scholarly journals Large differences in carbohydrate degradation and transport potential in the genomes of lichen fungal symbionts

2021 ◽  
Author(s):  
Philipp Resl ◽  
Adina R. Bujold ◽  
Gulnara Tagirdzhanova ◽  
Peter Meidl ◽  
Sandra Freire Rallo ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Cell Wall Degrading Enzymes ◽  
Sugar Transporters ◽  
Carbohydrate Degradation ◽  
Wide Range ◽  
Genes Encoding ◽  
Adaptive Processes ◽  
External Sources ◽  
Lichen Symbioses ◽  
Transport Potential

Lichen symbioses are generally thought to be stabilized by the transfer of fixed carbon compounds from a photosynthesizing unicellular symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with genomic reductions in the number of genes for plant cell wall-degrading enzymes (PCWDEs), but whether this is the case with lichen fungal symbionts (LFSs) is unknown. We predicted genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 17 existing and 29 newly sequenced genomes from across the class Lecanoromycetes, the largest extant clade of LFSs. Despite possessing lower mean numbers of PCWDE genes compared to non-symbiont Ascomycota, all LFS genomes possessed a robust suite of predicted PCWDEs. The largest CAZyme gene numbers, on par with model species such as Penicillium, were retained in genomes from the subclass Ostropomycetidae, which are found in crust lichens with highly specific ecologies. The lowest numbers were in the subclass Lecanoromycetidae, which are symbionts of many generalist macrolichens. Our results suggest that association with phototroph symbionts does not in itself result in functional loss of PCWDEs and that PCWDE losses may have been driven by adaptive processes within the evolution of specific LFS lineages. The inferred capability of some LFSs to access a wide range of carbohydrates suggests that some lichen symbioses may augment fixed CO2 with carbon from external sources.

scholarly journals Butyrivibrio hungateiMB2003 Competes Effectively for Soluble Sugars Released byButyrivibrio proteoclasticusB316Tduring Growth on Xylan or Pectin

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Nikola Palevich ◽  
William J. Kelly ◽  
Siva Ganesh ◽  
Jasna Rakonjac ◽  
Graeme T. Attwood
Keyword(s):  
Bacterial Species ◽  
Soluble Sugars ◽  
Plant Fiber ◽  
Content Type ◽  
Plant Polysaccharide ◽  
Rumen Microbes ◽  
Carbohydrate Degradation ◽  
Wide Range ◽  
Genes Encoding ◽  
Enzymatic Machinery

ABSTRACTRumen bacterial species belonging to the genusButyrivibrioare important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four species are recognized; they have very similar substrate utilization profiles, but little is known about how these microorganisms are able to coexist in the rumen. To investigate this question,Butyrivibrio hungateiMB2003 andButyrivibrio proteoclasticusB316Twere grown alone or in coculture on xylan or pectin, and their growth, release of sugars, fermentation end products, and transcriptomes were examined. In monocultures, B316Twas able to grow well on xylan and pectin, while MB2003 was unable to utilize either of these insoluble substrates to support significant growth. Cocultures of B316Tgrown with MB2003 revealed that MB2003 showed growth almost equivalent to that of B316Twhen either xylan or pectin was supplied as the substrate. The effect of coculture on the transcriptomes of B316Tand MB2003 was assessed; B316Ttranscription was largely unaffected by the presence of MB2003, but MB2003 expressed a wide range of genes encoding proteins for carbohydrate degradation, central metabolism, oligosaccharide transport, and substrate assimilation, in order to compete with B316Tfor the released sugars. These results suggest that B316Thas a role as an initiator of primary solubilization of xylan and pectin, while MB2003 competes effectively for the released soluble sugars to enable its growth and maintenance in the rumen.IMPORTANCEFeeding a future global population of 9 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation.Butyrivibriospecies are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings suggest that closely related species ofButyrivibriohave developed unique strategies for the degradation of plant fiber and the subsequent assimilation of carbohydrates in order to coexist in the competitive rumen environment. The identification of genes expressed during these competitive interactions gives further insight into the enzymatic machinery used by these bacteria as they degrade the xylan and pectin components of plant fiber.

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 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 Inactivation of pecS restores the virulence of mutants devoid of osmoregulated periplasmic glucans in the phytopathogenic bacterium Dickeya dadantii

Microbiology ◽  
2014 ◽  
Vol 160 (4) ◽  
pp. 766-777 ◽  
Author(s):  
Sébastien Bontemps-Gallo ◽  
Edwige Madec ◽  
Jean-Marie Lacroix
Keyword(s):  
Plant Cell Wall ◽  
Transcriptional Regulator ◽  
Soft Rot ◽  
Cellular Functions ◽  
Cell Wall Degrading Enzymes ◽  
Dickeya Dadantii ◽  
Phytopathogenic Bacterium ◽  
Wide Range ◽  
Severe Reduction ◽  
Rot Disease

Dickeya dadantii is a phytopathogenic enterobacterium that causes soft rot disease in a wide range of plant species. Maceration, an apparent symptom of the disease, is the result of the synthesis and secretion of a set of plant cell wall-degrading enzymes (PCWDEs), but many additional factors are required for full virulence. Among these, osmoregulated periplasmic glucans (OPGs) and the PecS transcriptional regulator are essential virulence factors. Several cellular functions are controlled by both OPGs and PecS. Strains devoid of OPGs display a pleiotropic phenotype including total loss of virulence, loss of motility and severe reduction in the synthesis of PCWDEs. PecS is one of the major regulators of virulence in D. dadantii, acting mainly as a repressor of various cellular functions including virulence, motility and synthesis of PCWDEs. The present study shows that inactivation of the pecS gene restored virulence in a D. dadantii strain devoid of OPGs, indicating that PecS cannot be de-repressed in strains devoid of OPGs.

scholarly journals Inositol pyrophosphate kinase (VIH2) impart drought resistance by promoting plant cell wall homeostasis

2019 ◽  
Author(s):  
Anuj Shukla ◽  
Mandeep Kaur ◽  
Swati Kanwar ◽  
Gazaldeep Kaur ◽  
Shivani Sharma ◽  
...  
Keyword(s):  
Cell Wall ◽  
Drought Tolerance ◽  
Plant Cell Wall ◽  
High Energy ◽  
Inositol Pyrophosphate ◽  
Signalling Molecules ◽  
Gus Reporter ◽  
Wide Range ◽  
Genes Encoding ◽  
Spatio Temporal

AbstractInositol pyrophosphates (PPx-InsPs) are important signalling molecules, those participate in multiple physiological processes across wide range of species. However, limited knowledge is available for their role in plants. Here, we characterized two diphosphoinositol pentakisphosphate kinase (PPIP5K) wheat homologs, TaVIH1 and TaVIH2 for their spatio-temporal expression and physiological functions. We demonstrated the presence of functional VIH-kinase domains through biochemical assays where high energy pyrophosphate forms (IP7/8) were generated. Our GUS-reporter assays in Arabidopsis, suggested the role of TaVIH2 in drought stress. Yeast two-hybrid screen of TaVIH2 by utilizing wheat library yielded multiple cell-wall related interacting partners. TaVIH2 overexpression in Arabidopsis provided growth advantage and drought tolerance. Further, transcriptomic studies of these overexpressing lines showed activation of genes encoding for abscisic acid metabolism, cell-wall biosynthesis and drought responsive element binding proteins. Biochemical analysis of their cell-wall components, confirmed enhanced accumulation of polysaccharides (arabinogalactan, cellulose and arabinoxylan) in transgenics. These results reveal novel function of VIH proteins in modulating cell wall homeostasis thereby providing drought tolerance.

Analysis of carbohydrate-active enzymes in Thermogemmatispora sp. strain T81 reveals carbohydrate degradation ability

2018 ◽  
Vol 64 (12) ◽  
pp. 992-1003 ◽  
Author(s):  
Atilio Tomazini ◽  
Sadhana Lal ◽  
Riffat Munir ◽  
Matthew Stott ◽  
Bernard Henrissat ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Type Strain ◽  
Whole Genome Sequence ◽  
Carbohydrate Active Enzymes ◽  
Bioinformatics Analyses ◽  
Carbohydrate Polymers ◽  
Carbohydrate Degradation ◽  
Wide Range ◽  
Genes Encoding ◽  
Degradation Ability

The phylum Chloroflexi is phylogenetically diverse and is a deeply branching lineage of bacteria that express a broad spectrum of physiological and metabolic capabilities. Members of the order Ktedonobacteriales, including the families Ktedonobacteriaceae, Thermosporotrichaceae, and Thermogemmatisporaceae, all have flexible aerobic metabolisms capable of utilizing a wide range of carbohydrates. A number of species within these families are considered cellulolytic and are capable of using cellulose as a sole carbon and energy source. In contrast, Ktedonobacter racemifer, the type strain of the order, does not appear to possess this cellulolytic phenotype. In this study, we confirmed the ability of Thermogemmatispora sp. strain T81 to hydrolyze cellulose, determined the whole-genome sequence of Thermogemmatispora sp. T81, and using comparative bioinformatics analyses, identified genes encoding putative carbohydrate-active enzymes (CAZymes) in the Thermogemmatispora sp. T81, Thermogemmatispora onikobensis, and Ktedonobacter racemifer genomes. Analyses of the Thermogemmatispora sp. T81 genome identified 64 CAZyme gene sequences belonging to 57 glycoside hydrolase families. The genome of Thermogemmatispora sp. T81 encodes 19 genes for putative extracellular CAZymes, similar to the number of putative extracellular CAZymes identified in T. onikobensis (17) and K. racemifer (17), despite K. racemifer not possessing a cellulolytic phenotype. These results suggest that these members of the order Ktedonobacteriales may use a broader range of carbohydrate polymers than currently described.

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