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Polymerization of the backbone of the pectic polysaccharide rhamnogalacturonan I
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Abstract
Rhamnogalacturonan I (RG-I) is a major plant cell wall pectic polysaccharide defined by its repeating disaccharide backbone structure of [4)-α-D-GalA-(1,2)-α-L-Rha-(1,]. A family of RG-I:Rhamnosyltransferases (RRT) has previously been identified, but synthesis of the RG-I backbone has not been demonstrated in vitro because the identity of Rhamnogalacturonan I:Galaturonosyltransferase (RG-I:GalAT) was unknown. Here a putative glycosyltransferase, At1g28240/MUCI70, is shown to be an RG-I:GalAT. The name RGGAT1 is proposed to reflect the catalytic activity of this enzyme. When incubated together with the rhamnosyltransferase RRT4, the combined activities of RGGAT1 and RRT4 result in elongation of RG-I acceptors in vitro into a polymeric product. RGGAT1 is a member of a new GT family categorized as GT116, which does not group into existing GT-A clades and is phylogenetically distinct from the GALACTURONOSYLTRANSFERASE (GAUT) family of GalA transferases that synthesize the backbone of the pectin homogalacturonan. RGGAT1 has a predicted GT-A fold structure but employs a metal-independent catalytic mechanism that is rare among glycosyltransferases with this fold type. The identification of RGGAT1 and the 8-member Arabidopsis GT116 family provides a new avenue for studying the mechanism of RG-I synthesis and the function of RG-I in plants.
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Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 63
- Atmodjo, M. A., Hao, Z. & Mohnen, D. Evolving views of pectin biosynthesis. Annu. Rev. Plant Biol. 64, 747–779 (2013). · DOI · Paper page
- Biswal, A. K. et al. Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis. Nat. Biotechnol. 36, 249–257 (2018). · DOI
- Wu, D. et al. Dietary pectic substances enhance gut health by its polycomponent: a review. Compr. Rev. Food Sci. Food Saf. 20, 2015–2039 (2021). · DOI
- Bonnin, E., Garnier, C. & Ralet, M. C. Pectin-modifying enzymes and pectin-derived materials: applications and impacts. Appl. Microbiol. Biotechnol. 98, 519–532 (2014). · DOI
- Atmodjo, M. A. et al. Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan:galacturonosyltransferase complex. Proc. Natl Acad. Sci. USA 108, 20225–20230 (2011). · DOI
- Amos, R. A. et al. A two-phase model for the non-processive biosynthesis of homogalacturonan polysaccharides by the GAUT1:GAUT7 complex. J. Biol. Chem. 293, 19047–19063 (2018). · DOI
- Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2014). · DOI
- Engle, K. A. et al. Multiple Arabidopsis galacturonosyltransferases synthesize polymeric homogalacturonan by oligosaccharide acceptor-dependent or de novo synthesis. Plant J. https://doi.org/10.1111/tpj.15640 (2021). · DOI
- Kaczmarska, A., Pieczywek, P. M., Cybulska, J. & Zdunek, A. Structure and functionality of rhamnogalacturonan I in the cell wall and in solution: a review. Carbohydr. Polym. 278, 118909 (2022). · DOI
- Pena, M. J. & Carpita, N. C. Loss of highly branched arabinans and debranching of rhamnogalacturonan I accompany loss of firm texture and cell separation during prolonged storage of apple. Plant Physiol. 135, 1305–1313 (2004). · DOI
- Molina-Hidalgo, F. J. et al. The strawberry (Fragaria×ananassa) fruit-specific rhamnogalacturonate lyase 1 (FaRGLyase1) gene encodes an enzyme involved in the degradation of cell-wall middle lamellae. J. Exp. Bot. 64, 1471–1483 (2013). · DOI
- Yapo, B. M., Lerouge, P., Thibault, J.-F. & Ralet, M.-C. Pectins from citrus peel cell walls contain homogalacturonans homogenous with respect to molar mass, rhamnogalacturonan I and rhamnogalacturonan II. Carbohydr. Polym. 69, 426–435 (2007). · DOI
- Arsovski, A. A., Haughn, G. W. & Western, T. L. Seed coat mucilage cells of Arabidopsis thaliana as a model for plant cell wall research. Plant Signal. Behav. 5, 796–801 (2010). · DOI
- Haughn, G. W. & Western, T. L. Arabidopsis seed coat mucilage is a specialized cell wall that can be used as a model for genetic analysis of plant cell wall structure and function. Front. Plant Sci. 3, 64 (2012). · DOI
- Macquet, A., Ralet, M. C., Kronenberger, J., Marion-Poll, A. & North, H. M. In situ, chemical and macromolecular study of the composition of Arabidopsis thaliana seed coat mucilage. Plant Cell Physiol. 48, 984–999 (2007). · DOI
- Takenaka, Y. et al. Pectin RG-I rhamnosyltransferases represent a novel plant-specific glycosyltransferase family. Nat. Plants 4, 669–676 (2018). · DOI
- Wachananawat, B. et al. Diversity of pectin rhamnogalacturonan I rhamnosyltransferases in glycosyltransferase family 106. Front. Plant Sci. 11, 997 (2020). · DOI
- Liwanag, A. J. et al. Pectin biosynthesis: GALS1 in Arabidopsis thaliana is a β-1,4-galactan β-1,4-galactosyltransferase. Plant Cell 24, 5024–5036 (2012). · DOI
- Ebert, B. et al. The three members of the Arabidopsis glycosyltransferase family 92 are functional β-1,4-galactan synthases. Plant Cell Physiol. 59, 2624–2636 (2018). · DOI
- Voiniciuc, C. et al. Identification of key enzymes for pectin synthesis in seed mucilage. Plant Physiol. 178, 1045–1064 (2018). · DOI
- Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021). · DOI · Paper page
- Nikolovski, N. et al. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol. 160, 1037–1051 (2012). · DOI
- Sterling, J. D. et al. Functional identification of an Arabidopsis pectin biosynthetic homogalacturonan galacturonosyltransferase. Proc. Natl Acad. Sci. USA 103, 5236–5241 (2006). · DOI
- Fabrissin, I. et al. Natural variation reveals a key role for rhamnogalacturonan I in seed outer mucilage and underlying genes. Plant Physiol. 181, 1498–1518 (2019). · DOI
- Moremen, K. W. et al. Expression system for structural and functional studies of human glycosylation enzymes. Nat. Chem. Biol. 14, 156–162 (2018). · DOI
- Urbanowicz, B. R., Pena, M. J., Moniz, H. A., Moremen, K. W. & York, W. S. Two Arabidopsis proteins synthesize acetylated xylan in vitro. Plant J. 80, 197–206 (2014). · DOI
- Urbanowicz, B. R. et al. Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism. Plant J. 91, 931–949 (2017). · DOI
- Soto, M. J. et al. AtFUT4 and AtFUT6 are arabinofuranose-specific fucosyltransferases. Front. Plant Sci. 12, 589518 (2021). · DOI
- Kofod, L. V. et al. Cloning and characterization of two structurally and functionally divergent rhamnogalacturonases from Aspergillus aculeatus. J. Biol. Chem. 269, 29182–29189 (1994). · DOI
- Azadi, P., O’Neill, M. A., Bergmann, C., Darvill, A. G. & Albersheim, P. The backbone of the pectic polysaccharide rhamnogalacturonan I is cleaved by an endohydrolase and an endolyase. Glycobiology 5, 783–789 (1995). · DOI
- Ishii, T., Ichita, J., Matsue, H., Ono, H. & Maeda, I. Fluorescent labeling of pectic oligosaccharides with 2-aminobenzamide and enzyme assay for pectin. Carbohydr. Res. 337, 1023–1032 (2002). · DOI
- Scheller, H. V., Doong, R. L., Ridley, B. L. & Mohnen, D. Pectin biosynthesis: a solubilized α1,4-galacturonosyltransferase from tobacco catalyzes the transfer of galacturonic acid from UDP-galacturonic acid onto the non-reducing end of homogalacturonan. Planta 207, 512–517 (1999). · DOI
- Moremen, K. W. & Haltiwanger, R. S. Emerging structural insights into glycosyltransferase-mediated synthesis of glycans. Nat. Chem. Biol. 15, 853–864 (2019). · DOI
- Drula, E. et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. https://doi.org/10.1093/nar/gkab1045 (2021). · DOI · Paper page
- Taujale, R. et al. Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases. eLife https://doi.org/10.7554/eLife.54532 (2020). · DOI
- Taujale, R. et al. Mapping the glycosyltransferase fold landscape using interpretable deep learning. Nat. Commun. 12, 5656 (2021). · DOI
- Kadirvelraj, R. et al. Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites. J. Biol. Chem. 296, 100110 (2021). · DOI
- Klepikova, A. V., Kasianov, A. S., Gerasimov, E. S., Logacheva, M. D. & Penin, A. A. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J. 88, 1058–1070 (2016). · DOI
- Round, A. N., Rigby, N. M., MacDougall, A. J. & Morris, V. J. A new view of pectin structure revealed by acid hydrolysis and atomic force microscopy. Carbohydr. Res. 345, 487–497 (2010). · DOI
- Zdunek, A., Pieczywek, P. M. & Cybulska, J. The primary, secondary, and structures of higher levels of pectin polysaccharides. Compr. Rev. Food Sci. Food Saf. 20, 1101–1117 (2021). · DOI
- Amos, R. A. & Mohnen, D. Critical review of plant cell wall matrix polysaccharide glycosyltransferase activities verified by heterologous protein expression. Front. Plant Sci. 10, 915 (2019). · DOI
- Meinke, D. W. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. New Phytol. 226, 306–325 (2020). · DOI
- Tzafrir, I. et al. Identification of genes required for embryo development in Arabidopsis. Plant Physiol. 135, 1206–1220 (2004). · DOI
- Chen, L. Y. et al. The Arabidopsis alkaline ceramidase TOD1 is a key turgor pressure regulator in plant cells. Nat. Commun. 6, 6030 (2015). · DOI
- Pham, T. T. et al. Structures of complexes of a metal-independent glycosyltransferase GT6 from Bacteroides ovatus with UDP-N-acetylgalactosamine (UDP-GalNAc) and its hydrolysis products. J. Biol. Chem. 289, 8041–8050 (2014). · DOI
- Wu, D. et al. Rethinking the impact of RG-I mainly from fruits and vegetables on dietary health. Crit. Rev. Food Sci. Nutr. 60, 2938–2960 (2020). · DOI
- Naqash, F., Masoodi, F. A., Rather, S. A., Wani, S. M. & Gani, A. Emerging concepts in the nutraceutical and functional properties of pectin—a review. Carbohydr. Polym. 168, 227–239 (2017). · DOI
- Singh, R. P. et al. Generation of structurally diverse pectin oligosaccharides having prebiotic attributes. Food Hydrocoll. 108, 105988 (2020). · DOI
- Cui, J. et al. Dietary fibers from fruits and vegetables and their health benefits via modulation of gut microbiota. Compr. Rev. Food Sci. Food Saf. 18, 1514–1532 (2019). · DOI
- Micoli, F. et al. Glycoconjugate vaccines: current approaches towards faster vaccine design. Expert Rev. Vaccines 18, 881–895 (2019). · DOI
- Barnes, W. J. et al. Protocols for isolating and characterizing polysaccharides from plant cell walls: a case study using rhamnogalacturonan-II. Biotechnol. Biofuels 14, 142 (2021). · DOI
- Klausen, M. S. et al. NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning. Proteins 87, 520–527 (2019). · DOI
- Rohl, C. A., Strauss, C. E., Misura, K. M. & Baker, D. Protein structure prediction using Rosetta. Methods Enzymol. 383, 66–93 (2004). · DOI
- Osawa, T. et al. Crystal structure of chondroitin polymerase from Escherichia coli K4. Biochem. Biophys. Res. Commun. 378, 10–14 (2009). · DOI
- Neuwald, A. F. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinformatics 25, 1869–1875 (2009). · DOI
- Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2012). · DOI
- Tamura, K., Stecher, G. & Kumar, S. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021). · DOI
- Hall, B. G. Building phylogenetic trees from molecular data with MEGA. Mol. Biol. Evol. 30, 1229–1235 (2013). · DOI
- Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021). · DOI
- Morris, G. M. et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009). · DOI
- Nivedha, A. K., Thieker, D. F., Makeneni, S., Hu, H. & Woods, R. J. Vina-Carb: improving glycosidic angles during carbohydrate docking. J. Chem. Theory Comput. 12, 892–901 (2016). · DOI
- Neelamegham, S. et al. Updates to the symbol nomenclature for glycans guidelines. Glycobiology 29, 620–624 (2019). · DOI
- Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256–2268 (2004). · DOI
Metadata
- Authors
- Amos, R. A., Atmodjo, M. A., Huang, C., Gao, Z., Venkat, A., Taujale, R., Kannan, N., Moremen, K. W., & Mohnen, D.
- Affiliations
- University of Georgia (US)
- Corresponding author
- Mohnen, Debra
- ORCID
- Venue
- Nature Plants
- Published
- 2022-11-10
- Volume
- 8
- Issue
- 11
- Pages
- 1289-1303
- ISSN
- 2055-026X (ISSN-L)
- 2055-0278
- PMC
- PMC10115348
- OpenAlex
- W4308695747
- Cited by
- 55
- References
- 1
- Citations by year
- 2026: 19 · 2025: 14 · 2024: 14 · 2023: 8
- FWCI
- 4.96
- Type
- journal article
- Language
- en
- Update notices
- correction (2023-03-20)
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Plants (publishedVersion)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Health & Human Services | National Institutes of Health (R35 GM139656, P41GM103390, R01GM130915)
- U.S. Department of Energy (DE-SC0015662, AC05-000R22725)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Polysaccharides and Plant Cell Walls
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Surface Properties and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
- Keywords
- rhamnogalacturonan I, pectin, rhamnosyltransferase, Arabidopsis thaliana, homogalacturonan
- MeSH terms
- Pectins, Polysaccharides, Glycosyltransferases, Arabidopsis, Polymerization
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