Editorial Material
Biochemistry & Molecular Biology
Ilona Faustova, Mart Loog
Summary: Study by Hossain et al. (2021) reveals that ORC1 and CDC6 interact during pre-replicative complex formation in G1, mediated by SLiMs in IDRs and regulated by CDKs.
Article
Multidisciplinary Sciences
Aina Maria Mas, Enrique Goni, Igor Ruiz de los Mozos, Aida Arcas, Luisa Statello, Jovanna Gonzalez, Lorea Blazquez, Wei Ting Chelsea Lee, Dipika Gupta, Alvaro Sejas, Shoko Hoshina, Alexandros Armaos, Gian Gaetano Tartaglia, Shou Waga, Jernej Ule, Eli Rothenberg, Maria Gomez, Maite Huarte
Summary: In this study, the authors demonstrate that ORC1, a subunit of the Origin Recognition Complex, interacts with RNAs transcribed from genes with origins of replication at their TSSs, and this interaction positively correlates with origin activation. They show that the binding of RNA to ORC1 facilitates chromatin release and activation of proximal origins, and this process is regulated by phosphorylation and degradation. These findings reveal a novel non-coding function of RNA in coordinating the activation of replication origins.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Mary E. Anderson, Janet L. Smith, Alan D. Grossman
Summary: DNA replication is regulated primarily at the initiation step, where DnaA and oriC are the key targets. Multiple mechanisms including elongation and initiation can compensate for over-initiation, highlighting the complexity of replication regulation.
MOLECULAR MICROBIOLOGY
(2022)
Article
Cell Biology
Benjamin Bourgeois, Tianshu Gui, Diana Hoogeboom, Henry G. Hocking, Gesa Richter, Emil Spreitzer, Martin Viertler, Klaus Richter, Tobias Madl, Boudewijn M. T. Burgering
Summary: The study demonstrates how the transcription factor FOXO4 regulates its transcriptional activity through interactions with the structured co-regulator b-catenin, modulated by phosphorylation and other regulatory mechanisms. Additionally, it reveals the role of the b-catenin inhibitor protein ICAT in acting as a molecular switch between anti-proliferative FOXO and pro-proliferative Wnt/TCF/LEF signaling pathways. These findings highlight the importance of intrinsically disordered regions, post-translational modifications, and co-factor binding in regulating transcription factor function.
Article
Genetics & Heredity
Amy E. Ikui, Noriko Ueki, Kresti Pecani, Frederick R. Cross
Summary: This study investigates the localization of MCM proteins and the regulation of CDC6 during DNA replication in Chlamydomonas, finding that the step-wise assembly of the pre-replicative complex is conserved in Chlamydomonas and the plant-specific CDKB kinase is not required for this assembly. A model is proposed where pre-RC assembly takes place right before the first replication cycle and is repeated in each cycle after the replication proteins diffuse in mitosis. This mechanism may contribute to timely replication in the multiple fission cycle.
Article
Biotechnology & Applied Microbiology
Aymeric Antoine-Lorquin, Peter Arensburger, Ahmed Arnaoty, Sassan Asgari, Martine Batailler, Linda Beauclair, Catherine Belleannee, Nicolas Buisine, Vincent Coustham, Serge Guyetant, Laura Helou, Thierry Lecomte, Bruno Pitard, Isabelle Stevant, Yves Bigot
Summary: The study found different forms of SETMAR present in colon tissues, with expression in both tumor and healthy tissues. SETMAR was observed to bind to thousands of Hsmar1 and MADE1 transposons in colorectal cell lines, mainly located in non-genic regions of active chromatin.
Article
Biochemistry & Molecular Biology
Sayoko Sanada, Masashi Maekawa, Sota Tate, Hiroki Nakaoka, Yasuhiro Fujisawa, Koji Sayama, Shigeki Higashiyama
Summary: In this study, the cellular functions of wild-type SPOP in non-cancerous human keratinocyte-derived HaCaT cells were evaluated. SPOP knockdown resulted in reduced cell growth and arrested cell cycles at G1/S phase. The downregulation of DNA replication licensing factors CDT1 and CDC6 and the subsequent induction of p21 expression without p53 activation were observed upon SPOP knockdown. These results highlight the importance of SPOP in DNA replication licensing in non-cancerous keratinocyte HaCaT cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biology
Jasmin Philip, Mihkel Ord, Andriele Silva, Shaneen Singh, John F. X. Diffley, Dirk Remus, Mart Loog, Amy E. Ikui
Summary: This study reveals that PP2A(Cdc55) dephosphorylates the N-terminal sites of Cdc6 to release Clb2, while Cdc14 dephosphorylates the C-terminal phospho-degron to stabilize Cdc6 in mitosis. Additionally, the Cdk1 inhibitor Sic1 releases Clb2·Cdk1·Cks1 from Cdc6 to load Mcm2-7 on the chromatin upon mitotic exit. The findings suggest that phosphatases promote pre-RC assembly and origin licensing through the attenuation of different Cdk1-dependent inhibitory mechanisms of Cdc6.
Article
Chemistry, Medicinal
Clement Monsarrat, Guillaume Compain, Christophe Andre, Sylvain Engilberge, Isabelle Martiel, Vincent Olieric, Philippe Wolff, Karl Brillet, Marie Landolfo, Cyrielle Silva da Veiga, Jerome Wagner, Gilles Guichard, Dominique Y. Burnouf
Summary: A study was conducted on a series of peptides interacting with the Escherichia coli SC binding pocket, showing improved affinity through various modifications. X-ray structure analysis revealed new peptide-protein interactions that explained the enhanced binding mechanism.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Virology
Shaoying Wang, Qunxin She, Li Huang
Summary: This study reveals that the thermophilic archaeon Sulfolobus islandicus employs DNA damage response to defend against virus infection. UV irradiation treatment enhances the inhibitory effect on virus genome replication in S. islandicus infected with the fusellovirus SSV2. Infection with SSV2 triggers the activation of Orc1-2-mediated DNA damage response, including the activation of homologous recombination repair, cell aggregation and DNA import, and the repression of cell division. Lack of Orc1-2 abolishes the inhibitory effect of UV irradiation on SSV2 genome replication. Our findings shed light on the defense mechanisms of extremophilic organisms against viral threats.
JOURNAL OF VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Thomas M. R. Harrison, Josip Rudar, Nicholas Ogden, Royce Steeves, David R. Lapen, Donald Baird, Nellie Gagne, Oliver Lung
Summary: Mosquitoes are important vectors for disease transmission and genetic markers can help classify and prevent diseases. The control region of the mosquito mitochondrial genome contains conserved motifs that can be used to differentiate mosquito species. By utilizing these motifs, it is possible to identify the mosquito genus compared to their dipteran relatives.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Meghan V. Petrie, Yiwei He, Yan Gan, Andrew Zachary Ostrow, Oscar M. Aparicio
Summary: Chromatin ImmunoPrecipitation (ChIP) is a widely used method for studying protein-DNA interactions, but it suffers from false-positive signal enrichment. We developed a new approach to control for non-specific enrichment in ChIP by co-expressing a non-genome-binding protein with the experimental target protein and using the shared epitope tags. This method improves data quality by normalizing the experimental data with the ChIP signal of the non-specific protein, and has been successfully validated with known binding sites of multiple proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Fiona Jenkinson, Kang Wei Tan, Barbara Schopf, Miguel M. Santos, Philip Zegerman
Summary: In eukaryotes, cyclin-dependent kinase (CDK) inhibits helicase loading factors to ensure the exact duplication of the genome. CDK activates origin firing by phosphorylating Sld2 and Sld3, forming a transient intermediate called the pre-initiation complex (pre-IC). In yeast, the CDK phosphorylations of Sld3 and Sld2 are rapidly turned over by the phosphatases PP2A and PP4 during S phase. This dephosphorylation is important for genome-wide origin firing, pre-IC formation, and maintaining Sld3 dephosphorylation in G1 phase. PP2ARts1 specifically targets Sld3 and its dephosphorylation is critical for replication and cell viability.
Article
Multidisciplinary Sciences
Jiawei Ding, Xiangting Li, Jiangchuan Shen, Yiling Zhao, Shuchen Zhong, Luhua Lai, Hengyao Niu, Zhi Qi
Summary: The authors investigated the behavior of the RPA protein in DNA replication and repair using single molecule DNA Curtains and Markov chain modeling. They discovered that the interaction between RPA and Rad52 regulates the accessibility of ssDNA, facilitating the loading of Rad51 recombinase. This study provides insights into the bimolecular dynamics of RPA on ssDNA and its crucial role in DNA metabolic pathways.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jiaxin Zhang, Lili Li, Yu Miao, Xiaojing Liu, Haitao Sun, Meiqian Jiang, Xiaoli Li, Zhen Li, Cong Liu, Baohua Liu, Xingzhi Xu, Qinhong Cao, Wenya Hou, Chunlai Chen, Huiqiang Lou
Summary: In addition to entrapping sister chromatids, cohesin also drives other high-order chromosomal structural dynamics such as looping, compartmentalization, and condensation. ESCO2 acetylates a specific subset of cohesin to establish cohesion between nascent sister chromatids. The precise mechanism of this process is still unknown. This study reveals that GSK3 family kinases provide higher hierarchical control through an ESCO2 regulator, CRL4(MMS22L), by phosphorylating Thr105 in MMS22L and promoting the dimerization of CRL4(MMS22L) and ESCO2 during S phase. This research helps understand the symmetric control of cohesion establishment in eukaryotes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Nihan Kara, Manzar Hossain, Supriya G. Prasanth, Bruce Stillman
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Multidisciplinary Sciences
Kuhulika Bhalla, Monika Chugh, Sonali Mehrotra, Sumit Rathore, Sultan Tousif, Ved Prakash Dwivedi, Prem Prakash, Sachin Kumar Samuchiwal, Sushil Kumar, Dhiraj Kumar Singh, Swapnil Ghanwat, Dhiraj Kumar, Gobardhan Das, Asif Mohmmed, Pawan Malhotra, Anand Ranganathan
NATURE COMMUNICATIONS
(2015)
Article
Biology
Manzar Hossain, Bruce Stillman
Article
Infectious Diseases
Sachin Kumar Samuchiwal, Sultan Tousif, Dhiraj Kumar Singh, Arun Kumar, Anamika Ghosh, Kuhulika Bhalla, Prem Prakash, Sushil Kumar, Maitree Bhattacharyya, Prashini Moodley, Gobardhan Das, Anand Ranganathan
BMC INFECTIOUS DISEASES
(2014)
Article
Cell Biology
Elisa Tramentozzi, Paola Ferraro, Manzar Hossain, Bruce Stillman, Vera Bianchi, Giovanna Pontarin
Article
Genetics & Heredity
Manzar J. Hossain, Reshma Korde, Prashant K. Singh, Shivani Kanodia, Ravi Ranjan, Geeta Ram, Gaganjot Singh Kalsey, Rita Singh, Pawan Malhotra
Article
Cell Biology
Manzar Hossain, Bruce Stillman
GENES & DEVELOPMENT
(2012)
Article
Biochemical Research Methods
Ravi Ranjan, Monika Chugh, Saravanan Kumar, Shivani Singh, Shivani Kanodia, Manzar J. Hossain, Reshma Korde, Amit Grover, Shikha Dhawan, Virander S. Chauhan, Vanga S. Reddy, Asif Mohmmed, Pawan Malhotra
JOURNAL OF PROTEOME RESEARCH
(2011)
Article
Infectious Diseases
Manzar Hossain, Shweta Sharma, Reshma Korde, Shivani Kanodia, Monika Chugh, Khushboo Rawat, Pawan Malhotra
Article
Multidisciplinary Sciences
Megha Tharad, Sachin Kumar Samuchiwal, Kuhulika Bhalla, Anamika Ghosh, Krishan Kumar, Sushil Kumar, Anand Ranganathan
Article
Multidisciplinary Sciences
Asish K. Ghosh, Sheila B. Murphy, Raj Kishore, Douglas E. Vaughan
Article
Multidisciplinary Sciences
Anamika Ghosh, Sultan Tousif, Debapriya Bhattacharya, Sachin K. Samuchiwal, Kuhulika Bhalla, Megha Tharad, Sushil Kumar, Prem Prakash, Purnima Kumar, Gobardhan Das, Anand Ranganathan
Article
Biochemistry & Molecular Biology
Sachin Kumar Samuchiwal, Sultan Tousif, Dhiraj Kumar Singh, Arun Kumar, Anamika Ghosh, Kuhulika Bhalla, Prem Prakash, Sushil Kumar, Ashish Chandra Trivedi, Maitree Bhattacharyya, Gobardhan Das, Anand Ranganathan