Improving wood properties for wood utilization through multi omics integration in lignin biosynthesis
Journal
Nature Communications
Journal Volume
9
Journal Issue
1
Date Issued
2018
Author(s)
J. P. Wang
M. L. Matthews
C. M. Williams
R. Shi
C. M. Yang
S. Tunlaya Anukit
H. C. Chen
Q. Z. Li
J. Liu
C. Y. Lin
P. Naik
Y. H. Sun
P. L. Loziuk
T. F. Yeh
H. Kim
E. Gjersing
T. Shollenberger
C. M. Shuford
J. N. Song
Z. Miller
Y. Y. Huang
C. W. Edmunds
B. G. Liu
Y. Sun
W. Li
H. Chen
I. Peszlen
J. J. Ducoste
J. Ralph
H. M. Chang
D. C. Muddiman
M. F. Davis
C. Smith
F. Isik
R. Sederoff
V. L. Chiang
Abstract
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux, metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation. © 2018 The Author(s).
Other Subjects
4cl3 protein; 4cl5 protein; adenosine phosphate; adenosine triphosphate; c3h3 protein; c4h1 protein; c4h2 protein; ccoaomt1 protein; coenzyme A; galactose; glucose; hct1 protein; hct6 protein; lignin; mannose; monolignol; monomer; nicotinamide adenine dinucleotide phosphate; pal1 protein; pal2 protein; pal3 protein; pal4 protein; pal5 protein; plant protein; pyrophosphate; reduced nicotinamide adenine dinucleotide phosphate; s adenosylhomocysteine; s adenosylmethionine; transcriptome; unclassified drug; xylose; lignin; transcriptome; bioactivity; lignin; polymerization; quantitative analysis; secondary metabolite; wood; adaptation; Article; biosynthesis; concentration (parameters); controlled study; density; fluxomics; gene expression regulation; genetic engineering; genetic trait; genomics; metabolic flux analysis; metabolite; nonhuman; nucleotide sequence; omics; phenomics; plant gene; plant genetics; plant genome; Populus trichocarpa; proteomics; quantitative analysis; saccharification; strength; transcriptomics; transgene; transgenic plant; transgenics; tree growth; upregulation; whole genome sequencing; chemistry; genetics; metabolism; physiology; Populus; tree; wood; xylem; Populus trichocarpa; Gene Expression Regulation, Plant; Lignin; Plants, Genetically Modified; Populus; Transcriptome; Trees; Wood; Xylem
Type
journal article