CaCA superfamily genes in Saccharum spp.

Avani Dave, Jai Hind College.

Calcium (Ca2+) is the most commonly occurring element in almost all organisms. This broad presence can be linked to calcium’s role as an essential nutrient that provides the basis of the secondary messengers. The movement of Ca2+ ions is regulated by specific transport molecules acting as “gatekeepers”. As per the registered data from prior studies, these transporters can be categorized into 3 distinct classes, Ca2+-ATPases, permeable channels, and Ca2+/cation antiporters (CaCAs). They are known to mediate the movement of Ca2+ through the membranes, allowing the regulation of Ca2+ levels in the cytosol. CaCA proteins form a superfamily that is present in archaea, bacteria, fungi, plants, and animals. This widespread presence can be attributed to their ability to elevate the active efflux of Ca2+ through the membranes. They do so in exchange for the influx of several other monovalent cations like H+, Na+, or K+ to provide the energy for this uphill transport. 

As a superfamily, CaCAs comprise several exchanger proteins. These clusters can be subdivided into the following families

• The YRBG – seen in prokaryotes but not in eukaryotes. 

• Na+ / Ca2+ exchanger (NCX) – seen in animal groups 

• Na+ / Ca2+, K+ exchanger (NCKX) – seen in animal groups

• Cation / Ca2+ exchanger (CCX) – seen in animal groups

• H+ / cation exchanger (CAX) families – seen in bacteria, protozoa, fungi, animals, algae, and plants.

80% of the overall global production of sugar arises from Saccharum spp. (sugarcane), it also accounts for more than 40% of biofuel production, making it an economically essential plant. What might affect the usefulness lies in the different stresses experienced by these plants. These unfavourable conditions can be categorized as either biotic or abiotic. The plants have designated specific revolutionary mechanisms to avert the ill effects of such unfavourable stimuli. One such mechanism involves the ability of CaCAs to regulate the concentration of ions thereby maintaining the functional activities of the cells. In a study conducted by Su, W., et al. a genome-wide analysis of the CaCA proteins in Saccharum was performed. The two Saccharum species selected for this study were R570 and AP85-441. Their response under hormonal (abscisic acid, ABA), biotic (Sporisorium scitamineum), and abiotic (cold) stresses was visualized and evaluated.

Results

The findings of the study highlighted the presence of a different number of CaCA genes in the targeted plants, 34 genes in Saccharum spontaneum, 5 genes in R570, and 14 genes in Sorghum bicolour. These CaCA genes contained multiple families like CAX, CCX, EFCAX, MHX. 

Synteny analysis of the superfamily genes availed the identification of their orthologous and paralogous nature as observed in S. spontaneum, R570, and S. bicolour. Along with this, the protein-protein studies demonstrated the direct or indirect interacting mechanisms in the CaCA proteins. Further, the response of the CaCA genes to the various stress stimuli was registered by the technique of quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The hormonal stress stimuli witnessed an identical response in all the species as opposed to the diverse expression in response to biotic and abiotic stresses. 

Conclusions

This study involved a comprehensive analysis of the genes in the CaCA superfamily which were demonstrated in S. spontaneum, R570, and S. bicolour. This analysis paved the way for a more detailed characterization of the sequence and structural feature determination, classification, evolutionary progression, and other functional aspects of the genes. The findings arising from the study enabled the researchers with a vast repository of gene resources, further assisting in the exploration of the underlying mechanistic pathways. This broad understanding of the genes in the CaCA superfamily can be extrapolated to various gene families observed in Saccharum.

Also read: The 180-year-old-mystery behind alpine moth species

Source:

Su, W., Zhang, C., Wang, D. et al. The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress. BMC Genomics 22, 549 (2021). https://doi.org/10.1186/s12864-021-07828-3

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About the author: Avani Dave is currently in the final year of her bachelor’s degree, majoring in Life Sciences. Holding a good academic and extra-curricular record, she is on a constant journey of acquiring exposure in her field of interest while simultaneously not limiting herself to just that. Avani likes studying Diseases and Syndromes and everything under this umbrella! That being said, she is adept at working across departments and promises to deliver.