A comprehensive appraisal of mechanism of anti-CRISPR proteins: an advanced genome editor to amend the CRISPR gene editing.

The development of precise and controlled CRISPR-Cas tools has been made possible by the discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs). The Acr protein has the ability to control off-targeted mutations and impede Cas protein-editing operations. Acr can help with selective breeding, which could help plants and animals improve their valuable features. In this review, the Acr protein-based inhibitory mechanisms that have been adopted by several Acrs, such as (a) the interruption of CRISPR-Cas complex assembly, (b) interference with target DNA binding, (c) blocking of target DNA/RNA cleavage, and (d) enzymatic modification or degradation of signalling molecules, were discussed. In addition, this review emphasizes the applications of Acr proteins in the plant research.

Towards further understanding the applications of endophytes: enriched source of bioactive compounds and bio factories for nanoparticles.

The most significant issues that humans face today include a growing population, an altering climate, an growing reliance on pesticides, the appearance of novel infectious agents, and an accumulation of industrial waste. The production of agricultural goods has also been subject to a great number of significant shifts, often known as agricultural revolutions, which have been influenced by the progression of civilization, technology, and general human advancement. Sustainable measures that can be applied in agriculture, the environment, medicine, and industry are needed to lessen the harmful effects of the aforementioned problems. Endophytes, which might be bacterial or fungal, could be a successful solution. They protect plants and promote growth by producing phytohormones and by providing biotic and abiotic stress tolerance. Endophytes produce the diverse type of bioactive compounds such as alkaloids, saponins, flavonoids, tannins, terpenoids, quinones, chinones, phenolic acids etc. and are known for various therapeutic advantages such as anticancer, antitumor, antidiabetic, antifungal, antiviral, antimicrobial, antimalarial, antioxidant activity. Proteases, pectinases, amylases, cellulases, xylanases, laccases, lipases, and other types of enzymes that are vital for many different industries can also be produced by endophytes. Due to the presence of all these bioactive compounds in endophytes, they have preferred sources for the green synthesis of nanoparticles. This review aims to comprehend the contributions and uses of endophytes in agriculture, medicinal, industrial sectors and bio-nanotechnology with their mechanism of action.

Compensatory phenolic induction dynamics in aspen after aphid infestation.

Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage.

Role of Diversity and Recombination in the Emergence of Chilli Leaf Curl Virus.

Chilli leaf curl virus (ChiLCV), (Genus Begomovirus, family Geminiviridae) and associated satellites pose a serious threat to chilli production, worldwide. This study highlights the factors accountable for genetic diversity, recombination, and evolution of ChiLCV, and associated chilli leaf curl alphasatellite (ChiLCA) and chilli leaf curl betasatellite (ChiLCB). Phylogenetic analysis of complete genome (DNA-A) sequences of 132 ChiLCV isolates from five countries downloaded from NCBI database clustered into three major clades and showed high population diversity. The dN/dS ratio and Tajima D value of all viral DNA-A and associated betasatellite showed selective control on evolutionary relationships. Negative values of neutrality tests indicated purified selection and an excess of low-frequency polymorphism. Nucleotide diversity (π) for C4 and Rep genes was higher than other genes of ChiLCV with an average value of π = 18.37 × 10-2 and π = 17.52 × 10-2 respectively. A high number of mutations were detected in TrAP and Rep genes, while ChiLCB has a greater number of mutations than ChiLCA. In addition, significant recombination breakpoints were detected in all regions of ChiLCV genome, ChiLCB and, ChiLCA. Our findings indicate that ChiLCV has the potential for rapid evolution and adaptation to a range of geographic conditions and could be adopted to infect a wide range of crops, including diverse chilli cultivars.

Host Plant Strategies to Combat Against Viruses Effector Proteins.

Viruses are obligate parasites that exist in an inactive state until they enter the host body. Upon entry, viruses become active and start replicating by using the host cell machinery. All plant viruses can augment their transmission, thus powering their detrimental effects on the host plant. To diminish infection and diseases caused by viruses, the plant has a defence mechanism known as pathogenesis-related biochemicals, which are metabolites and proteins. Proteins that ultimately prevent pathogenic diseases are called R proteins. Several plant R genes (that confirm resistance) and avirulence protein (Avr) (pathogen Avr gene-encoded proteins [effector/elicitor proteins involved in pathogenicity]) molecules have been identified. The recognition of such a factor results in the plant defence mechanism. During plant viral infection, the replication and expression of a viral molecule lead to a series of a hypersensitive response (HR) and affect the host plant's immunity (pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity). Avr protein renders the host RNA silencing mechanism and its innate immunity, chiefly known as silencing suppressors towards the plant defensive machinery. This is a strong reply to the plant defensive machinery by harmful plant viruses. In this review, we describe the plant pathogen resistance protein and how these proteins regulate host immunity during plant-virus interactions. Furthermore, we have discussed regarding ribosome-inactivating proteins, ubiquitin proteasome system, translation repression (nuclear shuttle protein interacting kinase 1), DNA methylation, dominant resistance genes, and autophagy-mediated protein degradation, which are crucial in antiviral defences.

Analysis of genome comparison of two Indian isolates of Cowpea aphid-borne mosaic virus from India.

The complete sequence of two Cowpea aphid-borne mosaic virus (CABMV) isolates (RR3 and RR4) from India was determined. Phylogenetic analysis showed that both isolates showed different closeness with other isolates of CABMV. CABMV-RR3 showed maximum identity of 99 % with CABMV-BR1 from Brazil at nucleotide and protein levels, whereas CABMV-RR4 showed identity of 73 and 95 % with CABMV-Z isolate from Zimbabwe at nucleotide and protein levels respectively. Similarity identity matrix revealed 69 % identity at nucleotide level and 91 % at protein level with each other. Recombination breakpoint detection showed that CABMV-MG-Avr from Brazil and CABMV-Z from Zimbabwe act as major parents in our isolates RR3 and RR4, respectively.

RNAi mediated gene silencing against betasatellite associated with Croton yellow vein mosaic begomovirus.

Plant viruses encode suppressors of posttranscriptional gene silencing, an adaptive antiviral defense responses that confines virus infection. Previously, we identified single-stranded DNA satellite (also known as DNA-ß) of ~1,350 nucleotides in length associated with Croton yellow vein mosaic begomovirus (CYVMV) in croton plants. The expression of genes from DNA-ß requires the begomovirus for packaged, replication, insect transmission and movement in plants. The present study demonstrates the effect of the ßC1 gene on the silencing pathway as analysed by using both transgenic systems and transient Agrobacterium tumefaciens based delivery. Plants that carry an intron-hairpin construct covering the ßC1 gene accumulated cognate small-interfering RNAs and remained symptom-free after exposure to CYVMV and its satellite. These results suggest that ßC1 interferes with silencing mechanism.

Rhizobacterium-mediated growth promotion and expression of stress enzymes in Glycine max L. Merrill against Fusarium wilt upon challenge inoculation.

Wilt disease of soybean caused by a very common soil-borne fungus, Fusarium oxysporum is one of the most destructive diseases of the crop. The aim of the present study was to characterize plant growth-promotion activities and induced resistance of a rhizobacterial strain for the soybean plant against F. oxysporum. Rhizobacterium strain SJ-5 exhibited plant growth-promotion characteristics and antagonistic activity against the test pathogen on dual plate assay. It was identified as a Carnobacterium sp. A 950 bp PCR product was amplified from Carnobacterium sp. strain SJ-5, using zwittermicin A self-resistance gene-specific primers (zmaR). The strain produced indole 3-acetic acid (19 µg/ml) in the presence of salt stress and exhibited growth in Dworkin and Foster salt medium amended with 1-aminocyclopropane-1-carboxylate (ACC) through ACC deaminase activity (277 nmol/mg/h) as compared to the control. Strain seeds treated with the strain significantly enhanced the quorum of healthy plants after challenge inoculation at 14 days after seeding. An increase in the activity of stress enzymes after challenge inoculation with the test pathogen is reported. Treatment with the bacterium resulted in an increase in the chlorophyll content in the leaves in comparison with challenge-inoculated plants.

Effect of nitric oxide signaling in bacterial-treated soybean plant under salt stress.

To understand protective roles of nitric oxide against salt stress, the effects of exogenous sodium nitroprusside on activities of lipoxygenase, peroxidase, phenylalanine ammonialyase, catalase, superoxide dismutase enzymes, proline accumulation, and distribution of sodium in soybean plants under salt were determined. Application of sodium nitroprusside + bacterium enhanced plant growth-promotion characteristics, activities of different enzymes, and proline accumulation in the presence of sodium nitroprusside under salt stress. Treatment with NaCl at 200 mM and sodium nitroprusside (0.1 mM) reduced Na⁺ levels but increased K⁺ levels in leaves in comparison with the NaCl-treated plants. Correspondingly, the plants treated with exogenous sodium nitroprusside and NaCl maintained a lower ratio of [Na⁺]/[K⁺] in NaCl-stressed plants.

Geminivirus database (GVDB): first database of family Geminiviridae and its genera Begomovirus.

Geminivirus Database (GVDB) is an online interactive database of Geminiviridae family. GVDB comprises of partial and complete nucleotide sequences along with duly annotated expressed genes of isolated Begomovirus species. The in silico homology modeling, docking and recombination results obtained for different begomoviral sequences are also mentioned. This database is endowed with comprehensive information about Geminivirus members which grounds infection in various plants species in India assorting from crops, ornamentals plants and common weeds. The home page of this database offers various links associated with current research projects and also the publications related to molecular and in silico study of Begomovirus infection. The main feature of GVDB includes flexible database designs based on platform of PHP allows easy retrieval of the information. The database is made available at www.wikigeminivirus.org.

Soybean growth-promotion by Pseudomonas sp. strain VS1 under salt stress.

In the present study, we employ Pseudomonas sp. strain VS1 showed in vitro plant growth-promotion characteristics and promoted soybean seed emergence under salt stress. Strain produced indole 3-acetic acid in the presence of salt stresses that exhibited high numbers of lateral root as compared to control. Bacterial strain exhibited growth in DF salt medium amended with 1-aminocyclopropane-1-carboxylate through ACC deaminase activity. Bacterial-treated soybean seeds were subjected to salt stress and significantly enhanced emergence at 7 days after seeding. Strain untreated soybean plants had a 33% seed germination when 200 mM NaCl was applied at 0 DAS and the root length was significantly decreased compared to the strain treated plants (LSD0.05 = 0.21). Most importantly, the application of 200 mM NaCl at 0 DAS resulted in only a 9% of lateral root in untreated plants as compared to strain treated plants.

Phenetic and functional characterization of endophytic root-nodule bacteria isolated from chickpea (Cicer arietinum L.) and mothbean (Vigna aconitifolia l.) of arid-and semi-arid regions of Rajasthan, India.

In the present study we recovered endophytic root-nodule bacteria from chickpea (Cicer arietinumi L.) and mothbean (Vigna aconitifolia L.). Phenotypic and genotypic characterization of isolates was performed by employing biochemical and genetic approaches. Sequencing data showed that most isolates belonged to genus, Pseudomonas spp. being a dominant species. They also showed similarity with Rhizobium, Agrobacterium and Erwinia spp. Isolates were screened functionally for indole-3-acetic acid, siderophore production and inorganic phosphorus (Pi) solubilization. All isolates showed Pi solubilization except CJS-2. Nine isolates (CSS-1, CBS-1, CLS-3, CCS-1, CHS-1, VS-1, VL-1, VN-1, VN-2) were found positive for IAA production and eight isolates (CBS-1, CCS-1, CHS-2, CKS-2, CNS-2, VS-1, VJ-1) exhibited positive results for siderophore production. An understanding of the phonetic and functional diversity of these microbes that interact with plants will be worthwhile to fully achieve the biotechnological potential of efficient plant-microbe partnerships for a range of applications.

Subcellular localization of V2 protein of Tomato leaf curl Java virus by using green fluorescent protein and yeast hybrid system.

Tomato leaf curl Java virus-A (ToLCJV-A[ID]) from Southeast Asia is a new member of the emerging group of monopartite begomoviruses that require a betasatellite component for symptom induction. Previously, we have elucidated the role of V1 ORF encoded by ToLCJV-A[ID] in cell-to-cell movement. In this study, the role of V2 (PreCP) in localization was determined. Subcellular localization of ToLCJV-A[ID] V2 in plant tissues showed that this protein is co-localized to the cell cytoplasm, perinuclear and associated with the endoplasmic reticulum network. The results obtained from deletion analysis indicate that fusion of N-terminal part of the V2, containing the nuclear export signals (NES), directed the accumulation of fluorescence towards the cell cytoplasm. Furthermore, functionality of the NES ((20)LAVKYLQLV(29)) in the N-terminal part of the V2 protein was confirmed by one-hybrid yeast system. Taken together, these results suggest that V2 enhances the coat protein-mediated nuclear export of ToLCJV-A[ID] and is consistent with the model in which V2 mediates viral DNA export from the nucleus to the plasmodesmata.