Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily

The completion of the grape genome sequencing project has paved the way for novel gene discovery and functional analysis. Aldehyde dehydrogenases (ALDHs) comprise a gene superfamily encoding NAD(P)(+)-dependent enzymes that catalyze the irreversible oxidation of a wide range of endogenous and exogenous aromatic and aliphatic aldehydes. Although ALDHs have been systematically investigated in several plant species including Arabidopsis and rice, our knowledge concerning the ALDH genes, their evolutionary relationship and expression patterns in grape has been limited.A total of 23 ALDH genes were identified in the grape genome and grouped into ten families according to the unified nomenclature system developed by the ALDH Gene Nomenclature Committee (AGNC). Members within the same grape ALDH families possess nearly identical exon-intron structures. Evolutionary analysis indicates that both segmental and tandem duplication events have contributed significantly to the expansion of grape ALDH genes. Phylogenetic analysis of ALDH protein sequences from seven plant species indicates that grape ALDHs are more closely related to those of Arabidopsis. In addition, synteny analysis between grape and Arabidopsis shows that homologs of a number of grape ALDHs are found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the speciation of the grape and Arabidopsis. Microarray gene expression analysis revealed large number of grape ALDH genes responsive to drought or salt stress. Furthermore, we found a number of ALDH genes showed significantly changed expressions in responses to infection with different pathogens and during grape berry development, suggesting novel roles of ALDH genes in plant-pathogen interactions and berry development.The genome-wide identification, evolutionary and expression analysis of grape ALDH genes should facilitate research in this gene family and provide new insights regarding their evolution history and functional roles in plant stress tolerance

De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis.

BackgroundBixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of Bixa orellana L. An enzymatic pathway for bixin biosynthesis was inferred from homology of putative proteins encoded by differentially expressed seed cDNAs. Some activities were later validated in a heterologous system. Nevertheless, much of the pathway remains to be clarified. For example, it is essential to identify the methylerythritol phosphate (MEP) and carotenoid pathways genes.ResultsIn order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds from B. orellana were used for the construction of indexed mRNA libraries, sequenced on the Illumina HiSeq 2500 platform and assembled de novo using Velvet, CLC Genomics Workbench and CAP3 software. A total of 52,549 contigs were obtained with average length of 1,924 bp. Two phylogenetic analyses of inferred proteins, in one case encoded by thirteen general, single-copy cDNAs, in the other from carotenoid and MEP cDNAs, indicated that B. orellana is closely related to sister Malvales species cacao and cotton. Using homology, we identified 7 and 14 core gene products from the MEP and carotenoid pathways, respectively. Surprisingly, previously defined bixin pathway cDNAs were not present in our transcriptome. Here we propose a new set of gene products involved in bixin pathway.ConclusionThe identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of B. orellana

Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea

Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class with promising potential for plant adaptation improvement. Aldehyde dehydrogenases constitute a superfamily of proteins with important functions as ‘aldehyde scavengers’ by detoxifying aldehydes molecules, and thus play important roles in stress responses. We performed a comprehensive study of the ALDH superfamily in the chickpea genome and identified 27 unique ALDH loci. Most chickpea ALDHs originated from duplication events and the ALDH3 gene family was noticeably expanded. Based on the physical locations of genes and sequence similarities, our results suggest that segmental duplication is a major driving force in the expansion of the ALDH family. Supported by expression data, the findings of this study offer new potential target genes for improving stress tolerance in chickpea that will be useful for breeding programs

Identificación y caracterización de la superfamilia génica ALDH en garbanzo (Cicer arietinum) mediante herramientas bioinformáticas de acceso libre

Premio extraordinario de Trabajo Fin de Máster curso 2017/2018. Máster en Producción, Protección y Mejora VegetalLas aldehído deshidrogenasas (ALDHs) son una superfamilia de proteínas con una función importante en la detoxificación de los aldehídos producidos en respuesta a estreses bióticos/abióticos. La disponibilidad del genoma de referencia de garbanzo (Cicer arietinum) da la oportunidad de identificar y caracterizar a los miembros de esta familia en una leguminosa de importancia agronómica. En este estudio, se han identificado 37 ALDHs en el genoma de garbanzo y se ha realizado una caracterización completa de las mismas. Los análisis filogenéticos comparativos con Medicago sugieren una gran conservación de la familia entre las dos especies y los análisis de duplicaciones indican una leve incidencia de eventos de duplicación con posterioridad a la especiación. El análisis de expresión in silico apoya el papel de la mayoría de miembros de la familia CaALDH en la tolerancia al estrés abiótico, con una mayor representación de las secuencias de la familia 18 en librerías EST de tolerancia a sequía. Todos los scripts escritos en este trabajo y la secuencia de ejecución para el análisis de las bases de datos están disponibles públicamente en un repositorio online de acceso libre. En resumen, este trabajo proporciona una visión general de la superfamilia génica ALDH en garbanzo. Es la primera vez que la familia se estudia en este cultivo. Nuestros resultados respaldan que las proteínas ALDHs están implicadas en una amplia gama de rutas metabólicas y que participan en la respuesta al estrés. Esto proporciona nuevos conocimientos sobre la la presencia y función de la familia en esta especie, lo que puede ser útil para desarrollar estrategias de mejora genética de respuesta a diferentes estreses. Este trabajo también proporciona una base para análisis genómicos comparativos posteriores en el estudio de la evolución de los genes ALDH dentro de la familia de las leguminosas.Aldehyde dehydrogenases (ALDHs) constitute a protein superfamily with an important function in the detoxification of the aldehydes produced in response to biotic/abiotic stresses. The availability of the chickpea (Cicer arietinum) reference genome provides an opportunity to identify and characterize the members of this family in a legume of agronomic importance. In this study, 37 ALDHs have been identified in the chickpea genome and a complete characterization of them has been carried out. The comparative phylogenetic analysis with Medicago suggests a high conservation of the family between both species and the duplication analysis indicates a slight duplication incidence after the speciation. In silico expression analysis supports the abiotic stress tolerance role of most CaALDH family members, showing the family 18 sequences overrepresented in drought tolerance EST libraries. All the code and scripts written for this work are publicly available in an online open access repository. In summary, this work provides the first general overview of the ALDH gene superfamily in this crop. Our results support that ALDH proteins are involved in a wide range of metabolic pathways and they participate in the stress response. This provides new knowledge of the family presence and function in this species, what may be useful to develop chickpea breeding strategies to improve development or stress responses. This work also supplies a basis for further comparative genomic analysis and a framework to study the ALDH genes evolution within the legume family

Recent development on plant aldehyde dehydrogenase enzymes and their functions in plant development and stress signaling

Abstract: Abiotic and biotic stresses induce the formation of reactive oxygen species (ROS), which subsequently causes the excessive accumulation of aldehydes in cells. Stress-derived aldehydes are commonly designated as reactive electrophile species (RES) as a result of the presence of an electrophilicα,β-unsaturated carbonyl group. Aldehyde dehydrogenases (ALDHs) are NAD(P)+-dependent enzymes that metabolize a wide range of endogenous and exogenous aliphatic and aromatic aldehyde molecules by oxidizing them to their corresponding carboxylic acids. The ALDH enzymes are found in nearly all organisms, and plants contain fourteen ALDH protein families. In this review, we performed a critical analysis of the research reports over the last decade on plant ALDHs. Newly discovered roles for these enzymes in metabolism, signaling and development have been highlighted and discussed. We concluded with suggestions for future investigations to exploit the potential of these enzymes in biotechnology and to improve our current knowledge about these enzymes in gene signaling and plant development

Transcriptome analysis of Thapsia laciniata rouy provides insights into terpenoid biosynthesis and diversity in apiaceae

Thapsia laciniata Rouy (Apiaceae) produces irregular and regular sesquiterpenoids with thapsane and guaiene carbon skeletons, as found in other Apiaceae species. A transcriptomic analysis utilizing Illumina next-generation sequencing enabled the identification of novel genes involved in the biosynthesis of terpenoids in Thapsia. From 66.78 million HQ paired-end reads obtained from T. laciniata roots, 64.58 million were assembled into 76,565 contigs (N50: 1261 bp). Seventeen contigs were annotated as terpene synthases and five of these were predicted to be sesquiterpene synthases. Of the 67 contigs annotated as cytochromes P450, 18 of these are part of the CYP71 clade that primarily performs hydroxylations of specialized metabolites. Three contigs annotated as aldehyde dehydrogenases grouped phylogenetically with the characterized ALDH1 from Artemisia annua and three contigs annotated as alcohol dehydrogenases grouped with the recently described ADH1 from A. annua. ALDH1 and ADH1 were characterized as part of the artemisinin biosynthesis. We have produced a comprehensive EST dataset for T. laciniata roots, which contains a large sample of the T. laciniata transcriptome. These transcriptome data provide the foundation for future research into the molecular basis for terpenoid biosynthesis in Thapsia and on the evolution of terpenoids in Apiaceae.Damian Paul Drew, Bjørn Dueholm, Corinna Weitzel, Ye Zhang, Christoph W. Sensen and Henrik Toft Simonse

Structural shifts of aldehyde dehydrogenase enzymes were instrumental for the early evolution of retinoiddependent axial patterning in metazoans

Aldehyde dehydrogenases (ALDHs) catabolize toxic aldehydes and process the vitamin A-derived retinaldehyde into retinoic acid (RA), a small diffusible molecule and a pivotal chordate morphogen. In this study, we combine phylogenetic, structural, genomic, and developmental gene expression analyses to examine the evolutionary origins of ALDH substrate preference. Structural modeling reveals that processing of small aldehydes, such as acetaldehyde, by ALDH2, versus large aldehydes, including retinaldehyde, by ALDH1A is associated with small versus large substrate entry channels (SECs), respectively. Moreover, we show that metazoan ALDH1s and ALDH2s are members of a single ALDH1/2 clade and that during evolution, eukaryote ALDH1/2s often switched between large and small SECs after gene duplication, transforming constricted channels into wide opened ones and vice versa. Ancestral sequence reconstructions suggest that during the evolutionary emergence of RA signaling, the ancestral, narrow-channeled metazoan ALDH1/2 gave rise to large ALDH1 channels capable of accommodating bulky aldehydes, such as retinaldehyde, supporting the view that retinoid-dependent signaling arose from ancestral cellular detoxification mechanisms. Our analyses also indicate that, on a more restricted evolutionary scale, ALDH1 duplicates from invertebrate chordates (amphioxus and ascidian tunicates) underwent switches to smaller and narrower SECs. When combined with alterations in gene expression, these switches led to neofunctionalization from ALDH1-like roles in embryonic patterning to systemic, ALDH2-like roles, suggesting functional shifts from signaling to detoxification

Physiological and molecular studies of different aldehyde dehydrogenase (<i>ALDH</i>) genes in response to high temperature and functional analyses of the <i>ALDH7B4</i> promoter in <i>Arabidopsis thaliana</i>

In this study, the function of aldehyde dehydrogenase (ALDH) genes in response to heat stress alone and in combination with dehydration, salinity, or wounding stress was investigated using selected ALDH genes and characterized transgenic A. thaliana ALDH double knock-out lines. As heat stress often occurs in combination with other stresses, the purpose of this study was to first investigate the response of selected ALDH genes to heat and secondly to a combination of heat and other abiotic stresses. Expression of selected ALDH genes was analyzed on the transcript and protein level at different time points of heat stress and in response to basal or acquired thermotolerance. The results showed that ALDH genes, particularly ALDH7B4, is strongly induced by heat and combination stresses, indicating that ALDH genes play a crucial role in protecting plants from high temperature damages. The comparison of the physiological and biological parameters (survival rates, photosynthesis, lipid peroxidation and chlorophyll content) in T-DNA double mutants of ALDH genes and wild-type plants demonstrated that mutant lines are more sensitive to heat and combination stresses. DRE/CRT and ACGT1 motifs in ALDH7B4 promoter are vital for the response to heat stress combined with wounding or salt stress. In addition, ACGT2 and ACGT3 promoter elements play a crucial role for ALDH7B4 gene expression and stress responsiveness. Using a yeast one-hybrid screen and EMSA technique demonstrated that ATAF1 activates ALDH7B4 by directly binding to a specific promoter region in vivo and in vitro. Moreover, ATAF1 acts as a DNA-binding transcription activator that involved in ALDH7B4 expression in different growth stages

Compartment-specific metabolism associated with acetyl-CoA and acyl carrier protein

A characteristic feature of plant cells is the subcellular compartmentation of metabolism. Duplicated enzymes or cofactors occur in the same or distinct compartments, posing a challenge to define the complex metabolic networks that are central to biological functions. Our knowledge regarding the compartment-specific metabolism in plants has been hampered by the limitations of current analytical methods to determine the subcellular location of metabolites. In this dissertation, we integrate reverse genetic and metabolomic analyses to characterize the physiological roles of several compartment-specific enzymes and cofactors. Two distinctly localized Arabidopsis acetate-activating enzymes, the plastidic acetyl-CoA synthetase (ACS) and the peroxisomal acetate non-utilizing 1 (ACN1), are functionally redundant, but their roles in metabolism are not clear. Mutations in both ACS and ACN1 lead to abnormal phenotypes of delayed growth and infertility, which are associated with hyperaccumulation of acetate levels and decreased accumulation of acetyl-CoA-derived metabolites. Cellular acetate is generated from either the oxidation of ethanol or the non-oxidative decarboxylation of pyruvate via the common intermediate acetaldehyde. These processes are induced by hypoxia, suggesting the role of ACS and ACN1 in reducing the carbon loss in the form of ethanol after hypoxia. Using 13C-acetate as a tracer, we demonstrate that the acetate metabolized by the plastidic ACS is used for the de novo synthesis of fatty acids and leucine, whereas the acetate activated by the peroxisomal ACN1 enters the glyoxylate cycle that generates the organic acid intermediates for amino acid biosynthesis. Collectively, these studies establish the significant role of these two enzymes in protecting plant cells from the toxic accumulation of excess acetate. Typical of plants, Arabidopsis expresses two distinct Type II fatty acid synthases (FASs), one mitochondrial and the other in plastids. These two systems are supported by a small, phosphopantetheinylated protein cofactor, acyl carrier protein (ACP). The Arabidopsis genome contains eight ACP-coding genes. We demonstrate that three of these genes encode mitochondrial ACP (mtACP) isozymes, supporting the mitochondrial fatty acid synthase (mtFAS) system. Functional redundancy among the three mtACPs was dissected by a genetic strategy, which demonstrate that the simultaneous loss of all three mtACP genes is associated with an embryo-lethal phenotype. Characterization of double mutant combinations revealed unequal functional redundancy among the three mtACP isoforms, with mtACP3 being the least effective of the three in supporting the mtFAS system