CBP60-DB: An AlphaFold-predicted plant kingdom-wide database of the CALMODULIN-BINDING PROTEIN 60 (CBP60) protein family with a novel structural clustering algorithm

Abstract

Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CAM-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation and diversification in most species remain unclear. Here we have created CBP60-DB, a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs (encoding 2376 unique transcripts and 1996 unique proteins) across 62 phylogenetically diverse genomes in the plant kingdom. We have employed deep learning-predicted structural analyses using AlphaFold2 and then generated dedicated web pages for all plant CBP60 proteins. Importantly, we have generated a novel clustering visualization algorithm to interrogate kingdom-wide structural similarities for more efficient inference of conserved functions across various plant taxa. Because well-characterized CBP60 proteins in Arabidopsis are known to be transcription factors with putative calmodulin-binding domains, we have integrated external bioinformatic resources to analyze protein domains and motifs. Collectively, we present a plant kingdom-wide identification of this important protein family in a user-friendly AlphaFold-anchored database, representing a novel and significant resource for the broader plant biology community.

Structural diversity and stress regulation of the plant immunity-associated CALMODULIN-BINDING PROTEIN 60 (CBP60) family of transcription factors inSolanum lycopersicum(tomato)

“…In this paper, we have successfully identified and characterized 11 CBP60 family members in tomato plants. Unlike CBP60 proteins in the model species Arabidopsis thaliana (Reddy et al, 2002;Wang et al, 2009;Truman et al, 2013;Amani et al, 2022;Zheng et al, 2022), CBP60 proteins in tomato and other species have remained unexplored. First, phylogenetic and structural analyses were conducted for the 11 SlCBP60 proteins (Figures 1-2).…”

“…CBP60g is a member of the CBP60 protein family (Reddy et al, 2002; Wang et al, 2009; Truman et al, 2013; Amani et al, 2022; Zheng et al, 2022) and serves as a key transcriptional regulator for SA biosynthetic genes ISOCHORISMATE SYNTHASE 1 ( ICS1 ) and AVRPPHB SUSCEPTIBLE 3 ( PBS3 ; Zhang et al, 2010; Wang et al, 2009; Sun et al, 2015; Kim et al, 2022). Like CBP60g, another CBP60 protein family member SYSTEMIC ACQUIRED RESISTANCE 1 (SARD1) plays a partially redundant role in SA biosynthesis (Zhang et al, 2010; Wang et al, 2011).…”

“…Although a recent study reported orthologs of CBP60g and SARD1 in tobacco plants (Takagi et al, 2022), the function and regulation of CBP60 proteins in other plant species have yet to be investigated. We recently identified CBP60 homologs cross various representative taxa in the plant kingdom (Amani et al, 2022); however, whether gene expression trends observed in Arabidopsis are conserved in other plants remain unclear. In this study, we report the identification of 11 homologous CBP60 ( SlCBP60 ) genes in tomato plants ( Solanum lycopersiucm ).…”

Structural diversity and stress regulation of the plant immunity-associated CALMODULIN-BINDING PROTEIN 60 (CBP60) family of transcription factors in Solanum lycopersicum (tomato)

“…Although a recent study reported orthologs of CBP60g and SARD1 in tobacco plants (Takagi et al, 2022), the function and regulation of CBP60 proteins in other plant species have yet to be investigated. We recently identified CBP60 homologs across various representative taxa in the plant kingdom (Amani et al, 2022); however, whether gene expression trends observed in Arabidopsis are conserved in other plants remain unclear. In this study, we report the identification of 11 homologous CBP60 (SlCBP60) genes in tomato plants (Solanum lycopersicum).…”