Journal of Microbiology

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Bacillus coreaensis sp. nov.: a xylan-hydrolyzing bacterium isolated from the soil of Jeju Island, Republic of Korea: Won-Jae Chi , Young Sang Youn , Jae-Seon Park , Soon-Kwang Hong; J. Microbiol. 2015;53(7):448-453. Published online June 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5140-2

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A xylan-degrading bacterium, designated as MS5T strain, was isolated from soil collected from the Jeju Island, Republic of Korea. Strain MS5T was Gram-stain-positive, aerobic, and motile by polar flagellum. The major fatty acids identified in this bacterium were iso-C15:0 (32.3%), C16:0 (27.3%), and anteiso-C15:0 (10.2%). A similarity search based on the 16S rRNA gene sequence revealed that the strain belongs to the class Bacilli and shared the highest similarity with the type strains Bacillus beringensis BR035T (98.7%) and Bacillus korlensis ZLC-26T (98.6%) which form a coherent cluster in a neighbor-joining phylogenetic tree. The DNA G+C content of strain MS5T was 43.0 mol%. The major menaquinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNADNA relatedness values between strain MS5T and two closely related species, B. beringensis BR035T and B. korlensis ZLC- 26T, were less than 70%. DNA-DNA relatedness analysis and 16S rRNA sequence similarity, as well as phenotypic and chemotaxonomic characteristics suggest that the strain MS5T constitutes a novel Bacillus species, for which the name Bacillus coreaensis sp. nov. is proposed. The type strain is MS5T (=DSM25506T =KCTC13895T).

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Molecular Characterization of Xylobiose- and Xylopentaose-Producing β-1,4-Endoxylanase SCO5931 from Streptomyces coelicolor A3(2)
Bolormaa Enkhbaatar, Chang-Ro Lee, Young-Soo Hong, Soon-Kwang Hong
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Molecular characterization of SCO0765 as a cellotriose releasing endo-β-1,4-cellulase from Streptomyces coelicolor A(3)
Joo-Bin Hong, Vijayalakshmi Dhakshnamoorthy, Chang-Ro Lee
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Biocatalytic Properties and Substrate-binding Ability of a Modular GH10 β-1,4-Xylanase from an Insect-symbiotic Bacterium, Streptomyces mexicanus HY-14: Do Young Kim , Dong-Ha Shin , Sora Jung , Jong Suk Lee , Han-Young Cho , Kyung Sook Bae , Chang-Keun Sung , Young Ha Rhee , Kwang-Hee Son , Ho-Yong Park; J. Microbiol. 2014;52(10):863-870. Published online October 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4390-8

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Abstract

The gene (1350-bp) encoding a modular β-1,4-xylanase (XylU), which consists of an N-terminal catalytic GH10 domain and a C-terminal carbohydrate-binding module 2 (CBM 2), from Streptomyces mexicanus HY-14 was cloned and functionally characterized. The purified His-tagged recombinant enzyme (rXylU, 44.0 kDa) was capable of efficiently hydrolyze diverse xylosidic compounds, p-nitrophenyl-cellobioside, and pnitrophenyl- xylopyranoside when incubated at pH 5.5 and 65°C. Especially, the specific activities (649.8 U/mg and 587.0 U/mg, respectively) of rXylU toward oat spelts xylan and beechwood xylan were relatively higher than those (<500.0 U/mg) of many other GH10 homologs toward the same substrates. The results of enzymatic degradation of birchwood xylan and xylooligosaccharides (xylotriose to xylohexaose) revealed that rXylU preferentially hydrolyzed the substrates to xylobiose (>75%) as the primary degradation product. Moreover, a small amount (4%<) of xylose was detected as the degradation product of the evaluated xylosidic substrates, indicating that rXylU was a peculiar GH10 β-1,4- xylanase with substrate specificity, which was different from its retaining homologs. A significant reduction of the binding ability of rXylU caused by deletion of the C-terminal CBM 2 to various insoluble substrates strongly suggested that the additional domain might considerably contribute to the enzyme-substrate interaction.

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Paenibacillus xylaniclasticus sp. nov., a Xylanolytic-Cellulolytic Bacterium Isolated from Sludge in an Anaerobic Digester: Chakrit Tachaapaikoon , Somboon Tanasupawat , Patthra Pason , Somphit Sornyotha , Rattiya Waeonukul , Khin Lay Kyu , Khanok Ratanakhanokchai; J. Microbiol. 2012;50(3):394-400. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1480-3

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Abstract

A mesophilic, facultative, anaerobic, xylanolytic-cellulolytic bacterium, TW1T, was isolated from sludge in an anaerobic digester fed with pineapple waste. Cells stained Gram-positive, were spore-forming, and had the morphology of straight to slightly curved rods. Growth was observed in the temperature range of 30 to 50°C (optimum 37°C) and the pH range of 6.0 to 7.5 (optimum pH 7.0) under aerobic and anaerobic conditions. The strain contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The predominant isoprenoid quinone was menaquinone with seven isoprene units (MK-7). Anteiso-C15:0, iso-C16:0, anteiso-C17:0, and C16:0 were the predominant cellular fatty acids. The G+C content of the DNA was 49.5 mol%. A phylogenetic analysis based on 16S rRNA showed that strain TW1T belonged within the genus Paenibacillus and was closely related to Paenibacillus cellulosilyticus LMG 22232T, P. curdlanolyticus KCTC 3759T, and P. kobensis KCTC 3761T with 97.7, 97.5, and 97.3% sequence similarity, respectively. The DNA-DNA hybridization values between the isolate and type strains of P. cellulosilyticus LMG 22232T, P. curdlanolyticus KCTC 3759T, and P. kobensis KCTC 3761T were found to be 18.6, 18.3, and 18.0%, respectively. The protein and xylanase patterns of strain TW1T were quite different from those of the type strains of closely related Paenibacillus species. On the basis of DNA-DNA relatedness and phenotypic analyses, phylogenetic data and the enzymatic pattern presented in this study, strain TW1T should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus xylaniclasticus sp. nov. is proposed. The type strain is TW1T (=NBRC 106381T =KCTC 13719T =TISTR 1914T).

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Synergistic xylan decomposition by a reducing-end xylose-releasing exo-oligoxylanase with other xylanolytic enzymes derived from Paenibacillus xylaniclasticus strain TW1
Koki Taniguchi, Shuichi Karita, Midori Umekawa
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A C1/C4-Oxidizing AA10 Lytic Polysaccharide Monooxygenase from Paenibacillus xylaniclasticus Strain TW1
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Daichi Ito, Emiri Nakano, Shuichi Karita, Midori Umekawa, Khanok Ratanakhanokchai, Chakrit Tachaapaikoon
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Draft genome sequence data of Paenbacillus curdlanolyticus B-6 possessing a unique xylanolytic-cellulolytic multienzyme system
Sirilak Baramee, Ayaka Uke, Chakrit Tachaapaikoon, Rattiya Waeonukul, Patthra Pason, Khanok Ratanakhanokchai, Akihiko Kosugi
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The Role of Carbohydrate-Binding Module (CBM) Repeat of a Multimodular Xylanase (XynX) from Clostridium thermocellum in Cellulose and Xylan Binding: Thangaswamy Selvaraj , Sung Kyum Kim , Yong Ho Kim , Yu Seok Jeong , Yu-Jeong Kim , Nguyen Dinh Phuong , Kyung Hwa Jung , Jungho Kim , Han Dae Yun , Hoon Kim; J. Microbiol. 2010;48(6):856-861. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0285-5

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Abstract

A non-cellulosomal xylanase from Clostridium thermocellum, XynX, consists of a family-22 carbohydratebinding module (CBM22), a family-10 glycoside hydrolase (GH10) catalytic module, two family-9 carbohydrate-binding modules (CBM9-I and CBM9-II), and an S-layer homology (SLH) module. E. coli BL21(DE3) (pKM29), a transformant carrying xynX', produced several truncated forms of the enzyme. Among them, three major active species were purified by SDS-PAGE, activity staining, gel-slicing, and diffusion from the gel. The truncated xylanases were different from each other only in their C-terminal regions. In addition to the CBM22 and GH10 catalytic modules, XynX1 had the CBM9-I and most of the CBM9-II, XynX2 had the CBM9-I and about 40% of the CBM9-II, and XynX3 had about 75% of the CBM9-I. The truncated xylanases showed higher binding capacities toward Avicel than those toward insoluble xylan. XynX1 showed a higher affinity toward Avicel (70.5%) than XynX2 (46.0%) and XynX3 (42.1%); however, there were no significant differences in the affinities toward insoluble xylan. It is suggested that the CBM9 repeat, especially CBM9-II, of XynX plays a role in xylan degradation in nature by strengthening cellulose binding rather than by enhancing xylan binding.

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Structure-Informed Insights into Catalytic Mechanism and Multidomain Collaboration in α-Agarase CmAga
Yuxian You, Bee Koon Gan, Min Luo, Xinzhe Zheng, Nanqing Dong, Yixiong Tian, Caiming Li, Haocun Kong, Zhengbiao Gu, Daiwen Yang, Zhaofeng Li
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Cellulolytic and hemicellulolytic capacity of Acetivibrio clariflavus
Katarína Šuchová, Vladimír Puchart
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Min Xiao, Ya-Jun Liu, Edward A. Bayer, Akihiko Kosugi, Qiu Cui, Yingang Feng
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Yuxian You, Haocun Kong, Caiming Li, Zhengbiao Gu, Xiaofeng Ban, Zhaofeng Li
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Pedro R. V. Hamann, Eliane F. Noronha
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Qinghua Zhang, Hanguang Li, Xiangdong Zhu, Fenju Lai, Zhijun Zhai, Yuanxiu Wang
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Biochemical characterization of a novel thermostable GH11 xylanase with CBM6 domain from Caldicellulosiruptor kronotskyensis
Weibo Qiao, Shuge Tang, Shuofu Mi, Xiaojing Jia, Xiaowei Peng, Yejun Han
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Thermophilic lignocellulose deconstruction
Sara E. Blumer-Schuette, Steven D. Brown, Kyle B. Sander, Edward A. Bayer, Irina Kataeva, Jeffrey V. Zurawski, Jonathan M. Conway, Michael W. W. Adams, Robert M. Kelly
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Yu‐Liang Jiao, Shu‐Jun Wang, Ming‐Sheng Lv, Yao‐Wei Fang, Shu Liu
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Warin Deesukon, Yuichi Nishimura, Tatsuji Sakamoto, Wasana Sukhumsirichart
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Rui Cheng, Jinping Chen, Xiaohong Yu, Yang Wang, Shiming Wang, Jianfa Zhang
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Production of XynX, a Large Multimodular Protein of Clostridium thermocellum, by Protease-Deficient Bacillus subtilis Strains
Nguyen Dinh Phuong, Yu Seok Jeong, Thangaswamy Selvaraj, Sung Kyum Kim, Yong Ho Kim, Kyung Hwa Jung, Jungho Kim, Han Dae Yun, Sui-Lam Wong, Jung-Kul Lee, Hoon Kim
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Yejun Han, Vinayak Agarwal, Dylan Dodd, Jason Kim, Brian Bae, Roderick I. Mackie, Satish K. Nair, Isaac K.O. Cann
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Purification and characterization of a xylanase from alkalophilic cephalosporium sp. RYM-202: Kang, Myoung Kyu , Kwon, Tae Ik , Yang, Young Ki , Rhee, Young Ha; J. Microbiol. 1995;33(2):109-114.

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Abstract: Alkalophilic Cephalosporium sp. RYM-202 produced multiple xylanases extracellularly. One of these xylanases was purified to electrophoretical homogeneity by chromatography with DEAE-Sephadex A-50, Sephacryl S-200 HR and Superose 12 HR. The purified xylanase differed from most other microbial xylanases in that it had low-molecular weight and acidic isoelectric point. The molecular weight of the xylanase in that it had low-molecular weight and acidic isoelectric point. The molecular weight of the xylanase was 23 kDa by SDS-polyacrylamide electrophoresis and 24 kDa by gel permeation chromatography, and the isoelectric point was 4.3. The xylanase had the highest activity permentation chromatography, and the isoelectric point was 4.3. The xylanase had the highest activity permeation chromatography, and the isoelectric point was 4.3. The xylanase had the highest activity at pH 8.0 and 50℃. It was stable over a wide range of pH and retained more than 80% of its original activity after 24 h of incubation even at pH 12. The Km values of this enzyme on birchwood xylan and oat spelts xylan were 2.33 and 3.45 mg/ml, respectively. The complete inhibition of the enzyme of n-bromosuccinimide suggests the involvement of tryptophan in the active site. The sylanase lacked activity towards crystalline cellulose and carboxymethyl cellulose.

Comparative Enzyme Production by Fungi from Diverse Lignocellulosic Substrates: Marie K. W. Sin , Kevin D. Hyde , Stephen B. Pointing; J. Microbiol. 2002;40(3):241-244.

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Abstract: Fungi commonly encountered on monocotyledonous substrates were evaluated for their in vitro ability to produce enzymes involved in lignocellulose breakdown. Most were capable of structural polysaccharide utilization, but few produced enzymes associated with lignin breakdown. None of the monocotyledon-inhabiting fungi produced reactions as strongly as wood decay fungi.

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