scholarly journals Genetic determinants of endophytism in the Arabidopsis root mycobiome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fantin Mesny ◽  
Shingo Miyauchi ◽  
Thorsten Thiergart ◽  
Brigitte Pickel ◽  
Lea Atanasova ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Gene Families ◽  
Plant Health ◽  
Transcriptional Program ◽  
Genetic Determinants ◽  
Cell Wall Degrading Enzymes ◽  
Arabidopsis Root ◽  
Disease States ◽  
Genes Encoding ◽  
Health And Disease

AbstractThe roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.

scholarly journals Genetic determinants of endophytism in the Arabidopsis root mycobiome

2021 ◽  
Author(s):  
Fantin Mesny ◽  
Shingo Miyauchi ◽  
Thorsten Thiergart ◽  
Brigitte Pickel ◽  
Lea Atanasova ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
Plant Cell Wall ◽  
Transcriptional Response ◽  
Gene Families ◽  
Genetic Determinants ◽  
Cell Wall Degrading Enzymes ◽  
Arabidopsis Root ◽  
Symbiotic Associations ◽  
Disease States ◽  
Health And Disease

AbstractRoots of Arabidopsis thaliana do not engage in symbiotic associations with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors with diverse lifestyles and retained large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.

scholarly journals The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

2020 ◽  
Vol 117 (11) ◽  
pp. 6003-6013 ◽  
Author(s):  
Vincent W. Wu ◽  
Nils Thieme ◽  
Lori B. Huberman ◽  
Axel Dietschmann ◽  
David J. Kowbel ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factors ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Carbon Sources ◽  
Cell Wall Degrading Enzymes ◽  
Degrading Enzymes ◽  
Genes Encoding

Filamentous fungi, such asNeurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling ofN. crassaon 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors inN. crassaand characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level.

scholarly journals A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Junhua Li ◽  
Huanzi Zhong ◽  
Yuliaxis Ramayo-Caldas ◽  
Nicolas Terrapon ◽  
Vincent Lombard ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Production Systems ◽  
Wall Material ◽  
Rumen Microbes ◽  
Bovine Rumen ◽  
Degrading Enzymes ◽  
Genes Encoding ◽  
Health And Disease ◽  
Metagenome Sequencing ◽  
Available Information

Abstract Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

scholarly journals Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

PLoS Genetics ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. e1007322 ◽  
Author(s):  
Irina S. Druzhinina ◽  
Komal Chenthamara ◽  
Jian Zhang ◽  
Lea Atanasova ◽  
Dongqing Yang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Lateral Transfer ◽  
Cell Wall Degrading Enzymes ◽  
Degrading Enzymes ◽  
Genes Encoding ◽  
Mycoparasitic Fungus

scholarly journals Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Saidi R. Achari ◽  
Jacqueline Edwards ◽  
Ross C. Mann ◽  
Jatinder K. Kaur ◽  
Tim Sawbridge ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Plant Cell Wall ◽  
Post Inoculation ◽  
Cell Wall Degrading Enzymes ◽  
Oxidation Reduction ◽  
Genes Encoding ◽  
Infection Mechanisms ◽  
Race 2 ◽  
Necrotrophic Stage ◽  
Comparative Transcriptomic Analysis

Abstract Background The fungal pathogen Fusarium oxysporum f.sp. pisi (Fop) causes Fusarium wilt in peas. There are four races globally: 1, 2, 5 and 6 and all of these races are present in Australia. Molecular infection mechanisms have been studied in a few other F. oxysporum formae speciales; however, there has been no transcriptomic Fop-pea pathosystem study. Results A transcriptomic study was carried out to understand the molecular pathogenicity differences between the races. Transcriptome analysis at 20 days post-inoculation revealed differences in the differentially expressed genes (DEGs) in the Fop races potentially involved in fungal pathogenicity variations. Most of the DEGs in all the races were engaged in transportation, metabolism, oxidation-reduction, translation, biosynthetic processes, signal transduction, proteolysis, among others. Race 5 expressed the most virulence-associated genes. Most genes encoding for plant cell wall degrading enzymes, CAZymes and effector-like proteins were expressed in race 2. Race 6 expressed the least number of genes at this time point. Conclusion Fop races deploy various factors and complex strategies to mitigate host defences to facilitate colonisation. This investigation provides an overview of the putative pathogenicity genes in different Fop races during the necrotrophic stage of infection. These genes need to be functionally characterised to confirm their pathogenicity/virulence roles and the race-specific genes can be further explored for molecular characterisation.

scholarly journals The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer

2013 ◽  
Vol 280 (1763) ◽  
pp. 20131021 ◽  
Author(s):  
Yannick Pauchet ◽  
David G. Heckel
Keyword(s):  
Cell Wall ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Genetic Material ◽  
Leaf Beetle ◽  
Glycoside Hydrolase Family ◽  
Cell Wall Degrading Enzymes ◽  
Genes Encoding

The primary plant cell wall comprises the most abundant polysaccharides on the Earth and represents a rich source of energy for organisms which have evolved the ability to digest them. Enzymes able to degrade plant cell wall polysaccharides are widely distributed in micro-organisms but are generally absent in animals, although their presence in insects, especially phytophagous beetles from the superfamilies Chrysomeloidea and Curculionoidea, has recently begun to be appreciated. The observed patchy distribution of endogenous genes encoding these enzymes in animals has raised questions about their evolutionary origins. Recent evidence suggests that endogenous plant cell wall degrading enzymes-encoding genes have been acquired by animals through a mechanism known as horizontal gene transfer (HGT). HGT describes how genetic material is moved by means other than vertical inheritance from a parent to an offspring. Here, we provide evidence that the mustard leaf beetle, Phaedon cochleariae , possesses in its genome genes encoding active xylanases from the glycoside hydrolase family 11 (GH11). We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals.

scholarly journals The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Stéphane Hacquard ◽  
Benjamin Petre ◽  
Pascal Frey ◽  
Arnaud Hecker ◽  
Nicolas Rouhier ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Rust Fungus ◽  
Gene Families ◽  
Genetic Determinants ◽  
Plant Host ◽  
Recombinant Protein Purification ◽  
Functional Studies ◽  
Regulated Expression ◽  
Genes Encoding ◽  
Host Tissues

Poplars are extensively cultivated worldwide, and their susceptibility to the leaf rust fungusMelampsora larici-populinaleads to considerable damages in plantations. Despite a good knowledge of the poplar rust life cycle, and particularly the epidemics on poplar, the perennial status of the plant host and the obligate biotrophic lifestyle of the rust fungus are bottlenecks for molecular investigations. Following the completion of bothM. larici-populinaandPopulus trichocarpagenome sequences, gene families involved in poplar resistance or in rust fungus virulence were investigated, allowing the identification of key genetic determinants likely controlling the outcome of the interaction. Specific expansions of resistance and defense-related genes in poplar indicate probable innovations in perennial species in relation with host-pathogen interactions. The genome ofM. Larici-populinacontains a strikingly high number of genes encoding small secreted proteins (SSPs) representing hundreds of candidate effectors. Transcriptome analyses of interacting partners in compatible and incompatible interactions revealed conserved set of genes involved in poplar defense reactions as well as timely regulated expression of SSP transcripts during host tissues colonisation. Ongoing functional studies of selected candidate effectors will be achieved mainly on the basis of recombinant protein purification and subsequent characterisation.

scholarly journals Diversity of Beetle Genes Encoding Novel Plant Cell Wall Degrading Enzymes

PLoS ONE ◽  
2010 ◽  
Vol 5 (12) ◽  
pp. e15635 ◽  
Author(s):  
Yannick Pauchet ◽  
Paul Wilkinson ◽  
Ritika Chauhan ◽  
Richard H. ffrench-Constant
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Degrading Enzymes ◽  
Degrading Enzymes ◽  
Genes Encoding
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