Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

Abstract

In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD+- or NADP+-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as ‘aldehyde scavengers’ by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried outgenome-wide identification of ALDH genes in a number of plant species—including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.

Plant development reprogramming by cynipid gall wasp: proteomic analysis

“…Compounds with aldehydic functional groups are generated as important intermediates in many catabolic and biosynthetic pathways of carbohydrates, lipids, vitamins, steroids, and amino acids. Moreover, the ALDH-mediated generation of NADH/NADPH represents a major source of reducing equivalents required for maintaining cellular redox balance (Brocker et al 2012). In addition, ALDHs act as 'aldehyde scavengers' during lipid peroxidation where they remove reactive aldehydes entailed by the oxidative degradation of lipid membranes (Brocker et al 2012).…”

“…Moreover, the ALDH-mediated generation of NADH/NADPH represents a major source of reducing equivalents required for maintaining cellular redox balance (Brocker et al 2012). In addition, ALDHs act as 'aldehyde scavengers' during lipid peroxidation where they remove reactive aldehydes entailed by the oxidative degradation of lipid membranes (Brocker et al 2012). ALDHs that have been characterised to date, the most have been involved in different processes and have putative substantial roles in growth and development of the plant (Tian et al 2015).…”

Plant ALDH10 Family

“…We also noticed that the activity on several aminoaldehyde substrates is affected by Trp-288. In order to predict the substrate specificity differences in AMADH pairs from a single species and between species and because only a few plant AMADH pairs were reported and studied (4,6,18), we cloned and biochemically characterized five ALDH10 members (19) (Table 1): two tomato (Solanum lycopersicum) isoenzymes SlAMADH1 and SlAMADH2 and three maize (Zea mays) isoenzymes ZmAMADH1a, ZmAMADH1b, and ZmAMADH2. Both tomato AMADHs share 80% sequence identity.…”

Alternative Acetate Production Pathways inChlamydomonas reinhardtiiduring Dark Anoxia and the Dominant Role of Chloroplasts in Fermentative Acetate Production

“…These include: (a) the spontaneous hydrolysis of acetate phosphate to acetate and P i (Koshland, 1952;Di Sabato and Jencks, 1961); (b) aldehyde dehydrogenase activity that oxidizes acetaldehyde (from pyruvate decarboxylation) to acetate (Kirch et al, 2004(Kirch et al, , 2005Brocker et al, 2013); (c) acetyl-CoA hydrolase, which hydrolyzes acetyl-CoA to acetate and CoA without the production of ATP (Tielens et al, 2010); (d) acetate formation by AMP-forming acetyl-CoA synthetase (Takasaki et al, 2004;Yoshii et al, 2009); and (e) ASCT and SCL activities (van Grinsven et al, 2008;Millerioux et al, 2012). ASCT transfers the CoA moiety of acetyl-CoA to succinate and SCL converts succinyl-CoA back to succinate.…”

“…Chlamydomonas acetate accumulation can be influenced by altering fermentation pathways through the generation of mutants (Dubini et al, 2009;Philipps et al, 2011;Burgess et al, 2012;Catalanotti et al, 2012;Magneschi et al, 2012). In addition to the activities of PAT-ACK, the Chlamydomonas genome encodes other enzymes that may play a role in the synthesis of acetate, including four enzymes with homology to AMP-forming ACS (ACS1-4) and eight with homology to aldehyde dehydrogenase (ALDH) (Kirch et al, 2004(Kirch et al, , 2005Brocker et al, 2013), which may catalyze the conversion of acetaldehyde to acetate with concomitant NAD(P)H production (Kirch et al, 2004(Kirch et al, , 2005Brocker et al, 2013).…”