Improving Wood Properties for Wood Utilization through Multi-Omics Integration in Lignin Biosynthesis

Todd Shollenberger; Mark Davis; Jack Wang; Megan Matthews; Cranos Williams; Rui Shi; Chenmin Yang; Sermsawat Tunlaya-Anukit; Hsi-Chuan Chen; Quanzi Li; Jie Liu; Chien-Yuan Lin; Punith Naik; Ying-Hsuan Sun; Philip Loziuk; Ting-Feng Yeh; Hoon Kim; Christopher Shuford; Jina Song; Zachary Miller; Yung-Yun Huang; Charles Edmunds; Baoguang Liu; Yi Sun; Ying-Chung Lin; Wei Li; Hao Chen; Ilona Peszlen; Joel Ducoste; John Ralph; Hou-Min Chang; David Muddiman; Chris Smith; Fikret Isik; Ronald Sederoff; Vincent Chiang; Erica Gjersing

doi:10.1038/s41467-018-03863-z

Improving Wood Properties for Wood Utilization through Multi-Omics Integration in Lignin Biosynthesis

Todd Shollenberger, Mark Davis, Jack Wang, Megan Matthews, Cranos Williams, Rui Shi, Chenmin Yang, Sermsawat Tunlaya-Anukit, Hsi-Chuan Chen, Quanzi Li, Jie Liu, Chien-Yuan Lin, Punith Naik, Ying-Hsuan Sun, Philip Loziuk, Ting-Feng Yeh, Hoon Kim, Christopher Shuford, Jina Song, Zachary MillerYung-Yun Huang, Charles Edmunds, Baoguang Liu, Yi Sun, Ying-Chung Lin, Wei Li, Hao Chen, Ilona Peszlen, Joel Ducoste, John Ralph, Hou-Min Chang, David Muddiman, Chris Smith, Fikret Isik, Ronald Sederoff, Vincent Chiang, Erica Gjersing

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185 Scopus Citations

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.

Original language	American English
Article number	1579
Number of pages	16
Journal	Nature Communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-03863-z https://doi.org/10.1038/s41467-018-03863-z
State	Published - 1 Dec 2018

Bibliographical note

Publisher Copyright:
© 2018 The Author(s).

NREL Publication Number

NREL/JA-2700-71418

Keywords

genetic engineering
molecular engineering
secondary metabolism

Access to Document

https://www.nrel.gov/docs/fy18osti/71418.pdf

Cite this

Shollenberger, T., Davis, M., Wang, J., Matthews, M., Williams, C., Shi, R., Yang, C., Tunlaya-Anukit, S., Chen, H.-C., Li, Q., Liu, J., Lin, C.-Y., Naik, P., Sun, Y.-H., Loziuk, P., Yeh, T.-F., Kim, H., Shuford, C., Song, J., ... Gjersing, E. (2018). Improving Wood Properties for Wood Utilization through Multi-Omics Integration in Lignin Biosynthesis. Nature Communications, 9(1), Article 1579. https://doi.org/10.1038/s41467-018-03863-z, https://doi.org/10.1038/s41467-018-03863-z

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title = "Improving Wood Properties for Wood Utilization through Multi-Omics Integration in Lignin Biosynthesis",

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.",

keywords = "genetic engineering, molecular engineering, secondary metabolism",

author = "Todd Shollenberger and Mark Davis and Jack Wang and Megan Matthews and Cranos Williams and Rui Shi and Chenmin Yang and Sermsawat Tunlaya-Anukit and Hsi-Chuan Chen and Quanzi Li and Jie Liu and Chien-Yuan Lin and Punith Naik and Ying-Hsuan Sun and Philip Loziuk and Ting-Feng Yeh and Hoon Kim and Christopher Shuford and Jina Song and Zachary Miller and Yung-Yun Huang and Charles Edmunds and Baoguang Liu and Yi Sun and Ying-Chung Lin and Wei Li and Hao Chen and Ilona Peszlen and Joel Ducoste and John Ralph and Hou-Min Chang and David Muddiman and Chris Smith and Fikret Isik and Ronald Sederoff and Vincent Chiang and Erica Gjersing",

note = "Publisher Copyright: {\textcopyright} 2018 The Author(s).",

year = "2018",

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doi = "10.1038/s41467-018-03863-z",

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Shollenberger, T, Davis, M, Wang, J, Matthews, M, Williams, C, Shi, R, Yang, C, Tunlaya-Anukit, S, Chen, H-C, Li, Q, Liu, J, Lin, C-Y, Naik, P, Sun, Y-H, Loziuk, P, Yeh, T-F, Kim, H, Shuford, C, Song, J, Miller, Z, Huang, Y-Y, Edmunds, C, Liu, B, Sun, Y, Lin, Y-C, Li, W, Chen, H, Peszlen, I, Ducoste, J, Ralph, J, Chang, H-M, Muddiman, D, Smith, C, Isik, F, Sederoff, R, Chiang, V & Gjersing, E 2018, 'Improving Wood Properties for Wood Utilization through Multi-Omics Integration in Lignin Biosynthesis', Nature Communications, vol. 9, no. 1, 1579. https://doi.org/10.1038/s41467-018-03863-z, https://doi.org/10.1038/s41467-018-03863-z

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AU - Shollenberger, Todd

AU - Davis, Mark

AU - Wang, Jack

AU - Matthews, Megan

AU - Williams, Cranos

AU - Shi, Rui

AU - Yang, Chenmin

AU - Tunlaya-Anukit, Sermsawat

AU - Chen, Hsi-Chuan

AU - Li, Quanzi

AU - Liu, Jie

AU - Lin, Chien-Yuan

AU - Naik, Punith

AU - Sun, Ying-Hsuan

AU - Loziuk, Philip

AU - Yeh, Ting-Feng

AU - Kim, Hoon

AU - Shuford, Christopher

AU - Song, Jina

AU - Miller, Zachary

AU - Huang, Yung-Yun

AU - Edmunds, Charles

AU - Liu, Baoguang

AU - Sun, Yi

AU - Lin, Ying-Chung

AU - Li, Wei

AU - Chen, Hao

AU - Peszlen, Ilona

AU - Ducoste, Joel

AU - Ralph, John

AU - Chang, Hou-Min

AU - Muddiman, David

AU - Smith, Chris

AU - Isik, Fikret

AU - Sederoff, Ronald

AU - Chiang, Vincent

AU - Gjersing, Erica

PY - 2018/12/1

Y1 - 2018/12/1

N2 - 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.

AB - 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.

KW - genetic engineering

KW - molecular engineering

KW - secondary metabolism

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U2 - 10.1038/s41467-018-03863-z

DO - 10.1038/s41467-018-03863-z

M3 - Article

C2 - 29679008

AN - SCOPUS:85045890118

SN - 2041-1723

VL - 9

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 1579

ER -

Improving Wood Properties for Wood Utilization through Multi-Omics Integration in Lignin Biosynthesis

Abstract

Bibliographical note

NREL Publication Number

Keywords

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