|Emery, Laura -|
|Whelan, Simon -|
|Hirschi, Kendal -|
|Pittman, Jon -|
Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 1, 2012
Publication Date: January 13, 2012
Citation: Emery, L., Whelan, S., Hirschi, K.D., Pittman, J.K. 2012. Protein phylogenetic analysis of Ca(2+)/cation antiporters and insights into their evolution in plants. Frontiers in Plant Science. 3(1):1-19. Interpretive Summary: Determining functionality of genes is difficult and time consuming, often taking years to assign biological meaning to a specific nucleic acid sequence. Given that plant genomes contain at least 20,000 genes, ascribing function to the entire genome is a daunting task. Here we seek to use computer models to obviate some of the time-consuming aspects of standard experimentation. Bioinformatics is the application of computer science and information technology to the field of biology. In this work, we use bioinformatics to infer the function and evolution of over 100 plant calcium transporters from an array of plant species. By comparing the transporters among apples and oranges we can model the important structural components in these proteins and build a map to highlight areas that are conserved across different plant species. We assume that these invariant domains have important functional attributes and we speculate about their roles in various plant responses. We suggest alterations that could be engineered in the proteins to modify their functions and possibly increase plant yield and nutrient content. We find that we can make accurate predictions for the functionality of many genes by using computer programs and we have verified these predictions through limited experimentation. This study builds models regarding function that can save time and effort for future biologist regarding transporter functions.
Technical Abstract: Cation transport is a critical process in all organisms and is essential for mineral nutrition, ion stress tolerance, and signal transduction. Transporters that are members of the Ca(2+)/cation antiporter (CaCA) superfamily are involved in the transport of Ca(2+) and/or other cations using the counter exchange of another ion such as H(+) or Na(+). The CaCA superfamily has been previously divided into five transporter families: (1) the YRBG; (2) Na(+)/Ca(2+) exchanger (NCX); (3) Na(+)/Ca(2+), K(+) exchanger (NCKX); (4) H(+)/cation exchanger (CAX); and (5) cation/Ca(2+) exchanger (CCX) families, that include the well-characterized NCX and CAX transporters. To examine the evolution of CaCA transporters within higher plants and the green plant lineage, CaCA genes were identified from the genomes of sequenced flowering plants, a bryophyte, lycophyte, and freshwater and marine algae, and compared with those from non-plant species. We found evidence of the expansion and increased diversity of flowering plant genes within the CAX and CCX families. Genes related to the NCX family are present in land plant though they encode distinct MHX homologs that probably have an altered transport function. In contrast, the NCX and NCKX genes that are absent in land plants have been retained in many species of algae, especially the marine algae, indicating that these organisms may share "animal-like" characteristics of Ca(2+) homeostasis and signaling. A group of genes encoding novel CAX-like proteins containing an EF-hand domain were identified from plants and selected algae but appeared to be lacking in any other species. Lack of functional data for most of the CaCA proteins make it impossible to reliably predict substrate specificity and function for many of the groups or individual proteins. The abundance and diversity of CaCA genes throughout all branches of life indicates the importance of this class of cation transporter, and that many transporters with novel functions are waiting to be discovered.