genética , Transportador 1 de Casete de Unión a ATP/genética , Vertebrados/genética , Transportador 1 de Casete de Unión a ATP/química , Secuencia de Aminoácidos , Animales , Composición de Base/genética , Secuencia de Bases , Secuencia Conservada/genética , Elementos de Facilitación Genéticos/genética , Humanos , Intrones/genética , Mamíferos/genética , Anotación de Secuencia Molecular , Conformación de Ácido Nucleico , Motivos de Nucleótidos/genética , Sistemas de Lectura Abierta/genética , Filogenia , Empalme del ARN/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo
17.
Genes (Basel) ; 10(6)2019 06 21.
Artículo en Inglés | MEDLINE | ID: mdl-31234429

RESUMEN

Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.


Asunto(s)
Gossypium/genética , Peroxidasas/genética , Filogenia , Proteínas de Plantas/genética , Secuencia de Aminoácidos/genética , Cromosomas de las Plantas/genética , Secuencia Conservada/genética , Duplicación de Gen/genética , Regulación de la Expresión Génica de las Plantas , Genoma de Planta/genética , Gossypium/enzimología , Familia de Multigenes/genética , Estrés Fisiológico/genética , Tetraploidía
18.
Nat Commun ; 10(1): 2682, 2019 06 18.
Artículo en Inglés | MEDLINE | ID: mdl-31213602

RESUMEN

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.


Asunto(s)
Evolución Molecular , Proteómica/métodos , Motivos de Unión al ARN/genética , Proteínas de Unión al ARN/genética , ARN/metabolismo , Secuencia de Aminoácidos/genética , Animales , Línea Celular , Secuencia Conservada/genética , Reactivos de Enlaces Cruzados/química , Drosophila , Humanos , Péptidos/química , Péptidos/genética , Unión Proteica/genética , Proteoma/genética , ARN/química , Proteínas de Unión al ARN/química
19.
Genes (Basel) ; 10(6)2019 06 12.
Artículo en Inglés | MEDLINE | ID: mdl-31210171

RESUMEN

Plant fatty acid desaturases (FADs) catalyze the desaturation of fatty acids in various forms and play important roles in regulating fatty acid composition and maintaining membrane fluidity under temperature stress. A total of 30 FADs were identified from a maize genome, including 13 soluble and 17 membrane-bound FADs, which were further classified into two and five sub-groups, respectively, via phylogenetic analysis. Although there is no evolutionary relationship between the soluble and the membrane-bound FADs, they all harbor a highly conserved FA_desaturase domain, and the types and the distributions of conserved motifs are similar within each sub-group. The transcriptome analysis revealed that genes encoding FADs exhibited different expression profiles under cold and heat stresses. The expression of ZmFAD2.1&2.2, ZmFAD7, and ZmSLD1&3 were significantly up-regulated under cold stress; moreover, the expression of ZmFAD2.1&2.3 and ZmSLD1&3 were obviously down-regulated under heat stress. The co-expression analysis demonstrated close correlation among the transcription factors and the significant responsive FAD genes under cold or heat stress. This study helps to understand the roles of plant FADs in temperature stress responses.


Asunto(s)
Respuesta al Choque por Frío/genética , Ácido Graso Desaturasas/genética , Respuesta al Choque Térmico/genética , Zea mays/genética , Cromosomas de las Plantas , Frío , Secuencia Conservada/genética , Ácido Graso Desaturasas/clasificación , Duplicación de Gen , Regulación de la Expresión Génica de las Plantas , Calor , Filogenia , Transcriptoma/genética , Zea mays/crecimiento & desarrollo
20.
Mol Phylogenet Evol ; 138: 31-42, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31125660

RESUMEN

The Tropical Andes contains exceptionally high diversity, much of it arising within the Quaternary period. The complex geology of the Andes and paleoclimate fluctuations within the Quaternary suggest complex speciation scenarios. This, in turn, has contributed to idiosyncratic speciation modes among shallowly diverged Amazonian taxa. Many relationships among these taxa remain poorly resolved. Here we use a sequence capture approach, ultraconserved elements (UCEs), to address the phylogenetic relationships among three recently diverged Peruvian Ameerega poison frog species (A. cainarachi, A. petersi, and A. smaragdina; family Dendrobatidae) and explore a possible mode of speciation in this group. We assess concordance among concatenated phylogenetic tree inference, gene-tree based species tree inference, SNP-based species tree inference, and Bayes factor lineage delimitation to resolve species boundaries. We complement these analyses with assessments of call divergence to address the presence of a prezygotic reproductive barrier. Additionally, we further explore the phylogeographic history of these species of Ameerega with demographic inference, considering evidence for admixture and population expansions. Our results support the synonymy of A. smaragdina as a junior synonym of A. petersi and we find that speciation in this group is characterized by admixture and signatures of a population bottleneck followed by expansion. We invoke the disturbance-vicariance hypothesis to explain the observed patterns and call for more, detailed investigations of in-situ speciation in the Tropical Andes.


Asunto(s)
Anuros/clasificación , Anuros/genética , Especiación Genética , Filogeografía , Animales , Teorema de Bayes , Secuencia Conservada/genética , Análisis Discriminante , Flujo Génico , Variación Genética , Funciones de Verosimilitud , Filogenia , Análisis de Componente Principal , Vocalización Animal/fisiología
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