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

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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 out genome-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.

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Acknowledgments

We thank our colleagues for critically reviewing this manuscript. This work was supported, in part, by the following National Institutes of Health grants: R01 EY17963 (VV), R21 AA017754 (VV), F31 AA018248 (CB), and P30 ES006096 (DWN). Further support was provided by grant P501/11/1591 from the Czech Science Foundation (DK). The authors have no conflicts of interest related to the work detailed within this manuscript. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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Authors and Affiliations

  1. Department of Pharmaceutical Sciences, Molecular Toxicology and Environmental Health Sciences Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA

    Chad Brocker, Melpomene Vasiliou, Sarah Carpenter, Christopher Carpenter & Vasilis Vasiliou

  2. Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, College of Horticulture, Ministry of Agriculture, Northwest A&F University, Yangling, Shanxi, 712100, People’s Republic of China

    Yucheng Zhang & Xiping Wang

  3. Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA

    Simeon O. Kotchoni

  4. Department of Plant Biology, Southern Illinois University Carbondale, Carbondale, IL, 62901, USA

    Andrew J. Wood

  5. Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53115, Bonn, Germany

    Hans-Hubert Kirch

  6. Faculty of Science, Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 11, 783 71, Olomouc, Czech Republic

    David Kopečný

  7. Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA

    Daniel W. Nebert

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  1. Chad Brocker
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Brocker, C., Vasiliou, M., Carpenter, S. et al. Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics. Planta 237, 189–210 (2013). https://doi.org/10.1007/s00425-012-1749-0

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