title: A genomics approach to deciphering lignin biosynthesis in switchgrass.
abstract: It is necessary to overcome recalcitrance of the biomass to saccharification (sugar release) to make switchgrass (Panicum virgatum) economically viable as a feedstock for liquid biofuels. Lignin content correlates negatively with sugar release efficiency in switchgrass, but selecting the right gene candidates for engineering lignin biosynthesis in this tetraploid outcrossing species is not straightforward. To assist this endeavor, we have used an inducible switchgrass cell suspension system for studying lignin biosynthesis in response to exogenous brassinolide. By applying a combination of protein sequence phylogeny with whole-genome microarray analyses of induced cell cultures and developing stem internode sections, we have generated a list of candidate monolignol biosynthetic genes for switchgrass. Several genes that were strongly supported through our bioinformatics analysis as involved in lignin biosynthesis were confirmed by gene silencing studies, in which lignin levels were reduced as a result of targeting a single gene. However, candidate genes encoding enzymes involved in the early steps of the currently accepted monolignol biosynthesis pathway in dicots may have functionally redundant paralogues in switchgrass and therefore require further evaluation. This work provides a blueprint and resources for the systematic genome-wide study of the monolignol pathway in switchgrass, as well as other C4 monocot species.
authors.affiliation: Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401.
authors.forename: Hui
authors.initials: H
authors.lastname: Shen
authors.forename: Mitra
authors.initials: M
authors.lastname: Mazarei
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Hisano
authors.forename: Luis
authors.initials: L
authors.lastname: Escamilla-Trevino
authors.forename: Chunxiang
authors.initials: C
authors.lastname: Fu
authors.forename: Yunqiao
authors.initials: Y
authors.lastname: Pu
authors.forename: Mary R
authors.initials: MR
authors.lastname: Rudis
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Tang
authors.forename: Xirong
authors.initials: X
authors.lastname: Xiao
authors.forename: Lisa
authors.initials: L
authors.lastname: Jackson
authors.forename: Guifen
authors.initials: G
authors.lastname: Li
authors.forename: Tim
authors.initials: T
authors.lastname: Hernandez
authors.forename: Fang
authors.initials: F
authors.lastname: Chen
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Ragauskas
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
authors.forename: Zeng-Yu
authors.initials: ZY
authors.lastname: Wang
authors.forename: Richard A
authors.initials: RA
authors.lastname: Dixon
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics; D018929:Cell Culture Techniques; D003001:Cloning, Molecular; D016000:Cluster Analysis; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D023281:Genomics / Q000379:methods*; D008031:Lignin / Q000096:biosynthesis* / Q000235:genetics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D008897:Panicum / Q000166:cytology / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D030821:Plants, Genetically Modified
chemical_list: D004798:Enzymes; D008031:Lignin