Abstract
The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.
Highlights
S-domain subfamily of receptor-like kinases (SDRLKs) family members have the variable gene and protein structures S-locus receptor kinase gene, the prototype member of the SDRLK gene family, consists of seven exons separated by introns: the first exon encodes the entire extracellular S-domain, the second exon encodes the transmembrane and juxta-membrane domains, and exons 3–7 encode the kinase domain (Stein et al, 1991)
Based on homology modeling, we have suggested that the S-domain of the SRK6 protein from Brassica oleracea consists of an N-terminal signal peptide (SP) and four structurally conserved domains, including two contiguous N-terminal Lectin-like domains (LLD) followed by an EGF-like domain and a C-terminal PAN_APPLE domain (Naithani et al, 2007)
The crystal structure of SRK9 bound to its cognate ligand the SCR9 confirmed this domain structure of S-locus receptor kinase (SRK) and further suggested that both N-terminal LLDs are globular and each consists of a nine-stranded β-barrel that forms a “Y”-shaped structure, the EGF-like domain contains an embedded short a-helix, and the PAN_APPLE domain is highly similar to the N-terminal domain of hepatocyte growth factor (HGF) (Ma et al, 2016)
Summary
Receptor-like kinases (RLKs) are major players in perceiving and transducing extracellular signals into appropriate cellular responses and have been associated with nearly every aspect of plant growth and development (Becraft, Stinard & McCarty, 1996; Berckmans et al, 2020; Cartwright, Humphries & Smith, 2009; Clark, Williams & Meyerowitz, 1997), organ differentiation (Hord et al, 2006; Jinn, Stone & Walker, 2000; Pu et al, 2017; Shpak, Lakeman & Torii, 2003), plant reproduction (Ahmadi et al, 2016; Escobar-Restrepo et al, 2007; Kachroo et al, 2001; Stein et al, 1991; Yu et al, 2016) and plant’s response to biotic (Chen et al, 2006; Fan et al, 2018; Gomez-Gomez & Boller, 2000; Pruitt et al, 2015), and abiotic stresses (Chen et al, 2013; Grison et al, 2019; Ouyang et al, 2010; Pan et al, 2020). An RLK protein consists of an extracellular N-terminal domain followed by a transmembrane domain, and a conserved C-terminal kinase domain. The extracellular domain of RLKs are involved in sensing the extracellular signals via interacting with ligands (i.e., small molecules such as hormones, glycoproteins, or short peptides), and the cytoplasmic Serine/Threonine (Ser/Thr) kinase domain transfers the signal by phosphorylating downstream targets to activate/inactivate the relevant physiological pathways (Wolf, 2017). RLKs display great variety in their extracellular domains, consistent with their role in recognizing the diverse ligands, whereas their kinase domains show high conservation in sequence and structure. Based on the structure of their extracellular domains and the phylogenetic relationships between kinase domains, RLKs are grouped into subfamilies, such as leucine-rich repeats, S-domains (SD), Wall-associated kinases, etc. Based on the structure of their extracellular domains and the phylogenetic relationships between kinase domains, RLKs are grouped into subfamilies, such as leucine-rich repeats, S-domains (SD), Wall-associated kinases, etc. (Shiu & Bleecker, 2001a, 2001b)
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