Investigating the evolutionary origins of calcium signalling proteins

Proteins involved in calcium signalling are critical for human health because of their involvement in the nervous system, muscle activity and cardiac operation. Many of these proteins and their functions are poorly understood at a molecular level. The evolutionary trajectories that have yielded extant proteins in biological systems are often overlooked, despite their importance in phenotypic development. Herein, we utilise computational and experimental approaches to elucidate the characteristics of bacterial homologs of proteins involved in calcium signalling.
We present a high-performance computing-based bioinformatics workflow for phylogenetic analysis, using a case study protein, aspartate 1-decarboxylase (ADC), not involved in calcium signalling, but of biomedical relevance as a target for antibiotics. Phylogenetic analysis of ADC identified homologs that could further elucidate the sequence-level requirements for the cofactor dependence of E. coli ADC.
We elucidate features in ionotropic glutamate receptor’s ligand binding domain and transmembrane domain that are present in bacteria but are little studied. Specifically, we outline a C-terminal H-bond network and a TMD-based dyad that we propose are important for function.
Similar application of the bioinformatic workflow located homologs of calmodulin, one of which, from the cyanobacterium Okeania sp. SIO2C9, was characterised by nuclear magnetic resonance spectroscopy studies to have similar conformational dynamics to calmodulin. Other cyanobacterial calmodulin-like domains, which are part of functionally diverse multidomain proteins located in this study, warrant further investigation.
Preliminary study of the calmodulin-dependent kinase II (CaMKII) association domain has revealed residues that could be involved in the oligomeric assembly of the CaMKII hub.
The multifaceted nature of this methodology also has led us to believe that cyanobacteria have contributed significantly to eukaryotic genomes, likely by horizontal gene transfer. This study demonstrates an evolutionary approach could generate lines of scientific enquiry that result in developed understanding of calcium signalling proteins and of bacterial contributions to eukaryogenesis.