Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (Phaseolus vulgaris L.)

Abstract

The hard-to-cook defect in common beans is dictated by the ability to achieve cell separation during cooking. Hydrolysis of pectin methyl-esters by the pectin methyl-esterase (PME) enzyme influences cell separation. However, the contributions of the PME enzyme and the cell wall to the hard-to-cook defect have not been studied using molecular tools. We compared relevant molecular processes in fast- and slow-cooking bean varieties to understand the mechanisms underpinning the hard-to-cook defect. A PME spectrophotometric assay showed minor differences in enzyme activity between varieties. Meanwhile, a PME HMMER search in the P. vulgaris genome unveiled 113 genes encoding PMEs and PME inhibitors (PMEIs). Through RNA sequencing, we compared the gene expression of the PME-related genes in both varieties during seed development. A PME (Phvul010g080300) and PMEI gene (Phvul005g007600) showed the highest expression in the fast- and slow-cooking beans, respectively. We further identified 2132 differentially expressed genes (DEGs). Genes encoding cell-wall-related enzymes, mainly glycosylphosphatidylinositol mannosyltransferase, xyloglucan O-acetyltransferase, pectinesterase, and callose synthase, ranked among the top DEGs, indicating novel relations to the hard-to-cook defect. Gene ontology mapping revealed hydrolase activity and protein phosphorylation as functional categories with the most abundant upregulated DEGs in the slow-cooking bean. Additionally, the cell periphery contained 8% of the DEGs upregulated in the slow-cooking bean. This study provides new insights into the role of pectin methyl-esterase-related genes and novel cell wall processes in the occurrence of the hard-to-cook defect.

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

“…In all, more information will be needed to determine why TZ‐27 has higher pectin methylesterase activity. It should be determined, for instance, whether pectin methylesterase and pectin methylesterase inhibitor proteins accumulate more in TZ‐27 prior to seed maturity, thereby increasing pectin methylesterase activity immediately following water uptake (Tolili et al., 2022). In addition, the effects of mutations on pectin methylesterase activity should be explored.…”

“…Significant changes in enzyme activity paired with changes in cell structure during soaking could indicate that soaking directly affects gene expression in beans, and that gene expression affects cooking time. However, few studies have measured the entire transcriptome in P. vulgaris L. seeds during soaking, and even fewer have used transcriptomic data as a tool to understand how gene expression affects cooking time and phenotypes related to cooking time (Astudillo‐Reyes et al., 2015; O'Rourke et al., 2014; Parreira et al., 2018; Perez de Souza et al., 2019; Toili et al., 2022). Thus, the aim of this study was to (1) contrast and compare transcript expression in fast‐ and slow‐cooking beans within market classes; (2) characterize the physiology of cooking time; and (3) identify candidate genes for marker‐assisted selection.…”

Induction of common beanOVATE Family Protein 7(PvOFP7) promotes resistance to common bacterial blight

“…Indeed, although successful transformation has been achieved in few cases (Bonfim et al, 2007;Aragão et al, 1998;Collado et al, 2015), protocols remain largely genotype-dependent and both transformation and regeneration rates are still extremely low (Veltcheva et al, 2005;Hnatuszko-Konka et al, 2019;Hnatuszko-konka et al, 2014). Thus, except for hairy-root systems (Voß et al, 2022;Estrada-Navarrete et al, 2007), gene editing methods such as CRISPR/Cas9 have yet to be democratized for common bean (Toili, 2022). Transient expression via Agrobacterium (Richard et al, 2021) and virus-induced gene silencing (VIGS) methods have been developed using the bean pod mottle virus (Pflieger et al, 2014;Zhang et al, 2013).…”