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Carpita, Nick; Tierney, Mary L.; Campbell, Malcolm M.

doi:10.1023/a:1010603527077

Cited by 134 publications

(29 citation statements)

References 3 publications

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“…More than one thousand gene products have been proposed to be dedicated to plant cell wall biogenesis and modification [29–31]. During the past years, characterization of plant cell wall mutants has revealed dozens of genes involved in cell wall synthesis and modification [28, 32–41].…”

Section: Introductionmentioning

confidence: 99%

An integrated genomic and metabolomic framework for cell wall biology in rice

et al. 2014

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BackgroundPlant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synthesis and maintenance. However, functional association for the majority of these gene products remains obscure. One useful approach to infer biological associations is via transcriptional coordination, or co-expression of genes. This approach has proved useful for several biological processes. Nevertheless, combining co-expression with other large-scale measurements may improve the biological inferences.ResultsIn this study, we used a combined approach of co-expression and cell wall metabolomics to obtain new insight into cell wall synthesis in rice. We initially created a weighted gene co-expression network from publicly available datasets, and then established a comprehensive cell wall dataset by determining cell wall compositions from 29 tissues that almost cover the whole life cycle of rice. We subsequently combined the datasets through the conversion of co-expressed gene modules into eigen-vectors, representing expression profiles for the genes in the modules, and performed comparative analyses against the cell wall contents. Here, we made three major discoveries. First, we confirmed our approach by finding primary and secondary wall cellulose biosynthesis modules, respectively. Second, we found co-expressed modules that strongly correlated with re-organization of the secondary cell walls and with modifications and degradation of hemicellulosic structures. Third, we inferred that at least one module is likely to play a regulatory role in the production of G-rich lignification.ConclusionsHere, we integrated transcriptomic associations and cell wall metabolism and found that certain co-expressed gene modules are positively correlated with distinct cell wall characteristics. We propose that combining multiple data-types, such as coordinated transcription and cell wall analyses, may be a useful approach to glean new insight into biological processes. The combination of multiple datasets, as illustrated here, can further improve the functional inferences that typically are generated via a single type of datasets. In addition, our data extend the typical co-expression approach to allow deeper insight into cell wall biology in rice.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-596) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

An integrated genomic and metabolomic framework for cell wall biology in rice

et al. 2014

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“…The importance of the plant cell wall is revealed in the shear number of genes that are likely to be involved in cell wall biogenesis, assembly, and modification. In Arabidopsis , over 400 proteins have been identified that reside in the wall and over 2,000 genes are likely to participate in wall biogenesis during plant development ( 15 ). Beyond this, some integral membrane-associated proteins, such as cellulose synthase, obviously function in cell wall biogenesis.…”

Section: Modification Of Cell Wall Biogenesismentioning

confidence: 99%

“…Of these, only small subsets have been characterized. Recently, functional genomics approaches have provided insight into the genes relevant to cell wall metabolism 15., 21., 23.. Reverse genetic and molecular biological approaches, based on discovery of homologous genes from bacteria, fungal, and animal systems, have augmented the collection of recognized wall-relevant genes considerably, but the functions of many of these genes still remain elusive 17., 18., 21., 23..…”

Section: Modification Of Cell Wall Biogenesismentioning

confidence: 99%

“…According to Carpita et al ( 15 ), the major steps in wall biogenesis and modification can be divided into six specific stages: (1) the synthesis of monomer building blocks, such as nucleotide sugars and monolignols; (2) the biosynthesis of oligomers and polysaccharides at the plasma membrane and ER-Golgi apparatus; (3) the targeting and secretion of Golgi-derived materials; (4) the assembly and architectural patterning of polymers; (5) dynamic rearrangement during cell growth and differentiation; and (6) wall disassembly and catabolism of the spent polymers. To put into perspective the challenges of gene discovery and determination of function, functional genomics is predicted to make significant advances in this field.…”

Section: Modification Of Cell Wall Biogenesismentioning

confidence: 99%

“…A challenge for forest biologists in the future is to ensure that the forest industry benefits from rapidly developing genomic and biotechnological advances 14., 15.. Forest biotechnology could derive enormous advantages from information generated through functional genomics approaches.…”

Section: Introductionmentioning

confidence: 99%

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Functional Genomics of Wood Quality and Properties

Tang

Luo

Nelson

et al. 2003

Genomics, Proteomics &Amp; Bioinformatics

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Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide. In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus. The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.

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The Use of Small Molecules to Dissect Cell Wall Biosynthesis and Manipulate the Cortical Cytoskeleton

Harris¹,

DeBolt²

2013

Plant Chemical Biology

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Cited by 134 publications

References 3 publications

An integrated genomic and metabolomic framework for cell wall biology in rice

An integrated genomic and metabolomic framework for cell wall biology in rice

Functional Genomics of Wood Quality and Properties

The Use of Small Molecules to Dissect Cell Wall Biosynthesis and Manipulate the Cortical Cytoskeleton

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