Characterization in vitro and in vivo of the putative multigene 4-coumarate:CoA ligase network in Arabidopsis: syringyl lignin and sinapate/sinapyl alcohol derivative formation

Costa, Michael A.; Bedgar, Diana L.; Moinuddin, Syed G. A.; Kim, Kye‐Won; Cardenas, Claudia L.; Cochrane, Fiona C.; Shockey, Jay; Helms, Gregory L.; Amakura, Yoshiaki; Takahashi, Hironobu; Milhollan, Jessica K.; Davin, Laurence B.; Browse, John; Lewis, Norman G.

doi:10.1016/j.phytochem.2005.06.022

Cited by 134 publications

(132 citation statements)

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“…Most ACOS genes identified in Arabidopsis and other species are predicted to localize to peroxisomes, based on the presence of C-terminal peroxisomal targeting sequences (Costa et al, 2005;Schneider et al, 2005;de Azevedo Souza et al, 2008), and this is consistent with their having roles in fatty acid and jasmonate metabolism, which occur in this cellular compartment (Schneider et al, 2005;Koo et al, 2006;Kienow et al, 2008). One ACOS clade identified in this analysis is unique in that it contains singlecopy genes from Arabidopsis, poplar, and rice, which all encode enzymes without predicted peroxisomal targeting sequences (de Azevedo Souza et al, 2008).…”

Section: Introductionsupporting

confidence: 67%

“…Initial analysis of the recombinant ACOS5 protein suggested a lack of activity against hydroxycinnamic acids, substrates typically used by 4CLs (Costa et al, 2005;Kienow et al, 2008), while work reported here (Table 2) demonstrated in vitro activity against oleic acid (C18:1) with kinetic constants comparable to those of other fatty acyl-CoA synthetases. Hydroxycinnamic acids failed to compete with oleic acid as ACOS5 substrates (Figure 9), verifying that ACOS5 is not a 4CL.…”

Section: Acos5 Is An Ancient Acyl-coa Synthetase Conserved In Land Plmentioning

confidence: 70%

“…Many such genes are conserved in the fully sequenced genomes of poplar (Populus trichocarpa) and rice (Oryza sativa) (Tuskan et al, 2006;Hamberger et al, 2007;de Azevedo Souza et al, 2008). An example of such a supergene family is the group of genes encoding adenylate-forming enzymes related to the phenylpropanoid enzyme 4-coumarate:CoA ligase (4CL) (Cukovic et al, 2001;Costa et al, 2003Costa et al, , 2005Schneider et al, 2003Schneider et al, , 2005Shockey et al, 2003;Ehlting et al, 2005;de Azevedo Souza et al, 2008). Recent biochemical characterizations of enzymes encoded by this family of 4CL-like genes show that they generally do not convert substrates accepted by true 4CL enzymes to the corresponding CoA esters (Costa et al, 2005;Kienow et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…An example of such a supergene family is the group of genes encoding adenylate-forming enzymes related to the phenylpropanoid enzyme 4-coumarate:CoA ligase (4CL) (Cukovic et al, 2001;Costa et al, 2003Costa et al, , 2005Schneider et al, 2003Schneider et al, , 2005Shockey et al, 2003;Ehlting et al, 2005;de Azevedo Souza et al, 2008). Recent biochemical characterizations of enzymes encoded by this family of 4CL-like genes show that they generally do not convert substrates accepted by true 4CL enzymes to the corresponding CoA esters (Costa et al, 2005;Kienow et al, 2008). Instead, many accept fatty acyl substrates, such as 12-oxo-phytodienoic acid (OPDA) and OPDA derivatives (jasmonic acid precursors; Koo et al, 2006;Kienow et al, 2008), and medium-to long-chain fatty acids (Kienow et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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A Novel Fatty Acyl-CoA Synthetase Is Required for Pollen Development and Sporopollenin Biosynthesis inArabidopsis

et al. 2009

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Acyl-CoA Synthetase (ACOS) genes are related to 4-coumarate:CoA ligase (4CL) but have distinct functions. The Arabidopsis thaliana ACOS5 protein is in clade A of Arabidopsis ACOS proteins, the clade most closely related to 4CL proteins. This clade contains putative nonperoxisomal ACOS enzymes conserved in several angiosperm lineages and in the moss Physcomitrella patens. Although its function is unknown, ACOS5 is preferentially expressed in the flowers of all angiosperms examined. Here, we show that an acos5 mutant produced no pollen in mature anthers and no seeds by selffertilization and was severely compromised in pollen wall formation apparently lacking sporopollenin or exine. The phenotype was first evident at stage 8 of anther development and correlated with maximum ACOS5 mRNA accumulation in tapetal cells at stages 7 to 8. Green fluorescent protein-ACOS5 fusions showed that ACOS5 is located in the cytoplasm. Recombinant ACOS5 enzyme was active against oleic acid, allowing kinetic constants for ACOS5 substrates to be established. Substrate competition assays indicated broad in vitro preference of the enzyme for medium-chain fatty acids. We propose that ACOS5 encodes an enzyme that participates in a conserved and ancient biochemical pathway required for sporopollenin monomer biosynthesis that may also include the Arabidopsis CYP703A2 and MS2 enzymes.

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Section: Introductionsupporting

confidence: 67%

Section: Acos5 Is An Ancient Acyl-coa Synthetase Conserved In Land Plmentioning

confidence: 70%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Novel Fatty Acyl-CoA Synthetase Is Required for Pollen Development and Sporopollenin Biosynthesis inArabidopsis

et al. 2009

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“…For the phenylpropanoidlignin genes, the reported homologs of Arabidopsis 47 , poplar, rice 29 and maize downloaded from the cell wall genomics browser (see URLs) were used as the seed sequences to detect the bamboo, Brachypodium and sorghum gene models by BLASTP with E values under 1 × 10 -10 and with over 50% identity over the whole protein sequence. Detected homologs consisted of not only phenylpropanoidlignin genes but also many phenylpropanoid-lignin-like genes, which might be involved in different pathways, even though they share high sequence identity (such as At4CL-like genes 48 ). To remove these phenylpropanoid-lignin-like genes, we used the phenylpropanoid-lignin genes from Arabidopsis, maize, rice and poplar to build an initial neighbor-joining tree to cluster the phenylpropanoidlignin and phenylpropanoid-lignin-like genes into different clades.…”

Section: Competing Financial Interestsmentioning

confidence: 99%

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

et al. 2013

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l e t t e r sBamboo represents the only major lineage of grasses that is native to forests and is one of the most important nontimber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between droughtresponsive and flowering genes.Bamboo is one of the most important non-timber forest products in the world. About 2.5 billion people depend economically on bamboo, and international trade in bamboo amounts to over 2.5 billion US dollars per year 1 . Bamboo has a rather striking life history, characterized by a prolonged vegetative phase lasting decades before flowering, thereby inhibiting genetic improvement. Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .Here, we report the draft genome of moso bamboo, a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area. Comparative genome-wide analyses of bamboo to other grass species, including rice, maize and sorghum, yielded new genetic insights into the rapid and marked phenotypic and ecological divergence of bamboo and closely related grasses.The moso bamboo genome contains 24 pairs of chromosomes 8 (2n = 48) and is characteristic of a diploid (Supplementary Fig. 1a). We conducted a flow cytometry analysis and estimated that it had a genome size of 2.075 Gb (2C = 4.24 pg; Supplementary Fig. 1b), which was very close to that estimated in a previous report 9 .Because it is difficult to generate an inbred line of moso bamboo, owing to its infrequent sexual reproduction and the long periods of time between flowering intervals, we selected five plants from a single individual rhizome of the moso bamboo ecotype (P. heterocycla var. pubescens) and performed whole-genome shotgun sequencing. We generated 295 Gb of raw sequence data (approximately 147-fold coverage), including Illumina short reads and 10,327 pairs of BAC end ...

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Monolignol Biosynthesis and its Genetic Manipulation: The Good, the Bad, and the Ugly

Dixon

Reddy

Gallego‐Giraldo³

2014

Recent Advances in Polyphenol Research

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Economic and environmental factors favor the adoption of lignocellulosic bioenergy crops for production of liquid transportation fuels. However, lignocellulosic biomass is recalcitrant to saccharification (sugar release from cell walls), and this is, at least in part, due to the presence of the phenylpropanoid-derived cell wall polymer lignin. A large body of evidence exists documenting the impacts of lignin modification in plants. This technology can lead to improved forage quality and enhanced processing properties for trees (paper pulping) and lignocellulosic energy crops. We here provide a comprehensive review of the literature on lignin modification in plants. The pathway has been targeted through down-regulating expression of the enzymes of the monolignol pathway, as well as through down-regulation or over-expression of transcription factors that control lignin biosynthesis and/or programs of secondary cell wall development. Targeting lignin modification at some steps in the monolignol pathway can result in impairment of plant growth and development, often associated with the triggering of endogenous host defense mechanisms. Recent studies suggest that it may be possible to decouple negative growth impacts from lignin reduction.Keywords: monolignol biosynthesis, genetic modification, transcription factor, gene silencing, saccharification. 2 IntroductionLignin is a major component of plant secondary cell walls, and the second most abundant plant polymer on the planet. Lignin constitutes about 15-35% of the dry mass of vascular plants (Adler, 1977). Considerable attention has been given over the past several years to the reduction of lignin content in model plant species, forages, trees, and dedicated bioenergy feedstocks. This is because forage digestibility, paper pulping and liquid fuel production from biomass through fermentation are all affected by recalcitrance of lignocellulose, primarily due to the presence of lignin, which blocks accessibility of the sugar-rich cell wall polysaccharides cellulose and hemicellulose to enzymes and microorganisms (Pilate et al., 2002;Reddy et al., 2005;.Much is now known of the biosynthesis of lignin and its control at the transcriptional level. This information informs the targets that have been selected for genetic modification of lignin content and composition in transgenic plants. There is considerable variation in the effects on lignin content and composition depending on the gene that is targeted for down-or up-regulation. Equally important, lignin modification can have profound impacts on plant growth and development, ranging from good through bad to "downright ugly", but these impacts are again strongly target dependent. Understanding the mechanisms that may impact plant growth, which equate to agronomic performance, in crop species "improved" through lignin modification is critical for economic advancement of the forage and biofuels industries. Although still poorly understood, these mechanisms may also throw light on basal plant developmental and de...

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Characterization in vitro and in vivo of the putative multigene 4-coumarate:CoA ligase network in Arabidopsis: syringyl lignin and sinapate/sinapyl alcohol derivative formation

Cited by 134 publications

References 62 publications

A Novel Fatty Acyl-CoA Synthetase Is Required for Pollen Development and Sporopollenin Biosynthesis inArabidopsis

A Novel Fatty Acyl-CoA Synthetase Is Required for Pollen Development and Sporopollenin Biosynthesis inArabidopsis

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

Monolignol Biosynthesis and its Genetic Manipulation: The Good, the Bad, and the Ugly

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