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| Status |
Public on Jul 18, 2016 |
| Title |
Localizing gene regulation by RNA-seq reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta |
| Organism |
Postia placenta |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and non-selective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that lignocellulose-oxidation (LOX) components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole transcriptome sequencing (RNAseq) and assayed relevant enzyme activities. We found a marked pattern of LOX upregulation in a narrow (5-mm; 48-hr) zone at the hyphal front, which included many genes likely involved in ROS generation. Upregulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin- and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization.
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| Overall design |
We sequenced mRNA from 9 Postia placenta samples taken from 3 wood sections of wafer design, with 3 bioreplicates for each wood section, to compare the gene expression during brown rot processes. Three wood sections of the wafer are representing early to late decay stages.
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| Contributor(s) |
Zhang J, Schilling JS, Hammel KE, Figueroa M |
| Citation(s) |
27621450 |
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| Submission date |
Jul 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonathan Schilling |
| E-mail(s) |
schillin@umn.edu
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| Phone |
612-624-1761
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| Organization name |
University of Minnesota
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| Street address |
2004 folwell ave
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| City |
saint paul |
| State/province |
minnesota |
| ZIP/Postal code |
55108 |
| Country |
USA |
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| Platforms (1) |
| GPL22164 |
Illumina HiSeq 2500 (Postia placenta) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA329543 |
| SRA |
SRP078846 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84529_FPKM_tracking_0-5_mm__15-20_mm_and_30-35_mm_Cuffidff.txt.gz |
860.1 Kb |
(ftp)(http) |
TXT |
| GSE84529_Paired_comparison_of_three_sections_Cuffdiff.xlsx |
4.8 Mb |
(ftp)(http) |
XLSX |
| GSE84529_RAW.tar |
4.8 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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