scholarly journals Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Monika Tõlgo ◽  
Silvia Hüttner ◽  
Peter Rugbjerg ◽  
Nguyen Thanh Thuy ◽  
Vu Nguyen Thanh ◽  
...  
Keyword(s):  
Gc Content ◽  
Carbohydrate Active Enzymes ◽  
Lytic Polysaccharide Monooxygenase ◽  
Thielavia Terrestris ◽  
Biomass Saccharification ◽  
Beechwood Xylan ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Polysaccharide Monooxygenase

Abstract Background Biomass-degrading enzymes with improved activity and stability can increase substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate low pH and high temperatures. Here, we aimed to illuminate the lignocellulose-degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail. Results We sequenced and analyzed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. 10,128 predicted genes were found in total, which included 411 CAZy domains. Compared to other fungi, auxiliary activity (AA) domains were particularly enriched. A higher GC content was found in coding sequences compared to the overall genome, as well as a high GC3 content, which is hypothesized to contribute to thermophilicity. Primarily auxiliary activity (AA) family 9 lytic polysaccharide monooxygenase (LPMO) and glycoside hydrolase (GH) family 7 glucanase encoding genes were upregulated when LPH172 was cultivated on cellulosic substrates. Conventional hemicellulose encoding genes (GH10, GH11 and various CEs), as well as AA9 LPMOs, were upregulated when LPH172 was cultivated on xylan. The observed co-expression and co-upregulation of genes encoding AA9 LPMOs, other AA CAZymes, and (hemi)cellulases point to a complex and nuanced degradation strategy. Conclusions Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal that the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterization of potential new enzymes for industrial biomass saccharification.

scholarly journals Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172

2020 ◽  
Author(s):  
Monika Tõlgo ◽  
Silvia Hüttner ◽  
Nguyen Than Thuy ◽  
Vu Nguyen Than ◽  
Johan Larsbrink ◽  
...  
Keyword(s):  
Gc Content ◽  
Low Ph ◽  
Biomass Degradation ◽  
Carbohydrate Active Enzymes ◽  
Thielavia Terrestris ◽  
Biomass Saccharification ◽  
Lignocellulosic Substrates ◽  
Lytic Polysaccharide Monooxygenases ◽  
Beechwood Xylan ◽  
Polysaccharide Monooxygenases

Abstract Background: Biomass-degrading enzymes with improved activity and stability can ameliorate substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate well low pH and high temperatures. Here, we aimed to illuminate the lignocellulose degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail.Results: We sequenced and analysed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. In total, 411 CAZy domains were found among 10,128 predicted genes. Compared to other fungi, auxiliary activity (AA) enzymes were particularly enriched. GC content was higher in coding sequences than in the overall genome. A high GC3 content was hypothesised to contribute to thermophilicity. T. terrestris employed mainly lytic polysaccharide monooxygenases (LPMOs) and glycoside hydrolase (GH) family 7 glucanases to attack cellulosic substrates, and conventional hemicellulases (GH10 and GH11) to degrade xylan. The observed co-expression and co-upregulation of AA9 LPMOs, other AA CAZymes, and (hemi)cellulases points to a complex and nuanced degradation strategy. Growth on more complex and heterogeneous substrates resulted in a more varied but generally lower gene expression. Conclusions: Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterisation of potential new enzymes for industrial biomass saccharification.

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

Identification and characterization of a novel AA9-type lytic polysaccharide monooxygenase from a bagasse metagenome

2020 ◽  
Vol 105 (1) ◽  
pp. 197-210
Author(s):  
Benjarat Bunterngsook ◽  
Wuttichai Mhuantong ◽  
Pattanop Kanokratana ◽  
Yu Iseki ◽  
Takashi Watanabe ◽  
...  
Keyword(s):  
Lytic Polysaccharide Monooxygenase ◽  
Identification And Characterization ◽  
Polysaccharide Monooxygenase

scholarly journals Identification and Characterization of Hemolysin-Like Proteins Similar to RTX Toxin in Pasteurella pneumotropica

2009 ◽  
Vol 191 (11) ◽  
pp. 3698-3705 ◽  
Author(s):  
Hiraku Sasaki ◽  
Eiichi Kawamoto ◽  
Yoshikazu Tanaka ◽  
Takuo Sawada ◽  
Satoshi Kunita ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Opportunistic Pathogen ◽  
Pcr Analysis ◽  
Type I ◽  
Secretion Systems ◽  
Rtx Toxin ◽  
Rtx Toxins ◽  
Genes Encoding ◽  
Encoding Genes

ABSTRACT Pasteurella pneumotropica is an opportunistic pathogen that causes lethal pneumonia in immunodeficient rodents. The virulence factors of this bacterium remain unknown. In this study, we identified the genes encoding two RTX toxins, designated as pnxI and pnxII, from the genomic DNA of P. pneumotropica ATCC 35149 and characterized with respect to hemolysis. The pnxI operon was organized according to the manner in which the genes encoded the structural RTX toxin (pnxIA), the type I secretion systems (pnxIB and pnxID), and the unknown orf. The pnxII gene was involved only with the pnxIIA that coded for a structural RTX toxin. Both the structural RTX toxins of deduced PnxIA and PnxIIA were involved in seven of the RTX repeat and repeat-like sequences. By quantitative PCR analysis of the structural RTX toxin-encoding genes in P. pneumotropica ATCC 35149, the gene expression of pnxIA was found to have increased from the early log phase, while that of pnxIIA increased from the late log to the early stationary phase. As expressed in Escherichia coli, both the recombinant proteins of PnxIA and PnxIIA showed weak hemolytic activity in both sheep and murine erythrocytes. On the basis of the results of the Southern blotting analysis, the pnxIA gene was detected in 82% of the isolates, while the pnxIIA gene was detected in 39%. These results indicate that the products of both pnxIA and pnxIIA were putative associations of virulence factors in the rodent pathogen P. pneumotropica.

scholarly journals Characterization of a lytic polysaccharide monooxygenase from Aspergillus fumigatus shows functional variation among family AA11 fungal LPMOs

2021 ◽  
pp. 101421
Author(s):  
Fredrik Gjerstad Støpamo ◽  
Åsmund Kjendseth Røhr ◽  
Sophanit Mekasha ◽  
Dejan M. Petrović ◽  
Anikó Várnai ◽  
...  
Keyword(s):  
Aspergillus Fumigatus ◽  
Functional Variation ◽  
Lytic Polysaccharide Monooxygenase ◽  
Polysaccharide Monooxygenase

scholarly journals Prospecting for Novel Biocatalysts in a Soil Metagenome

2003 ◽  
Vol 69 (10) ◽  
pp. 6235-6242 ◽  
Author(s):  
S. Voget ◽  
C. Leggewie ◽  
A. Uesbeck ◽  
C. Raasch ◽  
K.-E. Jaeger ◽  
...  
Keyword(s):  
Type I ◽  
The Novel ◽  
Gene Duplications ◽  
16S Rrna Sequence ◽  
Pectate Lyases ◽  
Dna Libraries ◽  
Genes Encoding ◽  
16S Rrna Sequence Analysis ◽  
Encoding Genes

ABSTRACT The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an α-amylase (amyA), a 1,4-α-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.

scholarly journals Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome

2020 ◽  
Vol 9 (1) ◽  
pp. 20
Author(s):  
Hye-Won Yu ◽  
Ji-Hoon Im ◽  
Won-Sik Kong ◽  
Young-Jin Park
Keyword(s):  
De Novo ◽  
Animal Feed ◽  
Gc Content ◽  
Industrial Applications ◽  
Glycoside Hydrolases ◽  
Flammulina Velutipes ◽  
Carbohydrate Binding ◽  
Carbohydrate Active Enzymes ◽  
Carbohydrate Binding Modules ◽  
Genes Encoding

The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F.velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54–95 AAs, 145–188 GHs, 55–73 GTs, 6–19 PLs, 13–59 CEs, and 7–67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.

scholarly journals Molecular Characterization of Baseline Enterobacterales and Pseudomonas aeruginosa Isolates from a Phase 3 Nosocomial Pneumonia (ASPECT-NP) Clinical Trial

2020 ◽  
pp. AAC.02461-20
Author(s):  
Mariana Castanheira ◽  
Matthew G. Johnson ◽  
Brian Yu ◽  
Jennifer A. Huntington ◽  
Patricia Carmelitano ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Pseudomonas Aeruginosa ◽  
Nosocomial Pneumonia ◽  
Resistance Mechanisms ◽  
Quantitative Real Time Pcr ◽  
Phase 3 ◽  
Genes Encoding ◽  
Elevated Expression ◽  
Encoding Genes

We evaluated β-lactam-resistant Enterobacterales species and Pseudomonas aeruginosa baseline lower respiratory tract isolates collected during the ASPECT-NP phase 3 clinical trial evaluating the safety and efficacy of ceftolozane-tazobactam compared with meropenem for treatment of ventilated nosocomial pneumonia in adults. Isolates were subjected to whole genome sequencing, quantitative real-time PCR for quantification of the expression levels of β-lactamase and efflux genes, and Western blot analysis for detection of OprD (P. aeruginosa only). ESBL genes were detected in 168 of 262 Enterobacterales isolates and among these blaCTXM-15 was the most common, detected in 125 isolates. Sixty-one Enterobacterales carried genes encoding carbapenemases while 33 isolates did not carry ESBLs or carbapenemases. Carbapenemase-producing isolates carried mainly NDM and OXA-48 variants, with ceftolozane-tazobactam MIC values ranging from 4 to 128 μg/mL. Most ceftolozane-tazobactam-nonsusceptible Enterobacterales isolates that did not carry carbapenemases were K. pneumoniae that exhibited disrupted OmpK35, specific mutations in OmpK36, and, in some isolates, elevated expression of blaCTXM-15. Among 89 P. aeruginosa isolates, carbapenemases and ESBL-encoding genes were observed among 12 and 22 isolates, respectively. P. aeruginosa isolates without acquired β-lactamases displaying elevated expression of AmpC (14 isolates), elevated expression of efflux pumps (11 isolates), and/or decrease or loss of OprD (22 isolates) were susceptible to ceftolozane-tazobactam. Ceftolozane-tazobactam was active against >75% of the Enterobacterales isolates from the ASPECT-NP trial that did not carry carbapenemases. K. pneumoniae resistant to ceftolozane-tazobactam might represent a challenge for treatment due to its multiple resistance mechanisms. Ceftolozane-tazobactam was among the agents displaying the greatest activity against P. aeruginosa isolates.

scholarly journals Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity

2015 ◽  
Vol 290 (38) ◽  
pp. 22955-22969 ◽  
Author(s):  
Anna S. Borisova ◽  
Trine Isaksen ◽  
Maria Dimarogona ◽  
Abhishek A. Kognole ◽  
Geir Mathiesen ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Functional Characterization ◽  
Lytic Polysaccharide Monooxygenase ◽  
Broad Substrate Specificity ◽  
Polysaccharide Monooxygenase
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