Genetic and expression changes in Lactate dehydrogenase as potential mechanism for promoting adaptation

Understanding the genetic basis of adaptation is a central task for evolutionary biology. Here, I examined how Ldh gene expression contributes to the adaptation of Daphnia pulex and Daphnia pulicaria by using a controlled acclimation experiment. There were no statistically significant changes (p>0.1) in gene expression due to changes in temperature, dissolved oxygen. However, both LdhA and LdhB expression were significantly different in each type of Daphnia (pond, lake or hybrid) suggesting that these genes could contribute to adaptation or could be linked to loci that do. LdhA was expressed significantly more than LdhB (p<0.005), in all clones. Analysis of the protein structures of LDHA and LDHB revealed that both are functional LDH proteins, with very similar secondary structures. These results confirm that while the protein structures of LdhA and LdhB where very similar, expression of these genes could contribute to the adaptation of pond and lake Daphnia

Genetic and expression changes in Lactate dehydrogenase as potential mechanism for promoting adaptation

Understanding the genetic basis of adaptation is a central task for evolutionary biology. Here, I examined how Ldh gene expression contributes to the adaptation of Daphnia pulex and Daphnia pulicaria by using a controlled acclimation experiment. There were no statistically significant changes (p>0.1) in gene expression due to changes in temperature, dissolved oxygen. However, both LdhA and LdhB expression were significantly different in each type of Daphnia (pond, lake or hybrid) suggesting that these genes could contribute to adaptation or could be linked to loci that do. LdhA was expressed significantly more than LdhB (p<0.005), in all clones. Analysis of the protein structures of LDHA and LDHB revealed that both are functional LDH proteins, with very similar secondary structures. These results confirm that while the protein structures of LdhA and LdhB where very similar, expression of these genes could contribute to the adaptation of pond and lake Daphnia

Pairwise comparison of <i>Ldh</i>A <i>and Ldh</i>B expression between genotypes in <i>Daphnia</i>.

<p>The results are based on post-hoc t-test with the Bonferroni correction. The number of <i>Ldh</i> transcripts per <i>Gapdh</i> transcript was calculated using the 2^−ΔCT method and is the dependent variable in this analysis. Genotype refers to <i>D. pulex</i>, <i>D. pulicaria</i>, and <i>D. pulex-pulicaria</i> hybrids; Gene is <i>Ldh</i>A or <i>Ldh</i>B. P-values that show a significant difference in gene expression (p<0.05) are in bold-face type.</p

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

<div><p>Lactate dehydrogenase (LDH) has been shown to play an important role in adaptation of several aquatic species to different habitats. The genomes of <i>Daphnia pulex</i>, a pond species, and <i>Daphnia pulicaria</i>, a lake inhabitant, encode two L-LDH enzymes, LDHA and LDHB. We estimated relative levels of <i>Ldh</i> 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 <i>Ldh</i>A expression were 4 to 48 times higher than <i>Ldh</i>B expression (p<0.005) in all three groups (the two parental species and hybrids). Moreover, levels of <i>LdhB</i> expression differed significantly (p<0.05) between <i>D. pulex</i> and <i>D. pulicaria,</i> but neither species differed from the hybrid. Consistently higher expression of <i>Ldh</i>A relative to <i>Ldh</i>B 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 <i>Daphnia</i> 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.</p></div

Analysis of variance of relative <i>Ldh</i> expression in 18 clones of <i>Daphnia pulex, D. pulicaria</i> and hybrids.

<p>The number of <i>Ldh</i> transcripts per <i>Gapdh</i> transcript was calculated using the 2^−ΔCT method and is the dependent variable in this analysis. Gene is <i>Ldh</i>A or <i>Ldh</i>B; Group refers to <i>D. pulex</i>, <i>D. pulicaria</i>, and <i>D. pulex-pulicaria</i> hybrids; temperature is 10°C or 20°C; dissolved oxygen is high (6.5–7 mg/l) or low (2–3 mg/l). Interactions are indicated by an asterisk (*). Sources of variation that show a significant difference in gene expression (p<0.05) are in bold-face type.</p

Aquarium set up.

<p>Each of the four aquaria contained 27 chambers that were filled with one of nine <i>D. pulex</i> clones (pond), nine <i>D. pulicaria</i> clones (lake), and nine hybrid clones. Each chamber had a mesh bottom allowing food and air/nitrogen to circulate freely within the aquarium while keeping the clones isolated from each other. There were four aquaria each characterized by different environmental conditions. Aquarium 1 corresponds to 20°C/High [6.5–7 mg/L] DO; aquarium 2 (20°C/Low [2–3 mg/L] DO); aquarium 3 (10°C/High DO); and aquarium 4 (10°C/Low DO).</p

Primers used for qPCR analyses of <i>Ldh</i> expression in <i>D. pulex</i> and <i>D. pulicaria</i>.

<p>*The gene ID refers to the <i>Daphnia pulex</i> draft genome annotation (dappu v1.1) at <a href="http://www.jgi.doe.gov" target="_blank">www.jgi.doe.gov</a>.</p

Expression of <i>Ldh</i>A and <i>Ldh</i>B relative to <i>Gapdh</i> in <i>Daphnia</i> under four combinations of temperature and dissolved oxygen.

<p>Each <i>Daphnia</i> group (<i>D. pulex</i>, <i>D. pulicaria</i> and hybrids) was represented by six clones in the final analysis. The Y-axis shows the number of <i>Ldh</i>A and <i>Ldh</i>B transcripts per 1000 <i>Gapdh</i> transcripts calculated using the 2^−ΔCT method. The four treatments consisted of two temperatures, 10°C or 20°C each combined with two levels of dissolved oxygen, 6.5–7 mg/L (hi) or 2–3 mg/L (lo). Blue bars represent <i>LdhA</i> and red bars represent <i>LdhB</i>. Error bars represent standard error of the mean (SEM). The numbers on the graph are the mean value of relative <i>Ldh</i> expression for each treatment in each group. Only the difference between mean relative <i>Ldh</i>B expression in <i>D. pulex</i> (3.1) and <i>D. pulicaria</i> (14.9) is significant (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103964#pone-0103964-t003" target="_blank">Table 3</a>).</p