Review
Gastroenterology & Hepatology
Pavol Sulo, Barbora Sipkova
Summary: Reliable diagnostics are crucial for detecting and treating Helicobacter pylori infection, with non-invasive urea breath test (UBT) and stool antigen test (SAT) currently leading the way. Nested PCR (NPCR) can achieve DNA amplification specificity by involving two rounds of PCR. Properly designed primers for the 16S rRNA gene can facilitate the development of an NPCR assay for unambiguous identification of H. pylori.
WORLD JOURNAL OF GASTROENTEROLOGY
(2021)
Article
Multidisciplinary Sciences
Sho Tsuyuki, Hideyuki Takeshima, Shigeki Sekine, Yukinori Yamagata, Takayuki Ando, Satoshi Yamashita, Shin Maeda, Takaki Yoshikawa, Toshikazu Ushijima
Summary: Analysis showed that gastric cancers with current and past H. pylori infection had similar profiles of genetic alterations in terms of point mutations and gene amplification.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Mehwish Noureen, Takeshi Kawashima, Masanori Arita
Summary: Helicobacter pylori displays a diverse genomic structure with high mutation and recombination rates. Through analysis of orthologous gene orders among 72 complete genomes, it was found that shared inversions reflect conserved genomic elements across strains from different geographical locations. Some rearrangements are region-specific, while others are global, indicating that highly shared rearrangements are more ancestral. The location of genomic islands plays a crucial role in the occurrence of rearrangements.
Review
Medicine, General & Internal
Hang Yang, Bing Hu
Summary: Helicobacter pylori infection is associated with various diseases, including gastric cancer. Eradication of H. pylori can prevent disease progression. Diagnosis methods include test-and-treat, endoscopy-based, and screen-and-treat strategies, but challenges like false-negative results and antibiotic resistance exist. Advances in imaging techniques and artificial intelligence have been made to improve accuracy.
Review
Immunology
Nina Gorle, Eva Bauwens, Freddy Haesebrouck, Annemieke Smet, Roosmarijn E. Vandenbroucke
Summary: Trillions of symbiotic microbial cells colonize our body, with a larger portion residing in the human gut. Changes in gut microbiota have been linked to various diseases, including neurological disorders. Helicobacter species, particularly H. suis, may play a role in neurological disorders via the microbiome-gut-brain axis, but further research is needed to understand their impact on the brain.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Microbiology
Victor E. Reyes
Summary: Helicobacter pylori infection is a major risk factor for gastric cancer and is associated with chronic inflammation and DNA damage. Understanding the mechanisms of H. pylori-induced carcinogenesis and immune evasion is crucial for preventing gastric cancer and reducing the burden of this disease.
Article
Gastroenterology & Hepatology
Xiao-Hua Li, Yong-Yi Huang, Lin-Ming Lu, Li-Juan Zhao, Xian-Ke Luo, Ru-Jia Li, Yuan-Yuan Dai, Chun Qin, Yan-Qiang Huang, Hao Chen
Summary: This study isolated drug-resistant H. pylori strains from Chinese patients and identified hp1181 and hp1184 genes associated with clarithromycin resistance. The findings suggest that mutations in hp1181 and hp1184 may be the earliest and most persistent response to clarithromycin resistance.
WORLD JOURNAL OF GASTROENTEROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yi-Wen Cheng, Cheng-Yao Chen
Summary: Helicobacter pylori is a highly infectious human pathogen causing various diseases. HpPol I, an essential protein for the viability of H. pylori, has multiple functions including DNA nick translation, strand-displacement synthesis, and exonuclease activities. The two catalytic domains of HpPol I may play a crucial role in DNA replication and repair in H. pylori.
Article
Cell Biology
Na Wang, Faying Zhou, Caiyu Chen, Hao Luo, Jingwen Guo, Wei Wang, Jian Yang, Liangpeng Li
Summary: Infection, particularly involving H. pylori, is believed to play a role in the development of atherosclerosis. Studies have shown that OMVs secreted by H. pylori accelerate atherosclerosis plaque formation by damaging endothelial cells. Components like CagA and LPS in H. pylori OMVs are implicated in this process, potentially through activation of the ROS/NF-kappa B signaling pathway.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Gastroenterology & Hepatology
Fabian Fellipe Bueno Lemos, Marcel Silva Luz, Samuel Luca Rocha Pinheiro, Kadima Nayara Teixeira, Fabricio Freire de Melo
Summary: Gastric mucosa-associated lymphoid tissue lymphoma (GML) is a low-grade B-cell neoplasia commonly associated with chronic gastritis induced by Helicobacter pylori (H. pylori) infection. However, a subset of GML patients are H. pylori-negative. Despite previous beliefs, it has been found that a considerable proportion of H. pylori-negative GML patients show complete remission after bacterial eradication therapy. The mechanisms underlying this treatment responsiveness are not fully understood, and further research is needed to establish the causal relationship between non-H. pylori gastric helicobacters (NHPHs) and GML.
WORLD JOURNAL OF GASTROENTEROLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Linqi Zhu, Yue Huang, Hong Li, Shihe Shao
Summary: Infection with Helicobacter pylori may promote the occurrence and progression of gastric cancer by influencing the tumor microenvironment (TME).
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Olga Sokolova, Michael Naumann
Summary: Infection with H. pylori triggers a robust cellular response in the host, potentially leading to gastric cancer. The regulation of cellular processes through ubiquitinylation mechanisms influences various pathologies including cancer, yet the exact impact of H. pylori on this process remains unclear.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Aura M. Rodriguez, Daniel A. Urrea, Carlos F. Prada
Summary: Helicobacter pylori is a pathogenic bacteria that causes diseases in the human stomach, with high genetic diversity among strains observed in different geographic lineages. Analysis of virulence factor genetic variability in H. pylori strains can provide key information in understanding their pathogenic behavior.
Review
Immunology
Daniel Sijmons, Andrew J. Guy, Anna K. Walduck, Paul A. Ramsland
Summary: This review discusses the importance of Helicobacter pylori infection and its impact on the host immune system, including mechanisms such as modulation of cell function, secretion of immune signaling molecules, and interference with immune cell differentiation. H. pylori also utilizes its unique lipopolysaccharide structure to mimic the host and interacts with the host through outer membrane proteins.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Florent Ailloud, Iratxe Estibariz, Gudrun Pfaffinger, Sebastian Suerbaum
Summary: Helicobacter pylori is a common and genetically diverse human bacterial pathogen responsible for chronic gastritis and gastric cancer. The integration of short DNA fragments in H. pylori during natural transformation is determined by the UvrC endonuclease, suggesting distinct pathways for importing short and long fragments.
Article
Biochemistry & Molecular Biology
Stephanie Marsin, Yazid Adam, Claire Cargemel, Jessica Andreani, Sonia Baconnais, Pierre Legrand, Ines Li de la Sierra-Gallay, Adeline Humbert, Magali Aumont-Nicaise, Christophe Velours, Francoise Ochsenbein, Dominique Durand, Eric Le Cam, Helene Walbott, Christophe Possoz, Sophie Quevillon-Cheruel, Jean-Luc Ferat
Summary: The study shows that VcDciA can stimulate the loading of VcDnaB on DNA, resulting in increased DNA unwinding. This work is the first step towards understanding the ancestral mode of loading bacterial replicative helicases on DNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Joseph M. Dahl, Natalie Thomas, Maxwell A. Tracy, Brady L. Hearn, Lalith Perera, Scott R. Kennedy, Alan J. Herr, Thomas A. Kunkel
Summary: We investigated two mutations in the exonuclease domain of Saccharomyces cerevisiae DNA polymerase epsilon. Both mutations increased the mutation rate and impaired the ability to degrade DNA. Additionally, the mutations reduced the concentration required to switch between proofreading and polymerization and increased the probability of mismatch incorporation and extension. These findings elucidate the association of homologous mutations in DNA polymerase epsilon with cancer.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Andrea M. Kaminski, Thomas A. Kunkel, Lars C. Pedersen, Katarzyna Bebenek
Summary: 8-oxo-guanine (8OG) is a common base lesion associated with human diseases such as cancer, aging-related neurodegenerative disorders, and atherosclerosis. It is highly mutagenic and poses challenges for DNA polymerases in replicating and repairing genomic or mitochondrial DNA correctly.
Review
Biochemistry & Molecular Biology
Jessica S. Williams, Thomas A. Kunkel
Summary: The focus of this review is on the incorporation of ribonucleotides into the eukaryotic nuclear genome during replication, their removal, and the consequences for genome stability and disease.
ANNUAL REVIEW OF BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Prashant P. Damke, Louisa Celma, Sumedha M. Kondekar, Anne Marie Di Guilmi, Stephanie Marsin, Jordane Depagne, Xavier Veaute, Pierre Legrand, Helene Walbott, Julien Vercruyssen, Raphael Guerois, Sophie Quevillon-Cheruel, J. Pablo Radicella
Summary: The ComFC protein is essential for natural transformation and is involved in transporting DNA through the cell membrane and handling single-stranded DNA in the cytoplasm. The crystal structure of ComFC and its affinity for single-stranded DNA suggest that it plays a crucial role in the recombination machinery.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Andrea M. Kaminski, Kishore K. Chiruvella, Dale A. Ramsden, Katarzyna Bebenek, Thomas A. Kunkel, Lars C. Pedersen
Summary: This study reveals the structural features of Pol lambda that allow it to bridge and stabilize DNA double-strand break ends, enabling the repair of genomic instability. The findings provide valuable insights into the mechanisms of DNA repair.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Zhi-Xiong Zhou, Thomas A. Kunkel
Summary: The high fidelity of replication of the nuclear DNA genome in eukaryotes involves three processes: incorporation of correct dNTPs, removal of mismatches by exonuclease activity, and DNA mismatch repair. This review focuses on two mechanisms of proofreading: intrinsic proofreading and extrinsic proofreading. The evidence suggests that extrinsic proofreading significantly enhances the fidelity of nuclear DNA replication.
Article
Cell Biology
Jessica S. Williams, Jessica L. Wojtaszek, Denise C. Appel, Juno Krahn, Bret D. Wallace, Evan Walsh, Thomas A. Kunkel, R. Scott Williams
Summary: This study investigates the mechanism of how Apn2 engages and processes DNA damage. The results show that Apn2 frays and cleaves DNA termini through a wedging mechanism. In a background with ribonucleotide excision repair defects, APN2 deletion and DNA-wedge mutant strains show mutator phenotypes, cell growth defects, and sensitivity to genotoxic stress. These findings reveal the important role of Apn2 nuclease activity in mitigating mutagenic and genome instability phenotypes caused by Top1 incision.
Article
Environmental Sciences
Sonia Abdallah, Amandine Jampy, Delphine Moison, Margaux Wieckowski, Sebastien Messiaen, Emmanuelle Martini, Anna Campalans, Juan Pablo Radicella, Virginie Rouiller-Fabre, Gabriel Livera, Marie-Justine Guerquin
Summary: Many endocrine disruptors, including bisphenols, impair the meiotic process and oocyte quality. This study investigates the effects of two bisphenol alternatives, BADGE and BPAF, on oogenesis in mice. The compounds delay meiosis initiation, induce DNA damage, and negatively affect gene expression in fetal premeiotic germ cells. These findings provide insights into the mechanisms underlying the deleterious effects of bisphenols and suggest oxidative DNA damage as a common mechanism for environmental pollutants.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemistry & Molecular Biology
Zhi-Xiong Zhou, Cindy Follonier, Scott A. Lujan, Adam B. Burkholder, Virginia A. Zakian, Thomas A. Kunkel
Summary: This study identifies a novel function for the Pif1 family 5'->3' DNA helicase Rrm3 in promoting mutation avoidance during DNA replication. The loss of Rrm3 leads to increased spontaneous mutations made by DNA polymerases Pols epsilon and delta, as well as higher mutagenesis by Pol zeta. The genomic loci affected by the loss of Rrm3 vary, and Rrm3 is particularly important for preventing Pol zeta-dependent mutagenesis at tRNA genes. The helicase activity of Rrm3 is essential for its role in mutation avoidance, and Pif1 serves as a backup for Rrm3 in suppressing mutagenesis. Additionally, the findings suggest that the sole human Pif1 family helicase may also play a role in replication fidelity, potentially contributing to its tumor-suppressor function.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Claire Cargemel, Stephanie Marsin, Magali Noiray, Pierre Legrand, Halil Bounoua, Ines Li De la Sierra-Gallay, Helene Walbott, Sophie Quevillon-Cheruel
Summary: During bacterial genome replication initiation, replicative helicases rely on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, many bacteria do not have these genes and instead have domesticated phage elements that have replaced the original loader gene dciA. A crystal structure study of the complex from Vibrio cholerae revealed that two VcDciA molecules interact with a dimer of VcDnaB without altering its canonical structure, providing insights into how DciA assists in DnaB loading. Surprisingly, DnaC from Escherichia coli also targets the same module on EcDnaB, suggesting functional interchangeability between VcDciA and EcDnaC despite their lack of structural similarity. This study represents a significant advancement in understanding the mechanism by which phage helicase loaders hijack bacterial replicative helicases during evolution.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Cell Biology
Xhaferr Tanushi, Guillaume Pinna, Marie Vandamme, Capucine Siberchicot, Ostiane D'Augustin, Anne-Marie Di Guilmi, J. Pablo Radicella, Bertrand Castaing, Rebecca Smith, Sebastien Huet, Francois Leteurtre, Anna Campalans
Summary: 8-oxoG is a mutagenic DNA lesion induced by ROS, and OGG1 plays a major role in repairing it. Two competitive inhibitors of OGG1, TH5487 and SU0268, have been identified. Our study uncovered two off-target effects of these inhibitors, inhibiting ABC family transporters and interfering with metaphase completion. These effects should be considered when interpreting studies using TH5487 and SU0268.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sandrine Ragu, Nathalie Droin, Gabriel Matos-Rodrigues, Aurelia Barascu, Sylvain Caillat, Gabriella Zarkovic, Capucine Siberchicot, Elodie Dardillac, Camille Gelot, Josee Guirouilh-Barbat, J. Pablo Radicella, Alexander A. Ishchenko, Jean-Luc Ravanat, Eric Solary, Bernard S. Lopez
Summary: In human primary cells, a noncanonical cellular response specific to nonblocking replication stress is discovered. This response generates reactive oxygen species (ROS) and activates detoxification genes. ROS are produced by DUOX1/DUOX2 and controlled by NF-kappa B.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Biochemistry & Molecular Biology
Ostiane D'Augustin, Virginie Gaudon, Capucine Siberchicot, Rebecca Smith, Catherine Chapuis, Jordane Depagne, Xavier Veaute, Didier Busso, Anne-Marie Di Guilmi, Bertrand Castaing, J. Pablo Radicella, Anna Campalans, Sebastien Huet
Summary: The DNA-glycosylase OGG1 constantly samples the DNA by rapidly alternating between diffusion within the nucleoplasm and short transits on the DNA, which is crucial for its recruitment to oxidative lesions. The sampling process is tightly regulated by the residue G245, while the residues Y203, N149, and N150 differentially regulate the sampling of the DNA and recruitment to oxidative lesions based on previous structural data.
NUCLEIC ACIDS RESEARCH
(2023)