Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.)
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 d...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-06-01
|
| Series: | Foods |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2304-8158/11/12/1692 |
| _version_ | 1797487505374707712 |
|---|---|
| author | Mary Esther Muyoka Toili Ramon de Koning Raphaël Kiekens Nelson Ndumba Samuel Wahome Sylvester Anami Stephen Mwangi Githiri Geert Angenon |
| author_facet | Mary Esther Muyoka Toili Ramon de Koning Raphaël Kiekens Nelson Ndumba Samuel Wahome Sylvester Anami Stephen Mwangi Githiri Geert Angenon |
| author_sort | Mary Esther Muyoka Toili |
| collection | DOAJ |
| description | 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 <i>HMMER</i> search in the <i>P. vulgaris</i> 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 (<i>Phvul010g080300</i>) and PMEI gene (<i>Phvul005g007600</i>) 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. |
| first_indexed | 2024-03-09T23:49:38Z |
| format | Article |
| id | doaj.art-525481545c51408fb011c610cc9f816d |
| institution | Directory Open Access Journal |
| issn | 2304-8158 |
| language | English |
| last_indexed | 2024-03-09T23:49:38Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Foods |
| spelling | doaj.art-525481545c51408fb011c610cc9f816d2023-11-23T16:37:31ZengMDPI AGFoods2304-81582022-06-011112169210.3390/foods11121692Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.)Mary Esther Muyoka Toili0Ramon de Koning1Raphaël Kiekens2Nelson Ndumba3Samuel Wahome4Sylvester Anami5Stephen Mwangi Githiri6Geert Angenon7Laboratory of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, BelgiumLaboratory of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, BelgiumLaboratory of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, BelgiumDepartment of Biochemistry, School of Biomedical Sciences, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, KenyaDepartment of Horticulture and Food Security, School of Agriculture and Environmental Sciences, College of Agriculture and Natural Resources, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, KenyaInstitute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, KenyaDepartment of Horticulture and Food Security, School of Agriculture and Environmental Sciences, College of Agriculture and Natural Resources, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, KenyaLaboratory of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, BelgiumThe 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 <i>HMMER</i> search in the <i>P. vulgaris</i> 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 (<i>Phvul010g080300</i>) and PMEI gene (<i>Phvul005g007600</i>) 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.https://www.mdpi.com/2304-8158/11/12/1692pectin methyl-esterase (PME)pectin methyl-esterase inhibitor (PMEI)<i>Phaseolus vulgaris</i>hard-to-cook defectRNA sequencing |
| spellingShingle | Mary Esther Muyoka Toili Ramon de Koning Raphaël Kiekens Nelson Ndumba Samuel Wahome Sylvester Anami Stephen Mwangi Githiri Geert Angenon Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.) Foods pectin methyl-esterase (PME) pectin methyl-esterase inhibitor (PMEI) <i>Phaseolus vulgaris</i> hard-to-cook defect RNA sequencing |
| title | Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_full | Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_fullStr | Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_full_unstemmed | Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_short | Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (<i>Phaseolus vulgaris</i> L.) |
| title_sort | transcriptome guided identification of pectin methyl esterase related enzymes and novel molecular processes effectuating the hard to cook defect in common bean i phaseolus vulgaris i l |
| topic | pectin methyl-esterase (PME) pectin methyl-esterase inhibitor (PMEI) <i>Phaseolus vulgaris</i> hard-to-cook defect RNA sequencing |
| url | https://www.mdpi.com/2304-8158/11/12/1692 |
| work_keys_str_mv | AT maryesthermuyokatoili transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil AT ramondekoning transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil AT raphaelkiekens transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil AT nelsonndumba transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil AT samuelwahome transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil AT sylvesteranami transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil AT stephenmwangigithiri transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil AT geertangenon transcriptomeguidedidentificationofpectinmethylesteraserelatedenzymesandnovelmolecularprocesseseffectuatingthehardtocookdefectincommonbeaniphaseolusvulgarisil |