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A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis

Ruben Vanholme (UGent) , Veronique Storme (UGent) , Bartel Vanholme (UGent) , Lisa Sundin (UGent) , Jørgen Holst Christensen (UGent) , Geert Goeminne (UGent) , Claire Halpin, Antje Rohde (UGent) , Kris Morreel (UGent) and Wout Boerjan (UGent)
(2012) PLANT CELL. 24(9). p.3506-3529
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Biotechnology for a sustainable economy (Bio-Economy)
Abstract
Lignin engineering is an attractive strategy to improve lignocellulosic biomass quality for processing to biofuels and other bio-based products. However, lignin engineering also results in profound metabolic consequences in the plant. We used a systems biology approach to study the plant's response to lignin perturbations. To this end, inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (phenylalanine ammonia-lyase1 [PAL1], PAL2, cinnamate 4-hydroxylase [C4H], 4-coumarate:CoA ligase1 [4CL1], 4CL2, caffeoyl-CoA O-methyltransferase1 [CCoAOMT1], cinnamoyl-CoA reductase1 [CCR1], ferulate 5-hydroxylase [F5H1], caffeic acid O-methyltransferase [COMT], and cinnamyl alcohol dehydrogenase6 [CAD6], two mutant alleles each), were analyzed by transcriptomics and metabolomics. A total of 566 compounds were detected, of which 187 could be tentatively identified based on mass spectrometry fragmentation and many were new for Arabidopsis. Up to 675 genes were differentially expressed in mutants that did not have any obvious visible phenotypes. Comparing the responses of all mutants indicated that c4h, 4cl1, ccoaomt1, and ccr1, mutants that produced less lignin, upregulated the shikimate, methyl-donor, and phenylpropanoid pathways (i.e., the pathways supplying the monolignols). By contrast, f5h1 and comt, mutants that provoked lignin compositional shifts, downregulated the very same pathways. Reductions in the flux to lignin were associated with the accumulation of various classes of 4-O- and 9-O-hexosylated phenylpropanoids. By combining metabolomic and transcriptomic data in a correlation network, system-wide consequences of the perturbations were revealed and genes with a putative role in phenolic metabolism were identified. Together, our data provide insight into lignin biosynthesis and the metabolic network it is embedded in and provide a systems view of the plant's response to pathway perturbations.
Keywords
TRANSCRIPTION FACTORS, DOWN-REGULATION, CELL-WALL FORMATION, PHENYLPROPANOID PATHWAY, CONTROL MAQC PROJECT, FALSE DISCOVERY RATE, GENE-EXPRESSION MEASUREMENTS, MASS-SPECTROMETRY DATA, O-METHYLTRANSFERASE, REVERSE GENETICS

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Chicago
Vanholme, Ruben, Veronique Storme, Bartel Vanholme, Lisa Sundin, Jørgen Holst Christensen, Geert Goeminne, Claire Halpin, Antje Rohde, Kris Morreel, and Wout Boerjan. 2012. “A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis.” Plant Cell 24 (9): 3506–3529.
APA
Vanholme, R., Storme, V., Vanholme, B., Sundin, L., Christensen, J. H., Goeminne, G., Halpin, C., et al. (2012). A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis. PLANT CELL, 24(9), 3506–3529.
Vancouver
1.
Vanholme R, Storme V, Vanholme B, Sundin L, Christensen JH, Goeminne G, et al. A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis. PLANT CELL. 2012;24(9):3506–29.
MLA
Vanholme, Ruben, Veronique Storme, Bartel Vanholme, et al. “A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis.” PLANT CELL 24.9 (2012): 3506–3529. Print.
@article{3062678,
  abstract     = {Lignin engineering is an attractive strategy to improve lignocellulosic biomass quality for processing to biofuels and other bio-based products. However, lignin engineering also results in profound metabolic consequences in the plant. We used a systems biology approach to study the plant's response to lignin perturbations. To this end, inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (phenylalanine ammonia-lyase1 [PAL1], PAL2, cinnamate 4-hydroxylase [C4H], 4-coumarate:CoA ligase1 [4CL1], 4CL2, caffeoyl-CoA O-methyltransferase1 [CCoAOMT1], cinnamoyl-CoA reductase1 [CCR1], ferulate 5-hydroxylase [F5H1], caffeic acid O-methyltransferase [COMT], and cinnamyl alcohol dehydrogenase6 [CAD6], two mutant alleles each), were analyzed by transcriptomics and metabolomics. A total of 566 compounds were detected, of which 187 could be tentatively identified based on mass spectrometry fragmentation and many were new for Arabidopsis. Up to 675 genes were differentially expressed in mutants that did not have any obvious visible phenotypes. Comparing the responses of all mutants indicated that c4h, 4cl1, ccoaomt1, and ccr1, mutants that produced less lignin, upregulated the shikimate, methyl-donor, and phenylpropanoid pathways (i.e., the pathways supplying the monolignols). By contrast, f5h1 and comt, mutants that provoked lignin compositional shifts, downregulated the very same pathways. Reductions in the flux to lignin were associated with the accumulation of various classes of 4-O- and 9-O-hexosylated phenylpropanoids. By combining metabolomic and transcriptomic data in a correlation network, system-wide consequences of the perturbations were revealed and genes with a putative role in phenolic metabolism were identified. Together, our data provide insight into lignin biosynthesis and the metabolic network it is embedded in and provide a systems view of the plant's response to pathway perturbations.},
  author       = {Vanholme, Ruben and Storme, Veronique and Vanholme, Bartel and Sundin, Lisa and Christensen, J{\o}rgen Holst and Goeminne, Geert and Halpin, Claire and Rohde, Antje and Morreel, Kris and Boerjan, Wout},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {TRANSCRIPTION FACTORS,DOWN-REGULATION,CELL-WALL FORMATION,PHENYLPROPANOID PATHWAY,CONTROL MAQC PROJECT,FALSE DISCOVERY RATE,GENE-EXPRESSION MEASUREMENTS,MASS-SPECTROMETRY DATA,O-METHYLTRANSFERASE,REVERSE GENETICS},
  language     = {eng},
  number       = {9},
  pages        = {3506--3529},
  title        = {A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis},
  url          = {http://dx.doi.org/10.1105/tpc.112.102574},
  volume       = {24},
  year         = {2012},
}

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