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Title: Three Novel Rice Genes Closely Related to the ArabidopsisIRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis

Abstract

Xylan is the second most abundant polysaccharide on Earth, and represents a major component of both dicot wood and the cell walls of grasses. Much knowledge has been gained from studies of xylan biosynthesis in the model plant, Arabidopsis. In particular, the irregular xylem (irx) mutants, named for their collapsed xylem cells, have been essential in gaining a greater understanding of the genes involved in xylan biosynthesis. In contrast, xylan biosynthesis in grass cell walls is poorly understood. We identified three rice genes Os07g49370 (OsIRX9), Os01g48440 (OsIRX9L), and Os06g47340 (OsIRX14), from glycosyltransferase family 43 as putative orthologs to the putative β-1,4-xylan backbone elongating Arabidopsis IRX9, IRX9L, and IRX14 genes, respectively. We demonstrate that the over-expression of the closely related rice genes, in full or partly complement the two well-characterized Arabidopsis irregular xylem (irx) mutants: irx9 and irx14. Complementation was assessed by measuring dwarfed phenotypes, irregular xylem cells in stem cross sections, xylose content of stems, xylosyltransferase (XylT) activity of stems, and stem strength. The expression of OsIRX9 in the irx9 mutant resulted in XylT activity of stems that was over double that of wild type plants, and the stem strength of this line increased to 124% above that of wildmore » type. Taken together, our results suggest that OsIRX9/OsIRX9L, and OsIRX14, have similar functions to the Arabidopsis IRX9 and IRX14 genes, respectively. Furthermore, our expression data indicate that OsIRX9 and OsIRX9L may function in building the xylan backbone in the secondary and primary cell walls, respectively. Our results provide insight into xylan biosynthesis in rice and how expression of a xylan synthesis gene may be modified to increase stem strength.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [2];  [6];  [2];  [5];  [7];  [8]
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  1. Univ. of California, Davis, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. of California, Davis, CA (United States)
  4. Univ. of Copenhagen (Denmark)
  5. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  6. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  7. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  8. Univ. of California, Davis, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Kyung Hee Univ., Yongin (Korea, Republic of)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1511360
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Volume: 4; Journal Issue: APR; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Chiniquy, Dawn, Varanasi, Patanjali, Oh, Taeyun, Harholt, Jesper, Katnelson, Jacob, Singh, Seema, Auer, Manfred, Simmons, Blake, Adams, Paul D., Scheller, Henrik V., and Ronald, Pamela C. Three Novel Rice Genes Closely Related to the ArabidopsisIRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. United States: N. p., 2013. Web. doi:10.3389/fpls.2013.00083.
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Chiniquy, Dawn, Varanasi, Patanjali, Oh, Taeyun, Harholt, Jesper, Katnelson, Jacob, Singh, Seema, Auer, Manfred, Simmons, Blake, Adams, Paul D., Scheller, Henrik V., & Ronald, Pamela C. Three Novel Rice Genes Closely Related to the ArabidopsisIRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. United States. doi:10.3389/fpls.2013.00083.
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Chiniquy, Dawn, Varanasi, Patanjali, Oh, Taeyun, Harholt, Jesper, Katnelson, Jacob, Singh, Seema, Auer, Manfred, Simmons, Blake, Adams, Paul D., Scheller, Henrik V., and Ronald, Pamela C. Wed . "Three Novel Rice Genes Closely Related to the ArabidopsisIRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis". United States. doi:10.3389/fpls.2013.00083. https://www.osti.gov/servlets/purl/1511360.
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@article{osti_1511360,
title = {Three Novel Rice Genes Closely Related to the ArabidopsisIRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis},
author = {Chiniquy, Dawn and Varanasi, Patanjali and Oh, Taeyun and Harholt, Jesper and Katnelson, Jacob and Singh, Seema and Auer, Manfred and Simmons, Blake and Adams, Paul D. and Scheller, Henrik V. and Ronald, Pamela C.},
abstractNote = {Xylan is the second most abundant polysaccharide on Earth, and represents a major component of both dicot wood and the cell walls of grasses. Much knowledge has been gained from studies of xylan biosynthesis in the model plant, Arabidopsis. In particular, the irregular xylem (irx) mutants, named for their collapsed xylem cells, have been essential in gaining a greater understanding of the genes involved in xylan biosynthesis. In contrast, xylan biosynthesis in grass cell walls is poorly understood. We identified three rice genes Os07g49370 (OsIRX9), Os01g48440 (OsIRX9L), and Os06g47340 (OsIRX14), from glycosyltransferase family 43 as putative orthologs to the putative β-1,4-xylan backbone elongating Arabidopsis IRX9, IRX9L, and IRX14 genes, respectively. We demonstrate that the over-expression of the closely related rice genes, in full or partly complement the two well-characterized Arabidopsis irregular xylem (irx) mutants: irx9 and irx14. Complementation was assessed by measuring dwarfed phenotypes, irregular xylem cells in stem cross sections, xylose content of stems, xylosyltransferase (XylT) activity of stems, and stem strength. The expression of OsIRX9 in the irx9 mutant resulted in XylT activity of stems that was over double that of wild type plants, and the stem strength of this line increased to 124% above that of wild type. Taken together, our results suggest that OsIRX9/OsIRX9L, and OsIRX14, have similar functions to the Arabidopsis IRX9 and IRX14 genes, respectively. Furthermore, our expression data indicate that OsIRX9 and OsIRX9L may function in building the xylan backbone in the secondary and primary cell walls, respectively. Our results provide insight into xylan biosynthesis in rice and how expression of a xylan synthesis gene may be modified to increase stem strength.},
doi = {10.3389/fpls.2013.00083},
journal = {Frontiers in Plant Science},
number = APR,
volume = 4,
place = {United States},
year = {2013},
month = {4}
}
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Journal Article:
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DOI:  10.3389/fpls.2013.00083
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Cited by: 40 works
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Figures / Tables:

FIGURE 1 FIGURE 1: Phylogenetic tree of glycosyltransferase family 43 including genes from rice, Arabidopsis, Poplar, Selaginella, and Physcomitrella genomes. The evolutionary relationships were inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 16.96637902 is shown. The tree is drawn to scale with branch lengths inmore » the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method and are in the units of the number of amino acid substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1). Evolutionary analyses were conducted in MEGA5.« less
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Works referencing / citing this record:

Hemicellulose biosynthesis
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Populus GT43 family members group into distinct sets required for primary and secondary wall xylan biosynthesis and include useful promoters for wood modification
journal, August 2014

  • Ratke, Christine; Pawar, Prashant Mohan-Anupama; Balasubramanian, Vimal K.
  • Plant Biotechnology Journal, Vol. 13, Issue 1
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A novel FC17/CESA4 mutation causes increased biomass saccharification and lodging resistance by remodeling cell wall in rice
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Biochemical characterization of rice xylan O-acetyltransferases
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Control of secondary cell wall patterning involves xylan deacetylation by a GDSL esterase
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Secondary cell walls: biosynthesis and manipulation
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  • Kumar, Manoj; Campbell, Liam; Turner, Simon
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  • DOI: 10.1093/jxb/erv533

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  • Torres, Andres F.; Visser, Richard G. F.; Trindade, Luisa M.
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journal, April 2018

  • Ratke, Christine; Terebieniec, Barbara K.; Winestrand, Sandra
  • New Phytologist, Vol. 219, Issue 1
  • DOI: 10.1111/nph.15160

Genetic engineering of grass cell wall polysaccharides for biorefining
journal, June 2017

  • Bhatia, Rakesh; Gallagher, Joe A.; Gomez, Leonardo D.
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Arabidopsis thaliana IRX10 and two related proteins from psyllium and Physcomitrella patens are xylan xylosyltransferases
journal, September 2014

  • Jensen, Jacob Krüger; Johnson, Nathan Robert; Wilkerson, Curtis Gene
  • The Plant Journal, Vol. 80, Issue 2
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journal, September 2014

  • Urbanowicz, Breeanna R.; Peña, Maria J.; Moniz, Heather A.
  • The Plant Journal, Vol. 80, Issue 2
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Functional conservation and divergence of Miscanthus lutarioriparius GT43 gene family in xylan biosynthesis
journal, April 2016

A review of xylan and lignin biosynthesis: Foundation for studying Arabidopsis irregular xylem mutants with pleiotropic phenotypes
journal, February 2014

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journal, January 2017

  • Hatfield, Ronald D.; Rancour, David M.; Marita, Jane M.
  • Frontiers in Plant Science, Vol. 7
  • DOI: 10.3389/fpls.2016.02056

Digital Gene Expression Analysis of Ponkan Mandarin (Citrus reticulata Blanco) in Response to Asia Citrus Psyllid-Vectored Huanglongbing Infection
journal, July 2016

  • Zhong, Yun; Cheng, Chunzhen; Jiang, Bo
  • International Journal of Molecular Sciences, Vol. 17, Issue 7
  • DOI: 10.3390/ijms17071063
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