Aldehyde dehydrogenase superfamily in sorghum: genome-wide identification, evolution, and transcript profiling during development stages and stress conditions

Identification of Mustard Aldehyde Dehydrogenase (ALDH) Gene Family and Expression Analysis Under Salt and Drought Stress

BACKGROUND/OBJECTIVES

Abiotic stresses severely constrain the yield of Brassica juncea, and aldehyde dehydrogenases (ALDHs) play a pivotal role in plant stress resistance. This study aims to systematically identify the ALDH gene family members in B. juncea and elucidate their expression patterns under salt and drought stress.

METHODS

Using the Arabidopsis thaliana AtALDH proteins as seed sequences, BLASTp alignment was performed against the B. juncea whole-protein sequence database, combined with the conserved domain PF00171 of the ALDH proteins. A total of 39 BjALDH gene family members were identified, and their physicochemical properties, structures, phylogenetic relationships, interspecies collinearity, and intraspecies collinearity were analyzed. The qRT-PCR method was employed to quantify the relative expression levels of the BjALDH genes potentially associated with stress resistance under various treatments, and their effects on drought and salt stress tolerance were evaluated.

RESULTS

The results demonstrated that BjALDH were universally significantly upregulated under salt stress, while exhibiting predominantly upregulated trends under drought stress. These findings suggest that BjALDH may enhance plant resistance to both salt and drought stress by modulating the aldehyde metabolic pathways.

CONCLUSIONS

This study provides a theoretical basis for elucidating the functional roles and molecular genetic mechanisms of the BjALDH gene family in B. juncea under salt and drought stress.

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.

Identification of Aldehyde Dehydrogenase Gene Family in Glycyrrhiza uralensis and Analysis of Expression Pattern Under Drought Stress

Aldehyde dehydrogenases (ALDHs) are a gene family that relies on NAD +/NADP + proteins to oxidize toxic aldehydes to non-toxic carboxylic acids, and they play a crucial role in the growth and development of plants, as well as in their ability to withstand stress. This study identified 26 ALDH genes from six Glycyrrhiza uralensis gene families distributed on six chromosomes. By analyzing the phylogeny, gene structure, conserved motifs, cis-regulatory elements, collinearity of homologs, evolutionary patterns, differentiation patterns, and expression variations under drought stress, we found that the ALDH gene is involved in phytohormones and exhibits responsiveness to various environmental stressors by modulating multiple cis-regulatory elements. In addition, GuALDH3H1, GuALDH6B1, GuALDH12A2, and GuALDH12A1 have been identified as playing a crucial role in the response to drought stress. By analyzing the expression patterns of different tissues under drought stress, we discovered that GuALDH3I2 and GuALDH2B2 exhibited the most pronounced impact in relation to the drought stress response, which indicates that they play a positive role in the response to abiotic stress. These findings provide a comprehensive theoretical basis for the ALDH gene family in Glycyrrhiza uralensis and enhance our understanding of the molecular mechanisms underlying ALDH genes in licorice growth, development, and adaptation to drought stress.

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.

Combined metabolome and transcriptome analysis reveals the key pathways involved in the responses of soybean plants to high Se stress

High selenium (Se) levels can induce toxicity, inhibit growth, and affect gene expression and metabolite content in plants. However, the molecular mechanism by which high Se stress affects soybean plants remains unclear. This study examined the responses of soybean leaves and roots to high Se stress using transcriptome and metabolome analyses. High Se stress significantly inhibited soybean root growth, reduced leaf area, and affected the antioxidant enzyme system in roots and leaves, resulting in the accumulation of malondialdehyde (MDA). High Se stress increased indoleacetic acid (IAA), abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA) in the roots by 3.34-fold, 8.94-fold, 0.25-fold, and 5.65-fold, respectively. Similarly, high Se stress increased IAA, ABA, JA, and SA in the leaves by 1.96-fold, 10.54-fold, 2.03-fold, and 4.22-fold, respectively. In addition, high Se stress affected ion absorption and transport in soybean plants. Transcriptome results showed that there were 10,038 differentially expressed genes (DEGs) in soybean roots and 5811 DEGs in leaves, which affected the expression of antioxidant enzymes, ion transport and hormone-related genes. Metabolome results revealed that there were 277 differentially expressed metabolites (DEMs) in soybean leaves and 312 DEMs in roots. Soybean roots and leaves were significantly enriched in the "β-alanine metabolism" pathway under high Se stress, with differential expression of Aldehyde dehydrogenase (ALDH), Amine oxidase (AO), and other related genes, thereby relieving oxidative stress. This study improves our understanding of the molecular mechanisms underlying the responses of soybean plants to high Se stress and provides a basis for breeding Se-enriched soybean plants.

Genome-Wide Identification and Expression Analysis of the Melon Aldehyde Dehydrogenase (ALDH) Gene Family in Response to Abiotic and Biotic Stresses

Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragmental duplications within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon's ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue- or stage-specific. We analyzed the ALDH gene's expression patterns under six stress types, namely salt, cold, waterlogged, powdery mildew, Fusarium wilt, and gummy stem blight. The results showed differential expression of CmALDH2C4 and CmALDH11A3 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR (quantitative reverse transcription PCR) analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Physiological and gene expression response mechanisms of dehydration process in Cinnamomum cassia (L.) J. Presl seeds

BACKGROUND

A critical factor in the storability of recalcitrant seeds is their moisture content (MC), but its effect on the viability of Cinnamomum cassia (L.) J. Presl (C. cassia) seeds is not fully understood.

METHODS AND RESULTS

Measured the germination rate, starch and soluble sugar content, and transcriptome of 8 seed samples with different MC obtained by low-temperature drying method. It was found that the germination rate was significantly negatively correlated with MC. The lethal MC was around 15.6%. During the dehydration process, there was a significant increase in the content of soluble sugars and starch. Transcriptome analysis was performed on CK, W3, W6 showed a total of 62.78 Gb of clean data. Among the 30,228 Unigenes, 28,195 were successfully annotated. In the three comparative groups (CK and W3, CK and W6, W3 and W6), 6,842, 7,640, and 11,628 differentially expressed genes (DEGs) were obtained, respectively. These DEGs were found to be involved in a variety of metabolic pathways, including carbon metabolism, amino acid biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and nucleotide and amino sugar metabolism. A total of 1,416 common genes were identified among all three comparison groups. Furthermore, among all the DEGs, a total of 71 transcription factor families were identified, with the C2H2 transcription factor family having the highest number of genes.

CONCLUSIONS

This ground-breaking study sheds light on the physiological response and gene expression profiles of C. cassia seeds after undergoing dehydration treatment, which will provide valuable insights for further research and understanding of this process.

Insights into cellular crosstalk regulating cytoplasmic male sterility and fertility restoration

Cytoplasmic male sterility has been a popular genetic tool in development of hybrids. The molecular mechanism behind maternal sterility varies from crop to crop. An understanding of underlying mechanism can help in development of new functional CMS gene in crops which lack effective and stable CMS systems. In crops where seed or fruit is the commercial product, fertility must be recovered in F1 hybrids so that higher yield gains can be realized. This necessitates the presence of fertility restorer gene (Rf) in nucleus of male parent to overcome the effect of sterile cytoplasm. Fertility restoring genes have been identified in crops like wheat, maize, sunflower, rice, pepper, sugar beet, pigeon pea etc. But in crops like eggplant, bell pepper, barley etc. unstable fertility restorers hamper the use of Cytoplasmic genic male sterility (CGMS) system. Stability of CGMS system is influenced by environment, genetic background or interaction of these factors. This review thus aims to understand the genetic mechanisms controlling mitochondrial-nuclear interactions required to design strong and stable restorers without any pleiotropic effects in F1 hybrids.

Comprehensive analysis of the aldehyde dehydrogenase gene family in Phaseolus vulgaris L. and their response to saline-alkali stress

Background

Aldehyde dehydrogenase (ALDH) scavenges toxic aldehyde molecules by catalyzing the oxidation of aldehydes to carboxylic acids. Although ALDH gene family members in various plants have been extensively studied and were found to regulate plant response to abiotic stress, reports on ALDH genes in the common bean (Phaseolus vulgaris L.) are limited. In this study, we aimed to investigate the effects of neutral (NS) and basic alkaline (AS) stresses on growth, physiological and biochemical indices, and ALDH activity, ALDH gene expression of common bean. In addition, We used bioinformatics techniques to analyze the physical and chemical properties, phylogenetic relationships, gene replication, collinearity, cis-acting elements, gene structure, motifs, and protein structural characteristics of PvALDH family members.

Results

We found that both NS and AS stresses weakened the photosynthetic performance of the leaves, induced oxidative stress, inhibited common bean growth, and enhanced the antioxidative system to scavenge reactive oxygen species. Furthermore, we our findings revealed that ALDH in the common bean actively responds to NS or AS stress by inducing the expression of PvALDH genes. In addition, using the established classification criteria and phylogenetic analysis, 27 PvALDHs were identified in the common bean genome, belonging to 10 ALDH families. The primary expansion mode of PvALDH genes was segmental duplication. Cis-acting elemental analysis showed that PvALDHs were associated with abiotic stress and phytohormonal responses. Gene expression analysis revealed that the PvALDH gene expression was tissue-specific. For instance, PvALDH3F1 and PvALDH3H1 were highly expressed in flower buds and flowers, respectively, whereas PvALDH3H2 and PvALDH2B4 were highly expressed in green mature pods and young pods, respectively. PvALDH22A1 and PvALDH11A2 were highly expressed in leaves and young trifoliates, respectively; PvALDH18B2 and PvALDH18B3 were highly expressed in stems and nodules, respectively; and PvALDH2C2 and PvALDH2C3 were highly expressed in the roots. PvALDHs expression in the roots responded positively to NS-AS stress, and PvALDH2C3, PvALDH5F1, and PvALDH10A1 were significantly (P < 0.05) upregulated in the roots.

Conclusion

These results indicate that AS stress causes higher levels of oxidative damage than NS stress, resulting in weaker photosynthetic performance and more significant inhibition of common bean growth. The influence of PvALDHs potentially modulates abiotic stress response, particularly in the context of saline-alkali stress. These findings establish a basis for future research into the potential roles of ALDHs in the common bean.

Genome-wide analysis of ALDH gene family in jujube and identification of ZjALDH3F3 for its important role in high-temperature tolerance

Aldehyde dehydrogenases (ALDHs) are NAD(P)-dependent enzymes that oxidize aliphatic and aromatic aldehydes. They play crucial roles in various biological processes and plant responses to stress. The impact of high temperatures on jujube quality and yield has been well documented. Nevertheless, the involvement of ALDHs in the response to heat stress remains poorly understood. This study aimed to identify ZjALDHs in the jujube genome (Ziziphus jujuba var. spinosa) and conducted in silico analyses. Phylogenetic analyses indicated that ALDHs in plants, including jujube, can be divided into ten families, and members from the same family share conserved gene and protein structures. Quantitative real-time PCR (qRT-PCR) and β-glucuronidase (GUS) histochemical staining were used to analyze the expression patterns of ZjALDHs in response to elevated temperatures. We identified a ZjALDH (ZjALDH3F3) gene displaying a significant upregulation and down-regulation, respectively in heat-resistant (HR) and heat-sensitive (HS) jujube in response to heat treatments. Such specific responses are probably attributed to the different heat-responsive cis-elements of ZjALDH3F3 in HR and HS jujubes. ZjALDH3F3 over-expressed in tobacco increased heat tolerance, as evidenced by the reduced accumulation of reactive oxygen species (ROS) and elevated activity of antioxidant enzymes. The qRT-PCR results indicated that the expression of antioxidant enzymes, abscisic acid (ABA), and stress-responsive genes was enhanced in transgenic tobacco. This study sheds novel light on the function of ZjALDHs in heat resistance of jujube.

Genome-wide characterization and gene expression analyses of ALDH gene family in response to drought stress in moso bamboo (Phyllostachys edulis)

Aldehyde dehydrogenase (ALDH) superfamily, comprising enzymes dependent on NAD+ or NADP+, plays an important role in controlling plant growth and development, as well as in responsing to phytohormone and environmental stress. These enzymes possess the ability to prevent toxic effects of aldehydes by converting them into their corresponding carboxylic acids. However, the potential function of ALDH genes in moso bamboo (Phyllostachys edulis) remains largely unknown. In this study, the ALDH gene superfamily in moso bamboo was analyzed through genome-wide screening, the evolutionary relationship of expansion genes was conducted. Tissue-specific expression patterns of ALDH genes were observed in 26 different tissues. Plant hormone and environmental stress responsive cis-elements were identified in the promoter of ALDH genes, which were supported by public databases data on the expression patterns under various abiotic stresses and hormone treatments. ALDH activity was increased in moso bamboo seedlings exposed to drought, compared to control condition. Furthermore, PeALDH2B2 was found to physically interact with PeGPB1 in response to drought. Overall, the study provides a comprehensive analysis of the ALDH family in moso bamboo and contributes to our understanding of the function of ALDH genes in growth, development, and adaptation to drought stresses.

The Overexpression of Peanut (Arachis hypogaea L.) AhALDH2B6 in Soybean Enhances Cold Resistance

Soybeans are the main source of oils and protein for humans and animals; however, cold stress jeopardizes their growth and limits the soybean planting area. Aldehyde dehydrogenases (ALDH) are conserved enzymes that catalyze aldehyde oxidation for detoxification in response to stress. Additionally, transgenic breeding is an efficient method for producing stress-resistant germplasms. In this study, the peanut ALDH gene AhALDH2B6 was heterologously expressed in soybean, and its function was tested. We performed RNA-seq using transgenic and wild-type soybeans with and without cold treatment to investigate the potential mechanism. Transgenic soybeans developed stronger cold tolerance, with longer roots and taller stems than P3 soybeans. Biochemically, the transgenic soybeans exhibited a decrease in malondialdehyde activity and an increase in peroxidase and catalase content, both of which are indicative of stress alleviation. They also possessed higher levels of ALDH enzyme activity. Two phenylpropanoid-related pathways were specifically enriched in up-regulated differentially expressed genes (DEGs), including the phenylpropanoid metabolic process and phenylpropanoid biosynthetic process. Our findings suggest that AhALDH2B6 specifically up-regulates genes involved in oxidoreductase-related functions such as peroxidase, oxidoreductase, monooxygenase, and antioxidant activity, which is partially consistent with our biochemical data. These findings established the function of AhALDH2B6, especially its role in cold stress processes, and provided a foundation for molecular plant breeding, especially plant-stress-resistance breeding.

Identification and characterization of aldehyde dehydrogenase (ALDH) gene superfamily in garlic and expression profiling in response to drought, salinity, and ABA

In response to biotic and abiotic stressors, aldehydes are detoxified and converted to carboxylic acids by aldehyde dehydrogenases (ALDHs), which are enzymes that use NAD+/NADP+ as cofactors. Garlic (Allium sativum L.) has not yet undergone a systematic examination of the ALDH superfamily, despite the genome sequence having been made public. In this investigation, we identified, characterized, and profiled the expression of the garlic ALDH gene family over the entire genome. The ALDH Gene Nomenclature Committee (AGNC) classification was used to classify and name the 34 ALDH genes that were discovered. Except for chromosome 8, all AsALDH genes were dispersed across the chromosomes. AsALDH genes have various localizations, according to predictions about subcellular localization. The AsALDH proteins are more varied and closely related to rice than to Arabidopsis, according to a study of conserved motifs and phylogenetic relationships. The presence of stress modulation pathways is indicated by the abundance of stress-related cis-elements in the AsALDH genes' promoter regions. Analysis of the RNA-seq data showed that AsALDHs expressed differently in various tissues and at various developmental stages. Nine AsALDHs were chosen for study using RT-qPCR, and the results revealed that the majority of the genes were upregulated in response to ABA and downregulated in response to salinity and drought. The results of this study improved our knowledge of the traits, evolutionary background, and biological functions of AsALDHs genes in growth and development.

Genome-wide characterization of aldehyde dehydrogenase gene family members in groundnut (Arachis hypogaea) and the analysis under saline-alkali stress

Groundnut or peanut (Arachis hypogaea) is a legume crop. Its seeds are rich in protein and oil. Aldehyde dehydrogenase (ALDH, EC: 1.2.1.3) is an important enzyme involved in detoxification of aldehyde and cellular reactive oxygen species, as well as in attenuation of lipid peroxidation-meditated cellular toxicity under stress conditions. However, few studies have been identified and analyzed about ALDH members in Arachis hypogaea. In the present study, 71 members of the ALDH superfamily (AhALDH) were identified using the reference genome obtained from the Phytozome database. A systematic analysis of the evolutionary relationship, motif, gene structure, cis-acting elements, collinearity, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and expression patterns was conducted to understand the structure and function of AhALDHs. AhALDHs exhibited tissue-specific expression, and quantitative real-time PCR identified significant differences in the expression levels of AhALDH members under saline-alkali stress. The results revealed that some AhALDHs members could be involved in response to abiotic stress. Our findings on AhALDHs provide insights for further study.

Trans-cinnamaldehyde-related overproduction of benzoic acid and oxidative stress on Arabidopsis thaliana

Introduction

Trans-cinnamaldehyde is a specialised metabolite that naturally occurs in plants of the Lauraceae family. This study focused on the phytotoxic effects of this compound on the morphology and metabolism of Arabidopsis thaliana seedlings.

Material and methods

To evaluate the phytotoxicity of trans-cinnamaldehyde, a dose-response curve was first performed for the root growth process in order to calculate the reference inhibitory concentrations IC50 and IC80 (trans-cinnamaldehyde concentrations inducing a 50% and 80% inhibition, respectively). Subsequently, the structure and ultrastructure of the roots treated with the compound were analysed by light and electron microscopy. Based on these results, the following assays were carried out to in depth study the possible mode of action of the compound: antiauxinic PCIB reversion bioassay, determination of mitochondrial membrane potential, ROS detection, lipid peroxidation content, hormone quantification, in silico studies and gene expression of ALDH enzymes.

Results

Trans-cinnamaldehyde IC50 and IC80 values were as low as 46 and 87 μM, reducing the root growth and inducing the occurrence of adventitious roots. At the ultrastructural level, the compound caused alterations to the mitochondria, which were confirmed by detection of the mitochondrial membrane potential. The morphology observed after the treatment (i.e., appearance of adventitious roots) suggested a possible hormonal mismatch at the auxin level, which was confirmed after PCIB bioassay and hormone quantification by GC-MS. The addition of the compound caused an increase in benzoic, salicylic and indoleacetic acid content, which was related to the increased gene expression of the aldehyde dehydrogenase enzymes that can drive the conversion of trans-cinnamaldehyde to cinnamic acid. Also, an increase of ROS was also observed in treated roots. The enzyme-compound interaction was shown to be stable over time by docking and molecular dynamics assays.

Discussion

The aldehyde dehydrogenases could drive the conversion of trans-cinnamaldehyde to cinnamic acid, increasing the levels of benzoic, salicylic and indoleacetic acids and causing the oxidative stress symptoms observed in the treated seedlings. This would result into growth and development inhibition of the trans-cinnamaldehyde-treated seedlings and ultimately in their programmed-cell-death.