Journal articles: 'GH15'

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Wang, Qiong, Mengmeng Xu, Liting Zhao, Lei Chen, and Zhongyang Ding. "Novel Insights into the Mechanism Underlying High Polysaccharide Yield in Submerged Culture of Ganoderma lucidum Revealed by Transcriptome and Proteome Analyses." Microorganisms 11, no. 3 (March 17, 2023): 772. http://dx.doi.org/10.3390/microorganisms11030772.

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Polysaccharides are crucial dietary supplements and traditional pharmacological components of Ganoderma lucidum; however, the mechanisms responsible for high polysaccharide yields in G. lucidum remain unclear. Therefore, we investigated the mechanisms underlying the high yield of polysaccharides in submerged cultures of G. lucidum using transcriptomic and proteomic analyses. Several glycoside hydrolase (GH) genes and proteins, which are associated with the degradation of fungal cell walls, were significantly upregulated under high polysaccharide yield conditions. They mainly belonged to the GH3, GH5, GH16, GH17, GH18, GH55, GH79, GH128, GH152, and GH154 families. Additionally, the results suggested that the cell wall polysaccharide could be degraded by GHs, which is beneficial for extracting more intracellular polysaccharides from cultured mycelia. Furthermore, some of the degraded polysaccharides were released into the culture broth, which is beneficial for obtaining more extracellular polysaccharides. Our findings provide new insights into the mechanisms underlying the roles that GH family genes play to regulate high polysaccharide yields in G. lucidum.

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Lam, Ming Quan, Nicola C. Oates, Daniel R. Leadbeater, Kian Mau Goh, Adibah Yahya, Madihah Md Salleh, Zaharah Ibrahim, Neil C. Bruce, and Chun Shiong Chong. "Genomic Analysis to Elucidate the Lignocellulose Degrading Capability of a New Halophile Robertkochia solimangrovi." Genes 13, no. 11 (November 17, 2022): 2135. http://dx.doi.org/10.3390/genes13112135.

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Robertkochia solimangrovi is a proposed marine bacterium isolated from mangrove soil. So far, the study of this bacterium is limited to taxonomy only. In this report, we performed a genomic analysis of R. solimangrovi that revealed its lignocellulose degrading ability. Genome mining of R. solimangrovi revealed a total of 87 lignocellulose degrading enzymes. These enzymes include cellulases (GH3, GH5, GH9 and GH30), xylanases (GH5, GH10, GH43, GH51, GH67, and GH115), mannanases (GH2, GH26, GH27 and GH113) and xyloglucanases (GH2, GH5, GH16, GH29, GH31 and GH95). Most of the lignocellulolytic enzymes encoded in R. solimangrovi were absent in the genome of Robertkochia marina, the closest member from the same genus. Furthermore, current work also demonstrated the ability of R. solimangrovi to produce lignocellulolytic enzymes to deconstruct oil palm empty fruit bunch (EFB), a lignocellulosic waste found abundantly in palm oil industry. The metabolic pathway taken by R. solimangrovi to transport and process the reducing sugars after the action of lignocellulolytic enzymes on EFB was also inferred based on genomic data. Collectively, genomic analysis coupled with experimental studies elucidated R. solimangrovi to serve as a promising candidate in seawater based-biorefinery industry.

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Gu, Jingmin, Xiaohe Liu, Mei Yang, Yue Li, Changjiang Sun, Rong Lu, Jun Song, et al. "Genomic characterization of lytic Staphylococcus aureus phage GH15: providing new clues to intron shift in phages." Journal of General Virology 94, no. 4 (April 1, 2013): 906–15. http://dx.doi.org/10.1099/vir.0.049197-0.

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Phage GH15 is a polyvalent phage that shows activity against a wide range of Staphylcoccus aureus strains. This study analysed the genome of GH15. The genome size of GH15 (139 806 bp) was found to be larger than that of the known staphylococcal phages, and the G+C content (30.23 mol%) of GH15 was lower than that of any other staphylococcal myovirus phages. By mass spectrometry, ten structural proteins were identified. Analysis revealed that GH15 was closely related to phages G1, ISP, A5W, Sb-1 and K, and was moderately related to Twort. In light of the variability in identity, coverage, G+C content and genome size, coupled with the large number of mosaicisms, there certainly were close evolutionary relationships from K to Sb-1, A5W, ISP, G1 and finally GH15. Interestingly, all the introns and inteins present in the above phages were absent in GH15 and there appeared to be intron loss in GH15 compared with the intron gain seen in other phages. A comparison of the intron- and intein-related genes demonstrated a clear distinction in the location of the insertion site between intron-containing and intron-free alleles, and this might lead to the establishment of a consensus sequence associated with the presence of an intron or intein. The comparative analysis of the GH15 genome sequence with other phages not only provides compelling evidence for the diversity of staphylococcal myovirus phages but also offers new clues to intron shift in phages.

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Gu, Jingmin, Xiaohe Liu, Rong Lu, Yue Li, Jun Song, Liancheng Lei, Changjiang Sun, et al. "Complete Genome Sequence of Staphylococcus aureus Bacteriophage GH15." Journal of Virology 86, no. 16 (July 27, 2012): 8914–15. http://dx.doi.org/10.1128/jvi.01313-12.

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GH15 is a polyvalent phage that shows activity against a wide range ofStaphylococcus aureusstrains. In this work, the complete genome sequence of GH15 was determined. With a genome size of 139,806 bp (double-stranded DNA), GH15 is the largest staphylococcal phage sequenced to date. The complete genome encodes 214 open reading frames (ORFs) and 4 tRNAs. The closest relatives are the class III staphylococcal myobacteriophages, including K, A5W, ISP, Sb-1, and G1. Interestingly, although corresponding gene sequences demonstrate very high similarity, all the introns and inteins present in the phages listed above are absent in GH15. As such, GH15 can be considered phylogenetically unique among the staphylococcal myobacteriophages, indicating the diversity of this family.

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Sakaguchi, Masayoshi, Satoru Shimodaira, Shin-nosuke Ishida, Miko Amemiya, Shotaro Honda, Yasusato Sugahara, Fumitaka Oyama, and Masao Kawakita. "Identification of GH15 Family Thermophilic Archaeal Trehalases That Function within a Narrow Acidic-pH Range." Applied and Environmental Microbiology 81, no. 15 (May 15, 2015): 4920–31. http://dx.doi.org/10.1128/aem.00956-15.

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ABSTRACTTwo glucoamylase-like genes,TVN1315andTa0286, from the archaeaThermoplasma volcaniumandT. acidophilum, respectively, were expressed inEscherichia coli. The gene products, TVN1315 and Ta0286, were identified as archaeal trehalases. These trehalases belong to the CAZy database family GH15, although they have putative (α/α)6barrel catalytic domain structures similar to those of GH37 and GH65 family trehalases from other organisms. These newly identified trehalases function within a narrow range of acidic pH values (pH 3.2 to 4.0) and at high temperatures (50 to 60°C), and these enzymes displayKmvalues for trehalose higher than those observed for typical trehalases. These enzymes were inhibited by validamycin A; however, the inhibition constants (Ki) were higher than those of other trehalases. Three TVN1315 mutants, corresponding to E408Q, E571Q, and E408Q/E571Q mutations, showed reduced activity, suggesting that these two glutamic acid residues are involved in trehalase catalysis in a manner similar to that of glucoamylase. To date, TVN1315 and Ta0286 are the first archaeal trehalases to be identified, and this is the first report of the heterologous expression of GH15 family trehalases. The identification of these trehalases could extend our understanding of the relationships between the structure and function of GH15 family enzymes as well as glycoside hydrolase family enzymes; additionally, these enzymes provide insight into archaeal trehalose metabolism.

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Janeček, Štefan. "Amylolytic enzymes - focus on the alpha-amylases from Archae and plants." Nova Biotechnologica et Chimica 9, no. 1 (November 29, 2021): 5–26. http://dx.doi.org/10.36547/nbc.1284.

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Amylolytic enzymes represent a group of starch hydrolases and related enzymes that are active towards the α-glycosidic bonds in starch and related poly- and oligosaccharides. The three best known amylolytic enzymes are α-amylase, β-amylase and glucoamylase that, however, differ from each other by their amino acid sequences, three-dimensional structures, reaction mechanisms and catalytic machineries. In the sequence-based classification of all glycoside hydrolases (GHs) they have therefore been classified into the three independent families: GH13 (α-amylases), GH14 (β-amylases) and GH15 (glucoamylases). Some amylolytic enzymes have been placed to the families GH31 and GH57. The family GH13 together with the families GH70 and GH77 constitutes the clan GH-H, well-known as the α-amylase family. It contains more than 6,000 sequences and covers 30 various enzyme specificities sharing the conserved sequence regions, catalytic TIM-barrel fold, retaining reaction mechanism and catalytic triad. Among the GH13 α-amylases, those produced by plants and archaebacteria exhibit common sequence similarities that distinguish them from the α-amylases of the remaining taxonomic sources. Despite the close evolutionary relatedness between the plant and archaeal α-amylases, there are also specific differences that discriminate them from each other. These specific differences could be used in an effort to reveal the sequence-structural features responsible for the high thermostability of the α-amylases from Archaea.

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Dai, Xin, Yan Tian, Jinting Li, Xiaoyun Su, Xuewei Wang, Shengguo Zhao, Li Liu, et al. "Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen." Applied and Environmental Microbiology 81, no. 4 (December 12, 2014): 1375–86. http://dx.doi.org/10.1128/aem.03682-14.

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ABSTRACTThe bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for ∼1% and ∼0.1% of the total non-rRNAs, respectively. The majority (∼98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized byRuminococcusandFibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the generaRuminococcus,Prevotella, andFibrobacter. Most (∼82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the generaRuminococcus,Fibrobacter, andPrevotellaare predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.

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Zhang, Junhua, Xuehua Yu, Bo Guan, Youzhen Hu, Xu Li, Jun Zeng, and Yongqing Ni. "Identification and Characterization of a Novel Cold-Adapted GH15 Family Trehalase from the Psychrotolerant Microbacterium phyllosphaerae LW106." Fermentation 8, no. 10 (September 21, 2022): 471. http://dx.doi.org/10.3390/fermentation8100471.

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Psychrophiles inhabiting various cold environments are regarded as having evolved diverse physiological and molecular strategies, such as the accumulation of trehalose to alleviate cold stress. To investigate the possible contributions of trehalose metabolism-related enzymes to cold-adaption in psychrotrophic bacteria and enrich the resource bank of trehalose hydrolysis enzymes, a novel cold-adapted GH15 GA-like trehalase (MpTre15A) from psychrotolerant Microbacteriumphyllosphaerae LW106 isolated from glacier sediments was cloned and characterized. The recombinant MpTre15A from M. phyllosphaerae LW106 was expressed and purified in Escherichia coli BL21(DE3). The purified MpTre15A functioned as a hexamer and displayed maximal activity at pH 5.0 and 50 °C. Substrate specificity assay proved MpTre15A only showed hydrolytic activity toward α,α-trehalose. Site-directed mutation verified the key catalytic sites of Glu392 and Glu557 in MpTre15A. The kcat and kcat/Km values of MpTre15A at 4 °C (104.50 s−1 and 1.6 s−1 mM−1, respectively) were comparable to those observed for thermophilic GH15 trehalases at 50 °C, revealing its typical cold-adaptability. MpTre15A showed a trehalose conversion rate of 100% and 99.4% after 10 min and 15 min of incubation at 50 °C and 37 °C, respectively. In conclusion, this novel cold-adapted α,α-trehalase MpTre15A showed potential application for developing therapeutic enzymes, enzyme-based biosensors, and enzyme additives in the fermentation industry.

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Huyen, Do Thi, Nguyen Minh Giang, Nguyen Thu Nguyet, and Truong Nam Hai. "Probe design for mining and selection of genes coding endo 1- 4 xylanase from dna metagenome data." TAP CHI SINH HOC 40, no. 1 (January 25, 2018): 39–50. http://dx.doi.org/10.15625/0866-7160/v40n1.9200.

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According to the CAZY classification, endo 1- 4 xylanase belongs to GH 5, 8, 10, 11, 30, 51, 98. However only 03 sequences of GH8, 27 sequences of GH10, 18 sequence of GH11, only one sequence of each GH30 and GH51 from CAZy and NCBI database were thouroughly experimentally studied for biological activity and characteristics of the enzyme. Through the collected sequences, two probes for endo 1- 4 xylanase of GH10 and GH11 were designed, based on the sequence homology. The GH10 probe was 338 amino acids lenghth contained all the conserved amino acid residues (16 conserved residues in all sequences, 13 residues similar in almost sequences, 14 residues conserved in many sequences) with the lowest maxscore of 189, coverage of 88% and identity of 39%. The GH11 probe was 204 amino acids contained all the conserved amino acid residues (54 conserved residues were identity in all sequences, 25 residues similar in almost sequences, 24 residues conserved in many sequences) with the lowest maxscore of 165, coverage of 84% and identity of 50%. Using the two probes, we mined only one sequence (GL0018509) for endo 1- 4 xylanase from metagenomic DNA data of free-living bacteria in Coptotermes termite gut. Prediction of three-dimention structure of GL0018509 sequence by Phyre2 and Swiss Prot showed that this sequence was high similarity (95% by Phyre2 and 93,4% by Swiss Prot) with endo 1- 4 xylanase with the 100% confidence.

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Wu, Xiaofeng, Chijioke O. Elekwachi, Shiping Bai, Yuheng Luo, Keying Zhang, and Robert J. Forster. "Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics." Microorganisms 10, no. 1 (December 30, 2021): 71. http://dx.doi.org/10.3390/microorganisms10010071.

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Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

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Song, Jun, Feifei Xia, Haiyan Jiang, Xinwei Li, Liyuan Hu, Pengjuan Gong, Liancheng Lei, et al. "Identification and characterization of HolGH15: the holin of Staphylococcus aureus bacteriophage GH15." Journal of General Virology 97, no. 5 (May 1, 2016): 1272–81. http://dx.doi.org/10.1099/jgv.0.000428.

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Sawhney, Neha, Casey Crooks, Franz St. John, and James F. Preston. "Transcriptomic Analysis of Xylan Utilization Systems in Paenibacillus sp. Strain JDR-2." Applied and Environmental Microbiology 81, no. 4 (December 19, 2014): 1490–501. http://dx.doi.org/10.1128/aem.03523-14.

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ABSTRACTXylans, including methylglucuronoxylans (MeGXn) and methylglucuronoarabinoxylans (MeGAXn), are the predominant polysaccharides in hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals.Paenibacillussp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGXnand MeGAXnand assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cell-associated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) transporters, an intracellular GH67 α-glucuronidase, and other glycoside hydrolases contributes to complete metabolism. This GH10/GH67 system has been proposed to account for preferential utilization of xylans compared to free oligo- and monosaccharides. To identify additional genes contributing to MeGXnand MeGAXnutilization, the transcriptome of Pjdr2 has been sequenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with different substrates identified pathways common or unique to the utilization of MeGXnor MeGAXn. Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 endoxylanase and a GH115 α-glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Elevated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAXnbut not on MeGXnsupports a process in which arabinose may be removed extracellularly followed by its rapid assimilation. Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems into fermentative strains of related bacteria may lead to biocatalysts for consolidated bioprocessing of hemicelluloses released from lignocellulose.

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Merkel, Seth T., Emily J. Pritchett, and Bryan H. Fong. "Randomized Benchmarking as Convolution: Fourier Analysis of Gate Dependent Errors." Quantum 5 (November 16, 2021): 581. http://dx.doi.org/10.22331/q-2021-11-16-581.

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We show that the Randomized Benchmarking (RB) protocol is a convolution amenable to Fourier space analysis. By adopting the mathematical framework of Fourier transforms of matrix-valued functions on groups established in recent work from Gowers and Hatami \cite{GH15}, we provide an alternative proof of Wallman's \cite{Wallman2018} and Proctor's \cite{Proctor17} bounds on the effect of gate-dependent noise on randomized benchmarking. We show explicitly that as long as our faulty gate-set is close to the targeted representation of the Clifford group, an RB sequence is described by the exponential decay of a process that has exactly two eigenvalues close to one and the rest close to zero. This framework also allows us to construct a gauge in which the average gate-set error is a depolarizing channel parameterized by the RB decay rates, as well as a gauge which maximizes the fidelity with respect to the ideal gate-set.

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Weon, Hang-Yeon, Byung-Yong Kim, Youn-Kyung Baek, Seung-Hee Yoo, Soon-Wo Kwon, Erko Stackebrandt, and Seung-Joo Go. "Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils." International Journal of Systematic and Evolutionary Microbiology 56, no. 5 (May 1, 2006): 947–51. http://dx.doi.org/10.1099/ijs.0.64095-0.

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Two bacterial strains were isolated from greenhouse soils of Daejeon and Yangpyeong regions in Korea. The strains, designated GH1-9T and GH19-3T, were Gram-negative and aerobic, with rod-shaped cells. Their DNA G+C contents were 61.7 and 67.3 mol%, respectively. The major fatty acids of strain GH1-9T were iso-C16 : 0, iso-C15 : 0, iso-C14 : 0, iso-C17 : 1 ω9c and iso-C11 : 0 3-OH and the major components of strain GH19-3T were iso-C16 : 0, iso-C15 : 0, C16 : 1 ω7c alcohol, iso-C17 : 1 ω9c and iso-C11 : 0 3-OH. None of the species of the genus Lysobacter with validly published names showed 16S rRNA gene sequence similarity values of more than 97 % with respect to the novel isolates. The closest sequence similarity of strain GH1-9T was with Lysobacter concretionis DSM 16239T (96.4 %), whereas strain GH19-3T showed the highest sequence similarity with Lysobacter enzymogenes DSM 2043T (96.6 %). Polyphasic taxonomic studies indicated that the two strains should be classified as representing novel members of the genus Lysobacter. The names Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov. are proposed, with strains GH1-9T (=KACC 11406T=DSM 17634T) and GH19-3T (=KACC 11407T=DSM 17635T), respectively, as the type strains.

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Hori, Chiaki, Jill Gaskell, Kiyohiko Igarashi, Phil Kersten, Michael Mozuch, Masahiro Samejima, and Dan Cullen. "Temporal Alterations in the Secretome of the Selective Ligninolytic Fungus Ceriporiopsis subvermispora during Growth on Aspen Wood Reveal This Organism's Strategy for Degrading Lignocellulose." Applied and Environmental Microbiology 80, no. 7 (January 17, 2014): 2062–70. http://dx.doi.org/10.1128/aem.03652-13.

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ABSTRACTThe white-rot basidiomycetes efficiently degrade all wood cell wall polymers. Generally, these fungi simultaneously degrade cellulose and lignin, but certain organisms, such asCeriporiopsis subvermispora, selectively remove lignin in advance of cellulose degradation. However, relatively little is known about the mechanism of selective ligninolysis. To address this issue,C. subvermisporawas grown in liquid medium containing ball-milled aspen, and nano-liquid chromatography-tandem mass spectrometry was used to identify and estimate extracellular protein abundance over time. Several manganese peroxidases and an aryl alcohol oxidase, both associated with lignin degradation, were identified after 3 days of incubation. A glycoside hydrolase (GH) family 51 arabinofuranosidase was also identified after 3 days but then successively decreased in later samples. Several enzymes related to cellulose and xylan degradation, such as GH10 endoxylanase, GH5_5 endoglucanase, and GH7 cellobiohydrolase, were detected after 5 days. Peptides corresponding to potential cellulose-degrading enzymes GH12, GH45, lytic polysaccharide monooxygenase, and cellobiose dehydrogenase were most abundant after 7 days. This sequential production of enzymes provides a mechanism consistent with selective ligninolysis byC. subvermispora.

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Waghmare, Pratima, Nuo Xu, Pankajkumar Waghmare, Guodong Liu, Yinbo Qu, Xuezhi Li, and Jian Zhao. "Production and Characterization of Cellulose Nanocrystals from Eucalyptus Dissolving Pulp Using Endoglucanases from Myceliophthora thermophila." International Journal of Molecular Sciences 24, no. 13 (June 26, 2023): 10676. http://dx.doi.org/10.3390/ijms241310676.

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Endoglucanase (EG) is a key enzyme during enzymatic preparation of cellulose nanocrystals (CNCs). Myceliophthora thermophila is a thermophilic fungus that has thermal properties and a high secretion of endoglucanases (EGs), and could serve as potential sources of EGs for the preparation of CNCs. In this work, four different GH families (GH5, GH7, GH12, and GH45) of EGs from M. thermophila were expressed and purified, and their enzymatic characteristics and feasibility of application in CNC preparation were investigated. It was shown that the MtEG5A from M. thermophila has good potential in the enzymatic preparation of CNCs using eucalyptus dissolving pulp as feedstock. It was also observed that there was a synergistic effect between the MtEG5A and other MtEGs in the preparation of CNCs, which improved the yield and properties of CNCs obtained by enzymatic hydrolysis. This study provides a reference for understanding the enzymatic characteristics of different families of EGs from M. thermophile and their potential application in nanocellulose production.

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Pervez, Sidra, Afsheen Aman, and Shah Ali Ul Qader. "Role of two polysaccharide matrices on activity, stability and recycling efficiency of immobilized fungal amyloglucosidase of GH15 family." International Journal of Biological Macromolecules 96 (March 2017): 70–77. http://dx.doi.org/10.1016/j.ijbiomac.2016.12.023.

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Vlădoiu, Diana Larisa, Marioara Nicoleta Filimon, Vasile Ostafe, and Adriana Isvoran. "Effects Of Herbicides And Fungicides On The Soil Chitinolytic Activity. A Molecular Docking Approach." Ecological Chemistry and Engineering S 22, no. 3 (September 1, 2015): 439–50. http://dx.doi.org/10.1515/eces-2015-0025.

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Abstract A molecular docking study was undertaken using the programs SwissDock and PatchDock to assess the interactions of the bacterial chitinases belonging to the GH18 and GH19 families with two herbicides (chlorsulfuron and nicosulfuron) and two fungicides (difenoconazole and drazoxolon). Both molecular docking programs predict that all considered pesticides bind to the active sites of chitinases produced by soil microorganisms. There are correlations for predicted binding energy values for receptor-ligand complexes obtained using the two programs consolidating the prediction of the chitinases-pesticides interactions. The interactions of chitinases with pesticides involve the same residues as their interactions with known inhibitors suggesting the inhibitory potential of pesticides. Pesticides interact stronger with chitinases belonging to the GH18 family, their active sites reflecting higher polarity than those of the GH19 chitinases. Also, herbicides reveal a higher inhibitory potential to bacterial chitinases than fungicides.

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Trong Khoa, Dao, Do Thi Huyen, and Truong Nam Hai. "Probe-mining of endo-1,4-beta-xylanase from goats-rumen bacterial metagenomic DNA data." Vietnam Journal of Biotechnology 19, no. 3 (October 13, 2021): 519–28. http://dx.doi.org/10.15625/1811-4989/16632.

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Endo-1,4-beta-xylanases (xylanases) are classified into 9 glycoside hydrolase families, GH5, 8, 10, 11, 30, 43, 51, 98, and 141 based on the CAZy database. The probe sequences representing the enzymes were constructed from published sequences of actual experimental studies with xylan decomposition activity. From online databases, we found one sequence belonging to the GH5 family, 6 sequences belonging to the GH8 family and 5 sequences belonging to the GH30 family exhibiting xylanase activity. Thus specific probes for xylanase GH8 and GH30 families were designed with the length of 351 and 425 amino acids respectively. The reference values for the probe of the GH8 family were defined as the sequences with maximum score greater than 168, the lowest coverage was 84%, the lowest similarity was 36%; for the probe GH30, the maximum score was greater than 316, the coverage was greater than 98%, the similarity was greater than 41%. Using the built probes, including the probe of the two GH10 and GH11 families, we found 41 xylanase-encoding sequences from the metagenomic DNA data of bacteria in Vietnamese goats’rumen. Of the 41 exploited sequences, 19 were identical to the BGI company's annotation result based on KEGG database, whereas there were 16 sequences that are not annotated by the BGI company. Total 28 of 41 exploited sequences were complete open reading frames, of which the predicted ternary structure was highly similar to the published structures of xylanase.

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Sawhney, Neha, and James F. Preston. "GH51 Arabinofuranosidase and Its Role in the Methylglucuronoarabinoxylan Utilization System in Paenibacillus sp. Strain JDR-2." Applied and Environmental Microbiology 80, no. 19 (July 25, 2014): 6114–25. http://dx.doi.org/10.1128/aem.01684-14.

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ABSTRACTMethylglucuronoarabinoxylan (MeGAXn) from agricultural residues and energy crops is a significant yet underutilized biomass resource for production of biofuels and chemicals. Mild thermochemical pretreatment of bagasse yields MeGAXnrequiring saccharifying enzymes for conversion to fermentable sugars. A xylanolytic bacterium,Paenibacillussp. strain JDR-2, produces an extracellular cell-associated GH10 endoxylanse (XynA1) which efficiently depolymerizes methylglucuronoxylan (MeGXn) from hardwoods coupled with assimilation of oligosaccharides for further processing by intracellular GH67 α-glucuronidase, GH10 endoxylanase, and GH43 β-xylosidase. This process has been ascribed to genes that comprise a xylan utilization regulon that encodes XynA1and includes a gene cluster encoding transcriptional regulators, ABC transporters, and intracellular enzymes that convert assimilated oligosaccharides to fermentable sugars. Here we show thatPaenibacillussp. JDR-2 utilized MeGAXnwithout accumulation of oligosaccharides in the medium. ThePaenibacillussp. JDR-2 growth rate on MeGAXnwas 3.1-fold greater than that on oligosaccharides generated from MeGAXnby XynA1. Candidate genes encoding GH51 arabinofuranosidases with potential roles were identified. Following growth on MeGAXn, quantitative reverse transcription-PCR identified a cluster of genes encoding a GH51 arabinofuranosidase (AbfB) and transcriptional regulators which were coordinately expressed along with the genes comprising the xylan utilization regulon. The action of XynA1on MeGAXngenerated arabinoxylobiose, arabinoxylotriose, xylobiose, xylotriose, and methylglucuronoxylotriose. Recombinant AbfB processed arabinoxylooligosaccharides to xylooligosaccharides and arabinose. MeGAXnprocessing byPaenibacillussp. JDR-2 may be achieved by extracellular depolymerization by XynA1coupled to assimilation of oligosaccharides and further processing by intracellular enzymes, including AbfB.Paenibacillussp. JDR-2 provides a GH10/GH67 system complemented with genes encoding intracellular GH51 arabinofuranosidases for efficient utilization of MeGAXn.

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Pervez, Sidra, Muhammad Asif Nawaz, Afsheen Aman, Sadia Qayyum, Faiza Nawaz, and Shah Ali Ul Qader. "Agarose Hydrogel Beads: An Effective Approach to Improve the Catalytic Activity, Stability and Reusability of Fungal Amyloglucosidase of GH15 Family." Catalysis Letters 148, no. 9 (June 20, 2018): 2643–53. http://dx.doi.org/10.1007/s10562-018-2460-y.

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KIRKWOOD, R. N., P. A. THACKER, B. L. GUEDO, and B. LAARVELD. "THE EFFECT OF EXOGENOUS GROWTH HORMONE ON THE ENDOCRINE STATUS AND THE OCCURRENCE OF ESTRUS IN GILTS." Canadian Journal of Animal Science 69, no. 4 (December 1, 1989): 931–37. http://dx.doi.org/10.4141/cjas89-107.

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Fifty-six gilts of Yorkshire and Landrace breeding were selected at 86.8 ± 0.8 kg body weight (BW) and given an intramuscular (im) injection of 400 IU PMSG plus 200 IU hCG to stimulate ovulation. From 14 d after gonadotropic stimulation, gilts were exposed to a boar to detect a subsequent spontaneous estrus. At the onset of this first observed estrus, gilts were allocated to receive daily injections (i.m.) of growth hormone (pGH, 90 μg kg−1) from either 14 d (GH14, n = 21) or 17 d (GH17, n = 20) until 22 d after the onset of the first observed estrus. A third group of gilts served as controls (n = 15) and received vehicle buffer. Blood samples were obtained by jugular vein puncture at 3-d intervals from 14 to 29 d, inclusively. Gilts were slaughtered 30–32 d after the first observed estrus at which time their ovaries were recovered for the determination of ovulation rates. All control gilts and all but one GH17 gilt exhibited normal estrous cycles. However, of the 21 gilts assigned to GH14, only 9 (43%) had normal estrous cycles (P < 0.001). In gilts exhibiting a second estrus, there was no effect of pGH treatment on the duration of the estrous cycle (20.4, 20.9 and 20.5 d) or on ovulation rate (14.6, 13.9 and 13.5) for GH14, GH17 and controls, respectively. Serum assays revealed that pGH injections resulted in decreased serum concentrations of thyroxine (P < 0.01) but increased concentrations of triiodothyronine, insulin and glucose (P < 0.001). The present data confirm an adverse effect of pGH on ovarian function. However, the adverse effect is only evident when the pGH injection regime encompasses days 14–16 of the estrous cycle. Key words: Gilts, growth hormone, estrus, ovulation rate

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Curiel, José Antonio, Ángela Peirotén, José María Landete, Ana Ruiz de la Bastida, Susana Langa, and Juan Luis Arqués. "Architecture Insight of Bifidobacterial α-L-Fucosidases." International Journal of Molecular Sciences 22, no. 16 (August 6, 2021): 8462. http://dx.doi.org/10.3390/ijms22168462.

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Fucosylated carbohydrates and glycoproteins from human breast milk are essential for the development of the gut microbiota in early life because they are selectively metabolized by bifidobacteria. In this regard, α-L-fucosidases play a key role in this successful bifidobacterial colonization allowing the utilization of these substrates. Although a considerable number of α-L-fucosidases from bifidobacteria have been identified by computational analysis, only a few of them have been characterized. Hitherto, α-L-fucosidases are classified into three families: GH29, GH95, and GH151, based on their catalytic structure. However, bifidobacterial α-L-fucosidases belonging to a particular family show significant differences in their sequence. Because this fact could underlie distinct phylogenetic evolution, here extensive similarity searches and comparative analyses of the bifidobacterial α-L-fucosidases identified were carried out with the assistance of previous physicochemical studies available. This work reveals four and two paralogue bifidobacterial fucosidase groups within GH29 and GH95 families, respectively. Moreover, Bifidobacterium longum subsp. infantis species exhibited the greatest number of phylogenetic lineages in their fucosidases clustered in every family: GH29, GH95, and GH151. Since α-L-fucosidases phylogenetically descended from other glycosyl hydrolase families, we hypothesized that they could exhibit additional glycosidase activities other than fucosidase, raising the possibility of their application to transfucosylate substrates other than lactose in order to synthesis novel prebiotics.

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Ratnasari, Agnes, Efri Efri, Muhammad Syamsoel Hadi, and Hasriadi Mat Akin. "KETAHANAN BEBERAPA GENOTIPE SORGUM (Sorghum bicolor [L]Moench) TERHADAP PENYAKIT ANTRAKNOSA (Colletotrichum graminicola) PADA DUA SISTEM POLA TANAM BERBEDA." Jurnal Agrotek Tropika 7, no. 2 (May 3, 2019): 351. http://dx.doi.org/10.23960/jat.v7i2.3258.

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Tujuan penelitian ini yaitu mengetahui ketahanan 15 genotipe sorgum yang ditanam pada dua sistem tanam berbeda yaitu monokultur dan tumpangsari. Penelitian ini dilaksanakan pada bulan April 2017- Februari 2018 di Desa Sukanegara, Kecamatan Tanjung Bintang, Kabupaten Lampung Selatan, Lampung dan di Laboratorium Hama dan Penyakit Tanaman Fakultas Pertanian Universitas Lampung. Perlakuan disusunmenggunakan rancangan acak kekompok dalam Split Plot Design dengan faktor utama adalah sistem pola tanam (tumpangsari, monokultur), dan anak petak adalah 15 genotipe sorgum (Numbu, Samurai 1, GH3, UPCA, GH4, P/I WHP, GH6, Super 2, GH13, P/F 51-93-C, Super 1, GH5, Mandau, GH7 dan TalagaBodas). Monokultur sorgum ditanam pada jarak 80 cm x 20 cm. Tumpangsari sorgum ubikayu dilakukan dengan cara menanam sorgum di antara tanaman ubikayusehingga jarak tanam sorgum tetap 80 cm x 20 cm, sedangkan jarak tanam ubikayu 80 cm x 60 cm, baik sorgum maupun ubikayu ditanam secara bersamaan. Hasil penelitian menunjukkan bahwa sistem tanam tumpangsari lebih efektif untuk menekan intensitas penyakit antraknosa. Pada penelitian ini intensitas penyakit antraknosa terhadap 15 genotipe sorgum yang diamati dikelompokan menjadi 3 kategori yaitu tinggi, sedang dan rendah. Genotipe Numbu, GH3, Talaga Bodas, Super 1, dan Mandau adalah genotipe dengan intensitas penyaki terendah dibandingkan genotipe Samurai 1, UPCA, GH4, P/I WHP, GH13, P/F 5-193-C, GH5, GH6 dan GH7 . Genotipe Samurai 1, UPCA, GH4, P/I WHP, GH13, P/F 5-193-C, GH5, GH6 dan GH7 adalah genotipe yang intensitas penyakitnya lebih rendah dibandingkan genotipe Super 2. Dan genotipe Super 2 adalah genotipe dengan intnsitas penyakit antraknosa tertinggi.

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Wang, Xiyan, Thomas Isbrandt, Mikael Lenz Strube, Sara Skøtt Paulsen, Maike Wennekers Nielsen, Yannick Buijs, Erwin M. Schoof, Thomas Ostenfeld Larsen, Lone Gram, and Sheng-Da Zhang. "Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059." Marine Drugs 19, no. 2 (February 12, 2021): 108. http://dx.doi.org/10.3390/md19020108.

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Genome mining of pigmented Pseudoalteromonas has revealed a large potential for the production of bioactive compounds and hydrolytic enzymes. The purpose of the present study was to explore this bioactivity potential in a potent antibiotic and enzyme producer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXchange with identifier PXD023249) indicated that a highly efficient chitin degradation machinery was present in the red-pigmented P. rubra S4059 when grown on chitin. Four GH18 chitinases and two GH20 hexosaminidases were significantly upregulated under these conditions. GH19 chitinases, which are not common in bacteria, are consistently found in pigmented Pseudoalteromonas, and in S4059, GH19 was only detected when the bacterium was grown on chitin. To explore the possible role of GH19 in pigmented Pseudoalteromonas, we developed a protocol for genetic manipulation of S4059 and deleted the GH19 chitinase, and compared phenotypes of the mutant and wild type. However, none of the chitin degrading ability, secondary metabolite profile, or biofilm-forming capacity was affected by GH19 deletion. In conclusion, we developed a genetic manipulation protocol that can be used to unravel the bioactive potential of pigmented pseudoalteromonads. An efficient chitinolytic enzyme cocktail was identified in S4059, suggesting that this strain could be a candidate with industrial potential.

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Xia, Feifei, Xin Li, Bin Wang, Pengjuan Gong, Feng Xiao, Mei Yang, Lei Zhang, et al. "Combination Therapy of LysGH15 and Apigenin as a New Strategy for Treating Pneumonia Caused by Staphylococcus aureus." Applied and Environmental Microbiology 82, no. 1 (October 16, 2015): 87–94. http://dx.doi.org/10.1128/aem.02581-15.

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ABSTRACTPneumonia is one of the most prevalentStaphylococcus aureus-mediated diseases, and the treatment of this infection is becoming challenging due to the emergence of multidrug-resistantS. aureus, especially methicillin-resistantS. aureus(MRSA) strains. It has been reported that LysGH15, the lysin derived from phage GH15, displays high efficiency and a broad lytic spectrum against MRSA and that apigenin can markedly diminish the alpha-hemolysin ofS. aureus. In this study, the combination therapy of LysGH15 and apigenin was evaluatedin vitroand in a mouseS. aureuspneumonia model. No mutual adverse influence was detected between LysGH15 and apigeninin vitro. In animal experiments, the combination therapy showed a more effective treatment effect than LysGH15 or apigenin monotherapy (P< 0.05). The bacterial load in the lungs of mice administered the combination therapy was 1.5 log units within 24 h after challenge, whereas the loads in unprotected mice or mice treated with apigenin or LysGH15 alone were 10.2, 4.7, and 2.6 log units, respectively. The combination therapy group showed the best health status, the lowest ratio of wet tissue to dry tissue of the lungs, the smallest amount of total protein and cells in the lung, the fewest pathological manifestations, and the lowest cytokine level compared with the other groups (P< 0.05). With regard to its better protective efficacy, the combination therapy of LysGH15 and apigenin exhibits therapeutic potential for treating pneumonia caused by MRSA. This paper reports the combination therapy of lysin and natural products derived from traditional Chinese medicine.

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Chow, Virginia, Young Sik Kim, Mun Su Rhee, Neha Sawhney, Franz J. St. John, Guang Nong, John D. Rice, and James F. Preston. "A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2." Applied and Environmental Microbiology 82, no. 6 (January 8, 2016): 1789–98. http://dx.doi.org/10.1128/aem.03526-15.

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ABSTRACTPaenibacillussp. strain JDR-2 (PaenibacillusJDR-2) secretes a multimodular cell-associated glycoside hydrolase family 10 (GH10) endoxylanase (XynA10A1) that catalyzes the depolymerization of methylglucuronoxylan (MeGXn) and rapidly assimilates the products of depolymerization. Efficient utilization of MeGXnhas been postulated to result from the coupling of the processes of exocellular depolymerization and assimilation of oligosaccharide products, followed by intracellular metabolism. Growth and substrate utilization patterns with barley glucan and laminarin similar to those observed with MeGXnas a substrate suggest similar processes for 1,3-1,4-β-glucan and 1,3-β-glucan depolymerization and product assimilation. ThePaenibacillusJDR-2 genome includes a cluster of genes encoding a secreted multimodular GH16 β-glucanase (Bgl16A1) containing surface layer homology (SLH) domains, a secreted GH16 β-glucanase with only a catalytic domain (Bgl16A2), transporter proteins, and transcriptional regulators. Recombinant Bgl16A1and Bgl16A2catalyze the formation of trisaccharides, tetrasaccharides, and larger oligosaccharides from barley glucan and of mono-, di-, tri-, and tetrasaccharides and larger oligosaccharides from laminarin. The lack of accumulation of depolymerization products during growth and a marked preference for polymeric glucan over depolymerization products support a process coupling extracellular depolymerization, assimilation, and intracellular metabolism for β-glucans similar to that ascribed to the GH10/GH67 xylan utilization system inPaenibacillusJDR-2. Coordinate expression of genes encoding GH16 β-glucanases, transporters, and transcriptional regulators supports their role as a regulon for the utilization of soluble β-glucans. As in the case of the xylan utilization regulons, this soluble β-glucan regulon provides advantages in the growth rate and yields on polymeric substrates and may be exploited for the efficient conversion of plant-derived polysaccharides to targeted products.

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Master, Emma R., Yun Zheng, Reginald Storms, Adrian Tsang, and Justin Powlowski. "A xyloglucan-specific family 12 glycosyl hydrolase from Aspergillus niger: recombinant expression, purification and characterization." Biochemical Journal 411, no. 1 (March 13, 2008): 161–70. http://dx.doi.org/10.1042/bj20070819.

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A new GH12 (glycosyl hydrolase 12) family XEG [xyloglucan-specific endo-β-1,4-glucanase (EC 3.2.1.151)] from Aspergillus niger, AnXEG12A, was overexpressed, purified and characterized. Whereas seven xyloglucanases from GH74 and two xyloglucanases from GH5 have been characterized previously, this is only the third characterized example of a GH12 family xyloglucanase. GH12 enzymes are structurally and mechanistically distinct from GH74 enzymes. Although over 100 GH12 sequences are now available, little is known about the structural and biochemical bases of xyloglucan binding and hydrolysis by GH12 enzymes. Comparison of the AnXEG12A cDNA sequence with the genome sequence of A. niger showed the presence of two introns, one in the coding region and the second one in the 333-nt-long 3′-untranslated region of the transcript. The enzyme was expressed recombinantly in A. niger and was readily purified from the culture supernatant. The isolated enzyme appeared to have been processed by a kexin-type protease, which removed a short prosequence. The substrate specificity was restricted to xyloglucan, with cleavage at unbranched glucose in the backbone. The apparent kinetic parameters were similar to those reported for other xyloglucan-degrading endoglucanases. The pH optimum (5.0) and temperature resulting in highest enzyme activity (50–60 °C) were higher than those reported for a GH12 family xyloglucanase from Aspergillus aculeatus, but similar to those of cellulose-specific endoglucanases from the GH12 family. Phylogenetic, sequence and structural comparisons of GH12 family endoglucanases helped to delineate features that appear to be correlated to xyloglucan specificity.

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Gullfot, Fredrika, Farid M. Ibatullin, Gustav Sundqvist, Gideon J. Davies, and Harry Brumer. "Functional Characterization of Xyloglucan Glycosynthases from GH7, GH12, and GH16 Scaffolds." Biomacromolecules 10, no. 7 (July 13, 2009): 1782–88. http://dx.doi.org/10.1021/bm900215p.

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Badur, Ahmet H., Ehab M. Ammar, Geethika Yalamanchili, Jan-Hendrik Hehemann, and Christopher V. Rao. "Characterization of the GH16 and GH17 laminarinases from Vibrio breoganii 1C10." Applied Microbiology and Biotechnology 104, no. 1 (November 21, 2019): 161–71. http://dx.doi.org/10.1007/s00253-019-10243-0.

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Liu, Liangwei, Xiaofeng Sun, Pengfei Yan, Linmin Wang, and Hongge Chen. "Non-Structured Amino-Acid Impact on GH11 Differs from GH10 Xylanase." PLoS ONE 7, no. 9 (September 21, 2012): e45762. http://dx.doi.org/10.1371/journal.pone.0045762.

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Meng, Dong-Dong, Yu Ying, Xiao-Hua Chen, Ming Lu, Kang Ning, Lu-Shan Wang, and Fu-Li Li. "Distinct Roles for Carbohydrate-Binding Modules of Glycoside Hydrolase 10 (GH10) and GH11 Xylanases from Caldicellulosiruptor sp. Strain F32 in Thermostability and Catalytic Efficiency." Applied and Environmental Microbiology 81, no. 6 (January 9, 2015): 2006–14. http://dx.doi.org/10.1128/aem.03677-14.

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ABSTRACTXylanases are crucial for lignocellulosic biomass deconstruction and generally contain noncatalytic carbohydrate-binding modules (CBMs) accessing recalcitrant polymers. Understanding how multimodular enzymes assemble can benefit protein engineering by aiming at accommodating various environmental conditions. Two multimodular xylanases, XynA and XynB, which belong to glycoside hydrolase families 11 (GH11) and GH10, respectively, have been identified fromCaldicellulosiruptorsp. strain F32. In this study, both xylanases and their truncated mutants were overexpressed inEscherichia coli, purified, and characterized. GH11 XynATM1 lacking CBM exhibited a considerable improvement in specific activity (215.8 U nmol−1versus 94.7 U nmol−1) and thermal stability (half-life of 48 h versus 5.5 h at 75°C) compared with those of XynA. However, GH10 XynB showed higher enzyme activity and thermostability than its truncated mutant without CBM. Site-directed mutagenesis of N-terminal amino acids resulted in a mutant, XynATM1-M, with 50% residual activity improvement at 75°C for 48 h, revealing that the disordered region influenced protein thermostability negatively. The thermal stability of both xylanases and their truncated mutants were consistent with their melting temperature (Tm), which was determined by using differential scanning calorimetry. Through homology modeling and cross-linking analysis, we demonstrated that for XynB, the resistance against thermoinactivation generally was enhanced through improving both domain properties and interdomain interactions, whereas for XynA, no interdomain interactions were observed. Optimized intramolecular interactions can accelerate thermostability, which provided microbes a powerful evolutionary strategy to assemble catalysts that are adapted to various ecological conditions.

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Malgas, Samkelo, Mpho S. Mafa, Brian N. Mathibe, and Brett I. Pletschke. "Unraveling Synergism between Various GH Family Xylanases and Debranching Enzymes during Hetero-Xylan Degradation." Molecules 26, no. 22 (November 9, 2021): 6770. http://dx.doi.org/10.3390/molecules26226770.

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Enzymes classified with the same Enzyme Commission (EC) that are allotted in different glycoside hydrolase (GH) families can display different mechanisms of action and substrate specificities. Therefore, the combination of different enzyme classes may not yield synergism during biomass hydrolysis, as the GH family allocation of the enzymes influences their behavior. As a result, it is important to understand which GH family combinations are compatible to gain knowledge on how to efficiently depolymerize biomass into fermentable sugars. We evaluated GH10 (Xyn10D and XT6) and GH11 (XynA and Xyn2A) β-xylanase performance alone and in combination with various GH family α-l-arabinofuranosidases (GH43 AXH-d and GH51 Abf51A) and α-d-glucuronidases (GH4 Agu4B and GH67 AguA) during xylan depolymerization. No synergistic enhancement in reducing sugar, xylose and glucuronic acid released from beechwood xylan was observed when xylanases were supplemented with either one of the glucuronidases, except between Xyn2A and AguA (1.1-fold reducing sugar increase). However, overall sugar release was significantly improved (≥1.1-fold reducing sugar increase) when xylanases were supplemented with either one of the arabinofuranosidases during wheat arabinoxylan degradation. Synergism appeared to result from the xylanases liberating xylo-oligomers, which are the preferred substrates of the terminal arabinofuranosyl-substituent debranching enzyme, Abf51A, allowing the exolytic β-xylosidase, SXA, to have access to the generated unbranched xylo-oligomers. Here, it was shown that arabinofuranosidases are key enzymes in the efficient saccharification of hetero-xylan into xylose. This study demonstrated that consideration of GH family affiliations of the carbohydrate-active enzymes (CAZymes) used to formulate synergistic enzyme cocktails is crucial for achieving efficient biomass saccharification.

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Abedi, Ehsan, Fataneh Fatemi, Yahya Sefidbakht, and Seyed Ehsan Ranaei Siadat. "Development and characterization of a thermostable GH11/GH10 xylan degrading chimeric enzyme." Enzyme and Microbial Technology 149 (September 2021): 109854. http://dx.doi.org/10.1016/j.enzmictec.2021.109854.

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Ghio, Silvina, Ornella Ontañon, Florencia E. Piccinni, Rubén Marrero Díaz de Villegas, Paola Talia, Daniel H. Grasso, and Eleonora Campos. "Paenibacillus sp. A59 GH10 and GH11 Extracellular Endoxylanases: Application in Biomass Bioconversion." BioEnergy Research 11, no. 1 (December 6, 2017): 174–90. http://dx.doi.org/10.1007/s12155-017-9887-7.

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Abstract The cost-efficient degradation of xylan to fermentable sugars is of particular interest in second generation bioethanol production, feed, food, and pulp and paper industries. Multiple potentially secreted enzymes involved in polysaccharide deconstruction are encoded in the genome of Paenibacillus sp. A59, a xylanolytic soil bacterium, such as three endoxylanases, seven GH43 β-xylosidases, and two GH30 glucuronoxylanases. In secretome analysis of xylan cultures, ten glycoside hydrolases were identified, including the three predicted endoxylanases, confirming their active role. The two uni-modular xylanases, a 32-KDa GH10 and a 20-KDa GH11, were recombinantly expressed and their activity on xylan was confirmed (106 and 85 IU/mg, respectively), with differences in their activity pattern. Both endoxylanases released mainly xylobiose (X2) and xylotriose (X3) from xylan and pre-treated biomasses (wheat straw, barley straw, and sweet corn cob), although only rGH10XynA released xylose (X1). rGH10XynA presented optimal conditions at pH 6, with thermal stability at 45–50 °C, while rGH11XynB showed activity in a wider range of pH, from 5 to 9, and was thermostable only at 45 °C. Moreover, GH11XynB presented sigmoidal kinetics on xylan, indicating possible cooperative binding, which was further supported by the structural model. This study provides a detailed analysis of the complete set of carbohydrate-active enzymes encoded in Paenibacillus sp. A59 genome and those effectively implicated in hemicellulose hydrolysis, contributing to understanding the mechanisms necessary for the bioconversion of this polysaccharide. Moreover, the two main free secreted xylanases, rGH10XynA and rGH11XynB, were fully characterized, supporting their potential application in industrial bioprocesses on lignocellulosic biomass.

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Madan, Bharat, and Sun-Gu Lee. "Sequence and Structural Features of Subsite Residues in GH10 and GH11 Xylanases." Biotechnology and Bioprocess Engineering 23, no. 3 (June 2018): 311–18. http://dx.doi.org/10.1007/s12257-018-0105-z.

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Kim, Sung Kyum, Jong Eun Park, Jong Min Oh, and Hoon Kim. "Molecular Characterization of Four Alkaline Chitinases from Three Chitinolytic Bacteria Isolated from a Mudflat." International Journal of Molecular Sciences 22, no. 23 (November 26, 2021): 12822. http://dx.doi.org/10.3390/ijms222312822.

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Four chitinases were cloned and characterized from three strains isolated from a mudflat: Aeromonas sp. SK10, Aeromonas sp. SK15, and Chitinibacter sp. SK16. In SK10, three genes, Chi18A, Pro2K, and Chi19B, were found as a cluster. Chi18A and Chi19B were chitinases, and Pro2K was a metalloprotease. With combinatorial amplification of the genes and analysis of the hydrolysis patterns of substrates, Chi18A and Chi19B were found to be an endochitinase and exochitinase, respectively. Chi18A and Chi19B belonged to the glycosyl hydrolase family 18 (GH18) and GH19, with 869 and 659 amino acids, respectively. Chi18C from SK15 belonged to GH18 with 864 amino acids, and Chi18D from SK16 belonged to GH18 with 664 amino acids. These four chitinases had signal peptides and high molecular masses with one or two chitin-binding domains and, interestingly, preferred alkaline conditions. In the activity staining, their sizes were determined to be 96, 74, 95, and 73 kDa, respectively, corresponding to their expected sizes. Purified Chi18C and Chi18D after pET expression produced N,N′-diacetylchitobiose as the main product in hydrolyzing chitooligosaccharides and colloidal chitin. These results suggest that Chi18A, Chi18C, and Chi18D are endochitinases, that Chi19B is an exochitinase, and that these chitinases can be effectively used for hydrolyzing natural chitinous sources.

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Gutiérrez, Diana, Dieter Vandenheuvel, Beatriz Martínez, Ana Rodríguez, Rob Lavigne, and Pilar García. "Two Phages, phiIPLA-RODI and phiIPLA-C1C, Lyse Mono- and Dual-Species Staphylococcal Biofilms." Applied and Environmental Microbiology 81, no. 10 (March 6, 2015): 3336–48. http://dx.doi.org/10.1128/aem.03560-14.

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ABSTRACTPhage therapy is a promising option for fighting against staphylococcal infections. Two lytic phages, vB_SauM_phiIPLA-RODI (phiIPLA-RODI) and vB_SepM_phiIPLA-C1C (phiIPLA-C1C), belonging to theMyoviridaefamily and exhibiting wide host ranges, were characterized in this study. The complete genome sequences comprised 142,348 bp and 140,961 bp and contained 213 and 203 open reading frames, respectively. The gene organization was typical ofSpounavirinaemembers, with long direct terminal repeats (LTRs), genes grouped into modules not clearly separated from each other, and several group I introns. In addition, four genes encoding tRNAs were identified in phiIPLA-RODI. Comparative DNA sequence analysis showed high similarities with two phages, GH15 and 676Z, belonging to theTwort-like virusgenus (nucleotide identities of >84%); for phiIPLA-C1C, a high similarity with phage phiIBB-SEP1 was observed (identity of 80%). Challenge assays of phages phiIPLA-RODI and phiIPLA-C1C against planktonic staphylococcal cells confirmed their lytic ability, as they were able to remove 5 log units in 8 h. Exposure of biofilms to phages phiIPLA-RODI and phiIPLA-C1C reduced the amount of adhered bacteria to about 2 log units in both monospecies and dual-species biofilms, but phiIPLA-RODI turned out to be as effective as the mixture of both phages. Moreover, the frequencies of bacteriophage-insensitive mutants (BIMs) ofStaphylococcus aureusandS. epidermidiswith resistance to phiIPLA-RODI and phiIPLA-C1C were low, at 4.05 × 10−7± 2.34 × 10−9and 1.1 × 10−7± 2.08 × 10−9, respectively. Overall, a generally reduced fitness in the absence of phages was observed for BIMs, which showed a restored phage-sensitive phenotype in a few generations. These results confirm that lytic bacteriophages can be efficient biofilm-disrupting agents, supporting their potential as antimicrobials against staphylococcal infections.

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Sabater, Carlos, Lorena Ruiz, and Abelardo Margolles. "A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium." Microorganisms 9, no. 5 (May 11, 2021): 1034. http://dx.doi.org/10.3390/microorganisms9051034.

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This study aimed to recover metagenome-assembled genomes (MAGs) from human fecal samples to characterize the glycosidase profiles of Bifidobacterium species exposed to different prebiotic oligosaccharides (galacto-oligosaccharides, fructo-oligosaccharides and human milk oligosaccharides, HMOs) as well as high-fiber diets. A total of 1806 MAGs were recovered from 487 infant and adult metagenomes. Unsupervised and supervised classification of glycosidases codified in MAGs using machine-learning algorithms allowed establishing characteristic hydrolytic profiles for B. adolescentis, B. bifidum, B. breve, B. longum and B. pseudocatenulatum, yielding classification rates above 90%. Glycosidase families GH5 44, GH32, and GH110 were characteristic of B. bifidum. The presence or absence of GH1, GH2, GH5 and GH20 was characteristic of B. adolescentis, B. breve and B. pseudocatenulatum, while families GH1 and GH30 were relevant in MAGs from B. longum. These characteristic profiles allowed discriminating bifidobacteria regardless of prebiotic exposure. Correlation analysis of glycosidase activities suggests strong associations between glycosidase families comprising HMOs-degrading enzymes, which are often found in MAGs from the same species. Mathematical models here proposed may contribute to a better understanding of the carbohydrate metabolism of some common bifidobacteria species and could be extrapolated to other microorganisms of interest in future studies.

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Xiao, Zhizhuang, Stephan Grosse, Hélène Bergeron, and Peter C. K. Lau. "Cloning and characterization of the first GH10 and GH11 xylanases from Rhizopus oryzae." Applied Microbiology and Biotechnology 98, no. 19 (April 24, 2014): 8211–22. http://dx.doi.org/10.1007/s00253-014-5741-4.

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Ghio, Silvina, Ornella Ontañon, Florencia E. Piccinni, Rubén Marrero Díaz de Villegas, Paola Talia, Daniel H. Grasso, and Eleonora Campos. "Correction to: Paenibacillus sp. A59 GH10 and GH11 Extracellular Endoxylanases: Application in Biomass Bioconversion." BioEnergy Research 12, no. 3 (May 8, 2019): 743. http://dx.doi.org/10.1007/s12155-019-09982-9.

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Shrestha, Prasansah, Jayram Karmacharya, So-Ra Han, Jun Hyuck Lee, Hyun Park, and Tae-Jin Oh. "Complete Genome Sequence and Comparative Genome Analysis of Variovorax sp. Strains PAMC28711, PAMC26660, and PAMC28562 and Trehalose Metabolic Pathways in Antarctica Isolates." International Journal of Microbiology 2022 (November 9, 2022): 1–13. http://dx.doi.org/10.1155/2022/5067074.

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The complete genomes of Variovorax strains were analyzed and compared along with the genomes of Variovorax strains PAMC28711, PAMC28562, and PAMC26660, Antarctic isolates. The genomic information was collected from the NCBI database and the CAZyme database, and Prokka annotation was used to find the genes that encode for the trehalose metabolic pathway. Likewise, CAZyme annotation (dbCAN2 Meta server) was performed to predict the CAZyme family responsible for trehalose biosynthesis and degradation enzymes. Trehalose has been found to respond to osmotic stress and extreme temperatures. As a result, the study of the trehalose metabolic pathway was carried out in harsh environments such as the Antarctic, where bacteria Variovorax sp. strains PAMC28711, PAMC28562, and PAMC26660 can survive in extreme environments, such as cold temperatures. The trehalose metabolic pathway was analyzed via bioinformatics tools, such as the dbCAN2 Meta server, Prokka annotation, Multiple Sequence Alignment, ANI calculator, and PATRIC database, which helped to predict trehalose biosynthesis and degradation genes’ involvement in the complete genome of Variovorax strains. Likewise, MEGA X was used for evolutionary and conserved genes. The complete genomes of Variovorax strains PAMC28711, PAMC26660, and PAMC28562 are circular chromosomes of length (4,320,000, 7,390,000, and 4,690,000) bp, respectively, with GC content of (66.00, 66.00, and 63.70)%, respectively. The GC content of these three Variovorax strains is lower than that of the other Variovorax strains with complete genomes. Strains PAMC28711 and PAMC28562 exhibit three complete trehalose biosynthetic pathways (OtsA/OtsB, TS, and TreY/TreZ), but strain PAMC26660 only possesses one (OtsA/OtsB). Despite the fact that all three strains contain trehalose, only strain PAMC28711 has two trehaloses according to CAZyme families (GH37 and GH15). Moreover, among the three Antarctica isolates, only strain PAMC28711 exhibits auxiliary activities (AAs), a CAZyme family. To date, although the Variovorax strains are studied for different purposes, the trehalose metabolic pathways in Variovorax strains have not been reported. Further, this study provides additional information regarding trehalose biosynthesis genes and degradation genes (trehalose) as one of the factors facilitating bacterial survival under extreme environments, and this enzyme has shown potential application in biotechnology fields.

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Patel, Pavan, and Stephen J. Free. "Characterization of Neurospora crassa GH16, GH17, and GH72 gene families of cell wall crosslinking enzymes." Cell Surface 8 (December 2022): 100073. http://dx.doi.org/10.1016/j.tcsw.2022.100073.

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Meng, Dong-Dong, Xi Liu, Sheng Dong, Ye-Fei Wang, Xiao-Qing Ma, Haixia Zhou, Xinquan Wang, Li-Shan Yao, Yingang Feng, and Fu-Li Li. "Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32." Biochemical Journal 474, no. 20 (September 26, 2017): 3373–89. http://dx.doi.org/10.1042/bcj20170328.

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Glycoside hydrolase (GH) family 5 is one of the largest GH families with various GH activities including lichenase, but the structural basis of the GH5 lichenase activity is still unknown. A novel thermostable lichenase F32EG5 belonging to GH5 was identified from an extremely thermophilic bacterium Caldicellulosiruptor sp. F32. F32EG5 is a bi-functional cellulose and a lichenan-degrading enzyme, and exhibited a high activity on β-1,3-1,4-glucan but side activity on cellulose. Thin-layer chromatography and NMR analyses indicated that F32EG5 cleaved the β-1,4 linkage or the β-1,3 linkage while a 4-O-substitued glucose residue linked to a glucose residue through a β-1,3 linkage, which is completely different from extensively studied GH16 lichenase that catalyses strict endo-hydrolysis of the β-1,4-glycosidic linkage adjacent to a 3-O-substitued glucose residue in the mixed-linked β-glucans. The crystal structure of F32EG5 was determined to 2.8 Å resolution, and the crystal structure of the complex of F32EG5 E193Q mutant and cellotetraose was determined to 1.7 Å resolution, which revealed that the exit subsites of substrate-binding sites contribute to both thermostability and substrate specificity of F32EG5. The sugar chain showed a sharp bend in the complex structure, suggesting that a substrate cleft fitting to the bent sugar chains in lichenan is a common feature of GH5 lichenases. The mechanism of thermostability and substrate selectivity of F32EG5 was further demonstrated by molecular dynamics simulation and site-directed mutagenesis. These results provide biochemical and structural insights into thermostability and substrate selectivity of GH5 lichenases, which have potential in industrial processes.

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Herold, Silvia, Robert Bischof, Benjamin Metz, Bernhard Seiboth, and Christian P. Kubicek. "Xylanase Gene Transcription in Trichoderma reesei Is Triggered by Different Inducers Representing Different Hemicellulosic Pentose Polymers." Eukaryotic Cell 12, no. 3 (January 4, 2013): 390–98. http://dx.doi.org/10.1128/ec.00182-12.

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ABSTRACTThe ascomyceteTrichoderma reeseiis a paradigm for the regulation and production of plant cell wall-degrading enzymes, including xylanases. Four xylanases, including XYN1 and XYN2 of glycosyl hydrolase family 11 (GH11), the GH10 XYN3, and the GH30 XYN4, were already described. By genome mining, we identified a fifth xylanase, XYN5, belonging to GH11. Transcriptional analysis reveals that the expression of all xylanases butxyn3is induced byd-xylose, dependent on the cellulase and xylanase regulator XYR1 and negatively regulated by the carbon catabolite repressor CRE1. Impairment ofd-xylose catabolism at thed-xylose reductase and xylitol dehydrogenase step strongly enhanced induction byd-xylose. Knockout of thel-xylulose reductase-encoding genelxr3, which connects thed-xylose andl-arabinose catabolic pathways, had no effect on xylanase induction. Besides the induction byd-xylose, theT. reeseixylanases were also induced byl-arabinose, and this induction was also enhanced in knockout mutants inl-arabinose reductase (xyl1),l-arabitol dehydrogenase (lad1), andl-xylulose reductase (lxr3). Induction byl-arabinose was also XYR1 dependent. Analysis of intracellular polyols revealed accumulation of xylitol in all strains only during incubation withd-xylose and accumulation ofl-arabitol only during incubation withl-arabinose. Induction byl-arabinose could be further stimulated by addition ofd-xylose. We conclude that the expression of theT. reeseixylanases can be induced by bothd-xylose andl-arabinose, but independently of each other and by using different inducing metabolites.

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Hu, Jinguang, and Jack N. Saddler. "Why does GH10 xylanase have better performance than GH11 xylanase for the deconstruction of pretreated biomass?" Biomass and Bioenergy 110 (March 2018): 13–16. http://dx.doi.org/10.1016/j.biombioe.2018.01.007.

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Rhee, Mun Su, Neha Sawhney, Young Sik Kim, Hyun Jee Rhee, Jason C. Hurlbert, Franz J. St. John, Guang Nong, John D. Rice, and James F. Preston. "GH115 α-glucuronidase and GH11 xylanase from Paenibacillus sp. JDR-2: potential roles in processing glucuronoxylans." Applied Microbiology and Biotechnology 101, no. 4 (October 21, 2016): 1465–76. http://dx.doi.org/10.1007/s00253-016-7899-4.

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Beaugrand, Johnny, Gérard Chambat, Vicky W. K. Wong, Florence Goubet, Caroline Rémond, Gabriel Paës, Samina Benamrouche, Philippe Debeire, Michael O’Donohue, and Brigitte Chabbert. "Impact and efficiency of GH10 and GH11 thermostable endoxylanases on wheat bran and alkali-extractable arabinoxylans." Carbohydrate Research 339, no. 15 (October 2004): 2529–40. http://dx.doi.org/10.1016/j.carres.2004.08.012.

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Liu, Zhuoyi, Wenfei Yu, Xiaowen Zhang, Jinfeng Huang, Wei Wang, Miao Miao, Li Hu, et al. "Genome-Wide Identification and Expression Analysis of Chitinase-like Genes in Petunia axillaris." Plants 11, no. 9 (May 9, 2022): 1269. http://dx.doi.org/10.3390/plants11091269.

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Chitinase (EC 3.2.1.14) is a kind of chitin-degrading glycosidase, which plays important roles in the abiotic and biotic defense of plants. In this study, we conducted whole-genome annotation, molecular evolution, and gene expression analyses on the chitinase-like (CTL) gene family members of Petunia axillaris. Thirty-three Petunia axillarischitinase-like genes (PaCTLs) were identified from the latest Petunia genome database. According to the phylogenetic analyses, these genes were divided into GH18 and GH19 subgroups and further subdivided into five classes (Class I to Class V). Conserved motif arrangements indicated their functional relevance within each group. The expansion and homeology analyses showed that gene replication events played an important role in the evolution of PaCTLs and the increase of the GH18 subgroup members was the main reason for the expansion of the PaCTL gene family in the evolution progress. By qRT-PCR analysis, we found that most of the PaCTLs showed a very low expression level in the normal growing plants. But lots of PaCTLs showed upregulated expression profiles when the plants suffered different abiotic stress conditions. Among them, five PaCTLs responded to high temperature and exhibited significantly upregulate expression level. Correspondingly, many hormone responses, as well as biotic and abiotic stress elements were found in the promoters of PaCTLs by using cis-acting element analysis. These results provide a foundation for the exploration of PaCTLs’ function and enrich the evolutionary process of the CTL gene family.

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Book, Adam J., Gina R. Lewin, Bradon R. McDonald, Taichi E. Takasuka, Drew T. Doering, Aaron S. Adams, Joshua A. V. Blodgett, et al. "Cellulolytic Streptomyces Strains Associated with Herbivorous Insects Share a Phylogenetically Linked Capacity To Degrade Lignocellulose." Applied and Environmental Microbiology 80, no. 15 (May 16, 2014): 4692–701. http://dx.doi.org/10.1128/aem.01133-14.

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ABSTRACTActinobacteria in the genusStreptomycesare critical players in microbial communities that decompose complex carbohydrates in the soil, and these bacteria have recently been implicated in the deconstruction of plant polysaccharides for some herbivorous insects. Despite the importance ofStreptomycesto carbon cycling, the extent of their plant biomass-degrading ability remains largely unknown. In this study, we compared four strains ofStreptomycesisolated from insect herbivores that attack pine trees: DpondAA-B6 (SDPB6) from the mountain pine beetle, SPB74 from the southern pine beetle, and SirexAA-E (SACTE) and SirexAA-G from the woodwasp,Sirex noctilio. Biochemical analysis of secreted enzymes demonstrated that only two of these strains, SACTE and SDPB6, were efficient at degrading plant biomass. Genomic analyses indicated that SACTE and SDPB6 are closely related and that they share similar compositions of carbohydrate-active enzymes. Genome-wide proteomic and transcriptomic analyses revealed that the major exocellulases (GH6 and GH48), lytic polysaccharide monooxygenases (AA10), and mannanases (GH5) were conserved and secreted by both organisms, while the secreted endocellulases (GH5 and GH9 versus GH9 and GH12) were from diverged enzyme families. Together, these data identify two phylogenetically related insect-associatedStreptomycesstrains with high biomass-degrading activity and characterize key enzymatic similarities and differences used by these organisms to deconstruct plant biomass.

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Journal articles on the topic 'GH15'

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