Article
Microbiology
Joep J. J. M. Stohr, Marjolein F. Q. Kluytmans-van den Bergh, Veronica A. T. C. Weterings, John W. A. Rossen, Jan A. J. W. Kluytmans
Summary: This study evaluated three approaches to distinguish epidemiologically related from unrelated bla(KPC)-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids, showing that phylogenetic distance had the highest discriminatory power.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Review
Biochemistry & Molecular Biology
Yuli Zhang, Linlin Hou
Summary: Sox proteins, known as crucial transcription factors, are not limited to transcription initiation but also involved in regulating alternative splicing networks and translational control.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Simon Beard, Ana Moya-Beltran, Danitza Silva-Garcia, Cesar Valenzuela, Tomas Perez-Acle, Alejandra Loyola, Raquel Quatrini
Summary: This study investigated the diversity, distribution, and functional roles of nucleoid-associated proteins (NAPs) within the acidithiobacillia class, focusing on their role in mobile genetic elements (MGEs) biology. The study revealed the presence of core NAPs that were highly conserved across species and flexible NAPs that were encoded in plasmids or larger integrated MGEs. These core and flexible NAPs proved valuable as markers and provided insights into the stabilization of MGEs in strains and species with larger genomes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Fiona Jenkinson, Philip Zegerman
Summary: Protein phosphatases play a crucial role in DNA replication initiation by dephosphorylating replication initiation factors, ensuring timely and stable replication of the genome. Understanding the role of phosphatases may provide critical insights into cancer treatment, as many kinases involved in replication control are targets for new chemotherapies.
Article
Genetics & Heredity
Anand P. Maurya, Alessandro Lazdins, Helen Wilson, Georgina S. Lloyd, Elton R. Stephens, Anthony S. Haines, Christopher M. Thomas
Summary: The replication control of plasmids is influenced by the interaction between Rep protein and repeated sequences known as iterons in the replication origin, oriV. Negative control is achieved through Rep protein handcuffing iterons. The well-studied oriV region of RK2 contains 9 iterons, but only iterons 5 to 9 are essential for replication. Flipping the orientation of iterons 1 and 10, which share the same upstream hexamer, does not increase but rather slightly decrease the copy-number. Mutagenesis of the hexamer upstream of iteron 10 suggests functional differences in the interaction with TrfA compared to the essential iterons.
Article
Microbiology
Adam Valcek, Petra Sismova, Kristina Nesporova, Soren Overballe-Petersen, Ibrahim Bitar, Ivana Jamborova, Arie Kant, Jaroslav Hrabak, Jaap A. Wagenaar, Jean-Yves Madec, Peter Damborg, Engeline van Duijkeren, Christa Ewers, Joost Hordijk, Henrik Hasman, Michael S. M. Brouwer, Monika Dolejska
Summary: The study found that the equine-associated Escherichia coli strains ST1250 and its variants ST1250-SLV/DLV exhibit high genetic diversity at the genomic level, with a portion of the samples carrying the epidemic multidrug resistance plasmid lineage IncHI1/ST9 and fos operon associated with E. coli-ST1250.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Review
Cell Biology
Ana Rita Ferreira, Mariana Marques, Bruno Ramos, Jonathan C. Kagan, Daniela Ribeiro
Summary: Peroxisomes, essential subcellular organelles, play crucial roles in lipid and reactive oxygen species metabolism, and have recently been recognized as key players in viral infections. They are involved in both cellular antiviral response and proviral functions. Targeting peroxisome-related mechanisms may represent a promising strategy for the development of novel antiviral approaches in the future.
TRENDS IN CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ching-Wen Chiu, Ya-Ru Li, Cheng-Yuan Lin, Hsin-Hung Yeh, Ming-Jung Liu
Summary: By experimentally profiling translation initiation sites, we have identified unannotated genes in tomato yellow leaf curl Thailand virus (TYLCTHV) and determined their association with transcriptional and/or translational start sites and flanking mRNA sequences. We have also discovered the importance of an unexplored gene, BV2, for pathogenicity. This study highlights the significance of coding complexity in plant viruses.
Article
Biology
Lorraine De Jesus-Kim, Larry J. Friedman, Marko Looke, Christian K. Ramsoomair, Jeff Gelles, Stephen P. Bell
Summary: The committed step of eukaryotic DNA replication occurs when Mcm2-7 replicative helicases are activated. Helicase activation requires the recruitment of Cdc45 and GINS to form CMGs. The study found that Cdc45 and GINS are recruited to Mcm2-7 in two stages, with phosphorylation modulating the process.
Article
Cell Biology
Hong-Lei Jin, Sujuan Duan, Pengxiang Zhang, Ziyue Yang, Yunping Zeng, Ziqi Chen, Liu Hong, Mengshu Li, Lujun Luo, Zhenyi Chang, Jiliang Hu, Hong -Bin Wang
Summary: This study reveals the role of CND1 protein in maintaining genome stability in both chloroplasts and nuclei. Loss of CND1 affects nuclear cell-cycle progression and photosynthetic activity. CND1 also plays a role in the coordination of genome status across organelles to regulate plant growth and development.
Article
Microbiology
Xheni Karaboja, Xindan Wang
Summary: Nucleoid-associated proteins (NAPs) play crucial roles in structuring bacterial genomes and various DNA transactions. While NAPs are generally nonessential, the HU homolog HBsu is essential for cell viability in Bacillus subtilis. This study demonstrates that HBsu is required for the initiation of DNA replication, likely by promoting origin melting by DnaA, as well as another unknown essential function.
JOURNAL OF BACTERIOLOGY
(2022)
Review
Cell Biology
Balwina Koopal, Sumanth K. Mutte, Daan C. Swarts
Summary: Argonaute proteins (Agos) utilize small 15-30 nucleotide-long guides to bind and/or cleave complementary target nucleic acids. While eukaryotic Agos mediate RNA-guided RNA silencing, prokaryotic Agos (pAgos) use RNA or DNA guides to interfere with invading plasmid and viral DNA. This review focuses on the function and mechanisms of truncated and highly divergent 'short' pAgos, which have only recently been characterized. Short pAgos retain the MID and PIWI domains crucial for guide-mediated target binding, but lack the ability to cleave targets. Instead, they interact with specific accessory enzymes to kill host cells and prevent invader spread.
TRENDS IN CELL BIOLOGY
(2023)
Article
Microbiology
Bahtiyar Yilmaz, Catherine Mooser, Irene Keller, Hai Li, Jakob Zimmermann, Lars Bosshard, Tobias Fuhrer, Mercedes Gomez de Agueero, Nerea Fernandez Trigo, Heidi Tschanz-Lischer, Julien P. Limenitakis, Wolf-Dietrich Hardt, Kathy D. McCoy, Baerbel Stecher, Laurent Excoffier, Uwe Sauer, Stephanie C. Ganal-Vonarburg, Andrew J. Macpherson
Summary: The study showed that isobiotic mice with stable microbiota can adapt to changes in the intestinal environment through long-term genomic positive selection and short-term transcriptional reprogramming and adjustments in sub-strain proportions.
CELL HOST & MICROBE
(2021)
Article
Chemistry, Multidisciplinary
Haoyang Peng, Simin Zhang, Yihan Peng, Shuangyi Zhu, Xin Zhao, Xiaocong Zhao, Shuangshuang Yang, Guangxue Liu, Yang Dong, Xiaoli Gan, Qing Li, Xinghua Zhang, Huadong Pei, Xuefeng Chen
Summary: Histone acetylation plays a key role in chromatin structure and function, with Bromodomain proteins like Bdf1 and TAF1 being essential in promoting DNA repair by homologous recombination. Their interaction with acetylated histones and RPA facilitates repair processes, highlighting a conserved mechanism in maintaining genome integrity.
Article
Microbiology
Yue Liu, Nikolaos Charamis, Sjef Boeren, Joost Blok, Alisha Geraldine Lewis, Eddy J. Smid, Tjakko Abee
Summary: This study investigated the impact of different forms of vitamin K2 produced by Lactococcus cremoris and L. lactis on bacterial survival, finding that long-chain forms are more effective in aerobic respiratory electron transport, while short-chain forms are preferred for facilitating extracellular electron transfer and reactions, supporting the growth and survival of these bacteria in various environments.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wesley Loftie-Eaton, Hirokazu Yano, Stephen Burleigh, Ryan S. Simmons, Julie M. Hughes, Linda M. Rogers, Samuel S. Hunter, Matthew L. Settles, Larry J. Forney, Jose M. Ponciano, Eva M. Top
MOLECULAR BIOLOGY AND EVOLUTION
(2016)
Article
Biochemistry & Molecular Biology
Hirokazu Yano, Katarznya Wegrzyn, Wesley Loftie-Eaton, Jenny Johnson, Gail E. Deckert, Linda M. Rogers, Igor Konieczny, Eva M. Top
MOLECULAR MICROBIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Yingbiao Zhang, Tomoyuki Matsuzaka, Hirokazu Yano, Yoshikazu Furuta, Toshiaki Nakano, Ken Ishikawa, Masaki Fukuyo, Noriko Takahashi, Yutaka Suzuki, Sumio Sugano, Hiroshi Ide, Ichizo Kobayashi
NUCLEIC ACIDS RESEARCH
(2017)
Article
Evolutionary Biology
Hirokazu Yano, Tomotada Iwamoto, Yukiko Nishiuchi, Chie Nakajima, Daria A. Starkova, Igor Mokrousov, Olga Narvskaya, Shiomi Yoshida, Kentaro Arikawa, Noriko Nakanishi, Ken Osaki, Ichiro Nakagawa, Manabu Ato, Yasuhiko Suzuki, Fumito Maruyama
GENOME BIOLOGY AND EVOLUTION
(2017)
Article
Multidisciplinary Sciences
Lisa Nonaka, Tatsuya Yamamoto, Fumito Maruyama, Yuu Hirose, Yuki Onishi, Takeshi Kobayashi, Satoru Suzuki, Nobuhiko Nomura, Michiaki Masuda, Hirokazu Yano
Article
Multidisciplinary Sciences
Ryo Miyazaki, Hirokazu Yano, Vladimir Sentchilo, Jan Roelof van der Meer
SCIENTIFIC REPORTS
(2018)
Article
Multidisciplinary Sciences
Thibault Stalder, Linda M. Rogers, Chris Renfrow, Hirokazu Yano, Zachary Smith, Eva M. Top
SCIENTIFIC REPORTS
(2017)
Article
Biotechnology & Applied Microbiology
Hirokazu Yano, Haruo Suzuki, Fumito Maruyama, Tomotada Iwamoto
Article
Infectious Diseases
Kentaro Arikawa, Tomoaki Ichijo, Satomi Nakajima, Yukiko Nishiuchi, Hirokazu Yano, Aki Tamaru, Shiomi Yoshida, Fumito Maruyama, Atsushi Ota, Masao Nasu, Daria A. Starkova, Igor Mokrousov, Olga Narvskaya, Tomotada Iwamoto
INFECTION GENETICS AND EVOLUTION
(2019)
Article
Biochemistry & Molecular Biology
Thibault Stalder, Brandon Cornwell, Jared Lacroix, Bethel Kohler, Seth Dixon, Hirokazu Yano, Ben Kerr, Larry J. Forney, Eva M. Top
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Microbiology
Shinnosuke Inaba, Hironori Sakai, Hiromi Kato, Takayuki Horiuchi, Hirokazu Yano, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata
Article
Microbiology
Hirokazu Yano, Md Zobaidul Alam, Emiko Rimbara, Tomoko F. Shibata, Masaki Fukuyo, Yoshikazu Furuta, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Lisa Nonaka, Michiaki Masuda, Hirokazu Yano
Summary: The exchange of antimicrobial resistance genes between aquaculture and terrestrial microbial populations is a serious public health concern. This study reveals the presence of SEs (strand-biased circularizing integrative elements) in marine bacteria, which could play a crucial role in the spread of antimicrobial resistance genes.
Article
Genetics & Heredity
Desmila Idola, Hiroshi Mori, Yuji Nagata, Lisa Nonaka, Hirokazu Yano
Summary: This study confirmed the transposition mode and prevalence of strand-biased circularizing integrative elements (SEs) by searching for hypothetical transposition intermediates in the genomic DNA fractions of an SE host. The experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. SEs were found to mainly exist in a subset of free-living Gammaproteobacteria, which represents a narrower host range compared to other mobile DNA element groups.
Review
Biochemistry & Molecular Biology
Hirokazu Yano, Masaki Shintani, Masaru Tomita, Haruo Suzuki, Taku Oshima
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2019)