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RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica.

Blackman LM, Cullerne DP, Torreña P, Taylor J, Hardham AR - PLoS ONE (2015)

Bottom Line: The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase.Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack.The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.

View Article: PubMed Central - PubMed

Affiliation: Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia.

ABSTRACT
RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.

No MeSH data available.


Related in: MedlinePlus

Total NRPKs from the multiple location data set for genes targeting major categories of wall components.Because many genes act on cellulose and hemicelluloses, counts for these two substrates have been combined. (A) Total NRPK counts show the relative transcript abundance for each substrate category. (B) Total NRPK counts expressed as a percentage of the maximum counts show trends in the expression profiles over time. Genes whose products target pectins have been assigned to the first and second halves of the 60-h infection time-course.
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pone.0136899.g002: Total NRPKs from the multiple location data set for genes targeting major categories of wall components.Because many genes act on cellulose and hemicelluloses, counts for these two substrates have been combined. (A) Total NRPK counts show the relative transcript abundance for each substrate category. (B) Total NRPK counts expressed as a percentage of the maximum counts show trends in the expression profiles over time. Genes whose products target pectins have been assigned to the first and second halves of the 60-h infection time-course.

Mentions: Evaluation of global patterns of expression of genes targeting the major categories of wall components, namely pectins, cellulose, hemicelluloses, β-1,3-glucans and glycoproteins used the multiple location data set. In terms of total transcript abundance, there are similar levels of pectinases and cellulases/hemicellulases at 30 hpi and about half that number of β-1,3-glucanases (Fig 2A). As infection proceeded, the CWDE transcriptome became dominated by cellulases/hemicellulases and β-1,3-glucanases. Calculation of the total NRPK values as a percentage of the maximum transcript number for each category of enzymes, revealed that a cohort of pectinases were expressed most strongly during the first half of the infection time-course (Fig 2B). This was not the case for enzymes targeting the other substrate categories. As transcript levels of the early cohort of pectinases decreased, transcript levels for the other pectinases and for enzymes targetting cellulose, hemicellulose, β-1,3-glucans and glycoproteins increased.


RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica.

Blackman LM, Cullerne DP, Torreña P, Taylor J, Hardham AR - PLoS ONE (2015)

Total NRPKs from the multiple location data set for genes targeting major categories of wall components.Because many genes act on cellulose and hemicelluloses, counts for these two substrates have been combined. (A) Total NRPK counts show the relative transcript abundance for each substrate category. (B) Total NRPK counts expressed as a percentage of the maximum counts show trends in the expression profiles over time. Genes whose products target pectins have been assigned to the first and second halves of the 60-h infection time-course.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4558045&req=5

pone.0136899.g002: Total NRPKs from the multiple location data set for genes targeting major categories of wall components.Because many genes act on cellulose and hemicelluloses, counts for these two substrates have been combined. (A) Total NRPK counts show the relative transcript abundance for each substrate category. (B) Total NRPK counts expressed as a percentage of the maximum counts show trends in the expression profiles over time. Genes whose products target pectins have been assigned to the first and second halves of the 60-h infection time-course.
Mentions: Evaluation of global patterns of expression of genes targeting the major categories of wall components, namely pectins, cellulose, hemicelluloses, β-1,3-glucans and glycoproteins used the multiple location data set. In terms of total transcript abundance, there are similar levels of pectinases and cellulases/hemicellulases at 30 hpi and about half that number of β-1,3-glucanases (Fig 2A). As infection proceeded, the CWDE transcriptome became dominated by cellulases/hemicellulases and β-1,3-glucanases. Calculation of the total NRPK values as a percentage of the maximum transcript number for each category of enzymes, revealed that a cohort of pectinases were expressed most strongly during the first half of the infection time-course (Fig 2B). This was not the case for enzymes targeting the other substrate categories. As transcript levels of the early cohort of pectinases decreased, transcript levels for the other pectinases and for enzymes targetting cellulose, hemicellulose, β-1,3-glucans and glycoproteins increased.

Bottom Line: The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase.Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack.The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.

View Article: PubMed Central - PubMed

Affiliation: Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia.

ABSTRACT
RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.

No MeSH data available.


Related in: MedlinePlus