Article
Biochemistry & Molecular Biology
Jing Wang, Chunjun Qin, Yujuan Xu, Jian Yin, Jing Hu, Xi Guo
Summary: In this study, the structure of a novel O-antigen from Escherichia coli strain SD2019180 was established, and its role in O-antigen synthesis was confirmed through experiments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jing Wang, Yujuan Xu, Chunjun Qin, Jing Hu, Jian Yin, Xi Guo
Summary: The study identified the structure of the O-antigen in Escherichia coli strain LL004, showing significant differences from traditional E. coli serogroups, indicating it belongs to a novel serogroup. The O-antigen biosynthesis of LL004 was confirmed to be assembled via the Wzx/Wzy dependent pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Chunjun Qin, Bin Hu, Yujuan Xu, Changqing Zhao, Wei Hao, Jing Wang, Xi Guo, Renpeng Li, Jing Hu, Jian Yin
Summary: The O-antigen is an important virulence factor involved in bacterial survival, virulence, and invasion. This study elucidates the structure of O-antigen from an Escherichia coli strain 2017LL031, which is completely unique compared to known E. coli serogroups. The analysis of the O-antigen gene cluster confirms its correlation to the O-antigen structure. Furthermore, experimental evidence confirms the role of the O-antigen gene cluster in O-antigen biosynthesis. Overall, a novel E. coli serotype, 2017LL031, is identified.
CARBOHYDRATE RESEARCH
(2022)
Article
Genetics & Heredity
Kazunori Murase, Eiji Arakawa, Hidemasa Izumiya, Atsushi Iguchi, Taichiro Takemura, Taisei Kikuchi, Ichiro Nakagawa, Nicholas R. Thomson, Makoto Ohnishi, Masatomo Morita
Summary: Approximately 200 O-serogroups of Vibrio cholerae have been identified, but only O1 and O139 are closely related to pandemic cholera. The study of non-O1 and non-O139 strains is limited. This study analyzed the genomes of V. cholerae O-serogroup reference strains, revealing structural diversity of O-antigen biosynthesis gene clusters and differences in serological patterns.
MICROBIAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Maria Kurzylewska, Arkadiusz Bomba, Katarzyna Dworaczek, Agnieszka P. Ekala-Safinska, Anna Turska-Szewczuk
Summary: This study reported the isolation of Aeromonas sobria K928 strain from a common carp during a disease outbreak on a Polish fish farm, which was classified into a new provisional PGO1 serogroup. The O-specific polysaccharide structure of A. sobria K928 was studied by mild acid hydrolysis, gel-permeation chromatography, sugar and methylation analyses, and NMR spectroscopy. The O-antigen gene cluster in the genome of A. sobria K928 was identified and characterized.
CARBOHYDRATE RESEARCH
(2023)
Article
Infectious Diseases
Pierre Lopez, Sebastien Bridel, Denis Saulnier, Rarahu David, Beatriz Magarinos, Beatriz S. Torres, Jean Francois Bernardet, Eric Duchaud
Summary: This study identified the genomic loci involved in the O-antigen biosynthesis of Tenacibaculum maritimum, a devastating bacterial pathogen affecting marine fish. By combining conventional serotyping and genome-wide association study, a robust multiplex PCR-based serotyping scheme was developed, outperforming traditional serotyping. This method could be useful for population structure analysis, disease surveillance, vaccine formulation, and efficacy follow-up.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Review
Chemistry, Multidisciplinary
Duncan J. Kountz, Emily P. Balskus
Summary: The genomic era has revolutionized the discovery and investigation of microbial biochemistry, providing researchers with vast amounts of sequence data to explore biochemical functions and mechanisms, as well as novel enzymes and metabolites. By analyzing genomic context and understanding enzyme mechanisms, new microbial metabolic activities, enzymes, and metabolites can be discovered at an accelerated pace. The canonical organization of microbial genomes into gene clusters presents a unique opportunity for the utilization of genomic data, allowing for effective chemical discovery in microbial systems by leveraging functional and physiological relationships between genes within gene clusters.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Javier O. Cifuente, Julia Schulze, Andrea Bethe, Valerio Di Domenico, Christa Litschko, Insa Budde, Lukas Eidenberger, Hauke Thiesler, Isabel Ramon Roth, Monika Berger, Heike Claus, Cecilia D'Angelo, Alberto Marina, Rita Gerardy-Schahn, Mario Schubert, Marcelo E. Guerin, Timm Fiebig
Summary: This study investigates the biosynthesis pathway of Haemophilus influenzae serotype b capsule and reveals the structure of the key enzyme. The findings provide insights into the critical role of the capsule in bacterial survival.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yiyuan Cheng, Xuan Yi, Yan Zhang, Qingli He, Dandan Chen, Weiguo Cao, Pengfei Fang, Wen Liu
Summary: By reconstituting the biosynthetic route of ABCH-containing unit, we found that the formation of ABCH is completed by an oxidase heterotetramer with the association of NRPS. DADH precursor was prepared and offloaded from an amino-group carrier protein. DADH was processed to form an aziridine ring and further cyclized to form a fused five-membered nitrogen heterocycle in the NRPS. The catalytic mechanism of the oxidase heterotetramer was rationalized through biochemical characterization, crystal structure, and site-specific mutagenesis.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Yingling Lu, Yi Wang, Xiaolong Yuan, Ou Huang, Quanying Dong, Dandan Li, Shujin Ding, Fuxian Ma, Hong Yu
Summary: The whole genome of Cordyceps pseudotenuipes was sequenced, annotated, and compared with three related species to characterize the genome. The study explored the secondary metabolites and biosynthesis gene clusters of Cordyceps genus using antiSMASH and local BLAST analysis. The analysis revealed differences in genome size, gene lengths, and GC contents among different species of Cordyceps. The study also identified putative secondary metabolite biosynthesis gene clusters and unique secondary metabolites in Cordyceps pseudotenuipes.
Article
Chemistry, Organic
Haochen Zou, Xin Xia, Qiushuang Xu, Haoxin Wang, Yuemao Shen, Yaoyao Li
Summary: The structural diversity of PoTeMs is mainly generated by cyclases and cytochrome P450s. In Saccharopolyspora hirsuta, six new cytotoxic PoTeMs, including the first examples of oxidized one-ring PoTeMs, were discovered through combinatorial reassembling and heterologous expression.
Article
Biology
Yuanyuan Feng, Xu Yang, Huining Ji, Zixin Deng, Shuangjun Lin, Jianting Zheng
Summary: Structural analysis of a Streptomyces viridochromogenes product template (PT) domain reveals molecular and functional similarities with known fungal PTs. The PT domain acts as an aldol cyclase to control the regiospecific aldol cyclization of reactive poly-beta-ketone intermediates. The bacterial PT closely resembles the dehydrase (DH) domains of modular type I polyketide synthases (PKSs) and represents an evolutionary intermediate between the two tailoring domains of type I PKSs.
COMMUNICATIONS BIOLOGY
(2022)
Article
Immunology
Nicole Inge Richardson, Neil Ravenscroft, Vanessa Arato, Davide Oldrini, Francesca Micoli, Michelle M. Kuttel
Summary: Shigella, a pathogenic bacterium, is a major cause of diarrheal disease and death, especially impacting young children in low-income countries. Given the increasing antibiotic resistance in Shigella, there is a need for an effective vaccine targeting the bacterial lipopolysaccharide O-antigen. Research on S. flexneri serotype 6 suggests that O-acetylation may not be essential for the antigenicity of the serotype, as confirmed by an in vivo study in mice.
Review
Biochemistry & Molecular Biology
Robert A. Hill, Andrew Sutherland
Summary: This paper presents a personal selection of 32 recent papers covering various aspects of current developments in bioorganic chemistry and novel natural products, including eurysoloid A from Eurysolen gracilis.
NATURAL PRODUCT REPORTS
(2021)
Article
Immunology
Zhenzhou Huang, Keyi Yu, Ruiting Lan, J. Glenn Morris, Yue Xiao, Julian Ye, Leyi Zhang, Longze Luo, He Gao, Xuemei Bai, Duochun Wang
Summary: This study describes the whole-genome features of V. metschnikovii strains and identifies two major lineages and 29 O-genotypes. Moreover, it identifies 19 virulence-associated factors and highlights the importance of lateral flagella in the early stages of infection.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Biotechnology & Applied Microbiology
Atsushi Jikumaru, Satoshi Ishii, Tomoko Fukudome, Yasuhiko Kawahara, Atsushi Iguchi, Yoshifumi Masago, Kei Nukazawa, Yoshihiro Suzuki
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2020)
Article
Microbiology
Thi Thu Huong Nguyen, Atsushi Iguchi, Ritsuko Ohata, Hisahiro Kawai, Tadasuke Ooka, Hiroshi Nakajima, Sunao Iyoda
Summary: This study screened 366 STEC strains isolated from healthy cattle, revealing 13 novel Og types and a strain carrying two types of O-AGCs. The DNA-based serotyping systems used here could be beneficial for future epidemiological studies and risk assessments of other STEC strains.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Infectious Diseases
Isaac Prah, Alafate Ayibieke, Thi Thu Huong Nguyen, Atsushi Iguchi, Samiratu Mahazu, Wakana Sato, Takaya Hayashi, Shoji Yamaoka, Toshihiko Suzuki, Shiroh Iwanaga, Anthony Ablordey, Ryoichi Saito
Summary: By characterizing DEC strains from stool samples of pediatric patients in the Western region of Ghana, diverse serotypic identities and phylogenetic relatedness were observed, highlighting the importance and novelty of these genotypes circulating in the area that should be monitored for public health purposes.
JAPANESE JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Microbiology
Daigo Tsubokawa, Taisei Kikuchi, Jae Man Lee, Takahiro Kusakabe, Yasuhiko Yamamoto, Haruhiko Maruyama
Summary: Parasitic helminths can disrupt host protective immunity by targeting the RAGE receptor, and the EF-hand Ca2+-binding protein venestatin secreted by Strongyloides venezuelensis plays a key role in this immune evasion process. Venestatin binds to RAGE and suppresses inflammatory responses, facilitating larval migration from the skin to the lungs. These findings suggest that targeting the anti-inflammatory mechanism of venestatin may offer new therapeutic approaches for RAGE-mediated inflammatory diseases.
Article
Microbiology
Thi Thu Huong Nguyen, Taisei Kikuchi, Tadaaki Tokunaga, Sunao Iyoda, Atsushi Iguchi
Summary: The study examined 106 E. coli strains from various animals and classified ter operons into four subtypes based on nucleotide sequence, revealing significant differences in their positions and tellurite resistance. The research provided insights into the genetic characteristics of ter operons, as well as their phenotypic and ecological traits related to diversity.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Taisei Kikuchi, Mehmet Dayi, Vicky L. Hunt, Kenji Ishiwata, Atsushi Toyoda, Asuka Kounosu, Simo Sun, Yasunobu Maeda, Yoko Kondo, Belkisyole Alarcon de Noya, Oscar Noya, Somei Kojima, Toshiaki Kuramochi, Haruhiko Maruyama
Summary: Kikuchi et al. sequenced the genomes of the fatal tapeworm Sparganum proliferum and a closely related non-life-threatening tapeworm Spirometra erinaceieuropaei, revealing distinct evolutionary history and pathogenic mechanisms. The findings highlight the importance of nonordinal extracellular matrix coordination for asexual reproduction in the host, and suggest that the loss of sexual maturity contributes to the fatal pathogenicity of S. proliferum to humans.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Ryoji Shinya, Simo Sun, Mehmet Dayi, Isheng Jason Tsai, Atsushi Miyama, Anthony Fu Chen, Koichi Hasegawa, Igor Antoshechkin, Taisei Kikuchi, Paul W. Sternberg
Summary: The authors demonstrate that sex determination in Bursaphelenchus nematodes is likely regulated by a random, epigenetic mechanism, rather than the more well-known mechanisms of chromosomal or environmental sex determination.
NATURE COMMUNICATIONS
(2022)
Article
Developmental Biology
Gina Broitman-Maduro, Simo Sun, Taisei Kikuchi, Morris F. Maduro
Summary: Endoderm specification in Caenorhabditis elegans is achieved through the activation of the GATA factor cascade MED-1,2-END-1,3-ELT-2,7 by maternally provided SKN-1/Nrf and input from POP-1/TCF. However, the absence of orthologues of MED, END, and ELT-7 factors in more distant nematode species raises the question of gut specification in those species. This study finds that the GATA factor gene elt-3 orthologues in C. angaria, C. portoensis, and C. monodelphis are expressed in the early E lineage, and the loss of Can-elt-3 results in a penetrant 'gutless' phenotype in C. angaria. The ancestral mechanism for gut specification and differentiation in Caenorhabditis involves a simpler POP-1-ELT-3-ELT-2 gene network.
Article
Biochemistry & Molecular Biology
Cheng-Kuo Lai, Yi-Chien Lee, Huei-Mien Ke, Min R. Lu, Wei-An Liu, Hsin-Han Lee, Yu-Ching Liu, Toyoshi Yoshiga, Taisei Kikuchi, Peichen J. Chen, Isheng Jason Tsai
Summary: In this study, the genomes of six Aphelenchoides species, including four strains of the A. besseyi species complex, were analyzed. The systematic identification of horizontal gene transfer (HGT) genes revealed that these genes were mostly acquired from bacteria, fungi, and plants. This study provides a comprehensive understanding of HGT in nematodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Ecology
Kohta Yoshida, Christian Roedelsperger, Waltraud Roeseler, Metta Riebesell, Simo Sun, Taisei Kikuchi, Ralf J. Sommer
Summary: Recent research on closely related nematode species showed that chromosome fusions have played a key role in their genomic evolution and reproductive isolation. The fusions altered recombination rates and drove the speciation process. Rating: 7/10.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Zoology
Chiho Kaneko, Akio Shinohara, Taisei Kikuchi, Asami Tokuda, Takao Irie, Kentaro Yamada, Naoaki Misawa, Ayako Yoshida
Summary: The study compared the gut microbiota of Japanese badgers and raccoon dogs and found that they had completely different gut microbiota. Badgers were dominated by the phyla Firmicutes and Proteobacteria, while raccoon dogs had abundant Firmicutes and Bacteroidota, and also exhibited richer and more diverse species. This suggests that badgers and raccoon dogs have distinct gut microbiota despite their similar diets and habitats.
Article
Biochemistry & Molecular Biology
Yi-Chien Lee, Huei-Mien Ke, Yu-Ching Liu, Hsin-Han Lee, Min-Chen Wang, Yung-Che Tseng, Taisei Kikuchi, Isheng Jason Tsai
Summary: Obtaining sufficient genetic material from limited biological sources is a major challenge in biodiversity and genome evolution studies. In this study, we successfully amplified nanograms of DNA and mRNA from individual Caenorhabditis elegans using multiple displacement amplification (MDA) and Smartseq2 techniques. We generated long-read sequences with Oxford Nanopore Technologies (ONT) and achieved high genome coverage. Through genome and transcriptome sequencing of multiple nematode species, we discovered genome diversity and phylogenetic relationships within the phylum Nematoda. This study demonstrates the robustness of MDA and ONT for studying genome diversity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Veterinary Sciences
Kentaro Okuno, Sharda Prasad Awasthi, German A. Kopprio, Atsushi Iguchi, Noritoshi Hatanaka, Atsushi Hinenoya, Ruben Jose Lara, Shinji Yamasaki
Summary: This study aimed to investigate the prevalence, O-genotypes, and virulence gene profiles of stx-producing Escherichia coli (STEC) in beef cattle from Bahia Blanca, Argentina. The study found that stx2a and stx2c were not only present in O145 and O157, but also in minor O-genotypes of STEC in Argentina.
JOURNAL OF VETERINARY MEDICAL SCIENCE
(2021)
Article
Immunology
Kenichi Lee, Atsushi Iguchi, Kazuhiro Uda, Sohshi Matsumura, Isao Miyairi, Kenji Ishikura, Makoto Ohnishi, Junji Seto, Kanako Ishikawa, Noriko Konishi, Hiromi Obata, Ichiro Furukawa, Hiromi Nagaoka, Hirotaka Morinushi, Natsuki Hama, Ryohei Nomoto, Hiroshi Nakajima, Hideaki Kariya, Mitsuhiro Hamasaki, Sunao Iyoda
Summary: This study reports a fatal case of hemolytic uremic syndrome caused by Shiga toxin-producing Escherichia coli in Japan. The genotype of the isolate was identified as OX18:H2, and whole-genome sequencing revealed 3 potentially pathogenic lineages (OX18:H2, H19, and H34) that have been continuously isolated in Japan.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Microbiology
Atsuko Minowa-Nozawa, Takashi Nozawa, Daisuke Takamatsu, Akemi Yoshida, Kazunori Murase, Taisei Kikuchi, Kasumi Ishida-Kuroki, Yoshihiro Nitta, Tsutomu Sekizaki, Ichiro Nakagawa
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)