Isolation of a new fungi and wound-induced chitinase class in corms of Crocus sativus

Integrated transcriptomic meta-analysis and comparative artificial intelligence models in maize under biotic stress

Biotic stress imposed by pathogens, including fungal, bacterial, and viral, can cause heavy damage leading to yield reduction in maize. Therefore, the identification of resistant genes paves the way to the development of disease-resistant cultivars and is essential for reliable production in maize. Identifying different gene expression patterns can deepen our perception of maize resistance to disease. This study includes machine learning and deep learning-based application for classifying genes expressed under normal and biotic stress in maize. Machine learning algorithms used are Naive Bayes (NB), K-Nearest Neighbor (KNN), Ensemble, Support Vector Machine (SVM), and Decision Tree (DT). A Bidirectional Long Short Term Memory (BiLSTM) based network with Recurrent Neural Network (RNN) architecture is proposed for gene classification with deep learning. To increase the performance of these algorithms, feature selection is made from the raw gene features through the Relief feature selection algorithm. The obtained finding indicated the efficacy of BiLSTM over other machine learning algorithms. Some top genes ((S)-beta-macrocarpene synthase, zealexin A1 synthase, polyphenol oxidase I, chloroplastic, pathogenesis-related protein 10, CHY1, chitinase chem 5, barwin, and uncharacterized LOC100273479 were proved to be differentially upregulated under biotic stress condition.

Isolation, Identification, and Determination of the Virulence of the Causal Agents of Corm Rot of Saffron (Crocus sativus L.) in Valle de Uco, Argentina

Saffron (Crocus sativus L.) presents an attractive opportunity for diversifying production and adding value, particularly for small-scale growers and family-based agriculture. However, the agamic propagation of the crop through corms raises concerns regarding disease dispersion. During the summers of 2013 and 2015, symptoms of corm rot were observed in saffron crops in La Consulta, Valle de Uco, Argentina. These symptoms manifested in the form of wilting plants and red-coloured areas on the surface of the corms, in some cases affecting deeper regions. This study aimed to isolate and identify the causal agent responsible for saffron corm rot while also comparing the virulence of four strains isolated on saffron plants. Consistent isolation of Fusarium spp. colonies from affected corms confirmed its association with the disease. The obtained isolates were inoculated into healthy corms, and the reproduction of symptoms was confirmed, as well as subsequent pathogen re-isolation. Morphological and molecular characterisation of the strains was performed using rDNA gene sequencing. Furthermore, disease progression was assessed with fitting epidemiological models to empirical data, which served as estimators of fungal strain aggressiveness. The results conclusively identified Fusarium oxysporum Schltdl. as the causal agent of corm rot, and variations in virulence were observed among the strains on the host plant. After basic molecular and pathological studies, it is postulated that the fungal strains possibly belong to the forma specialis gladioli, but further studies are necessary to confirm that. The present study provides findings that highlight the importance of early detection and the preservation of pathogen-free fields to sustain saffron cultivation. These findings may constitute the initial step for future projects aimed at understanding the epidemiology of the disease better, determining the species/races of the pathogen, and developing effective management strategies.

In silico characterization of bacterial chitinase: illuminating its relationship with archaeal and eukaryotic cousins

Background

Chitin is one of the most abundant biopolymers on Earth, only trailing second after cellulose. The enzyme chitinase is responsible for the degradation of chitin. Chitinases are found to be produced by wide range of organisms ranging from archaea to higher plants. Though chitin is a major component of fungal cell walls and invertebrate exoskeletons, bacterial chitinase can be industrially generated at low cost, in facile downstream processes at high production rate. Microbial chitinases are more stable, active, and economically practicable compared to the plant- and animal-derived enzymes.

Results

In the present study, computationally obtained results showed functional characteristics of chitinase with particular emphasis on bacterial chitinase which is fulfilling all the required qualities needed for commercial production. Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. Considering one suitable exemplary sequence from each group is being compared with others. Primary, secondary, and tertiary structures are determined by in silico models. Different physical parameters, viz., pI, molecular weight, instability index, aliphatic index, GRAVY, and presence of functional motifs, are determined, and a phylogenetic tree has been constructed to elucidate relationships with other groups of organisms.

Conclusions

This study provides novel insights into distribution of chitinase among four groups and their characterization. The results represent valuable information toward bacterial chitinase in terms of the catalytic properties and structural features, can be exploited to produce a range of chitin-derived products.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00121-6.

Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum)

Chitinase catalyzes the hydrolysis of chitin β-1,4 linkages. However, plants cannot produce chitin, suggesting that plant chitinases do not have the same function as animals. This study investigated the chitinase gene family in tomato and divided into eight groups via phylogenetic analyses with Arabidopsis and rice members. Conserved gene structures and motif arrangements indicated their functional relevance with each group. These genes were nonrandomly distributed across the tomato chromosomes, and tandem duplication contributed to the expansion of this gene family. Synteny analysis also established orthology relationships and functional linkages between Arabidopsis and tomato chitinase genes. Several positive selection sites were identified, which may contribute to the functional divergence of the protein family in evolution. In addition, differential expression profiles of the tomato chitinase genes were also investigated at some developmental stages, or under different biotic and abiotic stresses. Finally, functional network analysis found 124 physical or functional interactions, implying the diversity of physiological functions of the family proteins. These results provide a foundation for the exploration of the chitinase genes in plants and will offer some insights for further functional studies.

The Specialized Roles in Carotenogenesis and Apocarotenogenesis of the Phytoene Synthase Gene Family in Saffron

Crocus sativus stigmas are the main source of crocins, which are glucosylated apocarotenoids derived from zeaxanthin cleavage that give saffron its red color. Phytoene synthase (PSY) mediates the first committed step in carotenoid biosynthesis in plants. Four PSY genes encoding functional enzymes were isolated from saffron. All the proteins were localized in plastids, but the expression patterns of each gene, CsPSY1a, CsPSY1b, CsPSY2, and CsPSY3, in different saffron tissues and during the development of the stigma showed different tissue specialization. The CsPSY2 transcript was primarily detected in the stigmas where it activates and stimulates the accumulation of crocins, while its expression was very low in other tissues. In contrast, CsPSY1a and CsPSY1b were mainly expressed in the leaves, but only CsPSY1b showed stress-light regulation. Interestingly, CsPSY1b showed differential expression of two alternative splice variants, which differ in the intron retention at their 5' UTRs, resulting in a reduction in their expression levels. In addition, the CsPSY1a and CsPSY1b transcripts, together with the CsPSY3 transcript, were induced in roots under different stress conditions. The CsPSY3 expression was high in the root tip, and its expression was associated with mycorrhizal colonization and strigolactone production. CsPSY3 formed a separate branch to the stress-specific Poaceae homologs but was closely related to the dicot PSY3 enzymes.

A chitinase with antifungal activity from naked oat (Avena chinensis) seeds

A chitinase was purified from naked oat (Avena chinensis) seeds using simple chromatographic techniques. Its molecular weight and isoelectric point were determined as 35 kDa and 8.9, respectively. The purified chitinase exhibited specific activity of 3.6 U/mg and 15.6% yield using colloidal chitin as substrate. Partial amino acid sequence analysis and homology search indicated that it probably belonged to Class I plant chitinase, glycosyl hydrolase family 19. With chitin as substrate, the optimum pH and temperature of the chitinase were pH 7.0 and 40°C, respectively. The chitinase was remarkably stable from 30°C up to 50°C, but was inactivated at high temperatures above 85°C. Antifungal activity in vitro tests demonstrated this purified chitinase had potent, dose-dependent inhibitory activity against the fungi Panus conchatus and Trichoderma reesei. PRACTICAL APPLICATIONS: Chitinase has broad applications in many fields including the food industry and is recognized as one of the antifungal substances with potential use in plant disease resistance or biological control in agriculture. This study developed cost-effective purification methods for producing chitinase from naked oat (Avena chinensis) seeds, which may favor large-scale production of the enzyme. The remarkable stability of the chitinase at moderate temperatures (30°C-50°C), makes it a potentially useful enzyme in bioprocessing to produce chitooligosaccharides for various applications in the food, health, and agriculture sectors.

Molecular phylogeny, diversity, community structure, and plant growth promoting properties of fungal endophytes associated with the corms of saffron plant: An insight into the microbiome of Crocus sativus Linn

A total of 294 fungal endophytes were isolated from the corms of Crocus sativus at two stages of crocus life cycle collected from 14 different saffron growing sites in Jammu and Kashmir (J & K) State, India. Molecular phylogeny assigned them into 36 distinct internal transcribed spacer (ITS) genotypes which spread over 19 genera. The diversity of endophytes was higher at the dormant than at the vegetative stage. The Saffron microbiome was dominated by Phialophora mustea and Cadophora malorum, both are dark septate endophytes (DSEs). Some endophytes were found to possess antimicrobial properties that could be helpful for the host in evading the pathogens. These endophytes generally produced significant quantities of indole acetic acid (IAA) as well. However, thirteen of the endophytic taxa were found to cause corm rot in the host with different levels of severity under in vitro as well as in vivo conditions. This is the first report of community structure and biological properties of fungal endophytes associated with C. sativus, which may eventually help us to develop agro-technologies, based on plant-endophyte interactions for sustainable cultivation of saffron. The endophytes preserved ex situ, in this study, may also yield bioactive natural products for pharmacological and industrial applications.

Challenges of climate change: omics-based biology of saffron plants and organic agricultural biotechnology for sustainable saffron production

Kashmir Valley is a major saffron (Crocus sativus Kashmirianus) growing area of the world, second only to Iran in terms of production. In Kashmir, saffron is grown on uplands (termed in the local language as "Karewas"), which are lacustrine deposits located at an altitude of 1585 to 1677 m above mean sea level (amsl), under temperate climatic conditions. Kashmir, despite being one of the oldest historical saffron-producing areas, faces a rapid decline of saffron industry. Among many other factors responsible for decline of saffron industry the preponderance of erratic rainfalls and drought-like situation have become major challenges imposed by climate change. Saffron has a limited coverage area as it is grown as a 'niche crop' and is a recognized "geographical indication," growing under a narrow microclimatic condition. As such it has become a victim of climate change effects, which has the potential of jeopardizing the livelihood of thousands of farmers and traders associated with it. The paper discusses the potential and actual impact of climate change process on saffron cultivation in Kashmir; and the biotechnological measures to address these issues.

Purification, characterization of a CkChn134 protein from Cynanchum komarovii seeds and synergistic effect with CkTLP against Verticillium dahliae

Cynanchum komarovii Al Iljinski is a desert plant that has been used as analgesic, anthelminthic, and antidiarrheal, but also as herbal medicine to treat cholecystitis in people. In this work, an antifungal protein with sequence homology to chitinase was isolated from C. komarovii seeds and named CkChn134. The three-dimensional structure prediction of CkChn134 indicated that the protein has a loop domain formed a thin cleft, which is able to bind molecules and substrates. The protein and CkTLP synergistically inhibited the fungal growth of Verticillium dahliae, Fusarium oxysporum, Rhizoctonia solani, Botrytis cinerea, and Valsa mali in vitro. The full-length cDNA was cloned by RT-PCR and RACE-PCR according to the partial protein sequences obtained by nanoESI-MS/MS. The real-time PCR showed that the transcription level of CkChn134 had a significant increase under the stress of ethylene, NaCl, low temperature, drought, and pathogen infection, which indicates that CkChn134 may play an important role in response to abiotic and biotic stresses. The CkChn134 protein was located in the extracellular space/cell wall by CkChn134::GFP fusion protein in transgenic Arabidopsis. Furthermore, overexpression of CkChn134 significantly enhanced the resistance of transgenic Arabidopsis against V. dahliae. Interestingly, the coexpression of CkChn134 and CkTLP showed substantially greater protection against the fungal pathogen V. dahliae than either transgene alone. The results suggest that the CkChn134 is a good candidate protein or gene, and it had a potential synergistic effect with CkTLP for contributing to the development of disease-resistant crops.

Developmental and stress regulation of gene expression for a 9-cis-epoxycarotenoid dioxygenase, CstNCED, isolated from Crocus sativus stigmas

Oxidative cleavage of cis-epoxycarotenoids by 9-cis-epoxycarotenoid dioxygenase (NCED) is the critical step in the regulation of abscisic acid (ABA) synthesis in higher plants. ABA has been associated with dormancy and flower senescence, while also regulating plant adaptive responses to various environmental stresses. An NCED gene, CstNCED, was cloned from Crocus sativus stigmas. The deduced amino acid sequence of the CstNCED protein shared high identity with other monocot NCEDs, and was closely related to the liliopsida enzymes. At the N-terminus of CstNCED a chloroplast transit peptide sequence is located. However, its expression in chloroplast-free tissues suggested localization in other plastid types. The relationship between expression of CstNCED and the endogenous ABA level was investigated in the stigma and corms, where it was developmentally regulated. The senescence of the unpollinated stigma is preceded by an increase in ABA levels and CstNCED expression. In corms, a correlation was observed between CstNCED expression and dormancy. Furthermore, CstNCED expression was correlated with the presence of zeaxanthin in the dormant corms. When detached C. sativus leaves and stigmas were water and salt stressed, increases in CstNCED mRNA were observed. The results provided evidence of the involvement of CstNCED in the regulation of ABA-associated processes such as flower senescence and corm dormancy in monocotyledonous saffron.