Dataset Information

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.

SUBMITTER: Wang JP

PROVIDER: S-EPMC5910405 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis.

Wang Jack P JP Matthews Megan L ML Williams Cranos M CM Shi Rui R Yang Chenmin C Tunlaya-Anukit Sermsawat S Chen Hsi-Chuan HC Li Quanzi Q Liu Jie J Lin Chien-Yuan CY Naik Punith P Sun Ying-Hsuan YH Loziuk Philip L PL Yeh Ting-Feng TF Kim Hoon H Gjersing Erica E Shollenberger Todd T Shuford Christopher M CM Song Jina J Miller Zachary Z Huang Yung-Yun YY Edmunds Charles W CW Liu Baoguang B Sun Yi Y Lin Ying-Chung Jimmy YJ Li Wei W Chen Hao H Peszlen Ilona I Ducoste Joel J JJ Ralph John J Chang Hou-Min HM Muddiman David C DC Davis Mark F MF Smith Chris C Isik Fikret F Sederoff Ronald R Chiang Vincent L VL

Nature communications 20180420 1

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, ...[more]

PMID: 29679008

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Project description:Pinewood nematode (PWN), the causal agent of pine wilt disease (PWD), causes massive global losses of Pinus species each year. Bacteria and fungi existing in symbiosis with PWN are closely linked with the pathogenesis of PWD, but the relationship between PWN pathogenicity and the associated microbiota is still ambiguous. This study explored the relationship between microbes and the pathogenicity of PWN by establishing a PWN-associated microbe library, and used this library to generate five artificial PWN-microbe symbiont (APMS) assemblies with gnotobiotic PWNs. The fungal and bacterial communities of different APMSs (the microbiome) were explored by next-generation sequencing. Furthermore, different APMSs were used to inoculate the same Masson pine (Pinus massoniana) cultivar, and multi-omics (metabolome, phenomics, and transcriptome) data were obtained to represent the pathogenicity of different APMSs at 14 days post-inoculation (dpi). Significant positive correlations were observed between microbiome and transcriptome or metabolome data, but microbiome data were negatively correlated with the reactive oxygen species (ROS) level in the host. Five response genes, four fungal genera, four bacterial genera, and nineteen induced metabolites were positively correlated with the ROS level, while seven induced metabolites were negatively correlated. To further explore the function of PWN-associated microbes, single genera of functional microbes (Mb1-Mb8) were reloaded onto gnotobiotic PWNs and used to inoculate pine tree seedlings. Three of the genera (Cladophialophora, Ochroconis, and Flavobacterium) decreased the ROS level of the host pine trees, while only one genus (Penicillium) significantly increased the ROS level of the host pine tree seedlings. These results demonstrate a clear relationship between associated microbes and the pathogenicity of PWN, and expand the knowledge on the interaction between PWD-induced forest decline and the PWN-associated microbiome.

Dataset Information

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis.

Publications

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis.

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