This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 2 of this series (The Backstory) can be found below.
The reason you and I and all other animals (and most other forms of life) can do things (like live) is because we combine oxygen with sugars to make energy. Eventually, the oxygen you breathe makes it into the cells throughout your body. Additionally, some of the food you eat gets broken down into molecules that are also transported to the various cells in your body. The oxygen and sugars are combined to make energy in a process known as cellular respiration. The first steps of this process involve splitting glucose (a sugar) into two molecules of pyruvate -- this is known as glycolysis. The products of glycolysis are used in the energy yielding reactions of cellular respiration.
The enzyme fructose-1,6-bisphosphate aldolase (hereafter referred to as aldolase) is responsible for splitting fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate and dihydroxyacetone-phosphate during glycolysis. Multicellular animals have developed different ways to encode specialized aldolase enzymes for different tissues. Most vertebrates, for example, have separate genes for muscle tissue (Ald A), liver (Ald B), and brain (Ald C) (Rutter 1964; Horecker et al. 1972), while Drosophila melanogaster has one primary copy of aldolase which undergoes alternative splicing of the initial transcript into three different mRNAs (Shaw-Lee et al. 1992). The vertebrate genes have undergone two major duplication events since the divergence of jawless fish (e.g., lampreys) and jawed vertebrates (Merritt and Quattro 2002). The first duplication event gave rise to the Ald B and Ald A/C lineage, and the second event led to separate Ald A and Ald C genes. Jawless fishes only have two aldolase genes which have protein products that are similar in function to the vertebrate aldolase A and C (Zhang et al. 1997), but arose by a duplication event separate from that along the jawed vertebrate lineage.
The vertebrate aldolase gene family also contains pseudogenes (duplications that appear to be non-functional). In mammals, these pseudogenes tend to occur via retrotransposition of the Ald A transcript, and have been studied in humans (Serero et al. 1988), rabbits (Amsden et al. 1992), and mice (Cortinas and Lessa 2001).
With the complete sequence of the D. melanogaster genome, came the discovery of a duplicate copy of Aldolase (CG5432) located approximately 150kb from the previously characterized copy (Ald). Whether or not this gene encodes a functional protein is yet to be determined, but it does possess all the necessary flanking sequences for transcription and translation. In this analysis we will examine the evolution of these paralogs within the Drosophila genus. Both coding and non-coding sequences will be included, and the coding sequences will be studied at the nucleotide and amino acid levels. Our analysis will consist of comparisons of synonymous and non-synonymous substitutions, rates of evolution along the lineages, and phylogenies retrieved using different subsets of the data. As we progress through the study, suggestions regarding the data analysis may be left in the comments.
Amsden, A.B., E.E. Penhoet, and D.R. Tolan. 1992. A rabbit Ald A pseudogene derived from a partially spliced primary Aldolase A transcript. Gene 120: 323-324.
Cortinas, M.N., and E.P. Lessa. 2001. Molecular evolution of Aldolase A pseudogenes in mice: multiple origins, subsequent duplications, and heterogeneity of evolutionary rates. Mol. Biol. Evol. 18: 1643-1653.
Horecker, B.L., O. Tsola, C.Y. Lai. 1972. Pp. 213-258 in The Enzymes, Vol. 7. P.D. Boyer, ed. Academic Press, New York.
Merritt, T.J.S. and J.M. Quattro. 2002. Negative Charge Correlates with Neural Expression in Vertebrate Aldolase Isozymes. J. Mol. Evol. 55: 674 - 683.
Rutter, W.J. 1964. Metabolic control mechanisms in animal cells. Fed. Proc. 23: 1248-1257.
Serero, S., P. Maire, V.C. Nguyen, O. Cohen-Haguenauer, M.S. Gross, C. Jegou-Foubert, M.F. de Tand, A. Kahn, J. Frezal. 1988. Localization of the active gene of aldolase on chromosome 16, and two aldolase A pseudogenes on chromosomes 3 and 10. Hum. Genet. 78: 167-174.
Shaw-Lee, R., J.L. Lissemore, D.T. Sullivan, and D.R. Tolan. 1992. Alternative splicing of fructose 1,6-bisphosphate aldolase transcripts in Drosophila melanogaster predicts three isozymes. J. Biol. Chem. 267:3959-3967.
Zhang, R., T. Kusakabe, N. Iwanaga, Y. Sugimoto, K. Kondo, Y. Takasaki, T. Imai, M. Yoshida, and K. Hori. 1997. Lamprey fructose-1,6-bisphosphate aldolase: characterization of the muscle-type and non-muscle-type isozymes. Arch. Biochem. Biophys. 341: 170-176.