Influence of Populus Genotype on Gene Expression by the Wood Decay Fungus Phanerochaete chrysosporium

ABSTRACTWe examined gene expression patterns in the lignin-degrading fungusPhanerochaete chrysosporiumwhen it colonizes hybrid poplar (Populus alba×tremula) and syringyl (S)-rich transgenic derivatives. A combination of microarrays and liquid chromatography-tandem mass spectrometry (LC-MS/MS) allowed detection of a total of 9,959 transcripts and 793 proteins. Comparisons ofP. chrysosporiumtranscript abundance in medium containing poplar or glucose as a sole carbon source showed 113 regulated genes, 11 of which were significantly higher (>2-fold,P< 0.05) in transgenic line 64 relative to the parental line. Possibly related to the very large amounts of syringyl (S) units in this transgenic tree (94 mol% S), several oxidoreductases were among the upregulated genes. Peptides corresponding to a total of 18 oxidoreductases were identified in medium consisting of biomass from line 64 or 82 (85 mol% S) but not in the parental clone (65 mol% S). These results demonstrate thatP. chrysosporiumgene expression patterns are substantially influenced by lignin composition.

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Significant Alteration of Gene Expression in Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium by Plant Species

Applied and Environmental Microbiology ◽

10.1128/aem.00508-11 ◽

2011 ◽

Vol 77 (13) ◽

pp. 4499-4507 ◽

Cited By ~ 76

Author(s):

Amber Vanden Wymelenberg ◽

Jill Gaskell ◽

Michael Mozuch ◽

Sandra Splinter BonDurant ◽

Grzegorz Sabat ◽

...

Keyword(s):

Gene Expression ◽

Carbon Source ◽

Phanerochaete Chrysosporium ◽

Wood Decay ◽

Hydrolytic Cleavage ◽

Decay Fungi ◽

Transcript Levels ◽

Content Type ◽

Postia Placenta ◽

Wood Decay Fungi

ABSTRACTIdentification of specific genes and enzymes involved in conversion of lignocellulosics from an expanding number of potential feedstocks is of growing interest to bioenergy process development. The basidiomycetous wood decay fungiPhanerochaete chrysosporiumandPostia placentaare promising in this regard because they are able to utilize a wide range of simple and complex carbon compounds. However, systematic comparative studies with different woody substrates have not been reported. To address this issue, we examined gene expression of these fungi colonizing aspen (Populus grandidentata) and pine (Pinus strobus). Transcript levels of genes encoding extracellular glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose, showed little difference forP. placentacolonizing pine versus aspen as the sole carbon source. However, 164 genes exhibited significant differences in transcript accumulation for these substrates. Among these, 15 cytochrome P450s were upregulated in pine relative to aspen. Of 72P. placentaextracellular proteins identified unambiguously by mass spectrometry, 52 were detected while colonizing both substrates and 10 were identified in pine but not aspen cultures. Most of the 178P. chrysosporiumglycoside hydrolase genes showed similar transcript levels on both substrates, but 13 accumulated >2-fold higher levels on aspen than on pine. Of 118 confidently identified proteins, 31 were identified in both substrates and 57 were identified in pine but not aspen cultures. Thus,P. placentaandP. chrysosporiumgene expression patterns are influenced substantially by wood species. Such adaptations to the carbon source may also reflect fundamental differences in the mechanisms by which these fungi attack plant cell walls.

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Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

Applied and Environmental Microbiology ◽

10.1128/aem.00134-16 ◽

2016 ◽

Vol 82 (14) ◽

pp. 4387-4400 ◽

Cited By ~ 21

Author(s):

Oleksandr Skyba ◽

Dan Cullen ◽

Carl J. Douglas ◽

Shawn D. Mansfield

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

White Rot Fungi ◽

Wood Decay ◽

White Rot ◽

Decay Fungi ◽

Content Type ◽

Postia Placenta ◽

Substrate Composition ◽

Wood Decay Fungi

ABSTRACTIdentification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi,Rhodonia placenta(formerlyPostia placenta) andPhanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-oldPopulus trichocarpa(poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold,P< 0.05) inP. chrysosporiumandP. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold,P< 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles ofP. chrysosporiumandP. placentaare influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode “proteins of unknown function,” and determining their role in lignocellulose degradation presents opportunities and challenges for future research.IMPORTANCEThis study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.

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Analyzing Phanerochaete chrysosporium gene expression patterns controlling the molecular fate of lignocellulose degrading enzymes

Process Biochemistry ◽

10.1016/j.procbio.2017.10.007 ◽

2018 ◽

Vol 64 ◽

pp. 51-62 ◽

Cited By ~ 1

Author(s):

Ayyappa Kumar Sista Kameshwar ◽

Wensheng Qin

Keyword(s):

Gene Expression ◽

Phanerochaete Chrysosporium ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Degrading Enzymes

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Sensitivity of White and Opaque Candida albicans Cells to Antifungal Drugs

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00166-17 ◽

2017 ◽

Vol 61 (8) ◽

Cited By ~ 3

Author(s):

Veronica B. Craik ◽

Alexander D. Johnson ◽

Matthew B. Lohse

Keyword(s):

Gene Expression ◽

Candida Albicans ◽

Antifungal Agents ◽

Expression Patterns ◽

Antifungal Drugs ◽

Gene Expression Patterns ◽

Metabolic Profiles ◽

Strain Variation ◽

Content Type ◽

Terbinafine Hydrochloride

ABSTRACT White and opaque cells of Candida albicans have the same genome but differ in gene expression patterns, metabolic profiles, and host niche preferences. We tested whether these differences, which include the differential expression of drug transporters, resulted in different sensitivities to 27 antifungal agents. The analysis was performed in two different strain backgrounds; although there was strain-to-strain variation, only terbinafine hydrochloride and caspofungin showed consistent, 2-fold differences between white and opaque cells across both strains.

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Gene expression patterns underlying changes in xylem structure and function in response to increased nitrogen availability in hybrid poplar

Plant Cell & Environment ◽

10.1111/j.1365-3040.2012.02566.x ◽

2012 ◽

Vol 36 (1) ◽

pp. 186-199 ◽

Cited By ~ 56

Author(s):

LENKA PLAVCOVÁ ◽

UWE G. HACKE ◽

ADRIANA M. ALMEIDA-RODRIGUEZ ◽

ERYANG LI ◽

CARL J. DOUGLAS

Keyword(s):

Gene Expression ◽

Nitrogen Availability ◽

Expression Patterns ◽

Hybrid Poplar ◽

Structure And Function ◽

Gene Expression Patterns ◽

Xylem Structure ◽

And Function

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Time Course of Gene Expression during Porphyromonas gingivalis Strain ATCC 33277 Biofilm Formation

Applied and Environmental Microbiology ◽

10.1128/aem.00746-11 ◽

2011 ◽

Vol 77 (18) ◽

pp. 6733-6736 ◽

Cited By ~ 14

Author(s):

Reiko Yamamoto ◽

Yuichiro Noiri ◽

Mikiyo Yamaguchi ◽

Yoko Asahi ◽

Hazuki Maezono ◽

...

Keyword(s):

Gene Expression ◽

Porphyromonas Gingivalis ◽

Biofilm Formation ◽

Time Course ◽

Growth Stage ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Strain Atcc ◽

Content Type ◽

Number Of Genes

ABSTRACTChronological gene expression patterns of biofilm-forming cells are important to understand bioactivity and pathogenicity of biofilms. ForPorphyromonas gingivalisATCC 33277 biofilm formation, the number of genes differentially regulated by more than 1.5-fold was highest during the growth stage (312/2,090 genes), and some pathogen-associated genes were time-dependently controlled.

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Tight junction protein gene expression patterns and changes in transcript abundance during development of model fish gill epithelia

Journal of Experimental Biology ◽

10.1242/jeb.098731 ◽

2014 ◽

Vol 217 (10) ◽

pp. 1667-1681 ◽

Cited By ~ 27

Author(s):

D. Kolosov ◽

H. Chasiotis ◽

S. P. Kelly

Keyword(s):

Gene Expression ◽

Tight Junction ◽

Protein Gene ◽

Expression Patterns ◽

Transcript Abundance ◽

Tight Junction Protein ◽

Gene Expression Patterns ◽

Fish Gill ◽

Junction Protein ◽

Model Fish

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Global Transcriptome Analysis of Staphylococcus aureus Biofilms in Response to Innate Immune Cells

Infection and Immunity ◽

10.1128/iai.00819-13 ◽

2013 ◽

Vol 81 (12) ◽

pp. 4363-4376 ◽

Cited By ~ 34

Author(s):

Tyler D. Scherr ◽

Christelle M. Roux ◽

Mark L. Hanke ◽

Amanda Angle ◽

Paul M. Dunman ◽

...

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Defense Mechanisms ◽

Bacterial Infections ◽

Expression Patterns ◽

Immune Defense ◽

Innate Immune ◽

Gene Expression Patterns ◽

Content Type ◽

Affymetrix Microarrays

ABSTRACTThe potent phagocytic and microbicidal activities of neutrophils and macrophages are among the first lines of defense against bacterial infections. YetStaphylococcus aureusis often resistant to innate immune defense mechanisms, especially when organized as a biofilm. To investigate howS. aureusbiofilms respond to macrophages and neutrophils, gene expression patterns were profiled using Affymetrix microarrays. The addition of macrophages toS. aureusstatic biofilms led to a global suppression of the biofilm transcriptome with a wide variety of genes downregulated. Notably, genes involved in metabolism, cell wall synthesis/structure, and transcription/translation/replication were among the most highly downregulated, which was most dramatic at 1 h compared to 24 h following macrophage addition to biofilms. Unexpectedly, few genes were enhanced in biofilms after macrophage challenge. Unlike coculture with macrophages, coculture ofS. aureusstatic biofilms with neutrophils did not greatly influence the biofilm transcriptome. Collectively, these experiments demonstrate thatS. aureusbiofilms differentially modify their gene expression patterns depending on the leukocyte subset encountered.

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