Opossum Aldehyde Dehydrogenases: Evidence for Four ALDH1A1-like Genes on Chromosome 6 and ALDH1A2 and ALDH1A3 Genes on Chromosome 1

Holmes, Roger S.

doi:10.1007/s10528-009-9245-3

Cited by 4 publications

(3 citation statements)

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“…In silico methods were used to predict the primary, secondary, and tertiary structures for opossum ALDH3 isozymes and gene locations for opossum ALDH3-like genes, using data from the opossum genome sequence (Mikkelsen et al 2007). This paper extends previous studies that examined the tissue and subcellular distribution and biochemical properties of opossum ALDHs (Holmes et al , 1991 and the predicted structures and properties of opossum ALDH1-like genes and proteins (Holmes 2009). Phylogenetic analyses also describe the relationships and potential evolutionary origins of multiple opossum ALDH3A-like genes and an ALDH3B-like gene in the opossum.…”

Section: Introductionsupporting

confidence: 82%

Biochemical Genetics of Opossum Aldehyde Dehydrogenase 3: Evidence for Three ALDH3A-Like Genes and an ALDH3B-Like Gene

Holmes

2009

Biochem Genet

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Mammalian ALDH3 isozymes participate in peroxidic and fatty aldehyde metabolism, and in anterior eye tissue UV-filtration. BLAT analyses were undertaken of the opossum genome using rat ALDH3A1, ALDH3A2, ALDH3B1, and ALDH3B2 amino acid sequences. Two predicted opossum ALDH3A1-like genes and an ALDH3A2-like gene were observed on chromosome 2, as well as an ALDH3B-like gene, which showed similar intron-exon boundaries with other mammalian ALDH3-like genes. Opossum ALDH3 subunit sequences and structures were highly conserved, including residues previously shown to be involved in catalysis and coenzyme binding for rat ALDH3A1. Eleven glycine residues were conserved for all of the opossum ALDH3-like sequences examined, including two glycine residues previously located within the stem of the rat ALDH3A1 active site funnel. Phylogeny studies of human, rat, opossum, and chicken ALDH3-like sequences indicated that the common ancestor for ALDH3A- and ALDH3B-like genes predates the appearance of birds during vertebrate evolution.

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Section: Introductionsupporting

confidence: 82%

Biochemical Genetics of Opossum Aldehyde Dehydrogenase 3: Evidence for Three ALDH3A-Like Genes and an ALDH3B-Like Gene

Holmes

2009

Biochem Genet

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“…Structures for vertebrate ALDH3 isozymes and gene locations for ALDH3-like genes were obtained using data from the respective genome sequences. This paper extends previous studies which examined the structures and properties of opossum (Monodelphis domestica) ALDH3-like genes and proteins [15,16]. Phylogenetic analyses also describe the relationships and potential origins of ALDH3A-like and ALDH3B-like genes during mammalian and vertebrate evolution.…”

Section: Introductionsupporting

confidence: 76%

Comparative studies of vertebrate aldehyde dehydrogenase 3: Sequences, structures, phylogeny and evolution. Evidence for a mammalian origin for the ALDH3A1 gene

Holmes¹,

Hempel²

2011

Chemico-Biological Interactions

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Mammalian ALDH3 genes (ALDH3A1, ALDH3A2, ALDH3B1 and ALDH3B2) encode enzymes of peroxidic and fatty aldehyde metabolism. ALDH3A1 also plays a major role in anterior eye tissue UV-filtration. BLAT and BLAST analyses were undertaken of several vertebrate genomes using rat, chicken and zebrafish ALDH3-like amino acid sequences. Predicted vertebrate ALDH3 sequences and structures were highly conserved, including residues involved in catalysis, coenzyme binding and enzyme structure as reported by Liu et al. [27] for rat ALDH3A1. Phylogeny studies of human, rat, opossum, platypus, chicken, xenopus and zebrafish ALDH3-like sequences supported three hypotheses: (1) the mammalian ALDH3A1 gene was generated by a tandem duplication event of an ancestral vertebrate ALDH3A2 gene; (2) multiple mammalian and chicken ALDH3B-like genes were generated by tandem duplication events within genomes of related species; and (3) vertebrate ALDH3A and ALDH3B genes were generated prior to the appearance of bony fish more than 500 million years ago.

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“…The bioinformatic methodologies used in this investigation of pancreatic lipase-like genes and proteins may be also readily applied to other pancreatic proteins as well as other gene families encoding enzymes and proteins, including neutral lipases [35][36][37], acid lipases [66], carboxylesterases [67], enolases [68] and other gene families [69][70][71].…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics and Evolution of Vertebrate Pancreatic Lipase and Related Proteins and Genes

Holmes¹,

Cox²

2012

JDMGP

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Background: Pancreatic lipase (PTL) functions in the presence of colipase in the hydrolysis of emulsified fats in the small intestine following secretion from the pancreas. Pancreatic lipase related protein 1 (PLR1) is also found in pancreatic secretions and may perform a regulatory role in lipolysis; PLR2 catalyses pancreatic triglyceride and galactolipase reactions while PLR3 may serve a related but unknown lipase function. Comparative PTL, PLR1, PLR2 and PLR3 amino acid sequences and structures and gene locations and sequences were examined using data from several vertebrate genome projects. Methods:Sequence alignments and conserved predicted secondary and tertiary structures were studied and key amino acid residues and domains identified based on previous reports on human and pig PTL. Comparative analyses of vertebrate PTL-like genes were conducted using the UC Santa Cruz Genome Browser. Phylogeny studies investigated the evolution of these vertebrate PTL-like genes.Data: Human and mouse PTL sequences shared 78% identities but only 64-68% identities with human and mouse PLR1 and PLR2 sequences. Several vertebrate PTL and PTL-like protein domains were predicted using bioinformatics including an N-signal peptide; N-glycosylation site(s); an α/β hydrolase fold region containing a catalytic triad; a 'lid' region for the active site; a 'hinge' separating the lipase and PLAT regions; and a C-terminal PLAT region. Eutherian mammalian PLR1 sequences retained residues (196Val/198Ala) responsible for the loss of triacylglycerol lipase activity whereas lower vertebrate PLR1 sequences retained the 'active' lipase residues. In contrast, mammalian PTL, PLR2 and PLR3 sequences exhibited lipase 'active' residues (196Ala/198Pro); chicken and frog PLR1 sequences retained the lipase 'active' residues; and opossum and platypus PLR1 sequences exhibited 196Ala/Ser198 and 196Ser/198Pro residues. A phylogenetic tree analysis provided evidence for four distinct vertebrate PTL-like gene families. Conclusions:Pancreatic lipase (PTL) and related genes and proteins (PLR1 and PLR2) are present in all vertebrate genomes examined whereas PLR3 is found only in primate genomes. The 'inactive' form of vertebrate PLR1 is restricted to eutherian mammals. Vertebrate PTL-like genes apparently originated in a vertebrate ancestor following gene duplication events of an ancestral PTL-like ancestral gene. Two separate lines of PTL-like gene evolution are proposed in lower vertebrates (PTL/PLR1 and PLR2), with a further gene duplication event (PLR2/PLR3) for primate genomes.

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Opossum Aldehyde Dehydrogenases: Evidence for Four ALDH1A1-like Genes on Chromosome 6 and ALDH1A2 and ALDH1A3 Genes on Chromosome 1

Cited by 4 publications

References 50 publications

Biochemical Genetics of Opossum Aldehyde Dehydrogenase 3: Evidence for Three ALDH3A-Like Genes and an ALDH3B-Like Gene

Biochemical Genetics of Opossum Aldehyde Dehydrogenase 3: Evidence for Three ALDH3A-Like Genes and an ALDH3B-Like Gene

Comparative studies of vertebrate aldehyde dehydrogenase 3: Sequences, structures, phylogeny and evolution. Evidence for a mammalian origin for the ALDH3A1 gene

Bioinformatics and Evolution of Vertebrate Pancreatic Lipase and Related Proteins and Genes

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