RESUMEN
Papaya leaf curl disease (PaLCD) was primarily detected in India and causes major economic damage to agriculture crops grown globally, seriously threatening food security. Begomoviruses are communicated by the vector Bemisia tabaci, and their transmission efficiency and persistence in the vector are the highest, exhibiting the widest host range due to adaptation and evolution. Symptoms induced during PaLCD include leaf curl, leaf yellowing, interveinal chlorosis, and reduced fruit quality and yield. Consequently, plants have evolved several multi-layered defense mechanisms to resist Begomovirus infection and distribution. Subsequently, Begomovirus genomes organise circular ssDNA of size ~2.5-2.7 kb of overlapping viral transcripts and carry six-seven ORFs encoding multifunctional proteins, which are precisely evolved by the viruses to maintain the genome-constraint and develop complex but integrated interactions with a variety of host components to expand and facilitate successful infection cycles, i.e., suppression of host defense strategies. Geographical distribution is continuing to increase due to the advent and evolution of new Begomoviruses, and sweep to new regions is a future scenario. This review summarizes the current information on the biological functions of papaya-infecting Begomoviruses and their encoded proteins in transmission through vectors and modulating host-mediated responses, which may improve our understanding of how to challenge these significant plant viruses by revealing new information on the development of antiviral approaches against Begomoviruses associated with PaLCD.
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Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.
Asunto(s)
Grano Comestible/genética , Epigénesis Genética , Regulación de la Expresión Génica de las Plantas , Oryza/genética , Salinidad , Tolerancia a la Sal/genética , Ensamble y Desensamble de Cromatina/genética , Metilación de ADN/genética , Código de Histonas/genética , FenotipoRESUMEN
Petunia hybrida is an important ornamental plant grown in many countries including India. It is a good model plant for the study of genetics and molecular biology. During a survey in 2013-2014, severe leaf curling was observed on most of the P. hybrida grown in the Sikar district, Rajasthan. The infected plants were analyzed for begomovirus infection by rolling circular amplification (RCA) and sequenced. Full length sequences confirmed the association of monopartite begomovirus with betasatellites. Phylogenetic analysis showed the highest percentage of identity with Chilli leaf curl virus (ChLCuV) and therefore considered to be an isolate of ChLCuV. Recombination analysis showed that ChLCuV has broadened its host range by recombination process. To the best our knowledge, this is the first report of natural occurrence of ChLCuV on P. hybrida in India.
Asunto(s)
Begomovirus/clasificación , Begomovirus/aislamiento & purificación , Petunia/virología , Begomovirus/genética , Análisis por Conglomerados , ADN Satélite/química , ADN Satélite/genética , ADN Viral/química , ADN Viral/genética , Especificidad del Huésped , India , Datos de Secuencia Molecular , Filogenia , Enfermedades de las Plantas/virología , Recombinación Genética , Análisis de Secuencia de ADN , Homología de SecuenciaRESUMEN
Papaya leaf curl disease (PaLCuD) is widespread and classified in the genus begomovirus (Geminiviridae), disseminated by the vector whitefly Bemisia tabaci. RNA interference (RNAi)-based antiviral innate immunity stands as a pivotal defense mechanism and biological process in limiting viral genomes to manage plant diseases. The current study aims to identify and analyze Carica Papaya locus-derived capa-microRNAs with predicted potential for targeting divergent begomovirus species-encoded mRNAs using a 'four integrative in silico algorithms' approach. This research aims to experimentally activate the RNAi catalytic pathway using in silico-predicted endogenous capa-miRNAs and create papaya varieties capable of assessing potential resistance against begomovirus species and monitoring antiviral capabilities. This study identified 48 predicted papaya locus-derived candidates from 23 miRNA families, which were further investigated for targeting begomovirus genes. Premised all the four algorithms combined, capa-miR5021 was the most anticipated miRNA followed by capa-miR482, capa-miR5658, capa-miR530b, capa-miR3441.2, and capa-miR414 'effective' papaya locus-derived candidate capa-miRNA and respected putative binding sites for targets at the consensus nucleotide position. It was predicted to bind and target mostly to AC1 gene of the complementary strand and the AV1 gene of the virion strand of different begomovirus isolates, which were associated with replication-associated protein and encapsidation, respectively, during PaLCuD. These miRNAs were also found targeting betaC1 gene of betasatellite which were associated with retardation in leaf growth and developmental abnormalities with severe symptoms during begomovirus infection. To validate target prediction accuracy, we created an integrated Circos plot for comprehensive visualization of host-virus interaction. In silico-predicted papaya genome-wide miRNA-mediated begomovirus target gene regulatory network corroborated interactions that permit in vivo analysis, which could provide biological material and valuable evidence, leading to the development of begomovirus-resistant papaya plants. The integrative nature of our research positions it at the forefront of efforts to ensure the sustainable cultivation of papaya, particularly in the face of evolving pathogenic threats. As we move forward, the knowledge gained from this study provides a solid foundation for continued exploration and innovation in the field of papaya virology, and to the best of our knowledge, this study represents a groundbreaking endeavor, undertaken for the first time in the context of PaLCuD research.
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In the year 2012 leaf curl disease was observed on Marigold (Tagetes patula) in Lakshmangrh, Sikar province of India. Affected plants were severely stunted with apical leaf curl and crinkled leaves, symptoms typical of begomovirus infection. This is the first report of complete nucleotide sequence of a begomovirus associated with satellites molecules infecting a new host Tagetes patula in India.
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Begomovirus/aislamiento & purificación , Genoma Viral , Enfermedades de las Plantas/virología , Virus Satélites/aislamiento & purificación , Tagetes/virología , Secuencia de Bases , Begomovirus/clasificación , Begomovirus/genética , India , Datos de Secuencia Molecular , Filogenia , Hojas de la Planta/virología , Virus Satélites/clasificación , Virus Satélites/genéticaRESUMEN
Capsicum annuum, a valuable spice and vegetable crop belonging to the Solanaceae family, is extensively grown across the Indian subcontinent. Chilli production is restricted by a begomoviral infection named as chilli leaf curl disease (ChiLCD) mainly in tropical and subtropical regions which leads to considerable economic losses, thus affecting chilli cultivation. Here, we studied the genetic diversity with structural evaluation of chilli leaf curl disease and satellite molecules infecting Chilli in India. We retrieved 121 reference sequences of ChiLCD including DNA-A, DNA-B, beta-satellite and alpha-satellites from GenBank reported from India. The population diversity and genetic variation were estimated through various parameters which decipher the four major groups of phylogenetic divergence for DNA-A and five groups of beta-satellite showing percentage similarity with isolates within and across India. Further, transitional and transversional bias for ORFs were observed highest in C4 and REn genes, respectively, and for DNA-A and DNA-B, these values were 1.07 and 1.22, respectively. The recombination breakpoints for DNA-A were estimated 49 majorly in V1, C1,C2 and C4 genome region and highest 22 breakpoints were determined for Rep (AC1) of ORFs, similarly 9 events for beta-satellite were found less around ßC1ORF. Moreover, the evolution and genetic variability were also contributed through parameters such as nucleotide substitution which were found within the range of RNA viruses for DNA-A, DNA-B, for all 6 ORFs (relaxed clock) and beta-satellite. Additionally, total numbers of mutations (η) for DNA-A, DNA-B, alpha-satellites and beta-satellites were 2505, 419, 807 and 1288 detected, respectively, while it was found 987 highest for Rep gene among all ORFs. Further, neutrality tests determine the dominant nature of population expansion and purifying selection for all the genes of begomovirus associated with ChiLCD and satellite molecules supporting conserved nature of gene. The combined Tajima's D and Fu and Li'S D* negative values in tests indicated that population are under purified selection and an excess of low-frequency polymorphism. Our analysis indicates the potential contribution of genetic mutations and recombination of ChiLCD which leads to rapid adaptation and evolution of begomovirus and its satellite molecules accelerating its host range and diversity within and across the Indian subcontinent. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03139-w.
RESUMEN
The genus Begomovirus represents a group of multipartite viruses that significantly damage many agricultural crops, including papaya, and influence overall production. Papaya leaf curl disease (PaLCD) caused by the complex begomovirus species has several important implications and substantial losses in papaya production in many developing countries, including India. The increase in the number of begomovirus species poses a continuous threat to the overall production of papaya. Here, we attempted to map the genomic variation, mutation, evolution rate, and recombination to know the disease complexity and successful adaptation of PaLCD in India. For this, we retrieved 44 DNA-A and 26 betasatellite sequences from GenBank reported from India. An uneven distribution of evolutionary divergence has been observed using the maximum-likelihood algorithm across the branch length. Although there were phylogenetic differences, we found high rates of nucleotide substitution mutation in both viral and sub-viral genome datasets. We demonstrated frequent recombination of begomovirus species, with a maximum in intra-species recombinants. Furthermore, our results showed a high degree of genetic variability, demographic selection, and mean substitution rate acting on the population, supporting the emergence of a diverse and purifying selection of viruses and associated betasatellites. Moreover, variation in the genetic composition of all begomovirus datasets revealed a predominance of nucleotide diversity principally driven by mutation, which might further accelerate the advent of new strains and species and their adaption to various hosts with unique pathogenicity. Therefore, the finding of genetic variation and selection emphases on factors that contribute to the universal spread and evolution of Begomovirus and this unanticipated diversity may also provide guidelines toward future evolutionary trend analyses and the development of wide-ranging disease control strategies for begomoviruses associated with PaLCD.
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In subsistence agricultural systems, crop yields are directly dependent on the inherent soil fertility and on microbial processes that govern the mineralization and mobilization of nutrients required for plant growth. An impact of different crop species that are used in various combinations is likely to be an important factor in determining the structure of plant beneficial microbial communities that function in nutrient cycling, the production of plant growth hormones, and suppression of root diseases. In addition, studies are needed to elucidate the signal transduction pathways that result from treatment of plants with plant growth-promoting rhizobacteria under stress conditions. In the present review an emphasis has been given on plant-microbe interactions and their mitigation under abiotic and biotic stresses.
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Agricultura , Biotecnología , Ecosistema , Enfermedades de las Plantas/microbiología , Plantas/microbiología , Microbiología del Suelo , Estrés Fisiológico , Fenómenos Fisiológicos Bacterianos , Resistencia a la EnfermedadRESUMEN
A monopartite begomovirus associated with betasatellite was identified from Osteospermum fruticosum (Cape Daisy) showing severe yellowing vein net symptoms in Rajasthan, India through molecular characterization. The DNA-A shared the highest nucleotide (96.61%) identity to Chilli leaf curl Ahmedabad virus (KM880103), while the betasatellite depicted the highest sequence similarity (99.28%) to Chilli leaf curl betasatellite (JF706231, 99.28%). Based on the sequence identity with other begomoviruses known to date, they were recognized as Chilli leaf curl virus (CDI, MH355641) and Chilli leaf curl betasatellite (CDB1, MH355642), respectively. Phylogenetic analysis showed that DNA-A (CD1) clustered with ChiLCV Goa (KP235539), whereas the betasatellite (CDB1) clustered with ChiLCB Jodhapur (JF70623). Recombination events were observed among the clades of ChiLCV, showing intragenic recombination in Rep (C1) and coat protein (V1/AV1) regions. To our knowledge, this is the first report of ChiLC begomovirus strain affecting O. fruticosum.
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Watermelon mosaic virus (WMV) is an important virus causing adverse effects on cucurbits throughout the world. In this study, we recorded WMV infection in the watermelon (Citrullus lanatus)-growing area of Alwar and Sikar in districts of Rajasthan, India. The RT-PCR-based detection was performed to confirm the presence of WMV, by using potyvirus-degenerated coat protein primers. Further, the complete genome sequences of two WMV isolates were compared with previously reported genome sequences. The complete genome of each isolate was 10,030 nt long, excluding the poly-A tails. Phylogeny relationships of the WMV isolates in the present study revealed the presence of uneven evolutionary pressure among the different WMV viral genomic segments. The analysis revealed that all the WMV isolates were divided into three clusters and the Indian WMV isolates cluster together with the French isolate. Recombination analysis of WMV exhibited significant recombination hotspots in the P1, NIa-Pro and Nib-CP regions. Our finding highlights the importance of genetic variability and recombination analysis to provide a better understanding of WMV molecular diversity.
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Chili (Capsicum annuum L.) is an important vegetable and spice crop of tropical and sub-tropical regions. Chili plants showing upward leaf curling, leaf crinkling, and leaf yellowing symptoms, collected from Sikar district of Rajasthan, India, were found to be associated with begomovirus and satellite molecules. The presence of virus was confirmed by PCR using virus-specific primer. The full-length genomic DNA-A of three begomovirus (MM-1, CS-1 and RV-1) and two satellites (MM-2 and MM-3) were cloned which was identified from single symptomatic chili plant. The genome organization of isolated three viruses is similar to those of other Old World monopartite begomoviruses. The comparison of the sequences and closest phylogenetic relationships for the begomoviruses, betasatellite and alphasatellite DNAs revealed that MM-1 was designated as DNA-A of Chili leaf curl virus (ChiLCV), CS-1 is considered to be a new distinct species of Tomato leaf curl Gujrat virus (ToLCGV) whereas RV-1 as a new strain of Cotton leaf curl Multan virus (CLCuMuV). The DNA-A component of ChiLCV showed 8.6%, ToLCGV of 16.6% and CLCuMuV of 7.7% average evolutionary divergence, concomitantly, the betasatellite and alphasatellite molecule had 9.9% and 5.9% overall sequence divergence, respectively. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The dN/dS ratio and Tajima D value of all viral DNA-A component and their associated betasatellite showed their selective control on evolutionary relationships. The nucleotide substitution rates were determined for the DNA-A genomes of ChiLCV (7.22 × 10-4 substitutions site-1 year-1), CLCuMuV (1.49 × 10-4 substitutions site-1 year-1), ToLCGV (7.47 × 10-4 substitutions site-1 year-1), the genome of associated ChiLCB (4.20 × 10-4 substitutions site-1 year-1) and CLCuMuA (1.49 × 10-4 substitutions site-1 year-1). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms in N. benthamiana and chili, suggesting prerequisite association for typical disease development.
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The mammalian splicing factor U2AF65 binds to the polypyrimidine tract adjacent to the 3' splice site and promotes assembly of U2 small nuclear ribonucleoprotein on the upstream branch point, an interaction that involves base pairing with U2 small nuclear RNA (snRNA). U2AF65 contains an RNA binding domain, required for interaction with the polypyrimidine tract, and an arginine-serine-rich (RS) region, required for U2 snRNP recruitment and splicing. Here it is reported that binding of U2AF65 to the polypyrimidine tract directed the RS domain to contact the branch point and promoted U2 snRNA-branch point base pairing even in the absence of other splicing factors. Analysis of RS domain mutants indicated that the ability of U2AF65 to contact the branch point, to promote the U2 snRNA-branch point interaction, and to support splicing are related activities, requiring only a few basic amino acids. Thus, the U2AF65 RS domain plays a direct role in modulating spliceosomal RNA-RNA interactions.
Asunto(s)
Proteínas Nucleares , Precursores del ARN/metabolismo , Empalme del ARN , ARN Mensajero/metabolismo , ARN Nuclear Pequeño/metabolismo , Ribonucleoproteínas/metabolismo , Secuencia de Aminoácidos , Arginina/química , Composición de Base , Secuencia de Bases , Reactivos de Enlaces Cruzados , Modelos Genéticos , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , Ribonucleoproteínas/química , Serina/química , Empalmosomas/metabolismo , Factor de Empalme U2AFRESUMEN
Symptomless grape plants (Vitis vinifera) cultivated in Jind, Punjab, have been found to carry a Grapevine red blotch virus (GRBV). Evaluation of full length DNA sequence (3204 bp) of the virus (KU522121) has revealed similarity with mastrevirus, begomovirus, and other Grapevine red blotch viruses reported in the US and Canada. Similar to naturally growing plants, agroinfiltrated model plants with infectious clone of GRBV do not show any visible disease warning sign. To the best of our knowledge, this is the first report of a symptomless host Vitis vinifera from Indian vineyards harbouring a Grapevine geminivirus.
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Human apurinic/apyrimidinic endonuclease (hApe1) encodes two important functional activities: an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcription factors, AP-1, NFkappaB, HIF-1alpha, CREB, p53 and others. The BER function is highly conserved from prokaryotes (E. coli exonuclease III) to humans (hApe1). Here, we provide evidence supporting a redox function unique to mammalian Apes. An evolutionary analysis of Ape sequences reveals that, of the 7 Cys residues, Cys 93, 99, 208, 296, and 310 are conserved in both mammalian and non-mammalian vertebrate Apes, while Cys 65 is unique to mammalian Apes. In the zebrafish Ape (zApe), selected as the vertebrate sequence most distant from human, the residue equivalent to Cys 65 is Thr 58. The wild-type zApe enzyme was tested for redox activity in both in vitro EMSA and transactivation assays and found to be inactive, similar to C65A hApe1. Substitution of Thr 58 with Cys in zApe, however, resulted in a redox active enzyme, suggesting that a Cys residue in this position is indeed critical for redox function. In order to further probe differences between redox active and inactive enzymes, we have determined the crystal structures of vertebrate redox inactive enzymes, the C65A human Ape1 enzyme and the zApe enzyme at 1.9 and 2.3A, respectively. Our results provide new insights on the redox function and highlight a dramatic gain-of-function activity for Ape1 in mammals not found in non-mammalian vertebrates or lower organisms.
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ADN-(Sitio Apurínico o Apirimidínico) Liasa/química , Evolución Molecular , Pez Cebra/metabolismo , Secuencia de Aminoácidos , Animales , ADN-(Sitio Apurínico o Apirimidínico) Liasa/genética , ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , Ensayo de Cambio de Movilidad Electroforética , Humanos , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Oxidación-Reducción , Conformación Proteica , Homología de Secuencia de Aminoácido , Activación Transcripcional , Pez Cebra/genéticaRESUMEN
U2 snRNP auxiliary factor (U2AF) promotes U2 snRNP binding to pre-mRNAs and consists of two subunits of 65 and 35 kDa, U2AF(65) and U2AF(35). U2AF(65) binds to the polypyrimidine (Py) tract upstream from the 3' splice site and plays a key role in assisting U2 snRNP recruitment. It has been proposed that U2AF(35) facilitates U2AF(65) binding through a network of protein-protein interactions with other splicing factors, but the requirement and function of U2AF(35) remain controversial. Here we show that recombinant U2AF(65) is sufficient to activate the splicing of two constitutively spliced pre-mRNAs in extracts that were chromatographically depleted of U2AF. In contrast, U2AF(65), U2AF(35), and the interaction between them are required for splicing of an immunoglobulin micro; pre-RNA containing an intron with a weak Py tract and a purine-rich exonic splicing enhancer. Remarkably, splicing activation by U2AF(35) occurs without changes in U2AF(65) cross-linking to the Py tract. These results reveal substrate-specific requirements for U2AF(35) and a novel function for this factor in pre-mRNA splicing.
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Proteínas Nucleares , Pirimidinas/metabolismo , Empalme del ARN , Ribonucleoproteínas/metabolismo , Animales , beta-Globulinas/genética , Extractos Celulares , Proteínas de Unión al ADN/genética , Células HeLa , Humanos , Inmunoglobulina M/genética , Ratones , Precursores del ARN , Proteínas Recombinantes de Fusión/metabolismo , Factor de Empalme U2AF , Especificidad por Sustrato , Factores de Transcripción/genética , Proteínas ViralesRESUMEN
We have investigated the incorporation of 2'-deoxynucleoside-5'-O-(1-thiotriphosphates) into RNA transcripts using T7 RNA polymerase. With the exception of [alpha-S]dGTP, we obtained full-length transcripts of pre-tRNA(Phe) and pre-tRNA(Tyr) using an appropriate mixture of 2'-deoxynucleoside 5'-O-(1-thiotriphosphate) and the corresponding normal nucleoside triphosphate. The yields of the transcripts were comparable to those obtained with unmodified NTPs. Both substrates, [alpha-S]dTTP and [alpha-S]dATP, were inserted specifically. However, [alpha-S]dCTP was excluded at specific sites. We could not obtain transcripts using the deoxyguanosine derivative.
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ARN Polimerasas Dirigidas por ADN/metabolismo , Desoxirribonucleótidos/metabolismo , ARN/química , Tionucleótidos/metabolismo , Secuencia de Bases , Enlace de Hidrógeno , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , Precursores de Ácido Nucleico/química , Procesamiento Postranscripcional del ARN , ARN de Transferencia de Fenilalanina/química , Proteínas ViralesRESUMEN
In a medically pluralistic setting a range of health care providers offer not only different forms of treatment, but different ways of understanding illness. Even within a single tradition, these concepts evolve over time. Chapters in the classical texts of Ayurveda describe varieties of severe mental disorder (unmada) arising from a particular humoral imbalance (dosa) or arising in association with specific demons and deities (bhuta) that produce distinct character changes and symptom patterns. Patients currently presenting for treatment of mental disorder may describe their illness with reference to these concepts, but they also rely on other indigenous traditional concepts such as astrology, karma, the effects of other humoral relationships, such as semen loss and so forth; or they may rely on ideas derived from cosmopolitan medicine or both. Patients presenting to allopathic psychiatric centers in India were studied to determine whether patterns of help seeking could be predicted from the conceptual model by which they understood their illness. We elicited explanatory models from patients and obtained a history of prior consultations to other types of healer. Preliminary findings were notable for the pervasiveness of prior use of folk healers and the prominence of somatic symptoms among patients presenting to these allopathic physicians. Hypotheses regarding the impact of explanatory models on patterns of medical help seeking require further study from a larger and more diverse data base.
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Actitud Frente a la Salud , Medicina Tradicional , Trastornos Mentales/psicología , Femenino , Homeopatía , Humanos , India , Masculino , Medicina Ayurvédica , Trastornos Mentales/terapia , Curación Mental , Modelos TeóricosRESUMEN
A simple and sensitive method for the quantitative determination of free amino groups on solid support is described. This approach is a modification of Ngo's [(1986) J. Biochem. Biophys. Methods 12, 349-354] method reported earlier. The method is based on the reaction of the solid support with an excess of 5'-O-(4,4'-dimethoxytrityl)-thymidine-3'-O-(2,4-dinitrophenyl) succinate (DTDS) in the presence of a catalytic amount of 4-dimethylaminopyridine. After removing the excess reagent, solid support is treated with perchloric acid to release 4,4'-dimethoxytrityl cation into the solution. The released 4,4'-dimethoxytrityl cation, which has a strong absorption at 498 nm (epsilon 498 = 70,000), is then determined spectrophotometrically. A comparative study of DTDS, N-succinimidyl-3-(2-pyridyldithio)propionate and 4,4-dimethoxytrityl chloride is also included. The method was found to be very useful to determine those amino groups which are available for functionalization of solid supports, especially, monitoring the functionalization of solid supports for affinity chromatography and synthesis of biopolymers.
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Aminas/análisis , Resinas Sintéticas , Cromatografía de Afinidad/métodos , Modelos Químicos , Espectrofotometría/métodos , Timidina/análogos & derivados , Timidina/síntesis química , Compuestos de Tritilo/análisis , Compuestos de Tritilo/síntesis químicaRESUMEN
A case of right paraduodenal hernia is reported. Embryogenesis and treatment of this rare type of internal hernia is discussed.