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1.
PLoS One ; 15(1): e0227713, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31929605

RESUMO

In wheat, adult plant resistance (APR) to leaf rust (Puccinia triticina), is effective in restricting pathogen growth and provides durable resistance against a wide range of virulent forms of P. triticina. Despite the importance, there is limited knowledge on the molecular basis of this type of resistance. We isolated and characterized the wall-associated kinase encoding gene in wheat, and assigned it as TaWAK6. Localization of TaWAK6 homeologs in A and B wheat subgenomes was consistent with the presence of the gene's orthologs in T. urartu (AA) and T. dicoccoides (AABB) and with the absence of its orthologs in Aegilops tauschii (DD). Overexpression of TaWAK6 did not change the wheat phenotype, nor did it affect seedling resistance. However, the adult plants overexpressing TaWAK6 showed that important parameters of APR were significantly elevated. Infection types scored on the first (flag), second and third leaves indicated elevated resistance, which significantly correlated with expression of TaWAK6. Analysis of plant-pathogen interactions showed a lower number of uredinia and higher rates of necrosis at the infection sites and this was associated with smaller size of uredinia and a longer latent period. The results indicated a role of TaWAK6 in quantitative partial resistance similar to APR in wheat. It is proposed that TaWAK6, which is a non-arginine-aspartate (non-RD) kinase, represents a novel class of quantitative immune receptors in monocots.


Assuntos
Basidiomycota/fisiologia , Doenças das Plantas/genética , Proteínas de Plantas/genética , Proteínas Quinases/genética , Triticum/genética , Triticum/microbiologia , Resistência à Doença , Interações Hospedeiro-Patógeno , Doenças das Plantas/microbiologia , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/microbiologia , Triticum/enzimologia , Regulação para Cima
2.
Genome Biol ; 20(1): 144, 2019 07 25.
Artigo em Inglês | MEDLINE | ID: mdl-31345254

RESUMO

BACKGROUND: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. RESULTS: Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. CONCLUSION: The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.


Assuntos
Análise de Sequência , Benchmarking , Transferência Genética Horizontal , Internet , Filogenia , Sequências Reguladoras de Ácido Nucleico , Alinhamento de Sequência , Análise de Sequência de Proteína , Software
3.
PLoS One ; 13(6): e0199364, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29920545

RESUMO

GLYCOGEN SYNTHASE KINASE3/Shaggy-like kinases (GSKs) represent a highly conserved group of proteins found in all eukaryotes. In plants they are encoded by multigene families and integrate signaling of brassinosteroids, auxin and abscisic acid in wide range of physiological and developmental processes with a strong impact on plant responses to environmental and biotic factors. Based on comprehensively studied structures of 10 Arabidopsis thaliana GSK genes and encoded proteins we report identification and phylogenetic reconstruction of 7 transcriptionally active GSK genes in barley. We re-evaluated annotation of the GSK genes in the current barley genome (Hv_IBSC_PGSB_v2) and provided data that a single gene annotated in the previous barley genome ensemble should be retained in the current one. The novel structure of another GSK, predicted in Hv_IBSC_PGSB_v2 to encode both GSK and amine oxidase domains, was proposed and experimentally confirmed based on the syntenic region in Brachypodium distachyon. The genes were assigned to 4 groups based on their encoded amino acid sequences and protein kinase domains. The analysis confirmed high level of conservation of functional protein domains and motifs among plant GSKs and the identified barley orthologs. Each of the seven identified HvGSK genes was expressed indicating semi-constitutive regulation in all tested organs and developmental stages. Regulation patterns of GSKs from the indicated groups showed a shift in organ-preferential expression in A. thaliana and barley illustrating diversification of biological roles of individual HvGSKs in different plant species.


Assuntos
Glicogênio Sintase/genética , Hordeum/genética , Desenvolvimento Vegetal/genética , Transcriptoma/genética , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas/genética , Genoma de Planta , Hordeum/crescimento & desenvolvimento , Anotação de Sequência Molecular
4.
Plant Cell Physiol ; 59(1): e1, 2018 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-29145635

RESUMO

tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex (http://combio.pl/trex)-the first comprehensive data-driven online resource specifically dedicated to tRFs in the model plant Arabidopsis thaliana. The portal is based on verified Arabidopsis tRNA annotation and includes in-house-generated and publicly available small RNA sequencing experiments from various tissues, ecotypes, genotypes and stress conditions. The provided web-based tools are designed in a user-friendly manner and allow for seamless exploration of the data that are presented in the form of dynamic tables and cumulative coverage profiles. The tRex database is connected to external genomic and citation resources, which makes it a one-stop solution for Arabidopsis tRF-related research.


Assuntos
Arabidopsis/genética , Biologia Computacional/métodos , Bases de Dados Genéticas , RNA de Plantas/genética , RNA de Transferência/genética , Sequência de Bases , Internet , Conformação de Ácido Nucleico , RNA de Plantas/química , RNA de Transferência/química , Análise de Sequência de RNA/métodos , Homologia de Sequência do Ácido Nucleico
5.
Genome Biol ; 18(1): 186, 2017 10 03.
Artigo em Inglês | MEDLINE | ID: mdl-28974235

RESUMO

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.


Assuntos
Análise de Sequência/métodos , Algoritmos , Sequenciamento de Nucleotídeos em Larga Escala , Teoria da Informação , Alinhamento de Sequência , Homologia de Sequência , Software
6.
Methods Mol Biol ; 1640: 241-256, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28608348

RESUMO

WG/GW domains recruit ARGONAUTE (AGO) proteins to distinct silencing effector complexes using combinations of just two amino acids: tryptophan (W) and glycine (G), forming a wide arsenal of highly simplified interaction surfaces. These unstructured domains exhibit very low sequence identity and excessive length polymorphism, which makes identification of new AGO-binding proteins a challenging task as they escape detection with standard sequence comparison-based methods (e.g., BLAST, HMMER).In this chapter, we explain the use of tools for prediction of AGO-binding WG/GW domains in protein sequences. We also show how to computationally explore an up-to-date information about AGO-interacting proteins and discover new properties of WG/GW domains. Finally, we encourage readers to explore the game-like web application for in silico designing/modifying AGO-binding sequences as well as modeling mutagenesis experiments and predicting their potential effect on AGO-binding activity.


Assuntos
Proteínas Argonauta/metabolismo , Mapas de Interação de Proteínas , Proteínas/metabolismo , Proteômica/métodos , Software , Sequência de Aminoácidos , Animais , Arabidopsis/química , Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Proteínas Argonauta/química , Sítios de Ligação , Glicina/química , Glicina/metabolismo , Humanos , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Proteínas/química , Triptofano/química , Triptofano/metabolismo
7.
Bioinformatics ; 33(8): 1224-1226, 2017 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-28057683

RESUMO

Summary: ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1-2 percent points. Availability and Implementation: The service is available for free at http://www.combio.pl/orcan/ . Contact: wmk@amu.edu.pl. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Biologia Computacional/métodos , Internet , Análise de Sequência de Proteína/métodos , Homologia de Sequência de Aminoácidos , Software , Ontologia Genética , Domínios Proteicos , Leveduras/genética , Leveduras/metabolismo
8.
Drug Chem Toxicol ; 40(4): 470-483, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28049353

RESUMO

Nicotine may affect cell function by rearranging protein complexes. We aimed to determine nicotine-induced alterations of protein complexes in Caenorhabditis elegans (C. elegans) cells, thereby revealing links between nicotine exposure and protein complex modulation. We compared the proteomic alterations induced by low and high nicotine concentrations (0.01 mM and 1 mM) with the control (no nicotine) in vivo by using mass spectrometry (MS)-based techniques, specifically the cetyltrimethylammonium bromide (CTAB) discontinuous gel electrophoresis coupled with liquid chromatography (LC)-MS/MS and spectral counting. As a result, we identified dozens of C. elegans proteins that are present exclusively or in higher abundance in either nicotine-treated or untreated worms. Based on these results, we report a possible network that captures the key protein components of nicotine-induced protein complexes and speculate how the different protein modules relate to their distinct physiological roles. Using functional annotation of detected proteins, we hypothesize that the identified complexes can modulate the energy metabolism and level of oxidative stress. These proteins can also be involved in modulation of gene expression and may be crucial in Alzheimer's disease. The findings reported in our study reveal putative intracellular interactions of many proteins with the cytoskeleton and may contribute to the understanding of the mechanisms of nicotinic acetylcholine receptor (nAChR) signaling and trafficking in cells.


Assuntos
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/efeitos dos fármacos , Regulação da Expressão Gênica no Desenvolvimento/efeitos dos fármacos , Modelos Biológicos , Nicotina/toxicidade , Agonistas Nicotínicos/toxicidade , Estresse Oxidativo/efeitos dos fármacos , Animais , Caenorhabditis elegans/crescimento & desenvolvimento , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/química , Proteínas de Caenorhabditis elegans/genética , Biologia Computacional , Citoesqueleto/efeitos dos fármacos , Citoesqueleto/metabolismo , Metabolismo Energético/efeitos dos fármacos , Perfilação da Expressão Gênica , Redes Reguladoras de Genes/efeitos dos fármacos , Anotação de Sequência Molecular , Concentração Osmolar , Multimerização Proteica/efeitos dos fármacos , Transporte Proteico/efeitos dos fármacos , Proteômica/métodos , Receptores Nicotínicos/química , Receptores Nicotínicos/metabolismo , Transdução de Sinais/efeitos dos fármacos
9.
Nucleic Acids Res ; 44(D1): D180-3, 2016 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-26490961

RESUMO

Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces.


Assuntos
Bases de Dados de Ácidos Nucleicos , RNA Ribossômico 5S/química , RNA Ribossômico 5S/genética , Eucariotos/genética , Conformação de Ácido Nucleico , RNA Arqueal/química , RNA Arqueal/genética , RNA Bacteriano/química , RNA Bacteriano/genética
10.
BMC Plant Biol ; 15: 144, 2015 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-26141515

RESUMO

BACKGROUND: MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism. DESCRIPTION: The mirEX 2.0 web portal ( http://www.combio.pl/mirex ) provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time PCR and NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation (e.g., tooltips, exemplary videos and presentations). All data contained within the mirEX 2.0 database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page. CONCLUSIONS: The mirEX 2.0 portal provides the plant research community with easily accessible data and powerful tools for application in multi-conditioned analyses of miRNA expression from important plant species in different biological and developmental backgrounds.


Assuntos
Arabidopsis/genética , Bases de Dados de Ácidos Nucleicos/organização & administração , Hepatófitas/genética , Hordeum/genética , Internet , MicroRNAs/genética , RNA de Plantas/genética , Arabidopsis/metabolismo , Perfilação da Expressão Gênica , Hepatófitas/metabolismo , Hordeum/metabolismo , MicroRNAs/metabolismo , RNA de Plantas/metabolismo , Reação em Cadeia da Polimerase em Tempo Real
11.
RNA Biol ; 12(7): 761-70, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26106978

RESUMO

The GW182 proteins are a key component of the miRNA-dependent post-transcriptional silencing pathway in animals. They function as scaffold proteins to mediate the interaction of Argonaute (AGO)-containing complexes with cytoplasmic poly(A)-binding proteins (PABP) and PAN2-PAN3 and CCR4-NOT deadenylases. The AGO-GW182 complexes mediate silencing of the target mRNA through induction of translational repression and/or mRNA degradation. Although the GW182 proteins are a subject of extensive experimental research in the recent years, very little is known about their origin and evolution. Here, based on complex functional annotation and phylogenetic analyses, we reveal 448 members of the GW182 protein family from the earliest animals to humans. Our results indicate that a single-copy GW182/TNRC6C progenitor gene arose with the emergence of multicellularity and it multiplied in the last common ancestor of vertebrates in 2 rounds of whole genome duplication (WGD) resulting in 3 genes. Before the divergence of vertebrates, both the AGO- and CCR4-NOT-binding regions of GW182s showed significant acceleration in the accumulation of amino acid changes, suggesting functional adaptation toward higher specificity to the molecules of the silencing complex. We conclude that the silencing ability of the GW182 proteins improves with higher position in the taxonomic classification and increasing complexity of the organism. The first reconstruction of the molecular journey of GW182 proteins from the ancestral metazoan protein to the current mammalian configuration provides new insight into development of the miRNA-dependent post-transcriptional silencing pathway in animals.


Assuntos
Autoantígenos/metabolismo , Evolução Molecular , Interferência de RNA , Proteínas de Ligação a RNA/metabolismo , Animais , Autoantígenos/genética , Humanos , Invertebrados/genética , Invertebrados/metabolismo , Proteínas de Ligação a RNA/genética , Vertebrados/genética , Vertebrados/metabolismo
12.
Plant Mol Biol Report ; 33: 84-101, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25620837

RESUMO

The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mapping, and molecular cytogenetics, to localize and analyze L. angustifolius gene-rich regions (GRRs). A L. angustifolius genomic bacterial artificial chromosome (BAC) library was screened with short sequence repeat (SSR)-based probes. Selected BACs were fingerprinted and assembled into contigs. BAC-end sequence (BES) annotation allowed us to choose clones for sequencing, targeting GRRs. Additionally, BESs were aligned to the scaffolds of the genome sequence. The genetic map was supplemented with 35 BES-derived markers, distributed in 14 linkage groups and tagging 37 scaffolds. The identified GRRs had an average gene density of 19.6 genes/100 kb and physical-to-genetic distance ratios of 11 to 109 kb/cM. Physical and genetic mapping was supported by multi-BAC-fluorescence in situ hybridization (FISH), and five new linkage groups were assigned to the chromosomes. Syntenic links to the genome sequences of five legume species (Medicago truncatula, Glycine max, Lotus japonicus, Phaseolus vulgaris, and Cajanus cajan) were identified. The comparative mapping of the two largest lupin GRRs provides novel evidence for ancient duplications in all of the studied species. These regions are conserved among representatives of the main clades of Papilionoideae. Furthermore, despite the complex evolution of legumes, some segments of the nuclear genome were not substantially modified and retained their quasi-ancestral structures. Cytogenetic markers anchored in these regions constitute a platform for heterologous mapping of legume genomes.

13.
Bioinformatics ; 31(3): 332-9, 2015 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-25304778

RESUMO

MOTIVATION: Argonaute-interacting WG/GW proteins are characterized by the presence of repeated sequence motifs containing glycine (G) and tryptophan (W). The motifs seem to be remarkably adaptive to amino acid substitutions and their sequences show non-contiguity. Our previous approach to the detection of GW domains, based on scoring their gross amino acid composition, allowed annotation of several novel proteins involved in gene silencing. The accumulation of new experimental data and more advanced applications revealed some deficiency of the algorithm in prediction selectivity. Additionally, W-motifs, though critical in gene regulation, have not yet been annotated in any available online resources. RESULTS: We present an improved set of computational tools allowing efficient management and annotation of W-based motifs involved in gene silencing. The new prediction algorithms provide novel functionalities by annotation of the W-containing domains at the local sequence motif level rather than by overall compositional properties. This approach represents a significant improvement over the previous method in terms of prediction sensitivity and selectivity. Application of the algorithm allowed annotation of a comprehensive list of putative Argonaute-interacting proteins across eukaryotes. An in-depth characterization of the domains' properties indicates its intrinsic disordered character. In addition, we created a knowledge-based portal (whub) that provides access to tools and information on RNAi-related tryptophan-containing motifs. AVAILABILITY AND IMPLEMENTATION: The web portal and tools are freely available at http://www.comgen.pl/whub. CONTACT: wmk@amu.edu.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Algoritmos , Motivos de Aminoácidos/genética , Proteínas Argonauta/química , Proteínas Argonauta/metabolismo , Glicina/química , Ligação Proteica/genética , Sequências Repetitivas de Aminoácidos/genética , Triptofano/química , Proteínas Argonauta/genética , Estrutura Terciária de Proteína , Software
14.
Nucleic Acids Res ; 40(Database issue): D191-7, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22013167

RESUMO

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.


Assuntos
Arabidopsis/genética , Bases de Dados de Ácidos Nucleicos , MicroRNAs/metabolismo , RNA de Plantas/metabolismo , Mineração de Dados , Perfilação da Expressão Gênica , Internet , Software , Interface Usuário-Computador
15.
Bioinformatics ; 27(9): 1318-9, 2011 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-21385787

RESUMO

MOTIVATION: AGO(Argonaute)-binding domains, composed of repeated motifs, in which only binary combinations of tryptophan and glycine are conserved, bind AGO proteins and are essential during RNAi-mediated gene silencing. The amino acid sequence of this domain is extremely divergent and therefore very difficult to detect. Commonly used bioinformatic tools fail to identify tryptophan-glycine and/or glycine-tryptophan motifs (WG/GW) domains and currently there is no publicly available software which can detect these weakly conserved, but functional AGO-binding segments. RESULTS: Recently, we have developed an algorithm based on compositional analysis of the amino acid content of the domain. We have demonstrated that the algorithm can be successfully applied for the identification of the new WG/GW proteins in the Arabidopsis genome. Here we introduce Agos (Argonaute-binding domain screener), a novel universal web service for de novo identification of WG/GW domains in protein sequences. The web implementation of the algorithm contains several new features and enhancements: (i) one universal scoring matrix which allows identification of AGO-binding proteins in sequences representing all organisms; (ii) reduction of false positive predictions by improved selectivity of the algorithm; (iii) graphical interface to easily browse the prediction results; and (iv) the option to submit a DNA sequence which will be automatically translated in six frames before running the prediction algorithm. AVAILABILITY: Freely available at: http://bioinfo.amu.edu.pl/agos/.


Assuntos
Algoritmos , Motivos de Aminoácidos/genética , Proteínas de Arabidopsis/genética , Arabidopsis/genética , Proteínas Argonauta/genética , Internet , Sequência de Aminoácidos , Proteínas de Arabidopsis/metabolismo , Proteínas Argonauta/metabolismo , Sítios de Ligação , Dados de Sequência Molecular , Ligação Proteica/genética , Estrutura Terciária de Proteína/genética , Software
16.
Nucleic Acids Res ; 38(13): 4231-45, 2010 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-20338883

RESUMO

Domains in Arabidopsis proteins NRPE1 and SPT5-like, composed almost exclusively of repeated motifs in which only WG or GW sequences and an overall amino-acid preference are conserved, have been experimentally shown to bind multiple molecules of Argonaute (AGO) protein(s). Domain swapping between the WG/GW domains of NRPE1 and the human protein GW182 showed a conserved function. As classical sequence alignment methods are poorly-adapted to detect such weakly-conserved motifs, we have developed a tool to carry out a systematic analysis to identify genes potentially encoding AGO-binding GW/WG proteins. Here, we describe exhaustive analysis of the Arabidopsis genome for all regions potentially encoding proteins bearing WG/GW motifs and consider the possible role of some of them in AGO-dependent mechanisms. We identified 20 different candidate WG/GW genes, encoding proteins in which the predicted domains range from 92aa to 654aa. These mostly correspond to a limited number of families: RNA-binding proteins, transcription factors, glycine-rich proteins, translation initiation factors and known silencing-associated proteins such as SDE3. Recent studies have argued that the interaction between WG/GW-rich domains and AGO proteins is evolutionarily conserved. Here, we demonstrate by an in silico domain-swapping simulation between plant and mammalian WG/GW proteins that the biased amino-acid composition of the AGO-binding sites is conserved.


Assuntos
Proteínas de Arabidopsis/química , Arabidopsis/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Sítios de Ligação , Sequência Conservada , Genoma de Planta , Genômica , Dados de Sequência Molecular , Família Multigênica , Estrutura Terciária de Proteína
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