Comprehensive Characterization of Phospholipase A Genes in Sorghum bicolor: Insights into Growth, Defense, and Stress Response

  • SorghumBase Team
  • 28 October 2024

Sorghum, a critical crop within the Poaceae family, plays an essential role in agriculture, especially in semi-arid regions where it serves as a staple for over 750 million people. This versatile cereal crop supports human and animal nutrition, ranking as India’s third most significant crop overall. Integral to various cellular functions such as carbon partitioning, cell elongation, defense responses, and plant growth are the enzymatic activities of phospholipases, which hydrolyze phospholipids to produce free fatty acids (FFAs) and other essential compounds. These enzymes, divided into three main groups—PLA, PLC, and PLD—play crucial roles in processes like intracellular signaling, membrane maintenance, and lipid metabolism, with PLA subtypes (pPLA, PLA1, and PLA2) showing specific activities depending on their cleavage positions on phospholipids.

Through extensive analysis of the sorghum genome, researchers from ICRISAT, Osmania University, University of Nottingham and Rothamsted Research identified 32 SbPLA genes, grouped into pPLA, PLA1, and sPLA2 categories, akin to the classifications in Arabidopsis and rice. Subcellular localization studies revealed that these genes are predominantly found in chloroplasts, reflecting similar distribution patterns observed in other plant species. Domain analysis highlighted distinct features such as the ‘patatin’ domain in pPLA, ‘lipase3’ in PLA1, and ‘PA2c’ in sPLA2, marking their functional diversity. Chromosomal mapping showed the genes’ variable distribution across ten chromosomes, excluding chromosomes 6 and 9. Previous research has highlighted the crucial role of the phospholipase gene family in early developmental stages, with many genes showing developmental-specific elements in their promoter regions. Phospholipases are essential for developmental and hormone-specific gene functions and play a significant role in signaling pathways triggered by abiotic stress. The STRING analysis conducted in this study revealed that the SbPLA genes are predominantly involved in lipid degradation, lipid metabolism, and hydrolase activities. SbSDP1-L and SbPLA2a emerged as key regulators, playing significant roles in various processes and overseeing the PLA gene family network. As members of the lipolytic acyl hydrolase family, these proteins are crucial for regulating membrane functions.

Expression profiling suggested that certain SbPLA genes, particularly within the pPLA class, are upregulated during specific developmental stages like root and seedling growth, indicating their potential involvement in seed development and root elongation. Additionally, pollen-specific PLA genes point towards their role in haploid induction, crucial for breeding processes. These findings provide a foundational understanding for further functional and molecular characterization of PLA genes in sorghum, paving the way for advanced studies on their roles in stress responses, growth regulation, and lipid metabolism.

SorghumBase examples: 

This study identifies and characterizes 32 phospholipase A (PLA) genes in Sorghum bicolor. We selected the gene SbpPLA-1(Sobic.002G320900) from this published study as the candidate gene to explore SorghumBase (https://sorghumbase.org/).  

Figure 1: The Germplasm tab displays predicted loss-of-function alleles of the SbpPLA-1 gene (Sobic.002G320900; SORBI_3002G320900) in SorbMutDB, showing variants with a stop-gained consequence. This tab lists accessions harboring protein-truncating variants (PTVs), along with their predicted consequence, zygosity (homozygous or heterozygous), and the associated genotyping study where they were identified. The PTVs represent putative loss-of-function single nucleotide polymorphisms (SNPs) located within the canonical transcript of the gene model. The table also includes links to SorbMutDB (USDA-Lubbock-EMS lines) and provides search functionality to explore other genes with PTVs in specific germplasm accessions. The indexed PTVs encompass predicted functional effects such as start lost, stop gained, stop lost, splice site acceptor, and splice site donor.

Figure 2: The sequence tab displays the peptide sequence of SbpPLA-1 [Sobic.002G320900; SORBI_3002G320900] in the search results on SorghumBase. The figures also suggest the AT1G61850 as an ortholog of this gene with 64% identity.
Figure 3: This figure displays the chromosome location of SbpPLA-1 [Sobic.002G320900; SORBI_3002G320900] under the Location tab in the Search results on SorghumBase. The gene is located on chromosome 2; within 2:69222573-69234444. In addition to SorghumBase, links to are provided on to the internal Sorghumbase EnsemblBrowser and external resource Phytozome to explore this gene in detail.
Figure 4: This figure shows the expression profile of SbpPLA-1 [Sobic.002G320900; SORBI_3002G320900] under the Expression tab (All Studies) in the search display onSorghumBase. It displays the baseline expression of the gene across all 11 published sorghum BTx623 datasets curated and processed by EMBL-EBI Expression Atlas in collaboration with the SorghumBase team.
Figure 5: This figure shows the expression of SbpPLA-1 [Sobic.002G320900; SORBI_3002G320900] under the Expression tab (eFP Browser) in the search results on SorghumBase. The eFP browser provides “electronic fluorescent pictographic” representations of the expression patterns of Sobic.002G320900 based on the Developmental and Stress Atlases by McCormick et al (2018).
Figure 6: This figure shows the homology of SbpPLA-1 [Sobic.002G320900; SORBI_3002G320900] under the Homology tab in the SorghumBase. A total of 40 homologs and 37 orthologs of this gene are identified.
Reference: 

Sapara VJ, Shankhapal AR, Reddy PS. Genome-wide screening and characterization of phospholipase A (PLA)-like genes in sorghum (Sorghum bicolor L.). Planta. 2024 Jun 26;260(2):35. PMID: 38922509. doi: 10.1007/s00425-024-04467-2. Read more

Related Project Websites: