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      The DROOPING LEAF ( DR) gene encoding GDSL esterase is involved in silica deposition in rice ( Oryza sativa L.)

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      Author(s): 1 , 2 , 3 , 1 , *
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      Journal: PLoS ONE
      Publisher: Public Library of Science

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          Abstract

          Leaf morphology is one of the most important agronomic traits in rice breeding because of its contribution to crop yield. The drooping leaf ( dr) mutant was developed from the Ilpum rice cultivar by ethyl methanesulfonate (EMS) mutagenesis. Compared with the wild type, dr plants exhibited drooping leaves accompanied by a small midrib, short panicle, and reduced plant height. The phenotype of the dr plant was caused by a mutation within a single recessive gene on chromosome 2, dr (LOC_Os02g15230), which encodes a GDSL esterase. Analysis of wild-type and dr sequences revealed that the dr allele carried a single nucleotide substitution, glycine to aspartic acid. RNAi targeted to LOC_Os02g15230 produced same phenotypes to the dr mutation, confirming LOC_Os02g15230 as the dr gene. Microscopic observations and plant nutrient analysis of SiO 2 revealed that silica was less abundant in dr leaves than in wild-type leaves. This study suggests that the dr gene is involved in the regulation of silica deposition and that disruption of silica processes lead to drooping leaf phenotypes.

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          Silicon uptake and accumulation in higher plants.

          Jian Ma, Naoki Yamaji (2006)
          Silicon (Si) accumulation differs greatly between plant species because of differences in Si uptake by the roots. Recently, a gene encoding a Si uptake transporter in rice, a typical Si-accumulating plant, was isolated. The beneficial effects of Si are mainly associated with its high deposition in plant tissues, enhancing their strength and rigidity. However, Si might play an active role in enhancing host resistance to plant diseases by stimulating defense reaction mechanisms. Because many plants are not able to accumulate Si at high enough levels to be beneficial, genetically manipulating the Si uptake capacity of the root might help plants to accumulate more Si and, hence, improve their ability to overcome biotic and abiotic stresses.
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            The anomaly of silicon in plant biology.

            E. Epstein (1994)
            Silicon is the second most abundant element in soils, the mineral substrate for most of the world's plant life. The soil water, or the "soil solution," contains silicon, mainly as silicic acid, H4SiO4, at 0.1-0.6 mM--concentrations on the order of those of potassium, calcium, and other major plant nutrients, and well in excess of those of phosphate. Silicon is readily absorbed so that terrestrial plants contain it in appreciable concentrations, ranging from a fraction of 1% of the dry matter to several percent, and in some plants to 10% or even higher. In spite of this prominence of silicon as a mineral constituent of plants, it is not counted among the elements defined as "essential," or nutrients, for any terrestrial higher plants except members of the Equisitaceae. For that reason it is not included in the formulation of any of the commonly used nutrient solutions. The plant physiologist's solution-cultured plants are thus anomalous, containing only what silicon is derived as a contaminant of their environment. Ample evidence is presented that silicon, when readily available to plants, plays a large role in their growth, mineral nutrition, mechanical strength, and resistance to fungal diseases, herbivory, and adverse chemical conditions of the medium. Plants grown in conventional nutrient solutions are thus to an extent experimental artifacts. Omission of silicon from solution cultures may lead to distorted results in experiments on inorganic plant nutrition, growth and development, and responses to environmental stress.
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              GDSL family of serine esterases/lipases.

              Casimir Akoh, Guan-Chiun Lee, Yen-Chywan Liaw … (2004)
              GDSL esterases and lipases are hydrolytic enzymes with multifunctional properties such as broad substrate specificity and regiospecificity. They have potential for use in the hydrolysis and synthesis of important ester compounds of pharmaceutical, food, biochemical, and biological interests. This new subclass of lipolytic enzymes possesses a distinct GDSL sequence motif different from the GxSxG motif found in many lipases. Unlike the common lipases, GDSL enzymes do not have the so called nucleophile elbow. Studies show that GDSL hydrolases have a flexible active site that appears to change conformation with the presence and binding of the different substrates, much like the induced fit mechanism proposed by Koshland. Some of the GDSL enzymes have thioesterase, protease, arylesterase, and lysophospholipase activity, yet they appear to be the same protein with similar molecular weight ( approximately 22-60 kDa for most esterases), although some have multiple glycosylation sites with higher apparent molecular weight. GDSL enzymes have five consensus sequence (I-V) and four invariant important catalytic residues Ser, Gly, Asn, and His in blocks I, II, III, and V, respectively. The oxyanion structure led to a new designation of these enzymes as SGNH-hydrolase superfamily or subfamily. Phylogenetic analysis revealed that block IIA which belonged to the SGNH-hydrolases was found only in clade I. Therefore, this family of hydrolases represents a new example of convergent evolution of lipolytic enzymes. These enzymes have little sequence homology to true lipases. Another important differentiating feature of GDSL subfamily of lipolytic enzymes is that the serine-containing motif is closer to the N-terminus unlike other lipases where the GxSxG motif is near the center. Since the first classification of these subclass or subfamily of lipases as GDSL(S) hydrolase, progress has been made in determining the consensus sequence, crystal structure, active site and oxyanion residues, secondary structure, mechanism of catalysis, and understanding the conformational changes. Nevertheless, much still needs to be done to gain better understanding of in vivo biological function, 3-D structure, how this group of enzymes evolved to utilize many different substrates, and the mechanism of reactions. Protein engineering is needed to improve the substrate specificity, enantioselectivity, specific activity, thermostability, and heterologous expression in other hosts (especially food grade microorganisms) leading to eventual large scale production and applications. We hope that this review will rekindle interest among researchers and the industry to study and find uses for these unique enzymes.
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                Author and article information

                Contributors
                Yoye Yu: Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: Writing – original draft
                Mi-Ok Woo: Role: Data curationRole: InvestigationRole: MethodologyRole: Software
                Piao Rihua: Role: Data curationRole: InvestigationRole: Methodology
                Hee-Jong Koh:
                ORCID: http://orcid.org/0000-0002-4357-7008
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Jong-Seong Jeon: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 10 September 2020
                Publication date Collection: 2020
                Volume: 15
                Issue: 9
                Electronic Location Identifier: e0238887
                Affiliations
                [1 ] Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
                [2 ] Science & Technology Policy Division, Ministry of Agriculture, Food and Rural Affairs, Sejong, South Korea
                [3 ] Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, China
                Kyung Hee Univeristy, REPUBLIC OF KOREA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-4357-7008
                Article
                Publisher ID: PONE-D-20-15655
                DOI: 10.1371/journal.pone.0238887
                PMC ID: 7482962
                PubMed ID: 32913358
                SO-VID: c9f7afb9-1650-4a0b-a6e2-402f5320817b
                Copyright © © 2020 Yu et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 25 May 2020
                Date accepted : 25 August 2020
                Page count
                Figures: 9, Tables: 2, Pages: 16
                Funding
                Funded by: the Next-Generation BioGreen 21 Program, Rural Development Administration, Korea
                Award ID: No. PJ013165
                Award Recipient :
                ORCID: http://orcid.org/0000-0002-4357-7008
                This study was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ013165) of the Rural Development Administration, Korea.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Anatomy
                Subject: Leaves
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Phenotypes
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Single Nucleotide Polymorphisms
                Subject: Biology and life sciences
                Subject: Genetics
                Subject: Epigenetics
                Subject: RNA interference
                Subject: Biology and life sciences
                Subject: Genetics
                Subject: Gene expression
                Subject: RNA interference
                Subject: Biology and life sciences
                Subject: Genetics
                Subject: Genetic interference
                Subject: RNA interference
                Subject: Biology and life sciences
                Subject: Biochemistry
                Subject: Nucleic acids
                Subject: RNA
                Subject: RNA interference
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Eukaryota
                Subject: Plants
                Subject: Grasses
                Subject: Rice
                Subject: Research and Analysis Methods
                Subject: Animal Studies
                Subject: Experimental Organism Systems
                Subject: Plant and Algal Models
                Subject: Rice
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Anatomy
                Subject: Inflorescences
                Subject: Panicles
                Subject: Biology and Life Sciences
                Subject: Cell Biology
                Subject: Cellular Structures and Organelles
                Subject: Cell Walls
                Subject: Plant Cell Walls
                Subject: Biology and Life Sciences
                Subject: Cell Biology
                Subject: Cellular Types
                Subject: Plant Cells
                Subject: Plant Cell Walls
                Subject: Biology and Life Sciences
                Subject: Cell Biology
                Subject: Plant Cell Biology
                Subject: Plant Cells
                Subject: Plant Cell Walls
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Cell Biology
                Subject: Plant Cells
                Subject: Plant Cell Walls
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Bioinformatics
                Subject: Sequence Analysis
                Subject: Sequence Alignment
                Custom metadata
                Data Availability All relevant data are within the paper and its Supporting Information files.

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