Evolutionary History of d-Lactate Dehydrogenases: A Phylogenomic Perspective on Functional Diversity in the FAD Binding Oxidoreductase/Transferase Type 4 Family

Cristescu, Melania E.; Egbosimba, Emmanuel E.

doi:10.1007/s00239-009-9274-x

Cited by 18 publications

(26 citation statements)

References 41 publications

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“…This suggests that while both isozymes likely produce functional enzymes, Ldh A may be more important in Daphnia metabolism, which is also consistent with the observation that Ldh A expression is significantly higher than Ldh B expression in both species and their hybrids, in all four environmental conditions. Substantially higher levels of Ldh A than Ldh B expression were also observed in a previous study of Ldh in these two species under a single set of environmental conditions [37]. The pairwise comparisons show that mean levels of Ldh B expression differ significantly between D. pulicaria and D. pulex with the former group having higher expression of the gene compared to the latter.…”

Section: Discussionsupporting

confidence: 72%

Gene Expression Variation in Duplicate Lactate dehydrogenase Genes: Do Ecological Species Show Distinct Responses?

et al. 2014

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Lactate dehydrogenase (LDH) has been shown to play an important role in adaptation of several aquatic species to different habitats. The genomes of Daphnia pulex, a pond species, and Daphnia pulicaria, a lake inhabitant, encode two L-LDH enzymes, LDHA and LDHB. We estimated relative levels of Ldh gene expression in these two closely related species and their hybrids in four environmental settings, each characterized by one of two temperatures (10°C or 20°C), and one of two concentrations of dissolved oxygen (DO; 6.5–7 mg/l or 2–3 mg/l). We found that levels of LdhA expression were 4 to 48 times higher than LdhB expression (p<0.005) in all three groups (the two parental species and hybrids). Moreover, levels of LdhB expression differed significantly (p<0.05) between D. pulex and D. pulicaria, but neither species differed from the hybrid. Consistently higher expression of LdhA relative to LdhB in both species and the hybrid suggests that the two isozymes could be performing different functions. No significant differences in levels of gene expression were observed among the four combinations of temperature and dissolved oxygen (p>0.1). Given that Daphnia dwell in environments characterized by fluctuating conditions with long periods of low dissolved oxygen concentration, we suggest that these species could employ regulated metabolic depression to survive in such environments.

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Section: Discussionsupporting

confidence: 72%

Gene Expression Variation in Duplicate Lactate dehydrogenase Genes: Do Ecological Species Show Distinct Responses?

et al. 2014

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“…A reference sequence was created from the D. pulex genome sequence [18] for each of the Ldh genes indicating the location of exons, introns and the start and stop codons. Sequence electropherograms from each cloning experiment were aligned and edited in Sequencher v.4.5 (Gene Codes) using the reference sequences to orient the alignment and to trim the ends to the start and stop codons.…”

Section: Methodsmentioning

confidence: 99%

“…Surveys of allozyme variation in most Daphnia species are consistent with a one-locus model, but a recent analysis of the D. pulex genome sequence has identified two Ldh genes, Ldh A and Ldh B, that are approximately 26 cM apart [16,17]. Preliminary gene expression work suggests that Ldh A is expressed at a significantly higher level than Ldh B [18], but the link between the allozyme locus and the genome sequences has not yet been made. Nevertheless, the fixation of different LDH variants in D. pulex and D. pulicaria in different aquatic habitats, despite the fact that they share polymorphisms at other allozyme loci [19-21], suggests the possibility that Ldh variation is adaptive.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulexspecies complex

et al. 2011

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BackgroundEvidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB.ResultsWe sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA.ConclusionsAlthough lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive.

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“…The binding of two divalent metal ions at distinct sites is essential for substrate binding and for stabilising the reaction intermediate. The ordered binding of metals and substrates is accompanied with dramatic rearrangements of three loops near the catalytic site; when the site is occupied by substrate and metal ions, the loops are all in closed conformation (de A S Navarro et al, 2007).…”

Section: Enolasementioning

confidence: 99%

“…L-Lactate dehydrogenase (EC 1.1.1.27) is widely distributed among prokaryotes and eukaryotes and has been extensively studied (Madern, 2002). D-Lactate dehydrogenase (EC 1.1.1.28) is homologous to various other D-isomer-specific 2-hydroxyacid dehydrogenases, and has been detected in a variety of invertebrates, fungi and eubacteria (Cristescu and Egbosimba, 2009). Relatively limited information is available about this enzyme.…”

Section: Ancillary Glycolytic Enzymesmentioning

confidence: 99%

Glycolytic Enzymes

Michels¹,

Verlinde²,

Fothergill‐Gilmore³

2010

Encyclopedia of Life Sciences

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All cells must burn fuels to drive the myriad of cellular processes necessary for life. The most important organic fuel is glucose, a stable and soluble sugar that is particularly well suited for its role in biology. Cellular combustion of glucose occurs in 10 well‐controlled steps in which six‐carbon glucose molecules are broken apart (literally ‘glycolysis’) into three‐carbon compounds. In the same process chemical energy is captured through the production of ATP (adenosine triphosphate), the hydrolysis of which powers many cellular processes. The 10 enzymes which catalyse the steps of glycolysis are exceptionally well characterised. They provide a fascinating array of enzymes that have been perfected over long evolution to carry out their tasks swiftly, efficiently and with finely tuned control. Key concepts: Glycolysis is an ancient pathway that is present at least in part in all organisms. Ten enzymes catalyse the reactions of the glycolytic pathway. Many enzymes occur as isoenzymes in different tissues or in response to different metabolic conditions. Hexokinase activity is regulated by product inhibition. A hinge‐bending motion of the two‐lobed structures of hexokinase and phosphoglycerate kinase is induced by substrate binding, and is required to position the substrates correctly for catalysis. Several reactions of the glycolytic pathway can be catalysed by pairs of nonhomologous enzymes (i.e. glucose‐phosphate isomerase, aldolase, glyceraldehyde‐3‐phosphate dehydrogenase and phosphoglycerate mutase). Phosphofructokinase occurs as two distantly related types that use different phospho donors: ATP or inorganic pyrophosphate. Activities of phosphofructokinase and pyruvate kinase are allosterically regulated. A conserved protein fold of eight parallel β‐strands and eight parallel α helices, first identified in triosephosphate isomerase and therefore known as the ‘TIM barrel’ is found in several glycolytic enzymes and occurs in approximately 10% of all enzymes. The Rossmann fold that occurs in many nucleotide‐binding proteins was first identified in glyceraldehyde‐3‐phosphate dehydrogenase. Pyruvate kinase activity is sometimes regulated by posttranslational phosphorylation.

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Evolutionary History of d-Lactate Dehydrogenases: A Phylogenomic Perspective on Functional Diversity in the FAD Binding Oxidoreductase/Transferase Type 4 Family

Cited by 18 publications

References 41 publications

Gene Expression Variation in Duplicate Lactate dehydrogenase Genes: Do Ecological Species Show Distinct Responses?

Gene Expression Variation in Duplicate Lactate dehydrogenase Genes: Do Ecological Species Show Distinct Responses?

Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulexspecies complex

Glycolytic Enzymes

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