Comparative genomic analysis of the aldehyde dehydrogenase gene superfamily in Arabidopsis thaliana - searching for the functional key to hypoxia tolerance

OsHDAC1 deacetylates the aldehyde dehydrogenase OsALDH2B1, repressing OsGR3 and decreasing salt tolerance in rice

Salt stress poses a significant challenge to the growth and productivity of rice (Oryza sativa L.). Histone deacetylases (HDACs) play a vital role in modulating responses to various abiotic stresses. However, how OsHDAC1 responds to salt stress remains largely unknown. Here, we report that OsHDAC1 decreases salt tolerance in rice through posttranslational modification of metabolic enzymes. Specifically, the rice OsHDAC1 RNAi lines exhibited enhanced resilience to salt stress, while plants overexpressing OsHDAC1 were notably more sensitive. OsHDAC1 interacts with the aldehyde dehydrogenase (ALDH) OsALDH2B1 and deacetylates it at K311 and K531, triggering ubiquitin-proteasome-mediated degradation of OsALDH2B1. OsALDH2B1 can directly target OsGR3, which encodes a type of glutathione reductase critical for reactive oxygen species scavenging. Compared with wild-type plants, OsALDH2B1-overexpressing plants exhibited higher OsGR3 expression levels and increased salt resistance, whereas OsALDH2B1 RNAi lines showed reduced OsGR3 expression and lower salt resistance. Collectively, our data suggest that salt stress downregulates OsHDAC1, resulting in an increase in the acetylation level of OsALDH2B1, which in turn stabilizes OsALDH2B1 and promotes its activity in the regulation of OsGR3 transcription. This OsHDAC1/OsALDH2B1/OsGR3 regulatory module represents an alternative pathway for governing salt stress adaptation in rice.

The Aldehyde Dehydrogenase Superfamily in Brassica napus L.: Genome-Wide Identification and Expression Analysis Under Low-Temperature Conditions

The Aldehyde Dehydrogenase (ALDH) superfamily comprises a group of NAD+ or NADP+-dependent enzymes that play essential roles in responding to abiotic stresses in plants. In Brassica napus L., however, the increasing frequency of extremely low temperatures during winter in recent years has significantly affected both yield and quality. This study conducted a genome-wide screening of ALDH superfamily genes, analyzing their gene structures, evolutionary relationships, protein physicochemical properties, and expression patterns under low-temperature stress to explore the function of the ALDH superfamily gene in cold tolerance in Brassica napus L. A total of six BnALDH genes with significant differences in expression levels were verified utilizing quantitative real-time polymerase chain reaction (qRT-PCR), revealing that BnALDH11A2, BnALDH7B2, BnALDH3F5, BnALDH12A3, BnALDH2B6, and BnALDH7B3 all exhibited higher expression in cold-tolerant material 24W233 compared with cold-sensitive material 24W259. Additionally, a single nucleotide polymorphism (SNP) in the BnALDH11A2 promoter region shows differences between the cold-tolerant (24W233) and the cold-sensitive (24W259) Brassica napus varieties, and it may be associated with the cold tolerance of these two varieties. This comprehensive analysis offers valuable insights into the role of ALDH family genes in low-temperature stress adaptation in Brassica napus and offers genetic resources for the development of novel cold-tolerant cultivars.

Genome-wide identification, classification, and expression profiling of the aldehyde dehydrogenase gene family in pepper

Pepper (Capsicum annuum L.) is one of the most significant vegetable crops worldwide which is known for its pungency and nutritional value. The aldehyde dehydrogenase (ALDH) superfamily encompasses enzymes critical for the detoxification of toxic aldehydes into non-toxic carboxylic acids. A comprehensive genome-wide approach in pepper identified a total of 27 putative ALDH genes grouped into ten families based on the criteria of the ALDH gene nomenclature committee. Both segmental and tandem duplication assisted in the enhancement of CaALDH gene family members. The identified CaALDH members were found to be more closely related to the dicot plants, however, the members were distributed across the phylogenetic tree suggesting the pre-eudicot-monocot separation of the ALDH superfamily members. The gene structure and protein domain were found to be mostly conserved in separate phylogenetic classes, indicating that each family played an important role in evolution. Expression analysis revealed that CaALDHs were expressed in various tissues, developmental stages, and in response to abiotic stresses, indicating that they can play roles in plant growth, development, and stress adaptation. Interestingly, the majority of the CaALDH genes were found to be highly responsive to salinity stress, and only the CaALDH11A1 transcript showed upregulation in cold stress conditions. The presence of cis-acting elements in the promoter region of these genes might have a significant role in abiotic stress tolerance. Overall, these findings add to the current understanding, evolutionary history, and contribution of CaALDHs in stress tolerance, and smooth the path of further functional validation of these genes.

Increasing nitrogen use efficiency in agronomically important plants: An insight into gene characteristics on a genome-wide scale in barley

Nitrogen (N) is a critical element for plant growth and development. Hence, improving nitrogen use efficiency (NUE) is vital for reducing costs and the environmental impact of agricultural practices. Understanding the genetic control of N metabolism is crucial to improve NUE, especially in agronomically important plants, such as barley (Hordeum vulgare). Using bioinformatics and functional genomics tools, we identified and characterized sixteen barley nitrogen metabolism-related gene families (HvNMGs) on a genome-wide scale, analysing gene features and evolution. These genes, located on six of seven barley chromosomes, are highly conserved in plants (including barley, rice, and Arabidopsis), as shown by phylogenetic analysis. We further explored the evolutionary relationships of NMGs through a genome-to-genome synteny analysis, which indicated higher conservation of NMGs between barley and other monocots, suggesting that these orthologous pairs predate species divergence. Protein-protein interaction analyses revealed that all of the HvNMGs show interactions, mainly with each other. The H. vulgare miRNAs target sites (hvu-miR) prediction identified six hvu-miR in 4 HvNMGs (HvGABA-T2, HvALDH10-1, HvALDH10-2 and HvARGAH), indicating their potential involvement in stress responses. The expression patterns analysis of publicly available RNA-seq data revealed that HvNMGs are expressed in all developmental stages of barley, and they respond to different stress conditions, indicating their essential role in plant growth, development and stress response. The organ-specific expression analysis, conducted using qPCR, of HvNMGs revealed higher expression of HvNiR and HvNRs in the leaf and significantly higher expression of HvARGAH and HvALDH10 in the spike than in other tissues, showing that some of the genes may be particularly important in some tissues than others. This data provides a foundation for understanding HvNMG function and could be used to improve barley yield by enhancing NUE - an important goal for both crop productivity and environmental sustainability.

Proteome and metabolome of Caryocar brasiliense camb. fruit and their interaction during development

Considered the symbol fruit of the Brazilian Cerrado, pequi (Caryocar brasiliense Camb.) is an exotic and much-appreciated fruit with an internal mesocarp (edible part) with an eye-catching golden yellow color. In an unprecedented way, this study characterized the proteome throughout pequi development. The most influential and essential transcription factors operating in the regulation of pequi ripening identified were members of the MAD-box family. A group of proteins related to the methionine cycle indicates the high consumption and recycling of methionine. However this consumption does not occur mainly for the biosynthesis of ethylene, a process dependent on methionine consumption. In the bioactive compounds presented, different proteins could be correlated with the presence of these phytochemicals, such as monodehydroascorbate reductase and ascorbate peroxidase in ascorbic acid recycling; pyruvate kinase, fructose bisphosphate aldolase and phytoene synthase with carotenoid biosynthesis; S-adenosylmethionine synthase 1 as a donor of methyl groups in the formation of trigonelline and aspartate aminotransferase as a biomarker of initial regulation of the trigonelline biosynthetic pathway; phenylalanine ammonia lyase, chorismate synthesis and chalcone-flavononone isomerase in the biosynthesis of phenolic compounds. Among the volatile organic compounds identified, the majority compound in pequi was ethyl hexanoate ester, with an area of 50.68 % in the ripe fruit, and in this group of esters that was the most representative, alcohol dehydrogenase, a fundamental enzyme in the synthesis of esters, was identified with an increase of approximately 7.2 times between the first and last stages. Therefore, an extensive group of proteins and some metabolites can serve as biomarkers of ripening in pequi, as most were more expressed in the last stage, which is the ripe fruit suitable for consumption.

Functional Characterization of Aldehyde Dehydrogenase in Fusarium graminearum

Aldehyde dehydrogenase (ALDH), a common oxidoreductase in organisms, is an aldehyde scavenger involved in various metabolic processes. However, its function in different pathogenic fungi remains unknown. Fusarium graminearum causes Fusarium head blight in cereals, which reduces grain yield and quality and is an important global food security problem. To elucidate the pathogenic mechanism of F. graminearum, seven genes encoding ALDH were knocked out and then studied for their function. Single deletions of seven ALDH genes caused a decrease in spore production and weakened the pathogenicity. Furthermore, these deletions altered susceptibility to various abiotic stresses. FGSG_04194 is associated with a number of functions, including mycelial growth and development, stress sensitivity, pathogenicity, toxin production, and energy metabolism. FGSG_00139 and FGSG_11482 are involved in sporulation, pathogenicity, and SDH activity, while the other five genes are multifunctional. Notably, we found that FGSG_04194 has an inhibitory impact on ALDH activity, whereas FGSG_00979 has a positive impact. RNA sequencing and subcellular location analysis revealed that FGSG_04194 is responsible for biological process regulation, including glucose and lipid metabolism. Our results suggest that ALDH contributes to growth, stress responses, pathogenicity, deoxynivalenol synthesis, and mitochondrial energy metabolism in F. graminearum. Finally, ALDH presents a potential target and theoretical basis for fungicide development.

Study on molecular mechanism of volatiles variation during Bupleurum scorzonerifolium root development based on metabolome and transcriptome analysis

Bupleurum scorzonerifolium Willd. is a medicinal herb. Its root has a high content of volatile oil (BSVO), which shows a variety of biological activities. Currently, BSVO in the injectable form is used for treating fever in humans and livestock. The yield and quality of volatile oils depends on the developmental stages of plants. However, the changes in BSVO yield and quality during root development in Bupleurum scorzonerifolium and the underlying molecular regulatory mechanisms remain unclear. This knowledge gap is limiting the improvement in the quality of BSVO. In the present study, B. scorzonerifolium root was collected at germinative, vegetative, florescence, fruiting and defoliating stages. The yield of BSVO, metabolic profile of volatile components and transcriptome of root samples at various developmental stages were comprehensively determined and compared. BSVO continuously accumulated from the germinative to fruiting stages, and its level slightly decreased from the fruiting to defoliating stages. A total of 82 volatile components were detected from B. scorzonerifolium root, of which 22 volatiles were identified as differentially accumulated metabolites (DAMs) during the root development. Of these volatiles, fatty acids and their derivatives accounted for the largest proportion. The contents of most major volatiles were highest at the fruiting stage. A large number of differentially expressed genes (DEGs) were detected during B. scorzonerifolium root development, of which 65 DEGs encoded various enzymes and transcription factors regulating the biosynthesis of fatty acids and their derivatives. In further analysis, 42 DEGs were identified to be significantly correlated with DAMs, and these DEGs may be the key genes for the biosynthesis of volatiles. To the best of our knowledge, this is the first study to comprehensively report the changes in the composition and content of volatiles and underlying mechanism during B. scorzonerifolium root development. This study provided important reference for future studies to determine the harvest time of B. scorzonerifolium roots and improve the quality of BSVO.