Article
Multidisciplinary Sciences
Sandesh Acharya, Amol Dahal, Hitesh Kumar Bhattarai
Summary: DNA replication is a crucial process in life, with the sliding clamp playing a significant role in facilitating the attachment of replicative polymerase. While the structure and functionality of sliding clamps vary across different domains of life, there is a conservation of protein sequence among them. Analysis of sliding clamp and PCNA sequences from diverse species reveals insights into their evolutionary origins.
Article
Microbiology
Peter B. Bohall, Stephen D. Bell
Summary: The loss of putative repair polymerases PolB2 and/or PolB3 in the crenarchaeon Sulfolobus islandicus leads to a modest growth advantage and insensitivity to hydrogen peroxide. However, cells lacking PolB3 show enhanced sensitivity to the DNA damaging agent 4-NQO, suggesting that these non-essential DNA polymerases may influence DNA repair pathway choice in hyperthermophilic aerobes.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Stephanie-Jane Nobs, Fraser MacLeod, Hon Lun Wong, Brendan P. Burns
Summary: The origin of eukaryotic cells, which occurred approximately 2 billion years ago, is one of the most significant events in the evolution of life. Ground-breaking research has changed our understanding of the Tree of Life by unraveling the contributions of archaea and bacteria in eukaryogenesis. The discovery of complex cell machineries in Asgard archaeal lineages and the evidence of bacterial gene transfers challenge the uniqueness of eukaryotes as a distinct domain.
TRENDS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Mei-Jing Dong, Hao Luo, Feng Gao
Summary: Ori-Finder is a web server for predicting bacterial DNA replication origins. It integrates multiple methods and databases to provide accurate predictions and facilitate data mining and analysis. The updated Ori-Finder 2022 has improved prediction framework, visualization module, analysis module, and user-friendly interface.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Microbiology
Claudia Maturana-Martinez, Camila Fernandez, Humberto E. Gonzalez, Pierre E. Galand
Summary: The study revealed that in two Chilean Patagonian fjords, the active microbial communities showed higher diversity and stronger biogeographic patterns compared to the standing stock. Climate change could potentially alter the composition of surface microbial communities, with unique features distinct from oceanic waters.
FRONTIERS IN MICROBIOLOGY
(2021)
Editorial Material
Microbiology
Markus Goeker, Edward R. B. Moore, Aharon Oren, Martha E. Trujillo
Summary: The recent publication of the alternative nomenclatural code SeqCode raises questions about how to treat names 'validly published' under that code in IJSEM. It is reiterated that IJSEM must adhere to the ICNP and assign a nomenclatural status to all prokaryotic names, including those 'validly published' under SeqCode. Such names should be marked as Candidatus names or printed in quotation marks.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Yulia Fridman, Zihan Wang, Sergei Maslov, Akshit Goyal
Summary: Recent observations have shown that closely related strains of the same microbial species can stably coexist in different environments. A consumer-resource model of microbial ecosystems suggests that differentiation of strains based on their growth rates in high and low nutrient conditions enables coexistence. The model also demonstrates that between 1 and 3 strains of a species typically coexist, consistent with experimental observations.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Nazima Habibi, Saif Uddin, Hanan Al-Sarawi, Ahmed Aldhameer, Anisha Shajan, Farhana Zakir, Nasreem Abdul Razzack, Faiz Alam
Summary: In this study, the metagenomes of 12 coastal surface sediments were analyzed through whole genome shotgun sequencing. The results revealed that bacteria, archaea, and fungi were the dominant microbial communities in the area. Additionally, various viruses and plant pathogens were identified. This study provides valuable information on the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.
Review
Microbiology
S. Mayo-Perez, Y. Gama-Martinez, S. Davila, N. Rivera, I. Hernandez-Lucas
Summary: This review focuses on the distribution, abundance, evolution, structural organization, transcriptional regulation, and fundamental roles of LysR-type transcriptional regulators (LTTRs) in bacteria, archaea, and algae. It also discusses their involvement in free life, pathogenesis, and bacteria-plant interaction, providing a current understanding of LTTR biology.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Microbiology
Jan Bergsch, Jean-Christophe Devillier, Gunnar Jeschke, Georg Lipps
Summary: The study demonstrates how DNA primase terminates primer formation at a specific length and the impact of mutations in the unstructured linker connecting the catalytic domain to the template binding domain. Understanding these mechanisms can provide insights into the role of primase in DNA replication.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Hiroka Miyabayashi, Hiroyuki D. Sakai, Norio Kurosawa
Summary: The subunits PBP1 and PBP2 greatly influence the activity of DNA polymerase PolB1, with PBP1 deletion leading to sensitivity to various types of DNA damage and increased mutation rate, while PBP2 is crucial for the replication process.
Article
Biochemistry & Molecular Biology
Hong-Wei Pi, Jinn-Jy Lin, Chi-An Chen, Po-Hsiang Wang, Yin-Ru Chiang, Chieh-Chen Huang, Chiu-Chung Young, Wen-Hsiung Li
Summary: This study provides evidence supporting the bacteria-first hypothesis in the origin of nitrogen fixation. The researchers found that in the phylogenetic trees of nitrogen-fixing proteins, the earliest lineages are bacterial sequences and the archaeal sequences are nested inside bacterial sequences. Additionally, they observed that most Nif archaea carry bacterial Mo transporter proteins. Isotopic data also support the bacteria-first hypothesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Xinli Wang, Yun Wang, Fei Zhu, Chi Zhang, Peiyao Wang, Xuan Zhang
Summary: Different disturbance gradients in land use types affect the distribution of active nitrifier communities, with ammonia-oxidizing archaea and bacteria as well as nitrite-oxidizing bacteria being influenced by soil physicochemical properties.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Ecology
Emilie Lyautey, Elodie Billard, Nathalie Tissot, Stephan Jacquet, Isabelle Domaizon
Summary: This study investigated the spatial variability and temporal dynamics of methanogenic Archaea and methanotrophic bacteria in Lake Bourget, France. Changes in both structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics.
Review
Chemistry, Multidisciplinary
Eskandar Moghimipour, Samaneh Abedishirehjin, Maryam Abedini Baghbadorani, Somayeh Handali
Summary: Microorganisms are being considered for cancer treatment due to their ability to secrete bioactive compounds that inhibit cancer cell growth. Nanocarriers derived from microorganisms, such as OMVs and BGs, are also being explored as drug delivery systems. The combination of microbiology and nanotechnology shows promising potential for eradicating cancer by delivering more drugs into cancer cells.
JOURNAL OF CONTROLLED RELEASE
(2021)
Article
Multidisciplinary Sciences
Zuanning Yuan, Roxana Georgescu, Lin Bai, Dan Zhang, Huilin Li, Michael E. O'Donnell
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Fengwei Zheng, Roxana E. Georgescu, Huilin Li, Michael E. O'Donnell
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Grant D. Schauer, Lisanne M. Spenkelink, Jacob S. Lewis, Olga Yurieva, Stefan H. Mueller, Antoine M. van Oijen, Michael E. O'Donnell
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Huilin Li, Fengwei Zheng, Mike O'Donnell
Summary: Polymerase sliding clamps are ring-shaped proteins that encircle duplex DNA and interact with the DNA through water layers, providing nearly frictionless support for fast and processive DNA synthesis. The crystal structure of clamp-DNA complex shows a highly tilted DNA conformation through the clamp inner surface, while replicative polymerases position DNA straight through the clamp without direct protein-DNA contacts. This unique interaction mechanism allows the clamps to 'water skate' on DNA during function with replicative polymerases, ensuring efficient DNA synthesis across all domains of life.
Article
Multidisciplinary Sciences
Xiang Feng, Yasunori Noguchi, Marta Barbon, Bruce Stillman, Christian Speck, Huilin Li
Summary: The Origin Recognition Complex (ORC) specifies the location of DNA replication origins by binding to specific DNA sequences throughout the cell cycle. It becomes active only when it binds to the replication initiator Cdc6, which contributes to origin DNA recognition through its winged helix domain (WHD) and initiator-specific motif. Cdc6 binding rearranges certain protein domains in ORC, leading to the activation of Cdc6 ATPase and the formation of sites for recruiting Mcm2-7.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Nina Y. Yao, Dan Zhang, Olga Yurieva, Michael E. O'Donnell
Summary: While ATP gamma S is often used to prevent CMG from unwinding DNA, this study found that CMG can actually hydrolyze ATP gamma S and perform DNA unwinding. The rate of unwinding is only slightly reduced when using ATP gamma S compared to ATP, suggesting that a conformational change is the limiting step for CMG unwinding, rather than hydrolysis. Furthermore, the study demonstrates that nonhydrolyzable AMP-PNP can be used to load CMG onto DNA without unwinding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Fengwei Zheng, Roxana E. Georgescu, Nina Y. Yao, Michael E. O'Donnell, Huilin Li
Summary: The Cryo-EM analysis shows that Rad24-RFC loads the 9-1-1 clamp onto 5'-recessed DNA to activate the DNA damage checkpoint. This loading mechanism is different from RFC, and involves a unique way of threading DNA into the clamp.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biology
Fengwei Zheng, Roxana Georgescu, Nina Y. Yao, Huilin Li, Michael E. O'Donnell
Summary: The RFC complex has been shown to have a second DNA binding site, located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. This 5' DNA site exhibits ideal binding to a 7-nt gap and shows enhanced binding to 5 and 10 nt gaps. It is proposed that the 5' site facilitates RFC's PCNA loading activity at DNA damage-induced gaps and plays a potential role in lagging strand DNA synthesis.
Review
Biochemistry & Molecular Biology
Huilin Li, Mike O'Donnell, Brian Kelch
Summary: Clamp loaders are pentameric AAA+ assemblies that open and close circular DNA sliding clamps using ATP, showing homology across different organisms. Recent studies have revealed unexpected DNA binding sites on both the clamp loader Rad24-RFC and RFC, shedding light on the loading mechanisms and introducing new features of the clamp loaders. These new findings have transformed our understanding of the clamp loader mechanism.
Article
Multidisciplinary Sciences
Sai Li, Michael R. Wasserman, Olga Yurieva, Lu Bai, Michael E. O'Donnell, Shixin Liu
Summary: This study found that the ORC can eject histones from a nucleosome in an ATP-dependent manner. It selectively evicts H2A-H2B dimers but leaves the (H3-H4)2 tetramer on DNA. It also discriminates canonical H2A from the H2A.Z variant, evicting the former while retaining the latter. These findings suggest that the ORC is a bona fide nucleosome remodeler that functions to create a local chromatin environment optimal for origin activity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Yixin Hu, Bruce Stillman
Summary: Errors during DNA replication can lead to genome instability, causing diseases like cancer or autism. Understanding the process of DNA replication and its regulation has made significant progress. This review focuses on the role of the origin recognition complex (ORC) in determining replication initiation sites in eukaryotic cells, as well as methods for mapping DNA replication. Origin specification varies between species and may have co-evolved with gene-silencing mechanisms. Centromeres and replication origins may have originated from a common element and separated during evolution.
Article
Multidisciplinary Sciences
Lance D. Langston, Zuanning Yuan, Roxana Georgescu, Huilin Li, Michael E. O'Donnell
Summary: This article investigates the mechanism of double-strand DNA unwinding during DNA genome replication. The researchers found that two helicases move inward together and unwind the double helix by pulling on opposite strands. They also discovered that in some cases, a single strand helicase can unwind a 150-base pair duplex. These findings contribute to our understanding of the initiation process of DNA replication.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Jeremy T-H Chang, Shibai Li, Emily C. Beckwitt, Thane Than, Cory Haluska, Joshua Chandanani, Michael E. O'Donnell, Xiaolan Zhao, Shixin Liu
Summary: In this study, the behavior of the Smc5/6 complex was visualized using single-molecule fluorescence and force microscopy. The complex displayed distinct behaviors towards different types of DNA, dynamically associating with double-stranded DNA and stably binding to junction DNA. The association with double-stranded DNA was enhanced by the Nse1-3-4 subcomplex and ATP binding, while the assembly onto single-stranded DNA originating from junction DNA depended mainly on the Nse1-3-4 subcomplex and not on ATP. Additionally, Smc5/6 was shown to protect the stability of junction DNA by preventing single-stranded DNA annealing.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Yi-Jun Sheu, Risa Karakida Kawaguchi, Jesse Gillis, Bruce Stillman
Summary: The Rad53 checkpoint kinase plays a major role in coordinating genome-wide replication and transcription under replication stress conditions. It binds to sites of active DNA replication initiation and fork progression, as well as to the promoters of genes involved in multiple cellular functions.
