Genomics of plant cell wall biogenesis

Yong, Weidong; Link, Bruce M.; O’Malley, Ronan; Tewari, Jagdish; Hunter, Charles T.; Lu, Chung An; Li, Xuemei; Bleecker, Anthony B.; Koch, Karen E.; McCann, Maureen C.; McCarty, Donald R.; Patterson, Sara E.; Reiter, Wolf Dieter; Staiger, Chris J.; Thomas, Steven R.; Vermerris, Wilfred; Carpita, Nicholas C.

doi:10.1007/s00425-005-1563-z

Cited by 99 publications

(80 citation statements)

References 37 publications

(22 reference statements)

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“…This is >5 times more than the estimated 2000 genes corresponding to <10% of the Arabidopsis genome that are predicted to have such a function (Yong et al, 2005). Among the 19 genes repressed in lrx1 rol1-2, three genes (16%) are presumed to be cell wall related.…”

Section: Rol1-1 and Rol1-2 Display Different Phenotypesmentioning

confidence: 95%

TheArabidopsisRoot Hair Cell Wall Formation Mutantlrx1Is Suppressed by Mutations in theRHM1Gene Encoding a UDP-L-Rhamnose Synthase

et al. 2006

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Cell and cell wall growth are mutually dependent processes that must be tightly coordinated and controlled. LRR-extensin1 (LRX1) of Arabidopsis thaliana is a potential regulator of cell wall development, consisting of an N-terminal leucine-rich repeat domain and a C-terminal extensin-like domain typical for structural cell wall proteins. LRX1 is expressed in root hairs, and lrx1 mutant plants develop distorted root hairs that often swell, branch, or collapse. The aberrant cell wall structures found in lrx1 mutants point toward a function of LRX1 during the establishment of the extracellular matrix. To identify genes that are involved in an LRX1-dependent developmental pathway, a suppressor screen was performed on the lrx1 mutant, and two independent rol1 (for repressor of lrx1) alleles were isolated. ROL1 is allelic to Rhamnose Biosynthesis1, which codes for a protein involved in the biosynthesis of rhamnose, a major monosaccharide component of pectin. The rol1 mutations modify the pectic polysaccharide rhamnogalacturonan I and, for one allele, rhamnogalacturonan II. Furthermore, the rol1 mutations cause a change in the expression of a number of cell wall-related genes. Thus, the lrx1 mutant phenotype is likely to be suppressed by changes in pectic polysaccharides or other cell wall components.

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Section: Rol1-1 and Rol1-2 Display Different Phenotypesmentioning

confidence: 95%

TheArabidopsisRoot Hair Cell Wall Formation Mutantlrx1Is Suppressed by Mutations in theRHM1Gene Encoding a UDP-L-Rhamnose Synthase

et al. 2006

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“…To optimize the structure, amount and composition of cell walls for efficient biofuel production, it is important to understand the molecular mechanisms underlying cell wall biosynthesis, modification and degradation. With an estimated 10% of plant genomes encoding proteins involved in cell wall-related functions, a concerted effort to elucidate their functions is needed (Yong et al 2005). Various high-throughput transcriptomics and proteomicsbased technologies have been employed to shortlist candidate genes for detailed investigation (Bonetta et al 2002;Imoto et al 2005;Manfield et al 2004;Yang et al 2008;Cao et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice

et al. 2011

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TitleTranscriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice. Abstract Efficient and cost-effective conversion of plant biomass to usable forms of energy requires a thorough understanding of cell wall biosynthesis, modification and degradation. To elucidate these processes, we assessed the expression dynamics during enzymatic removal and regeneration of rice cell walls in suspension cells over time. In total, 928 genes exhibited significant up-regulation during cell wall removal, whereas, 79 genes were up-regulated during cell wall regeneration. Both gene sets are enriched for kinases, transcription factors and genes predicted to be involved in cell wall-related functions. Integration of the gene expression datasets with a catalog of known and/or predicted biochemical pathways from rice, revealed metabolic and hormonal pathways involved in cell wall degradation and regeneration. Rice lines carrying Tos17 mutations in genes up-regulated during cell wall removal exhibit dwarf phenotypes. Many of the genes up-regulated during cell wall development are also up-regulated in response to infection and environmental perturbations indicating a coordinated response to diverse types of stress.

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“…It has been successfully used to investigate contaminated cotton fibers and yarn defects [14,15]. Furthermore, FTIR has emerged as a key technique for the study of plant growth and development [16][17][18][19][20][21][22][23][24][25]. Hyperspectral imaging (HI) data are acquired with line-scanning devices in which individual pixels are associated with a reflectance profile with reflectance values in narrow wavelength bands.…”

Section: Introductionmentioning

confidence: 99%

Using Spatial Structure Analysis of Hyperspectral Imaging Data and Fourier Transformed Infrared Analysis to Determine Bioactivity of Surface Pesticide Treatment

et al. 2010

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Many food products are subjected to quality control analyses for detection of surface residue/contaminants, and there is a trend of requiring more and more documentation and reporting by farmers regarding their use of pesticides. Recent outbreaks of food borne illnesses have been a major contributor to this trend. With a growing need for food safety measures and -smart applications‖ of insecticides, it is important to develop methods for rapid and accurate assessments of surface residues on food and feed items. As a model system, we investigated detection of a miticide applied to maize leaves and its miticidal bioactivity over time, and we compared two types of reflectance data: fourier transformed infrared (FTIR) data and hyperspectral imaging (HI) data. The miticide (bifenazate) was applied at a commercial field rate to maize leaves in the field, with or without application of a surfactant, and with or without application of a simulated -rain event‖. In addition, we collected FTIR and HI from untreated control leaves (total of five treatments). Maize leaf data were collected at seven time intervals from 0 to 48 hours after application. FTIR data were analyzed using conventional analysis of variance of miticide-specific vibration peaks. Two unique FTIR vibration peaks were associated with miticide application (1,700 cm −1 and 763 cm −1 ). The integrated intensities of these two OPEN ACCESSRemote Sensing 2010, 2 909 peaks, miticide application, surfactant, rain event, time between miticide application, and rain event were used as explanatory variables in a linear multi-regression fit to spider mite mortality. The same linear multi-regression approach was applied to variogram parameters derived from HI data in five selected spectral bands (664, 683, 706, 740, and 747 nm). For each spectral band, we conducted a spatial structure analysis, and the three standard variogram parameters (-sill‖, -range‖, and -nugget‖) were examined as possible -indicators‖ of miticide bioactivity. We demonstrated that both FTIR peaks and standard variogram parameters could be used to accurately predict spider mite mortality, but linear multi-regression fits based on standard variogram parameters had the highest accuracy and were successfully validated with independent data. Based on experimental manipulation of HI data, the use of spatial structure analysis in classification of HI data was discussed.

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Genomics of plant cell wall biogenesis

Cited by 99 publications

References 37 publications

TheArabidopsisRoot Hair Cell Wall Formation Mutantlrx1Is Suppressed by Mutations in theRHM1Gene Encoding a UDP-L-Rhamnose Synthase

TheArabidopsisRoot Hair Cell Wall Formation Mutantlrx1Is Suppressed by Mutations in theRHM1Gene Encoding a UDP-L-Rhamnose Synthase

Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice

Using Spatial Structure Analysis of Hyperspectral Imaging Data and Fourier Transformed Infrared Analysis to Determine Bioactivity of Surface Pesticide Treatment

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