| As a major component of the atmosphere, carbon dioxide has an important role in the environmental change. To plants and some animals, the CO2 detection ability influences their ecological activities. Recent studies found that three coding genes, carbonic anhydrase II (CAII), guanylyl cyclase D (GC-D) and phosphodiesterase 2A (PDE2A), consists the functional pathway of the CO2 detection in animals. The evolutionary analysis indicates that GC-D has been a pseudogene in higher primates and experiences negative selection in some mammals. It is meaningful to conduct bioinformatic study on the CAII and PDE2A, integrated with their pathway background. However, there has been no systematic evolutionary study on the other genes of this pathway yet.Our study utilized the data from GenBank and Ensembl and the CDS we sequenced to reconstruct phylogenetic trees of CAII and PDE2A. And we analyzed the sequences, phylogenetic reconstruction and adaptive evolution by various bioinformatic tools such as PHYLIP. PAML. MEGA. RRTree, MO Tree Comparison and KTreeDist. The content of this study is listed below:1) We sequenced CDS sequences of CAII of one lemur and two new world monkeys, and screened 13 ortholog sequences of CAII from the online database. We reconstructed phylogenetic tree of CAII with the removal of the interference of paralogs.9 common species were selected from the available data from the literature, and 2 species were added from database. We reconstructed phylogenetic trees according to the alignment of exons. The correlation in the genetic distance of CAII and GC-D was estimated by molecular evolutionary analysis tools. And then we compared their topological structure, branch length and relative evolutionary rate. At last, we analyzed and discussed whether PDE2A and GC-D have concert evolutionary patterns in the respects of genetic distance, phylogenetic tree structure and relative evolutionary rate, respectively. It is found that CAII has similar pattern in the genetic distance, tree structure and relative evolutionary rate with GC-D, which suggests that these two gene in same pathway have approximate trend.2) We screened 9 CDS sequences of PDE2A out of 37 species by multiple alignments from the online database, with which we reconstructed a phylogenetic tree. And we re- selected common species of GC-D and PDE2A to reconstruct two phylogenetic trees, respectively. We also analyzed and discussed whether PDE2A and GC-D have concert evolutionary patterns in the respects of genetic distance, phylogenetic tree structure and relative evolutionary rate, respectively. Meanwhile, we double selected the CAII sequences and compared them with PDE2A counterparts in the three respects. It is proved that PDE2A has significant correlation to GC-D in the genetic distance and tree structure, however, they diverge in the relative evolutionary rate.3) Considering the negative selection of GC-D in the evolutional process, we conducted adaptive evolutional analysis on CAII and PDE2A. It is found that CAII experiences significant negative selection in the primates and has similar pattern with GC-D. Though the same situation has been detected in PDE2A as a whole, we found different domains have different evolutionary patterns for their distinct functions. In addition, there is no positive selection detected in CAII and PDE2A.4) In order to further analyze the functional change of CAII and PDE2A, we conducted computer simulation of the 3D structure of the two proteins in some species, and compared them to the human counterparts. It is found that they have few diverges in the active sites among species which means little functional difference, however, it still shows the possibility of the catalyst activity reduction.By the evolutionary analysis, our study has proved that there may exist pathway evolution of the genes in the CO2 detection pathway of primates, which will help to reveal the relationship between the evolutionary pattern of this pathway and the environmental change.
|
PDF Full Text Request