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This editorial summarizes the main scientific contributions from 11 papers comprising the Special Issue (SI) "Molecular Basis of Crops and Fruit Plants in Response to Stress". Here, we collected papers from different research groups encompassing molecular studies from monocots (ginger, rice, maize) and eudicots (common hazel, cowpea, pepper, soybean, tomato) species submitted to abiotic stresses as heat, cold, salt, drought, and heavy metals or biotic stresses induced by different viruses, such as BPEV, PepGMV, PMMoV, and TEV. These studies explored different aspects of molecular mechanisms involved in plant stress tolerance, establishing comparative analyses among genotypes/cultivars to identify potential molecular markers of stresses that are now available for future application in biotechnological studies. This SI presents a collection of advanced concepts and emerging strategies for readers and researchers aiming to accelerate plant breeding.
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Pepper (Capsicum annuum L.) is a vegetable consumed worldwide, primarily used for vitamin C uptake and condiment purposes. Ascorbate (Asc) is a multifunctional metabolite, acting as an antioxidant and enzymatic cofactor involved in multiple cellular processes. Nevertheless, there is no evidence about the contribution of biosynthesis pathways and regulatory mechanisms responsible for Asc reserves in pepper plants. Here, we present a genome- and transcriptome-wide investigation of genes responsible for Asc biosynthesis in pepper during fruit development, stresses, and phytohormone exposures. A total of 21 genes, scattered in ten of twelve pepper chromosomes were annotated. Gene expression analyses of nine transcriptomic experiments supported the primary role of the L-galactose pathway in the Asc-biosynthesizing process, given its constitutive, ubiquitous, and high expression profile observed in all studied conditions. However, genes from alternative pathways generally exhibited low expression or were unexpressed and appeared to play some secondary role under specific stress conditions and phytohormone treatments. Taken together, our findings provide a deeper spatio-temporal understanding of expression levels of genes involved in Asc biosynthesis, and they highlight GGP2, GME1 and 2, and GalLDH members from L-galactose pathway as promising candidates for future wet experimentation, addressing the attainment of increase in ascorbate content of peppers and other crops.
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Identifying cultivars of leguminous crops exhibiting drought resistance has become crucial in addressing water scarcity issues. This investigative study aimed to select soybean and cowpea cultivars with enhanced potential to grow under water restriction during the vegetative stage. Two parallel trials were conducted using seven soybean (AS3810IPRO, M8644IPRO, TMG1180RR, NS 8338IPRO, BMX81I81IPRO, M8808IPRO, and BÔNUS8579IPRO) and cowpea cultivars (Aracê, Novaera, Pajeú, Pitiúba, Tumucumaque, TVU, and Xique-xique) under four water levels (75, 60, 45, and 30% field capacity-FC) over 21 days. Growth, water content, membrane damage, photosynthetic pigments, organic compounds, and proline levels were analyzed. Drought stress significantly impacted the growth of both crops, particularly at 45 and 30% FC for soybean and 60 and 45% FC for cowpea plants. The BÔNUS8579IPRO and TMG1180RR soybean cultivars demonstrated the highest performance under drought, a response attributed to increased amino acids and proline contents, which likely help to mitigate membrane damage. For cowpea, the superior performance of the drought-stressed Xique-xique cultivar was associated with the maintenance of water content and elevated photosynthetic pigments, which contributed to the preservation of the photosynthetic efficiency and carbohydrate levels. Our findings clearly indicate promising leguminous cultivars that grow under water restriction, serving as viable alternatives for cultivating in water-limited environments.
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We investigated SNPs in alternative oxidase (AOX) genes and their connection to ecotype origins (climate, altitude, and rainfall) by using genomic data sets of Arabidopsis and rice populations from 1190 and 90 ecotypes, respectively. Parameters were defined to detect non-synonymous SNPs in the AOX ORF, which revealed amino acid (AA) changes in AOX1c, AOX1d, and AOX2 from Arabidopsis and AOX1c from rice in comparison to AOX references from Columbia-0 and Japonica ecotypes, respectively. Among these AA changes, Arabidopsis AOX1c_A161E&G165R and AOX1c_R242S revealed a link to high rainfall and high altitude, respectively, while all other changes in Arabidopsis and rice AOX was connected to high altitude and rainfall. Comparative 3D modeling showed that all mutant AOX presented structural differences in relation to the respective references. Molecular docking analysis uncovered lower binding affinity values between AOX and the substrate ubiquinol for most of the identified structures compared to their reference, indicating better enzyme-substrate binding affinities. Thus, our in silico data suggest that the majority of the AA changes found in the available ecotypes will confer better enzyme-subtract interactions and thus indicate environment-related, more efficient AOX activity.
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Arabidopsis , Oryza , Arabidopsis/metabolismo , Oryza/metabolismo , Ecótipo , Altitude , Simulação de Acoplamento Molecular , Proteínas de Plantas/metabolismo , Proteínas Mitocondriais/metabolismoRESUMO
The molecule vitamin C, in the chemical form of ascorbic acid (AsA), is known to be essential for the metabolism of humans and animals. Humans do not produce AsA, so they depend on plants as a source of vitamin C for their food. The AsA synthesis pathway occurs partially in the cytosol, but the last oxidation step is physically linked to the respiratory chain of plant mitochondria. This oxidation step is catalyzed by l-galactono-1,4-lactone dehydrogenase (l-GalLDH). This enzyme is not considered a limiting step for AsA production; however, it presents a distinguishing characteristic: the l-GalLDH can introduce electrons directly into the respiratory chain through cytochrome c (Cytc) and therefore can be considered an extramitochondrial electron source that bypasses the phosphorylating Complex III. The use of Cytc as electron acceptor has been debated in terms of its need for AsA synthesis, but little has been said in relation to its impact on the functioning of the respiratory chain. This work seeks to offer a new view about the possible changes that result of the link between AsA synthesis and the mitochondrial respiration. We hypothesized that some physiological alterations related to low AsA may be not only explained by the deficiency of this molecule but also by the changes in the respiratory function. We discussed some findings showing that respiratory mutants contained changes in AsA synthesis. Besides, recent works that also indicate that the excessive electron transport via l-GalLDH enzyme may affect other respiratory pathways. We proposed that Cytc reduction by l-GalLDH may be part of an alternative respiratory pathway that is active during AsA synthesis. Also, it is proposed that possible links of this pathway with other pathways of alternative electron transport in plant mitochondria may exist. The review suggests potential implications of this relationship, particularly for situations of stress. We hypothesized that this pathway of alternative electron input would serve as a strategy for adaptation of plant respiration to changing conditions.
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Plants subjected to stress need to respond rapidly and efficiently to acclimatize and survive. In this paper, we investigated a selected gene set potentially involved in early cell reprogramming in two rice genotypes with contrasting salinity tolerance (Pokkali tolerant and IR29 susceptible) in order to advance knowledge of early molecular mechanisms of rice in dealing with salt stress. Selected genes were evaluated in available transcriptomic data over a short period of 24 h and involved enzymes that avoid ROS formation (AOX, UCP and PTOX), impact ATP production (PFK, ADH and COX) or relate to the antioxidant system. Higher transcript accumulation of AOX (ROS balancing), PFK and ADH (alcohol fermentation) was detected in the tolerant genotype, while the sensitive genotype revealed higher UCP and PTOX transcript levels, indicating a predominant role for early transcription of AOX and fermentation in conferring salt stress tolerance to rice. Antioxidant gene analyses supported higher oxidative stress in IR29, with transcript increases of cytosolic CAT and SOD from all cell compartments (cytoplasm, peroxisome, chloroplast and mitochondria). In contrast, Pokkali increased mRNA levels from the AsA-GSH cycle as cytosolic/mitochondrial DHAR was involved in ascorbate recovery. In addition, these responses occurred from 2 h in IR29 and 10 h in Pokkali, indicating early but ineffective antioxidant activity in the susceptible genotype. Overall, our data suggest that AOX and ADH can play a critical role during early cell reprogramming for improving salt stress tolerance by efficiently controlling ROS formation in mitochondria. We discuss our results in relation to gene engineering and editing approaches to develop salinity-tolerant crops.
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KEY MESSAGE: We found 34 and 71 key genes potentially involved in flavonoid biosynthesis and cell wall disassembly, respectively, which could be associated with specific peel coloration and softening of each genotype. Cashew apple (Anacardium occidentale) has a great economic importance worldwide due to its high nutritional value, peculiar flavor and aroma. During ripening, the peduncle develops different peel color and becomes quickly fragile due to its oversoftening, impacting its consumers' acceptance. In view of this, the understanding about its transcriptional dynamics throughout ripening is imperative. In this study, we performed a transcriptome sequencing of two cashew apple genotypes (CCP 76 and BRS 265), presenting different firmness and color peel, in the immature and ripe stages. Comparative transcriptome analysis between immature and ripe cashew apple revealed 4374 and 3266 differentially expressed genes (DEGs) to CCP 76 and BRS 265 genotypes, respectively. These genes included 71 and 34 GDEs involved in the cell wall disassembly and flavonoid biosynthesis, respectively, which could be associated with firmness loss and anthocyanin accumulation during cashew apple development. Then, softer peduncle of CCP 76 could be justified by down-regulated EXP and up-regulation of genes involved in pectin degradation (PG, PL and PAE) and in cell wall biosynthesis. Moreover, genes related to flavonoid biosynthesis (PAL, C4H and CHS) could be associated with early high accumulation of anthocyanin in red-peel peduncle of BRS 265. Finally, expression patterns of the selected genes were tested by real-time quantitative PCR (qRT-PCR), and the qRT-PCR results were consistent with transcriptome data. The information generated in this work will provide insights into transcriptome responses to cashew apple ripening and hence, it will be helpful for cashew breeding programs aimed at developing genotypes with improved quality traits.
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Anacardium , Anacardium/genética , Antocianinas , Frutas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genótipo , Melhoramento Vegetal , TranscriptomaRESUMO
BACKGROUND: Early metabolic reorganization was only recently recognized as an essentially integrated part of immunology. In this context, unbalanced ROS/RNS levels connected to increased aerobic fermentation, which is linked to alpha-tubulin-based cell restructuring and control of cell cycle progression, were identified as a major complex trait for early de novo programming ('CoV-MAC-TED') during SARS-CoV-2 infection. This trait was highlighted as a critical target for developing early anti-viral/anti-SARS-CoV-2 strategies. To obtain this result, analyses had been performed on transcriptome data from diverse experimental cell systems. A call was released for wide data collection of the defined set of genes for transcriptome analyses, named 'ReprogVirus', which should be based on strictly standardized protocols and data entry from diverse virus types and variants into the 'ReprogVirus Platform'. This platform is currently under development. However, so far, an in vitro cell system from primary target cells for virus attacks that could ideally serve for standardizing the data collection of early SARS-CoV-2 infection responses has not been defined. RESULTS: Here, we demonstrate transcriptome-level profiles of the most critical 'ReprogVirus' gene sets for identifying 'CoV-MAC-TED' in cultured human nasal epithelial cells infected by two SARS-CoV-2 variants differing in disease severity. Our results (a) validate 'Cov-MAC-TED' as a crucial trait for early SARS-CoV-2 reprogramming for the tested virus variants and (b) demonstrate its relevance in cultured human nasal epithelial cells. CONCLUSION: In vitro-cultured human nasal epithelial cells proved to be appropriate for standardized transcriptome data collection in the 'ReprogVirus Platform'. Thus, this cell system is highly promising to advance integrative data analyses with the help of artificial intelligence methodologies for designing anti-SARS-CoV-2 strategies.
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In a perspective entitled 'From plant survival under severe stress to anti-viral human defense' we raised and justified the hypothesis that transcript level profiles of justified target genes established from in vitro somatic embryogenesis (SE) induction in plants as a reference compared to virus-induced profiles can identify differential virus signatures that link to harmful reprogramming. A standard profile of selected genes named 'ReprogVirus' was proposed for in vitro-scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait. For data collection, the 'ReprogVirus platform' was initiated. This initiative aims to identify in a common effort across scientific boundaries critical virus footprints from diverse virus origins and variants as a basis for anti-viral strategy design. This approach is open for validation and extension. In the present study, we initiated validation by experimental transcriptome data available in public domain combined with advancing plant wet lab research. We compared plant-adapted transcriptomes according to 'RegroVirus' complemented by alternative oxidase (AOX) genes during de novo programming under SE-inducing conditions with in vitro corona virus-induced transcriptome profiles. This approach enabled identifying a major complex trait for early de novo programming during SARS-CoV-2 infection, called 'CoV-MAC-TED'. It consists of unbalanced ROS/RNS levels, which are connected to increased aerobic fermentation that links to alpha-tubulin-based cell restructuration and progression of cell cycle. We conclude that anti-viral/anti-SARS-CoV-2 strategies need to rigorously target 'CoV-MAC-TED' in primary infected nose and mouth cells through prophylactic and very early therapeutic strategies. We also discuss potential strategies in the view of the beneficial role of AOX for resilient behavior in plants. Furthermore, following the general observation that ROS/RNS equilibration/redox homeostasis is of utmost importance at the very beginning of viral infection, we highlight that 'de-stressing' disease and social handling should be seen as essential part of anti-viral/anti-SARS-CoV-2 strategies.