Journal of Microbiology

Journal Articles

Autotrophy to Heterotrophy: Shift in Bacterial Functions During the Melt Season in Antarctic Cryoconite Holes: Aritri Sanyal, Runa Antony, Gautami Samui, Meloth Thamban; J. Microbiol. 2024;62(8):591-609. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00140-1

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Microbes residing in cryoconite holes (debris, water, and nutrient-rich ecosystems) on the glacier surface actively participate in carbon and nutrient cycling. Not much is known about how these communities and their functions change during the summer melt-season when intense ablation and runoff alter the influx and outflux of nutrients and microbes. Here, we use high-throughput-amplicon sequencing, predictive metabolic tools and Phenotype MicroArray techniques to track changes in bacterial communities and functions in cryoconite holes in a coastal Antarctic site and the surrounding fjord, during the summer season. The bacterial diversity in cryoconite hole meltwater was predominantly composed of heterotrophs (Proteobacteria) throughout the season. The associated functional potentials were related to heterotrophic-assimilatory and -dissimilatory pathways. Autotrophic Cyanobacterial lineages dominated the debris community at the beginning and end of summer, while heterotrophic Bacteroidota- and Proteobacteria-related phyla increased during the peak melt period. Predictive functional analyses based on taxonomy show a shift from predominantly phototrophy-related functions to heterotrophic assimilatory pathways as the melt-season progressed. This shift from autotrophic to heterotrophic communities within cryoconite holes can affect carbon drawdown and nutrient liberation from the glacier surface during the summer. In addition, the flushing out and export of cryoconite hole communities to the fjord could influence the biogeochemical dynamics of the fjord ecosystem.

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Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park
Journal of Microbiology.2024; 62(11): 933. CrossRef

Comparison of Ganoderma boninense Isolate’s Aggressiveness Using Infected Oil Palm Seedlings: Mei Lieng Lo , Tu Anh Vu Thanh , Frazer Midot , Sharon Yu Ling Lau , Wei Chee Wong , Hun Jiat Tung , Mui Sie Jee , Mei-Yee Chin , Lulie Melling; J. Microbiol. 2023;61(4):449-459. Published online April 25, 2023; DOI: https://doi.org/10.1007/s12275-023-00040-w

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Abstract

Basal stem rot incidence caused by a white-rot fungus, Ganoderma boninense, is the major disease of oil palm in Southeast Asia. The rate of disease transmission and host damage are affected by variations in pathogen aggressiveness. Several other studies have used the disease severity index (DSI) to determine G. boninense aggressiveness levels while verifying disease using a culture-based method, which might not provide accurate results or be feasible in all cases. To differentiate G. boninense aggressiveness, we employed the DSI and vegetative growth measurement of infected oil palm seedlings. Disease confirmation was performed through scanning electron microscopy and molecular identification of fungal DNA from both infected tissue and fungi isolated from Ganoderma selective medium. Two-month-old oil palm seedlings were artificially inoculated with G. boninense isolates (2, 4A, 5A, 5B, and 7A) sampled from Miri (Lambir) and Mukah (Sungai Meris and Sungai Liuk), Sarawak. The isolates were categorized into three groups: highly aggressive (4A and 5B), moderately aggressive (5A and 7A), and less aggressive (2). Isolate 5B was identified as the most aggressive, and it was the only one to result in seedling mortality. Out of the five vegetative growth parameters measured, only the bole size between treatments was not affected. The integration of both conventional and molecular approaches in disease confirmation allows for precise detection.

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An In-Depth Study of Phytopathogenic Ganoderma: Pathogenicity, Advanced Detection Techniques, Control Strategies, and Sustainable Management
Samantha C. Karunarathna, Nimesha M. Patabendige, Wenhua Lu, Suhail Asad, Kalani K. Hapuarachchi
Journal of Fungi.2024; 10(6): 414. CrossRef
Advancements in the nanodelivery of azole-based fungicides to control oil palm pathogenic fungi
Azren Aida Asmawi, Fatmawati Adam, Nurul Aini Mohd Azman, Mohd Basyaruddin Abdul Rahman
Heliyon.2024; 10(18): e37132. CrossRef
Characterizations of Ganoderma species causing basal stem rot disease in coconut tree
Umesh Sajjan, Manjunath Hubballi, Abhay K. Pandey, V. Devappa, H. P. Maheswarappa
3 Biotech.2024;[Epub] CrossRef

Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons): Qian Liu , Guoying Fan , Kui Wu , Xiangning Bai , Xi Yang , Wentao Song , Shengen Chen , Yanwen Xiong , Haiying Chen; J. Microbiol. 2022;60(7):668-677. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2089-9

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Abstract

Two novel Gram-positive, non-spore-forming, facultatively anaerobic, non-motile, and short rods to coccoid strains were isolated from the feces of the greater white-fronted geese (Anser albifrons) at Poyang Lake. The 16S rRNA gene sequences of strains 4H37-19T and 3HC-13 shared highest identity to that of Corynebacterium uropygiale Iso10T (97.8%). Phylogenetic and phylogenomic analyses indicated that strains 4H37-19T and 3HC-13 formed an independent clade within genus Corynebacterium and clustered with Corynebacterium uropygiale Iso10T. The average nucleotide identity and digital DNA-DNA hybridization value between strains 4H37-19T and 3HC-13 and members within genus Corynebacterium were all below 95% and 70%, respectively. The genomic G + C content of strains 4H37-19T and 3HC-13 was 52.5%. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidylcholine, and phosphatidyl inositol mannosides (PIM) were the major polar lipids, with C18:1ω9c, C16:0, and C18:0 as the major fatty acids, and MK-8 (H4), MK-8(H2), and MK-9(H2) as the predominant respiratory quinones. The major whole cell sugar was arabinose, and the cell wall included mycolic acids. The cell wall peptidoglycan contained meso-diaminopimelic acid (meso-DAP). The polyphasic taxonomic data shows that these two strains represent a novel species of the genus Corynebacterium, for which the name Corynebacterium poyangense sp. nov. is proposed. The type strain of Corynebacterium poyangense is 4H37-19T (=GDMCC 1.1738T = KACC 21671T).

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Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023
Erik Munson, Claire R. Burbick, Sara D. Lawhon, Trinity Krueger, Elena Ruiz-Reyes, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Keratokonjunktivitisli bir tavuktan Corynebacterium spp. ve Arcanobacterium spp. izolasyonu
Hüban GÖÇMEN, Banur BOYNUKARA
Veteriner Hekimler Derneği Dergisi.2023; 94(2): 161. CrossRef

Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase: Jisub Hwang , Chang-Sook Jeong , Chang Woo Lee , Seung Chul Shin , Han-Woo Kim , Sung Gu Lee , Ui Joung Youn , Chang Sup Lee , Tae-Jin Oh , Hak Jun Kim , Hyun Park , Hyun Ho Park , Jun Hyuck Lee; J. Microbiol. 2020;58(7):606-613. Published online April 22, 2020; DOI: https://doi.org/10.1007/s12275-020-0089-1

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Abstract

Crystal structures of enoyl-coenzyme A (CoA) isomerase from Bosea sp. PAMC 26642 (BoECI) and enoyl-CoA hydratase from Hymenobacter sp. PAMC 26628 (HyECH) were determined at 2.35 and 2.70 Å resolution, respectively. BoECI and HyECH are members of the crotonase superfamily and are enzymes known to be involved in fatty acid degradation. Structurally, these enzymes are highly similar except for the orientation of their C-terminal helix domain. Analytical ultracentrifugation was performed to determine the oligomerization states of BoECI and HyECH revealing they exist as trimers in solution. However, their putative ligand-binding sites and active site residue compositions are dissimilar. Comparative sequence and structural analysis revealed that the active site of BoECI had one glutamate residue (Glu135), this site is occupied by an aspartate in some ECIs, and the active sites of HyECH had two highly conserved glutamate residues (Glu118 and Glu138). Moreover, HyECH possesses a salt bridge interaction between Glu98 and Arg152 near the active site. This interaction may allow the catalytic Glu118 residue to have a specific conformation for the ECH enzyme reaction. This salt bridge interaction is highly conserved in known bacterial ECH structures and ECI enzymes do not have this type of interaction. Collectively, our comparative sequential and structural studies have provided useful information to distinguish and classify two similar bacterial crotonase superfamily enzymes.

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ECHDC2 inhibits the proliferation of gastric cancer cells by binding with NEDD4 to degrade MCCC2 and reduce aerobic glycolysis
Jiancheng He, Jianfeng Yi, Li Ji, Lingchen Dai, Yu Chen, Wanjiang Xue
Molecular Medicine.2024;[Epub] CrossRef
Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite
Zhenhong Chen, Bo Song, Hongyu Guo, Dapin Xia, Yidong Cai, Yongjun Wang, Weizhong Zhao
Environmental Research.2023; 227: 115777. CrossRef
Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex
Hyeoncheol Francis Son, Jae-Woo Ahn, Jiyeon Hong, Jihye Seok, Kyeong Sik Jin, Kyung-Jin Kim
Archives of Biochemistry and Biophysics.2022; 730: 109391. CrossRef
Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8
Sivaraman Padavattan, Sneha Jos, Hemanga Gogoi, Bagautdin Bagautdinov
Acta Crystallographica Section F Structural Biology Communications.2021; 77(5): 148. CrossRef

Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis: Huaxian Zhao , Bing Yan , Shuming Mo , Shiqing Nie , Quanwen Li , Qian Ou , Bo Wu , Gonglingxia Jiang , Jinli Tang , Nan Li , Chengjian Jiang; J. Microbiol. 2019;57(7):575-586. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8679-5

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Abstract

Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that “Carbohydrate metabolism” was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and β-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.

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Habitat variations of sediment microbial community structure and functions and the influential environmental factors in a Ramsar protected wetland in South China
Kit-Ling Lam, Nora Fung-Yee Tam, Steven Jing-Liang Xu, Wing-Yin Mo, Yuet-Tung Tse, Kaze King-Yip Lai, Ping-Lung Chan, Fred Wang-Fat Lee
Marine Pollution Bulletin.2024; 209: 117166. CrossRef
Unraveling the role of bacterial communities in mangrove habitats under the urban influence, using a next-generation sequencing approach
Mayukhmita Ghose, Ashutosh Shankar Parab, Cathrine Sumathi Manohar, Deepika Mohanan, Ashwini Toraskar
Journal of Sea Research.2024; 198: 102469. CrossRef
Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome
Marcele Laux, Luciane Prioli Ciapina, Fabíola Marques de Carvalho, Alexandra Lehmkuhl Gerber, Ana Paula C. Guimarães, Moacir Apolinário, Jorge Eduardo Santos Paes, Célio Roberto Jonck, Ana Tereza R. de Vasconcelos
BMC Microbiology.2024;[Epub] CrossRef
Metagenomic 16S rRNA analysis and predictive functional profiling revealed intrinsic organohalides respiration and bioremediation potential in mangrove sediment
Sultan M. Alsharif, Mohamed Ismaeil, Ali M. Saeed, Wael S. El-Sayed
BMC Microbiology.2024;[Epub] CrossRef
Novosphingobium album sp. nov., Novosphingobium organovorum sp. nov. and Novosphingobium mangrovi sp. nov. with the organophosphorus pesticides degrading ability isolated from mangrove sediments
Wenjin Hu, Zhe Li, Haisheng Ou, Xiaochun Wang, Qiaozhen Wang, Zhanhua Tao, Shushi Huang, Yuanlin Huang, Guiwen Wang, Xinli Pan
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Taxonomy and anticancer potential of Streptomyces niphimycinicus sp. nov. against nasopharyngeal carcinoma cells
Yiying Huang, Wenjin Hu, Shushi Huang, Jiemei Chu, Yushan Liang, Zhanhua Tao, Guiwen Wang, Junlian Zhuang, Zhe Zhang, Xiaoying Zhou, Xinli Pan
Applied Microbiology and Biotechnology.2023; 107(20): 6325. CrossRef
Screening of marine sediment-derived microorganisms and their bioactive metabolites: a review
Hongli Yao, Shuangping Liu, Tiantian Liu, Dongliang Ren, Qilin Yang, Zhilei Zhou, Jian Mao
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef
Novosphingobium beihaiensis sp. nov., a novel pesticide-tolerant bacterium isolated from mangrove sediments
Wenjin Hu, Yiying Huang, Yingjing Liu, Xiaoying Zhou, Shushi Huang, Jiemei Chu, Xinli Pan
Antonie van Leeuwenhoek.2023; 116(11): 1151. CrossRef
Mycolicibacterium aurantiacum sp. nov. and Mycolicibacterium xanthum sp. nov., two novel actinobacteria isolated from mangrove sediments
Xinli Pan, Zhe Li, Shushi Huang, Yuanlin Huang, Qiaozhen Wang, Zhanhua Tao, Wenjin Hu
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef
Role of calcium and magnesium on dramatic physiological and anatomical responses in tomato plants
Ayshah A. ALRASHIDI, Haifa Abdulaziz Sakit ALHAITHLOUL, Mona H. SOLIMAN, Mohamed S. ATTIA, Salah M. ELSAYED, Mohamed M. ALI , Ahmed M. SADEK, Marwa A. FAKHR
Notulae Botanicae Horti Agrobotanici Cluj-Napoca.2022; 50(1): 12614. CrossRef
Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals
Gang Zhou, Hong-bing Tao, Xia Wen, Ying-si Wang, Hong Peng, Hui-zhong Liu, Xiu-jiang Yang, Xiao-mo Huang, Qing-shan Shi, Xiao-bao Xie
Chemosphere.2022; 291: 132766. CrossRef
Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem
Anwesha Ghosh, Ratul Saha, Punyasloke Bhadury
PeerJ.2022; 10: e13169. CrossRef
Diversity, metabolism and cultivation of archaea in mangrove ecosystems
Cui-Jing Zhang, Yu-Lian Chen, Yi-Hua Sun, Jie Pan, Ming-Wei Cai, Meng Li
Marine Life Science & Technology.2021; 3(2): 252. CrossRef
Thermohalobaculum xanthum gen. nov., sp. nov., a moderately thermophilic bacterium isolated from mangrove sediment
Xinli Pan, Zhe Li, Fei Li, Yuanlin Huang, Qiaozhen Wang, Shushi Huang, Wenjin Hu, Mingguo Jiang
Antonie van Leeuwenhoek.2021; 114(11): 1819. CrossRef
16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya
Edith M. Muwawa, Chinedu C. Obieze, Huxley M. Makonde, Joyce M. Jefwa, James H. P. Kahindi, Damase P. Khasa, Marco Fusi
PLOS ONE.2021; 16(3): e0248485. CrossRef
Microbial enrichment and meta-omics analysis identify CAZymes from mangrove sediments with unique properties
Douglas Antonio Alvaredo Paixão, Geizecler Tomazetto, Victoria Ramos Sodré, Thiago A. Gonçalves, Cristiane Akemi Uchima, Fernanda Büchli, Thabata Maria Alvarez, Gabriela Felix Persinoti, Márcio José da Silva, Juliano Bragatto, Marcelo Vizoná Liberato, Joã
Enzyme and Microbial Technology.2021; 148: 109820. CrossRef
Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils
Tianli Tong, Ruili Li, Minwei Chai, Qian Wang, Yuyin Yang, Shuguang Xie
Science of The Total Environment.2021; 792: 148486. CrossRef
Acuticoccus mangrovi sp. nov., with an antibacterial property, isolated from mangrove sediment
Zhe Li, Wenjin Hu, Shushi Huang, Yuanlin Huang, Fei Li, Qiaozhen Wang, Zhanhua Tao, Xinli Pan
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Extraordinary diversity of viruses in deep‐sea sediments as revealed by metagenomics without prior virion separation
Xiaowei Zheng, Wang Liu, Xin Dai, Yaxin Zhu, Jinfeng Wang, Yongqiang Zhu, Huajun Zheng, Ying Huang, Zhiyang Dong, Wenbin Du, Fangqing Zhao, Li Huang
Environmental Microbiology.2021; 23(2): 728. CrossRef
Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition
Panmeng Wang, Jianping Xu, Gang Wu, Tiezhi Liu, Zhu L. Yang
Journal of Fungi.2021; 7(8): 679. CrossRef

FgIlv3a is crucial in branched-chain amino acid biosynthesis, vegetative differentiation, and virulence in Fusarium graminearum: Xin Liu , Yichen Jiang , Yinghui Zhang , Mingzheng Yu , Hongjun Jiang , Jianhong Xu , Jianrong Shi; J. Microbiol. 2019;57(8):694-703. Published online May 11, 2019; DOI: https://doi.org/10.1007/s12275-019-9123-6

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Abstract

Dihydroxyacid dehydratase (DHAD), encoded by ILV3, catalyses the third step in the biosynthetic pathway of branchedchain amino acids (BCAAs), which include isoleucine (Ile), leucine (Leu), and valine (Val). Enzymes involved in BCAA biosynthesis exist in bacteria, plants, and fungi but not in mammals and are therefore attractive targets for antimicrobial or herbicide development. In this study, three paralogous ILV3 genes (FgILV3A, FgILV3B, and FgILV3C) were identified in the genome of Fusarium graminearum, the causal agent of Fusarium head blight (FHB). Deletion of FgILV3A alone or combined with FgILV3B or FgILV3C indicated an important role for FgILV3A in BCAA biosynthesis. FgILV3A deletion mutants lost the ability to grow on medium lacking amino acids. Exogenous supplementation of 1 mM Ile and Val rescued the auxotrophy of ΔFgIlv3A, though 5 mM was required to recover the growth defects in ΔFgIlv3AB and ΔFgIlv3AC strains, indicating that FgIlv3b and FgIlv3c exhibit redundant but accessory roles with FgIlv3a in BCAA biosynthesis. The auxotrophy of ΔFgIlv3A resulted in pleiotropic defects in aerial hyphal growth, in conidial formation and germination, and in aurofusarin accumulation. In addition, the mutants showed reduced virulence and deoxynivalenol production. Overall, our study demonstrates that FgIlv3a is crucial for BCAA biosynthesis in F. graminearum and a candidate fungicide target for FHB management.

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AflaILVB/G/I and AflaILVD are involved in mycelial production, aflatoxin biosynthesis, and fungal virulence in Aspergillus flavus
Yarong Zhao, Chulan Huang, Rui Zeng, Peirong Chen, Kaihang Xu, Xiaomei Huang, Xu Wang
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Histone H3 N-Terminal Lysine Acetylation Governs Fungal Growth, Conidiation, and Pathogenicity through Regulating Gene Expression in Fusarium pseudograminearum
Hang Jiang, Lifang Yuan, Liguo Ma, Kai Qi, Yueli Zhang, Bo Zhang, Guoping Ma, Junshan Qi
Journal of Fungi.2024; 10(6): 379. CrossRef
Identification and Characterization of an Antifungal Gene Mt1 from Bacillus subtilis by Affecting Amino Acid Metabolism in Fusarium graminearum
Pei Song, Wubei Dong
International Journal of Molecular Sciences.2023; 24(10): 8857. CrossRef
Branched-chain amino acid biosynthesis in fungi
Gary Jones, Jane Usher, Joel T. Steyer, Richard B. Todd
Essays in Biochemistry.2023; 67(5): 865. CrossRef
FgLEU1 Is Involved in Leucine Biosynthesis, Sexual Reproduction, and Full Virulence in Fusarium graminearum
Shaohua Sun, Mingyu Wang, Chunjie Liu, Yilin Tao, Tian Wang, Yuancun Liang, Li Zhang, Jinfeng Yu
Journal of Fungi.2022; 8(10): 1090. CrossRef
Acetolactate synthases regulatory subunit and catalytic subunit genes VdILVs are involved in BCAA biosynthesis, microscletotial and conidial formation and virulence in Verticillium dahliae
ShengNan Shao, Biao Li, Qi Sun, PeiRu Guo, YeJuan Du, JiaFeng Huang
Fungal Genetics and Biology.2022; 159: 103667. CrossRef
Molecular targets for antifungals in amino acid and protein biosynthetic pathways
Aleksandra Kuplińska, Kamila Rząd
Amino Acids.2021; 53(7): 961. CrossRef
MoCpa1-mediated arginine biosynthesis is crucial for fungal growth, conidiation, and plant infection of Magnaporthe oryzae
Osakina Aron, Min Wang, Anjago Wilfred Mabeche, Batool Wajjiha, Meiqin Li, Shuai Yang, Haixia You, Yan Cai, Tian Zhang, Yunxi Li, Baohua Wang, Dongmei Zhang, Zonghua Wang, Wei Tang
Applied Microbiology and Biotechnology.2021; 105(14-15): 5915. CrossRef
Metabolic, structural, and proteomic changes in Candida albicans cells induced by the protein-carbohydrate fraction of Dendrobaena veneta coelomic fluid
Marta J. Fiołka, Paulina Czaplewska, Sylwia Wójcik-Mieszawska, Aleksandra Lewandowska, Kinga Lewtak, Weronika Sofińska-Chmiel, Tomasz Buchwald
Scientific Reports.2021;[Epub] CrossRef
The pyruvate dehydrogenase kinase 2 (PDK2) is associated with conidiation, mycelial growth, and pathogenicity in Fusarium graminearum
Tao Gao, Dan He, Xin Liu, Fang Ji, Jianhong Xu, Jianrong Shi
Food Production, Processing and Nutrition.2020;[Epub] CrossRef
The Intermediates in Branched-Chain Amino Acid Biosynthesis Are Indispensable for Conidial Germination of the Insect-Pathogenic Fungus Metarhizium robertsii
Feifei Luo, Hongxia Zhou, Xue Zhou, Xiangyun Xie, You Li, Fenglin Hu, Bo Huang, Karyn N. Johnson
Applied and Environmental Microbiology.2020;[Epub] CrossRef

SucA-dependent uptake of sucrose across the outer membrane of Caulobacter crescentus: Samantha K. Modrak , Martha E. Melin , Lisa M. Bowers; J. Microbiol. 2018;56(9):648-655. Published online July 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8225-x

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Abstract

Caulobacter crescentus is an aquatic Gram-negative bacterium that lives in nutrient-poor environments. Like several other aquatic and phytopathogenic bacteria, Caulobacter cells have a relatively large number of genes predicted to encode TonB-dependent receptors (TBDRs). TBDRs transport nutrients across the outer membrane using energy from the proton motive force. We identified one TBDR gene, sucA, which is situated within a cluster of genes predicted to encode a lacIfamily transcription factor (sucR), amylosucrase (sucB), fructokinase (sucC), and an inner membrane transporter (sucD). Given its genomic neighborhood, we proposed that sucA encodes a transporter for sucrose. Using RT-qPCR, we determined that expression of sucABCD is strongly induced by sucrose in the media and repressed by the transcription factor, SucR. Furthermore, cells with a deletion of sucA have a reduced uptake of sucrose. Although cells with a non-polar deletion of sucA can grow with sucrose as the sole carbon source, cells with a polar deletion that eliminates expression of sucABCD cannot grow with sucrose as the sole carbon source. These results show that the suc locus is essential for sucrose utilization while SucA functions as one method of sucrose uptake in Caulobacter crescentus. This work sheds light on a new carbohydrate utilization locus in Caulobacter crescentus.

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Effect of Ferredoxin Receptor FusA on the Virulence Mechanism of Pseudomonas plecoglossicida
Rongchao He, Jiajia Wang, Miaozhen Lin, Jing Tian, Bi Wu, Xiaohan Tan, Jianchuan Zhou, Jiachen Zhang, Qingpi Yan, Lixing Huang
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Benzo[a]pyrene might be transported by a TonB-dependent transporter in Novosphingobium pentaromativorans US6-1
Jiaqing Liang, Jiantao Xu, Weijun Zhao, Jiaofeng Wang, Kai Chen, Yuqian Li, Yun Tian
Journal of Hazardous Materials.2021; 404: 124037. CrossRef
iTRAQ analysis reveals the effect of gabD and sucA gene knockouts on lysine metabolism and crystal protein formation in Bacillus thuringiensis
Zixian Yi, Tong Zhang, Junyan Xie, Zirong Zhu, Sisi Luo, Kexuan Zhou, Pengji Zhou, Wenhui Chen, Xiaoli Zhao, Yunjun Sun, Liqiu Xia, Xuezhi Ding
Environmental Microbiology.2021; 23(4): 2230. CrossRef
Structure and Stoichiometry of the Ton Molecular Motor
Herve Celia, Nicholas Noinaj, Susan K Buchanan
International Journal of Molecular Sciences.2020; 21(2): 375. CrossRef

Carbohydrate-binding specificities of potential probiotic Lactobacillus strains in porcine jejunal (IPEC-J2) cells and porcine mucin: Valerie Diane Valeriano , Bernadette B. Bagon , Marilen P. Balolong , Dae-Kyung Kang; J. Microbiol. 2016;54(7):510-519. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-6168-7

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Abstract

Bacterial lectins are carbohydrate-binding adhesins that recognize glycoreceptors in the gut mucus and epithelium of hosts. In this study, the contribution of lectin-like activities to adhesion of Lactobacillus mucosae LM1 and Lactobacillus johnsonii PF01, which were isolated from swine intestine, were compared to those of the commercial probiotic Lactobacillus rhamnosus GG. Both LM1 and PF01 strains have been reported to have good adhesion ability to crude intestinal mucus of pigs. To confirm this, we quantified their adhesion to porcine gastric mucin and intestinal porcine enterocytes isolated from the jejunum of piglets (IPEC-J2). In addition, we examined their carbohydrate-binding specificities by suspending bacterial cells in carbohydrate solutions prior to adhesion assays. We found that the selected carbohydrates affected the adherences of LM1 to IPEC-J2 cells and of LGG to mucin. In addition, compared to adhesion to IPEC-J2 cells, adhesion to mucin by both LM1 and LGG was characterized by enhanced specific recognition of glycoreceptor components such as galactose, mannose, and N-acetylglucosamine. Hydrophobic interactions might make a greater contribution to adhesion of PF01. A similar adhesin profile between a probiotic and a pathogen, suggest a correlation between shared pathogen–probiotic glycoreceptor recognition and the ability to exclude enteropathogens such as Escherichia coli K88 and Salmonella Typhimurium KCCM 40253. These findings extend our understanding of the mechanisms of the intestinal adhesion and pathogen-inhibition abilities of probiotic Lactobacillus strains.

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Effects of Probiotics on Gut Microbiota: An Overview
Preethi Chandrasekaran, Sabine Weiskirchen, Ralf Weiskirchen
International Journal of Molecular Sciences.2024; 25(11): 6022. CrossRef
Safety assessment of five candidate probiotic lactobacilli using comparative genome analysis
Patrick Josemaria d.R Altavas, Mia Beatriz C. Amoranto, Sang Hoon Kim, Dae-Kyung Kang, Marilen P. Balolong, Leslie Michelle M. Dalmacio
Access Microbiology .2024;[Epub] CrossRef
Galacto-oligosaccharides regulate intestinal mucosal sialylation to counteract antibiotic-induced mucin dysbiosis
Laipeng Xu, Xuan Li, Shuibing Han, Chunlong Mu, Weiyun Zhu
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Review

Microbial ecology in Hydra: Why viruses matter: Thomas C.G. Bosch , Juris A. Grasis , Tim Lachnit; J. Microbiol. 2015;53(3):193-200. Published online March 3, 2015; DOI: https://doi.org/10.1007/s12275-015-4695-2

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Abstract

While largely studied because of their harmful effects on human health, there is growing appreciation that viruses are also important members of the animal holobiont. This review highlights recent findings on viruses associated with Hydra and related Cnidaria. These early evolutionary diverging animals not only select their bacterial communities but also select for viral communities in a species-specific manner. The majority of the viruses associating with these animals are bacteriophages. We demonstrate that the animal host and its virome have evolved into a homeostatic, symbiotic relationship and propose that viruses are an important part of the Hydra holobiont by controlling the species-specific microbiome. We conclude that beneficial virus-bacterial-host interactions should be considered as an integral part of animal development and evolution.

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Caijiao Dai, Xin Chen, Shiyu Qian, Yihui Fan, Lijuan Li, Junfa Yuan
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Periodontology 2000.2021; 86(1): 14. CrossRef
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Research Support, Non-U.S. Gov'ts

X-ray Structure of Prephenate Dehydratase from Streptococcus mutans: Min Hyung Shin , Hyung-Keun Ku , Jin Sue Song , Saehae Choi , Se Young Son , Hee-Dai Kim , Sook-Kyung Kim , Il Yeong Park , Soo Jae Lee; J. Microbiol. 2014;52(6):490-495. Published online March 7, 2014; DOI: https://doi.org/10.1007/s12275-014-3645-8

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Abstract

Prephenate dehydratase is a key enzyme of the biosynthesis of L-phenylalanine in the organisms that utilize shikimate pathway. Since this enzymatic pathway does not exist in mammals, prephenate dehydratase can provide a new drug targets for antibiotics or herbicide. Prephenate dehydratase is an allosteric enzyme regulated by its end product. The enzyme composed of two domains, catalytic PDT domain located near the N-terminal and regulatory ACT domain located near the C-terminal. The allosteric enzyme is suggested to have two different conformations. When the regulatory molecule, phenylalanine, is not bound to its ACT domain, the catalytic site of PDT domain maintain open (active) state conformation as Sa-PDT structure. And the open state of its catalytic site become closed (allosterically inhibited) state if the regulatory molecule is bound to its ACT domain as Ct-PDT structure. However, the X-ray structure of prephenate dehydratase from Streptococcus mutans (Sm-PDT) shows that the catalytic site of Sm-PDT has closed state conformation without phenylalanine molecule bound to its regulatory site. The structure suggests a possibility that the binding of phenylalanine in its regulatory site may not be the only prerequisite for the closed state conformation of Sm-PDT.

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Immunostimulatory Activity of Dendritic Cells Pulsed with Carbonic Anhydrase IX and Acinetobacter baumannii Outer Membrane Protein A for Renal Cell Carcinoma: Bo Ra Kim , Eun Kyoung Yang , Sun Hee Kim , Dong Chan Moon , Hwa Jung Kim , Je Chul Lee , Duk Yoon Kim; J. Microbiol. 2011;49(1):115-120. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1037-x

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Abstract: Dendritic cell (DC)-based immunotherapy is a potent therapeutic modality for treating renal cell carcinoma (RCC), but development of antigens specific for tumor-targeting and anti-tumor immunity is of great interest for clinical trials. The present study investigated the ability of DCs pulsed with a combination of carbonic anhydrase IX (CA9) as an RCC-specific biomarker and Acinetobacter baumannii outer membrane protein A (AbOmpA) as an immunoadjuvant to induce anti-tumor immunity against murine renal cell carcinoma (RENCA) in a murine model. Murine bone-marrow-derived DCs pulsed with a combination of RENCA lysates and AbOmpA were tested for their capacity to induce DC maturation and T cell responses in vitro. A combination of RENCA lysates and AbOmpA up-regulated the surface expression of co-stimulatory molecules, CD80 and CD86, and the antigen presenting molecules, major histocompatibility (MHC) class I and class II, in DCs. A combination of RENCA lysates and AbOmpA also induced interleukin-12 (IL-12) production in DCs. Next, the immunostimulatory activity of DCs pulsed with a combination of CA9 and AbOmpA was determined. A combination of CA9 and AbOmpA up-regulated the surface expression of co-stimulatory molecules and antigen presenting molecules in DCs. DCs pulsed with a combination of CA9 and AbOmpA effectively secreted IL-12 but not IL-10. These cells interacted with T cells and formed clusters. DCs pulsed with CA9 and AbOmpA elicited the secretion of interferon-γ and IL-2 in T cells. In conclusion, a combination of CA9 and AbOmpA enhanced the immunostimulatory activity of DCs, which may effectively induce anti-tumor immunity against human RCC.

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.

Journal Article

Alternative Production of Avermectin Components in Streptomyces avermitilis by Gene Replacement: Joon-Hyoung Yong , Woo-Hyeon Byeon; J. Microbiol. 2005;43(3):277-284.; DOI: https://doi.org/2212 [pii]

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Abstract: The avermectins are composed of eight compounds, which exhibit structural differences at three positions. A family of four closely-related major components, A1a, A2a, B1a and B2a, has been identified. Of these components, B1a exhibits the most potent antihelminthic activity. The coexistence of the "1" components and "2" components has been accounted for by the defective dehydratase of aveAI module 2, which appears to be responsible for C22-23 dehydration. Therefore, we have attempted to replace the dehydratase of aveAI module 2 with the functional dehydratase from the erythromycin eryAII module 4, via homologous recombination. Erythromycin polyketide synthetase should contain the sole dehydratase domain, thus generating a saturated chain at the C6-7 of erythromycin. We constructed replacement plasmids with PCR products, by using primers which had been derived from the sequences of avermectin aveAI and the erythromycin eryAII biosynthetic gene cluster. If the original dehydratase of Streptomyces avermitilis were exchanged with the corresponding erythromycin gene located on the replacement plasmid, it would be expected to result in the formation of precursors which contain alkene at C22-23, formed by the dehydratase of erythromycin module 4, and further processed by avermectin polyketide synthase. Consequently, the resulting recombinant strain JW3105, which harbors the dehydratase gene derived from erythromycin, was shown to produce only C22,23-unsaturated avermectin compounds. Our research indicates that the desired compound may be produced via polyketide gene replacement.

Purification and charactedrization of cysteine desulfhydrase from streptomyces albidoflavus SMF301: Ryu, Jae Gon , Kang, Sung Gyun , Kim, In Seop , Rho, Young Taik , Lee, Sang Hee , Lee, Kye Joon; J. Microbiol. 1997;35(2):97-102.

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Abstract: Cysteine desulfhydrase (EC 4, 4, 1. 1. ) was purified from the culture supernatant of Streptomyces albidoflavus SMF301 by hydroxyapatite, gel filtration and Resource Q ion-exchange chromatography with a purification fold of six identical subunits. The enzyme was stabilized by dithiothreitol and pyridoxal 5'-phosphate during the purification procedures. The optimum pH and temperature were pH 8.6 and 35℃, respectively. The N-terminal amino acid sequence was identified as A-P-L-P-T-A-D-V-R-S-D-P-G-Y-E-W-L-G-E-A-V. The purified cystein desulfhydrase had a high substrate specificity toward cysteine, and exhibited no cystahionine λ-lyase activity. The K_m value for cysteine was determined to be 0.37 mM.

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