Article
Biochemistry & Molecular Biology
David G. Nickens, Matthew L. Bochman
Summary: Pif1 helicase plays a critical role in DNA metabolism, relying on DNA binding and ATP hydrolysis to unwind DNA. Studies have shown that Pif1 preferentially binds to structured G-rich single-stranded DNA, but its preferred binding substrates do not maximally stimulate ATP hydrolysis activity.
Article
Biochemistry & Molecular Biology
Jinghua Li, Jianbing Ma, Vikash Kumar, Hang Fu, Chunhua Xu, Shuang Wang, Qi Jia, Qinkai Fan, Xuguang Xi, Ming Li, Haiguang Liu, Ying Lu
Summary: In this study, the authors used single-molecule techniques and computational modeling to investigate the dynamic conformations and their impact on structure-function relationships in two Pif1 helicases. They found that solvent-exposed nucleotides interact dynamically with the helicase surfaces and these interactions play a crucial role in the enzymatic activities of the helicases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yang-Xue Dai, Wei-Fei Chen, Na-Nv Liu, Fang-Yuan Teng, Hai-Lei Guo, Xi-Miao Hou, Shuo-Xing Dou, Stephane Rety, Xu-Guang Xi
Summary: The study reveals the crystal structures of ToPif1 and its mechanism of forming a stable dimer when binding to single-stranded DNA. Moreover, it is found that dimerization of ToPif1 has an inhibitory effect on its helicase activity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jia-Hsin Huang, You-Rou Liao, Tzu-Chieh Lin, Cheng-Hung Tsai, Wei-Yun Lai, Yang-Kai Chou, Jun-Yi Leu, Huai-Kuang Tsai, Cheng-Fu Kao
Summary: iTARGEX, a new association framework, can identify novel regulators involved in biological traits without prior functional annotations. Experimental validation of the novel candidates provides solid evidence for their roles in the respective traits, converting genome-wide observations into causal gene function predictions. Further application of iTARGEX is expected to facilitate the discovery of new regulators and provide observations for novel mechanistic hypotheses regarding different biological traits and phenotypes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Sandy Ibanes, Fatima El-Alaoui, Josephine Lai-Kee-Him, Chantal Cazevieille, Francois Hoh, Sebastien Lyonnais, Patrick Bron, Luca Cipelletti, Laura Picas, Simonetta Piatti
Summary: This study reveals that Syp1 is able to align and pack septin filaments laterally, aiding in the assembly of septin collar. It also emphasizes the conserved protein functions and the functional diversity of unstructured protein domains.
Article
Cell Biology
Nitish Dua, Akshaya Seshadri, Anjana Badrinarayanan
Summary: Mitochondria are essential organelles involved in cell growth and survival. Recent research has shown that maintaining the distribution and organization of mitochondria is crucial for maintaining the stability of the mitochondrial genome. However, the impact of DNA damage on mitochondrial dynamics and the loss of mtDNA is not well understood. This study developed a tool to induce mitochondria-specific DNA damage and observed dynamic reorganization of mitochondrial networks and mtDNA loss. Surprisingly, perturbation to the exonuclease function of mtDNA replicative polymerase also resulted in rapid mtDNA loss. The findings highlight the importance of genome maintenance for mitochondrial function and organelle organization.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Manuel Hotz, Nathaniel H. Thayer, David G. Hendrickson, Elizabeth L. Schinski, Jun Xu, Daniel E. Gottschling
Summary: This study discovered a previously unappreciated relationship between the number of copies of the ribosomal RNA gene and the replicative lifespan in budding yeast. The data suggest that regulatory mechanisms involving ribosomal DNA copy number limit lifespan and changes in rDNA copy number might explain the effects of lifespan-enhancing mutations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Alejandro Collin, Araceli Gonzalez-Jimenez, Maria del Carmen Gonzalez-Jimenez, Manuel J. Alfonso, Olga Calvo
Summary: Saccharomyces cerevisiae Sub1 is a transcriptional stimulatory protein that shares homology with the ssDNA binding domain (ssDBD) of human PC4. This study reveals the key residues responsible for DNA-ScSub1 interaction in vivo, localized in the ssDBD, and demonstrates that the carboxyl-terminal (CT) region is required for transcription elongation. These findings indicate that Sub1 plays a dual role in transcription, participating in initiation through the ssDBD and in elongation through the CT region.
Article
Biochemistry & Molecular Biology
Reena R. Varma, Juhee G. Pandya, Jyoti Sharma, Chandramani Pathak, Mohan N. Patel
Summary: In this study, five N, S donor ligands were synthesized and their complexes with rhenium were evaluated for their activity against DNA, cells, and bacteria. The synthesized compounds showed toxicity towards yeast cells and exhibited antiproliferative activity against bacteria and cancer cells.
MOLECULAR DIVERSITY
(2021)
Article
Genetics & Heredity
Andrew Ziesel, Qixuan Weng, Jasvinder S. Ahuja, Abhishek Bhattacharya, Raunak Dutta, Evan Cheng, G. Valentin Borner, Michael Lichten, Nancy M. Hollingsworth
Summary: During meiosis, recombination between homologous chromosomes generates crossovers that promote proper segregation. Recombination is initiated by Spo11-catalyzed DNA double strand breaks. Rad51 and Dmc1 bind to single strand tails to form presynaptic filaments, mediate strand invasion and generate D-loops. D-loop processing forms crossover and noncrossover recombinants. Meiotic recombination occurs in two phases: Rad51 is inhibited in Phase 1 and Dmc1 mediates interhomolog recombination, while Rad51 becomes active in Phase 2 and functions with Rad54 to repair residual DSBs, making increasing use of sister chromatids. The transition from Phase 1 to Phase 2 is controlled by the meiotic recombination checkpoint. Constitutive activation of Rad51 in Phase 1 leads to delay in meiotic recombination and increases chromosome nondisjunction.
Article
Biochemical Research Methods
David G. Nickens, Matthew L. Bochman
Summary: DNA helicases play a crucial role in nucleic acid transactions and genome integrity. Research has shown that the PIF1 (Pif1 and Rrm3) and RecQ (Hrq1 and Sgs1) family helicases exhibit genetic and biochemical interactions in vivo, affecting genome integrity pathways and telomerase activity.
Article
Biochemistry & Molecular Biology
Steven Timmermans, Nicolette J. D. Verhoog, Kelly Van Looveren, Sylviane Dewaele, Tino Hochepied, Melanie Eggermont, Barbara Gilbert, Anne Boerema-de Munck, Tineke Vanderhaeghen, Joke Vanden Berghe, Natalia Garcia Gonzalez, Jolien Vandewalle, Yehudi Bloch, Mathias Provost, Savvas N. Savvides, Karolien De Bosscher, Wim Declercq, Robbert J. Rottier, Ann Louw, Claude Libert
Summary: The GR(dim/dim) mice with reduced dimerization propensity have helped define the functions of GR monomers and dimers, while the newly generated GR(D+L/D+L) mice exhibit insufficient ligand binding, leading to perinatal lethality.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biology
Ching-Hua Shih, Justin Fay
Summary: The evolution of cis-regulatory sequences is influenced by their impact on gene expression. Studies have shown that allele-specific expression dynamics are affected by cis-acting variations within and between species, suggesting a key role of cis-regulatory sequences in tuning gene expression dynamics.
Article
Biochemistry & Molecular Biology
Sabrine Hedouin, Glennis A. Logsdon, Jason G. Underwood, Sue Biggins
Summary: This study used a targeted RNA isoform sequencing approach to identify the transcriptional landscape at and surrounding all centromeres in budding yeast. They found that most pericentromeres are transcribed throughout the cell cycle, but centromere accessibility to the transcription machinery is restricted to S-phase, which is controlled by the centromere-binding transcription factor Cbf1. Deletion of Cbf1 leads to an accumulation of cenRNAs at all phases of the cell cycle and increased chromosome mis-segregation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Li Cheng, Xuetong Yue, Zhaoyu Qin, Xiaogang Sun, Fuchu He, Junbiao Dai, Chen Ding
Summary: This study reports a genome-wide quantitative proteomic system that uses unique code peptides to achieve precise protein quantification. By systematically tagging and decoding 40 yeast proteins using mass spectrometry, the researchers successfully recovered all code peptides with a large and consistent quantitative dynamic range. Additionally, they verified the alterations in glucose and galactose metabolism pathways in yeast under different carbon source conditions.
Article
Biochemistry & Molecular Biology
Erik A. Feldmann, Katrina N. Koc, Roberto Galletto
BIOPHYSICAL CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Saurabh P. Singh, Katrina N. Koc, Joseph L. Stodola, Roberto Galletto
JOURNAL OF MOLECULAR BIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Katrina N. Koc, Saurabh P. Singh, Joseph L. Stodola, Peter M. Burgers, Roberto Galletto
NUCLEIC ACIDS RESEARCH
(2016)
Article
Multidisciplinary Sciences
Joshua E. Sokoloski, Alexander G. Kozlov, Roberto Galletto, Timothy M. Lohman
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biochemistry & Molecular Biology
Carly L. Geronimo, Saurabh P. Singh, Roberto Galletto, Virginia A. Zakian
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Saurabh P. Singh, Vandna Kukshal, Paolo De Bona, Edwin Antony, Roberto Galletto
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Saurabh P. Singh, Vandna Kukshal, Roberto Galletto
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Danielle Dahan, Ioannis Tsirkas, Daniel Dovrat, Melanie A. Sparks, Saurabh P. Singh, Roberto Galletto, Amir Aharoni
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Tanumoy Mondol, Joseph L. Stodola, Roberto Galletto, Peter M. Burgers
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Melanie A. Sparks, Saurabh P. Singh, Peter M. Burgers, Roberto Galletto
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Sarem Hailemariam, Paolo De Bona, Roberto Galletto, Marcel Hohl, John H. Petrini, Peter M. Burgers
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Multidisciplinary Sciences
Saurabh P. Singh, Andrea Soranno, Melanie A. Sparks, Roberto Galletto
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Melanie A. Sparks, Peter M. Burgers, Roberto Galletto
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Cell Biology
Mohamed E. Ashour, Andrea K. Byrum, Alice Meroni, Jun Xia, Saurabh Singh, Roberto Galletto, Susan M. Rosenberg, Alessandro Vindigni, Nima Mosammaparast
Summary: The primary method for studying DNA replication dynamics, DNA fiber analysis, has limitations in terms of time, bias, and adaptability. In this study, a mass spectrometry-based analysis technique (MS-BAND) was introduced as a rapid and unbiased alternative for quantifying and analyzing DNA replication. MS-BAND accurately detects replication alterations in various cell compartments and has high-throughput capability, making it a potential alternative to the DNA fiber technique.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Kacey N. Mersch, Joshua E. Sokoloski, Binh Nguyen, Roberto Galletto, Timothy M. Lohman
Summary: RPA is an essential single-stranded DNA-binding protein that can bind and diffuse along single-stranded DNA. It has been shown that Pif1 can use its ATP-dependent translocase activity to push RPA along single-stranded DNA. Furthermore, Pif1 can also push RPA from single-stranded DNA into double-stranded DNA, resulting in stable disruption of at least 9 base pairs of duplex DNA. These findings highlight the dynamic nature of RPA and provide insights into the mechanism of directional DNA unwinding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)