Identificación y filogenia de la familia de proteínas tipo receptoras en tomate

The receptor-like proteins (RLPs) play multiple roles in development and defense. In the current work 75 RLPs were identified in tomato (Solanum lycopersicum L.) using iterative BLAST searches and domain prediction. A phylogenetic tree including all the identified RLPs from tomato and some functionally characterized RLPs from other species was built to identify their putative homologues in tomato. We first tested whether C3-F-based phylogeny was a good indicator of functional relation between related proteins of different species. Indeed, the functionally characterized CLAVATA2 (CLV2), the maize ortholog FASCIATED EAR2 (FEA2) and a putative tomato CLV2 described in Uniprot clustered together, which validates the approach. Using this approach Solyc12g042760.1.1 was identified as the putative tomato homologue of TOO MANY MOUTHS (TMM). It was shown that proteins in the same cluster of the phylogenetic tree share functional relations since several clusters of functionally related proteins i.e. the Ve cluster, the Cf cluster, and the Eix clade were formed. Keywords: phylogeny, receptors, RLP, tomatoLas proteínas tipo receptoras juegan múltiples papeles en procesos de desarrollo y defensa. En este trabajo se identificaron 75 RLPs en tomate (Solanum lycopersicum L.) mediante el empleo de búsquedas BLAST iterativas y predicción de dominios. Se construyó un árbol filogenético que incluyó todas las RLPs identificadas en tomate y otras proteínas de este tipo caracterizadas funcionalmente en otras especies. Primero se comprobó si la filogenia basada en la región C3-F constituía un buen indicador de la relación funcional entre proteínas relacionadas de diferentes especies. Se comprobó que, de hecho, las proteínas CLAVATA2 y su ortólogo en maíz FEA2 (FASCIATED EAR2) y la probable CLAVATA2 de tomate descrita en Uniprot se agruparon en una misma rama, lo que valida el enfoque. Con este procedimiento se identificó Solyc12g042760.1.1 como el probable homólogo en tomate del gen TMM. Se demostró que las proteínas en el mismo cluster en el árbol comparten relaciones funcionales, pues se formaron varios cluster de proteínas relacionadas funcionalmente como por ejemplo el cluster Ve, el cluster Cf, y la clada Eix. Palabras clave: filogenia, receptores, RLP, tomat

REPORTE CORTO/SHORT REPORT - MOLECULES MODULATING IMMUNE/INFLAMMATORY RESPONSES, DESIGN AND DEVELOPMENT OF POTENTIAL THERAPEUTICS

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Dataset on protein composition of a human plasma sub-proteome able to modulate the Dengue 2 virus infection in Huh 7.5 cells

The four serotypes of dengue virus (DENV1-4) are the causal agents of the emerging disease Dengue Fever and its severe forms. DENV is inoculated into human blood through a mosquito bite. Thus, plasma is an important media for DENV dissemination in infected persons and several important interactions should take place for the virus with human plasma proteins that strongly influence or may determine the course of the infection. This dataset contains 239 proteins identified in the elution fractions of human plasma subjected to DE-52 anion exchange chromatography. Data on DENV2 infection of Huh 7.5 cells in presence of the human plasma fraction is also presented. Keywords: Human plasma, Anion exchange chromatography, Dengue viru

Molecular Docking Study of Flavonoids to Block the Aryl Hydrocarbon Receptor

Anti-HIF flavonoids have been described for their antitumor activity by interfering with a presumed antioxidant mechanism through direct and indirect ways of overexpression of the hypoxia inducible factor (HIF-1α). The aryl hydrocarbon receptor (AhR) is a protein homologous to HIF-1α and is overexpressed in smoking patients suffering from lung and breast cancer. The interaction of thirteen flavonoids with the AhR has been evaluated by molecular docking. The AhR:ARNT model obtained by SwissModel has been used for docking with the MOE 2019.01 program, as well as several servers for the determination of protein–protein interactions and alanine mutations. Different interaction sites were identified for blocking the AhR: functional ARNT, the interface between the bHLH and PAS-A domains, being important. The blocking capacity to AhR:ARNT proved to be between 50 and 60% for flavonoids 4′,7-dihydroxy-flavone, fisetin, luteolin, 5-hydroxy-2-(4′-hydroxy)-7-methoxy-flavonone, flavone, apigenin, galangin and 7-hydroxy-5-methoxy-flavonone. None of the flavonoids evaluated interact with the PAS-B domain (AhR active site). All the studied flavonoids interact with AhR, except flavone, and with ARNT except the compounds 3,7-dihydroxy-flavone and kaempferol. The best flavonoid for blocking the formation of the AhR:ARNT heterodimer proved to be fisetin, which is found in food sources such as strawberries, apples and grapes, and has shown the ability to reduce pro-cancer inflammatory markers in colorectal cancer patients and lung cancer

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report

The workshop "Bioinformatics for Biotechnology Applications (HavanaBioinfo 2012)", held December 8-11, 2012 in Havana, aimed at exploring new bioinformatics tools and approaches for large-scale proteomics, genomics and chemoinformatics. Major conclusions of the workshop include the following: (i) development of new applications and bioinformatics tools for proteomic repository analysis is crucial; current proteomic repositories contain enough data (spectra/identifications) that can be used to increase the annotations in protein databases and to generate new tools for protein identification; (ii) spectral libraries, de novo sequencing and database search tools should be combined to increase the number of protein identifications; (iii) protein probabilities and FDR are not yet sufficiently mature; (iv) computational proteomics software needs to become more intuitive; and at the same time appropriate education and training should be provided to help in the efficient exchange of knowledge between mass spectrometrists and experimental biologists and bioinformaticians in order to increase their bioinforrnatics background, especially statistics knowledge. (c) 2013 Elsevier B.V. All rights reserved