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Stylosanthes scabra is a scientifically orphaned legume found in the Brazilian Caatinga biome (a semi-arid environment). This work utilized omics approaches to investigate some ecophysiological aspects of stress tolerance/resistance in S. scabra, study its genomic landscape, and predict potential metabolic pathways. Considering its high-confidence conceptual proteome, 1694 (~2.6%) proteins were associated with resistance proteins, some of which were found in soybean QTL regions that confer resistance to Asian soybean rust. S. scabra was also found to be a potential source of terpenes, as biosynthetic gene clusters associated with terpene biosynthesis were identified in its genome. The analysis revealed that mobile elements comprised approximately 59% of the sequenced genome. In the remaining 41% of the sections, some of the 22,681 protein-coding gene families were categorized into two informational groups: those that were specific to S. scabra and those that expanded significantly compared to their immediate ancestor. Biological process enrichment analyses indicated that these gene families play fundamental roles in the adaptation of S. scabra to extreme environments. Additionally, phylogenomic analysis indicated a close evolutionary relationship between the genera Stylosanthes and Arachis. Finally, this study found a high number (57) of aquaporin-encoding loci in the S. scabra genome. RNA-Seq and qPCR data suggested that the PIP subfamily may play a key role in the species' adaptation to water deficit conditions. Overall, these results provide valuable insights into S. scabra biology and a wealth of gene/transcript information for future legume omics studies.
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Abstract Globodera pallida is a white potato cyst nematode present in the Andes, which causes huge losses to Peruvian farmers. An RNA-seq analysis allowed the identification of candidate genes that could mediate resistance against this pathogen. Two varieties, "María Huanca" (Solanum andigena) clone resistant (CIP 279142.12) and "Chimbina Colorada" (Solanum chaucha) (CIP 701013) clone susceptible to G. pallida, were used to identify differentially expressed genes. Total RNA from roots was extracted 72 hours post inoculation with second stage juveniles. Sequencing was done using the Illumina Hiseq 2500 platform. Reads were screened for quality issues and then mapped to the reference potato genome (clone DM1-3516 R44 v4.03). Here, we report 27717 and 27750 genes expressed in the resistant and susceptible variety respectively. The comparative analysis of expression identified 100 candidate genes. 91 genes were associated with resistance to G. pallida with Fold Change ≥ 2 (p <0.05). The remaining 9 R genes had Fold Change ≤ 1. We show differences in the expression of an NBS-LRR protein similar to Gro1-8, genes linked to late blight and TMV virus resistance.
Resumen Globodera pallida es un nemátodo formador de quistes. En la papa (Solanum tuberosum) ocasiona daños atrofiando las raíces. En los Andes peruanos ocasiona grandes pérdidas económicas a los agricultores. A través del análisis por RNA-seq, se identificaron genes candidatos que podrían mediar la resistencia contra este nemátodo. Dos variedades de papa: "María Huanca" (S. andigena) clon resistente (CIP 279142.12) y "Chimbina Colorada" (S. chaucha) clon susceptible (CIP 701013) a G. pallida, fueron utilizados para identificar genes expresados diferencialmente. Las raíces fueron inoculadas con G. pallida en segundo estadío juvenil (J2). El ARN total fue extraído a 72 horas post inoculación. El secuenciamiento fue realizado en plataforma Illumina HiSeq 2500. Las lecturas de buena calidad fueron mapeadas al genoma de referencia de S. tuberosum (clon DM1-3516 R44 v4.03). Reportamos 27717 y 27750 genes expresados en la variedad resistente y susceptible, respectivamente. El análisis comparativo identificó 100 genes candidatos, de ellos 91 genes fueron asociados con la resistencia a G. pallida (Fold Change ≥ 2 , p <0.05) y los 9 restantes con genes R ( Fold Change ≤ 1). En este último grupo se observaron diferencias en la expresión de genes NBS-LRR similar a Gro 1-8, genes relacionados a late blight y resistencia al Virus TMV.
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Glycoprotein-A repetitions predominant (GARP) is a transmembrane protein that is highly expressed in breast cancer. Its overexpression correlates with worse survival, and antibodies to GARP appear to play a protective role in a mouse model. No large-scale studies of immunity to GARP in humans have yet been undertaken. In this investigation, using a large multiethnic cohort (1738 subjects), we aimed to determine whether the magnitude of anti-GARP antibody responsiveness was significantly different in patients with breast cancer from that in matched healthy controls. We also investigated whether the allelic variation at the immunoglobulin GM (γ marker), KM (κ marker), and Fcγ receptor (FcγR) loci contributed to the interindividual variability in anti-GARP IgG antibody levels. A combined analysis of all subjects showed that levels of anti-GARP antibodies were significantly higher in patients with breast cancer than in healthy controls (mean⯱â¯SD: 7.4⯱â¯3.5 vs. 6.9⯱â¯3.5 absorbance units per mL (AU/µL), pâ¯<â¯0.0001). In the two populations with the largest sample size, the probability of breast cancer generally increases as anti-GARP antibody levels increase. Several significant individual and epistatic effects of GM, KM, and FcγR genotypes on anti-GARP antibody responsiveness were noted in both patients and controls. These results, if confirmed by independent investigations, will aid in devising personalized GARP-based immunotherapeutic strategies against breast cancer and other GARP-overexpressing malignancies.
Assuntos
Neoplasias da Mama/genética , Genótipo , Alótipos Gm de Imunoglobulina/genética , Alótipos Km de Imunoglobulina/genética , Imunoterapia/métodos , Proteínas de Membrana/imunologia , Receptores de IgG/genética , Formação de Anticorpos , Brasil , Neoplasias da Mama/imunologia , Estudos de Casos e Controles , Estudos de Coortes , Epistasia Genética , Etnicidade , Feminino , Humanos , Imunoglobulina G/sangue , Proteínas de Membrana/genética , Polimorfismo Genético , Medicina de PrecisãoRESUMO
MAIN CONCLUSION: The overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136, suggesting that RXam1 might be implicated in strain-specific resistance. Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) is a prevalent disease in all regions, where cassava is cultivated. CBB is a foliar and vascular disease usually controlled through host resistance. Previous studies have found QTLs explaining resistance to several Xam strains. Interestingly, one QTL called XM5 that explained 13% of resistance to XamCIO136 was associated with a similar fragment of the rice Xa21-resistance gene called PCR250. In this study, we aimed to further identify and characterize this fragment and its role in resistance to CBB. Screening and hybridization of a BAC library using the molecular marker PCR250 as a probe led to the identification of a receptor-like kinase similar to Xa21 and were called RXam1 (Resistance to Xam 1). Here, we report the functional characterization of susceptible cassava plants overexpressing RXam1. Our results indicated that the overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136. This suggests that RXAM1 might be implicated in strain-specific resistance to XamCIO136.
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Resistência à Doença/genética , Manihot/genética , Doenças das Plantas/microbiologia , Xanthomonas axonopodis , Receptores de Ativinas/genética , Receptores de Ativinas/metabolismo , Genes de Plantas/genética , Imunidade Vegetal/genética , Reação em Cadeia da Polimerase , Locos de Características Quantitativas/genéticaRESUMO
High levels of naturally occurring IgG antibodies to mucin 1 (MUC1), a membrane-bound glycoprotein that is overexpressed in patients with breast cancer, are associated with good prognosis. This suggests that endogenous anti-MUC1 antibodies have a protective effect and, through antibody-mediated host immunosurveillance mechanisms, might contribute to a cancer-free state. To test this possibility, we characterized a large number of multiethnic patients with breast cancer and matched controls for IgG antibodies to MUC1. We also aimed to determine whether the magnitude of anti-MUC1 antibody responsiveness was associated with particular immunoglobulin GM (γ marker), KM (κ marker), and Fcγ receptors (FcγR) genotypes. After adjusting for the confounding variables in a multivariate analysis, we found no significant difference in the levels of anti-MUC1 IgG antibodies between patients and cancer-free controls. However, in patients and controls, particular GM, KM, and FcγR genotypes-individually or epistatically-were significantly associated with the levels of anti-MUC1 IgG antibodies in a racially restricted manner. These findings, if confirmed in an independent investigation, could help identify individuals most likely to benefit from a MUC1-based therapeutic or prophylactic vaccine for MUC1-overexpressing malignancies.
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Neoplasias da Mama/imunologia , Etnicidade , Genótipo , Imunoglobulinas/genética , Mucina-1/imunologia , Grupos Raciais , Receptores de IgG/genética , Formação de Anticorpos , Brasil/epidemiologia , Neoplasias da Mama/epidemiologia , Estudos de Coortes , Feminino , Humanos , Imunoglobulinas/sangue , Vigilância Imunológica , Japão/epidemiologia , Análise MultivariadaRESUMO
Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of these proteins is codified by the Arabidopsis thaliana HR4 gene in the Col-0 ecotype that is homologous to RPW8 genes present in the Ms-0 ecotype. In this study, we investigated the expression patterns of the HR4 gene in Arabidopsis seedlings interacting with the beneficial fungus Trichoderma atroviride. We observed the induction of the HR4 gene mainly at 96 hpi when the fungus interaction was established. Furthermore, we found that the HR4 gene was differentially regulated in interactions with the beneficial bacterium Pseudomonas fluorescens and the pathogenic bacterium P. syringae. When hormone treatments were applied to A. thaliana (Col-0), each hormone treatment induced changes in HR4 gene expression. On the other hand, the expression of the RPW8.1 and RPW8.2 genes of Arabidopsis ecotype Ms-0 in interaction with T. atroviride was assessed. Interestingly, these genes are interaction-responsive; in particular, the RPW8.1 gene shows a very high level of expression in the later stages of interaction. These results indicate that HR4 and RPW8 genes could play a role in the establishment of Arabidopsis interactions with beneficial microbes.