1
|
Abramczyk D, Del Carmen Sanchez Olmos M, Rojas AAR, Schindler D, Robertson D, McColm S, Marston AL, Barlow PN. A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. Microb Cell Fact 2023; 22:259. [PMID: 38104077 PMCID: PMC10724962 DOI: 10.1186/s12934-023-02262-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Komagataella phaffii (Pichia pastoris) is a methylotrophic commercially important non-conventional species of yeast that grows in a fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored in this organism to facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes in K. phaffii could offer unique advantages by accommodating multiple integrations of extraneous genes and their promoters without accumulating perturbations of native chromosomes or exhausting the availability of selection markers. RESULTS Here, we describe a linear "nano"chromosome (of 15-25 kb) that, according to whole-genome sequencing, persists in K. phaffii over many generations with a copy number per cell of one, provided non-homologous end joining is compromised (by KU70-knockout). The nanochromosome includes a copy of the centromere from K. phaffii chromosome 3, a K. phaffii-derived autonomously replicating sequence on either side of the centromere, and a pair of K. phaffii-like telomeres. It contains, within its q arm, a landing zone in which genes of interest alternate with long (approx. 1-kb) non-coding DNA chosen to facilitate homologous recombination and serve as spacers. The landing zone can be extended along the nanochromosome, in an inch-worming mode of sequential gene integrations, accompanied by recycling of just two antibiotic-resistance markers. The nanochromosome was used to express PDI, a gene encoding protein disulfide isomerase. Co-expression with PDI allowed the production, from a genomically integrated gene, of secreted murine complement factor H, a plasma protein containing 40 disulfide bonds. As further proof-of-principle, we co-expressed, from a nanochromosome, both PDI and a gene for GFP-tagged human complement factor H under the control of PAOX1 and demonstrated that the secreted protein was active as a regulator of the complement system. CONCLUSIONS We have added K. phaffii to the list of organisms that can produce human proteins from genes carried on a stable, linear, artificial chromosome. We envisage using nanochromosomes as repositories for numerous extraneous genes, allowing intensive engineering of K. phaffii without compromising its genome or weakening the resulting strain.
Collapse
Affiliation(s)
| | | | | | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Robertson
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Paul N Barlow
- School of Chemistry, University of Edinburgh, Edinburgh, UK.
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
2
|
Mukherjee S, Das S, Sriram N, Chakraborty S, Sah MK. In silico investigation of the role of vitamins in cancer therapy through inhibition of MCM7 oncoprotein. RSC Adv 2022; 12:31004-31015. [PMID: 36349041 PMCID: PMC9619486 DOI: 10.1039/d2ra03703c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022] Open
Abstract
An overabundance of MCM7 protein, a component of the minichromosome maintenance complex that normally initiates DNA replication, has been reported to cause different types of cancers with aggressive malignancy. Inhibition of MCM7 may lead to a significant reduction in cancer-associated cell proliferation. Despite such significance of MCM7 in cancer, the protein structure is yet to be resolved experimentally. This significantly halts the structure-guided ligand designing for cancer therapy targeting the MCM7. The present study aims to resolve the tertiary structure of MCM7 and repurpose the FDA-approved clinically used drugs for cancer therapy by targeting MCM7 protein. The secondary and 3D structures of MCM7 were generated using multiple bioinformatics tools, including the Self-Optimized Prediction Method with Alignment (SOPMA), SWISS-MODEL, and I-TASSER. The reliability of the modeled structure was assessed using PROCHECK. Initially, a structure-guided virtual screening was performed on the approved drug library to identify potential hits against MCM7. The detailed molecular mechanism of receptor interactions of the identified hits was evaluated using extensive molecular dynamics simulation. The results from this study reveal an intriguing discovery of the potential of ergocalciferol (vitamin D2), cholecalciferol (vitamin D3), ergosterol (precursor of vitamin D2) and menaquinone (vitamin K2) as oncoprotein inhibitors for cancer therapy via inhibition of MCM7.
Collapse
Affiliation(s)
- Sunny Mukherjee
- Department of Biotechnology, Dr B. R. Ambedkar National Institute of TechnologyJalandharPunjab-144011India
| | - Sucharita Das
- Department of Microbiology, University of Calcutta35 BallygungeKolkata700 019India
| | - Navneeth Sriram
- Department of Biotechnology, Dr B. R. Ambedkar National Institute of TechnologyJalandharPunjab-144011India,Department of Biosciences and Bioengineering, Indian Institute of TechnologyGuwahatiAssam-781039India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr Reddy's Institute of Life Sciences, University of Hyderabad CampusGachibowliHyderabad 500046India
| | - Mahesh Kumar Sah
- Department of Biotechnology, Dr B. R. Ambedkar National Institute of TechnologyJalandharPunjab-144011India
| |
Collapse
|
3
|
Ahammad F, Alam R, Mahmud R, Akhter S, Talukder EK, Tonmoy AM, Fahim S, Al-Ghamdi K, Samad A, Qadri I. Pharmacoinformatics and molecular dynamics simulation-based phytochemical screening of neem plant (Azadiractha indica) against human cancer by targeting MCM7 protein. Brief Bioinform 2021; 22:6217720. [PMID: 33834183 DOI: 10.1093/bib/bbab098] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022] Open
Abstract
Minichromosome maintenance complex component 7 (MCM7) belongs to the minichromosome maintenance family that is important for the initiation of eukaryotic DNA replication. Overexpression of the MCM7 protein is relative to cellular proliferation and responsible for aggressive malignancy in various cancers. Mechanistically, inhibition of MCM7 significantly reduces the cellular proliferation associated with cancer. To date, no effective small molecular candidate has been identified that can block the progression of cancer induced by the MCM7 protein. Therefore, the study has been designed to identify small molecular-like natural drug candidates against aggressive malignancy associated with various cancers by targeting MCM7 protein. To identify potential compounds against the targeted protein a comprehensive in silico drug design including molecular docking, ADME (Absorption, Distribution, Metabolism and Excretion), toxicity, and molecular dynamics (MD) simulation approaches has been applied. Seventy phytochemicals isolated from the neem tree (Azadiractha indica) were retrieved and screened against MCM7 protein by using the molecular docking simulation method, where the top four compounds have been chosen for further evaluation based on their binding affinities. Analysis of ADME and toxicity properties reveals the efficacy and safety of the selected four compounds. To validate the stability of the protein-ligand complex structure MD simulations approach has also been performed to the protein-ligand complex structure, which confirmed the stability of the selected three compounds including CAS ID:105377-74-0, CID:12308716 and CID:10505484 to the binding site of the protein. In the study, a comprehensive data screening process has performed based on the docking, ADMET properties, and MD simulation approaches, which found a good value of the selected four compounds against the targeted MCM7 protein and indicates as a promising and effective human anticancer agent.
Collapse
Affiliation(s)
- Foysal Ahammad
- Department of Biological Science, Faculty of science, King Abdul-Aziz University, Jeddah-21589, Saudi Arabia.,Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Rahat Alam
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Rasel Mahmud
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail-1902, Bangladesh
| | - Shahina Akhter
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC) Block # D, Floor # 11, Foy's Lake, Khulshi, Chittagong 4202, Bangladesh
| | - Enamul Kabir Talukder
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Al Mahmud Tonmoy
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Zoology, Institute of Dhaka College, University of Dhaka, Dhaka-1000, Bangladesh
| | - Salman Fahim
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Bachelor of medicine and Bachelor of Surgery (MBBS), CARe Medical College, 2, 1-A Iqbal Road, Dhaka-1207, Bangladesh
| | - Khalid Al-Ghamdi
- Department of Biological Science, Faculty of science, King Abdul-Aziz University, Jeddah-21589, Saudi Arabia
| | - Abdus Samad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Ishtiaq Qadri
- Department of Biological Science, Faculty of science, King Abdul-Aziz University, Jeddah-21589, Saudi Arabia
| |
Collapse
|
4
|
Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
Collapse
Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
5
|
Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R. Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. PLoS Genet 2020; 16:e1008390. [PMID: 32084124 PMCID: PMC7055916 DOI: 10.1371/journal.pgen.1008390] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/04/2020] [Accepted: 01/08/2020] [Indexed: 11/18/2022] Open
Abstract
Base J, β-D-glucosyl-hydroxymethyluracil, is a modification of thymine DNA base involved in RNA Polymerase (Pol) II transcription termination in kinetoplastid protozoa. Little is understood regarding how specific thymine residues are targeted for J-modification or the mechanism of J regulated transcription termination. To identify proteins involved in J-synthesis, we expressed a tagged version of the J-glucosyltransferase (JGT) in Leishmania tarentolae, and identified four co-purified proteins by mass spectrometry: protein phosphatase (PP1), a homolog of Wdr82, a potential PP1 regulatory protein (PNUTS) and a protein containing a J-DNA binding domain (named JBP3). Gel shift studies indicate JBP3 is a J-DNA binding protein. Reciprocal tagging, co-IP and sucrose gradient analyses indicate PP1, JGT, JBP3, Wdr82 and PNUTS form a multimeric complex in kinetoplastids, similar to the mammalian PTW/PP1 complex involved in transcription termination via PP1 mediated dephosphorylation of Pol II. Using RNAi and analysis of Pol II termination by RNA-seq and RT-PCR, we demonstrate that ablation of PNUTS, JBP3 and Wdr82 lead to defects in Pol II termination at the 3'-end of polycistronic gene arrays in Trypanosoma brucei. Mutants also contain increased antisense RNA levels upstream of transcription start sites, suggesting an additional role of the complex in regulating termination of bi-directional transcription. In addition, PNUTS loss causes derepression of silent Variant Surface Glycoprotein genes involved in host immune evasion. Our results suggest a novel mechanistic link between base J and Pol II polycistronic transcription termination in kinetoplastids.
Collapse
Affiliation(s)
- Rudo Kieft
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Alexandre P. Marand
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Jose Dagoberto Moran
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Robert Bridger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| |
Collapse
|
6
|
Abstract
Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.
Collapse
|
7
|
Candelli T, Gros J, Libri D. Pervasive transcription fine-tunes replication origin activity. eLife 2018; 7:40802. [PMID: 30556807 PMCID: PMC6314782 DOI: 10.7554/elife.40802] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase (RNAPII) transcription occurs pervasively, raising the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have neglected the role of non-annotated transcription. We studied the relationships between pervasive transcription and replication origin activity using high-resolution transcription maps. We show that ARSs alter the pervasive transcription landscape by pausing and terminating neighboring RNAPII transcription, thus limiting the occurrence of pervasive transcription within origins. We propose that quasi-symmetrical binding of the ORC complex to ARS borders and/or pre-RC formation are responsible for pausing and termination. We show that low, physiological levels of pervasive transcription impact the function of replication origins. Overall, our results have important implications for understanding the impact of genomic location on origin function.
Collapse
Affiliation(s)
- Tito Candelli
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Julien Gros
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
8
|
Soudet J, Gill JK, Stutz F. Noncoding transcription influences the replication initiation program through chromatin regulation. Genome Res 2018; 28:1882-1893. [PMID: 30401734 PMCID: PMC6280764 DOI: 10.1101/gr.239582.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023]
Abstract
In eukaryotic organisms, replication initiation follows a temporal program. Among the parameters that regulate this program in Saccharomyces cerevisiae, chromatin structure has been at the center of attention without considering the contribution of transcription. Here, we revisit the replication initiation program in the light of widespread genomic noncoding transcription. We find that noncoding RNA transcription termination in the vicinity of autonomously replicating sequences (ARSs) shields replication initiation from transcriptional readthrough. Consistently, high natural nascent transcription correlates with low ARS efficiency and late replication timing. High readthrough transcription is also linked to increased nucleosome occupancy and high levels of H3K36me3. Moreover, forcing ARS readthrough transcription promotes these chromatin features. Finally, replication initiation defects induced by increased transcriptional readthrough are partially rescued in the absence of H3K36 methylation. Altogether, these observations indicate that natural noncoding transcription into ARSs influences replication initiation through chromatin regulation.
Collapse
Affiliation(s)
- Julien Soudet
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Jatinder Kaur Gill
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Françoise Stutz
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| |
Collapse
|
9
|
Cao SN, Yuan Y, Qin YH, Zhang MZ, de Figueiredo P, Li GH, Qin QM. The pre-rRNA processing factor Nop53 regulates fungal development and pathogenesis via mediating production of reactive oxygen species. Environ Microbiol 2018; 20:1531-1549. [PMID: 29488307 DOI: 10.1111/1462-2920.14082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 11/28/2022]
Abstract
Botrytis cinerea is a necrotrophic plant fungal pathogen that annually causes enormous economic losses worldwide. The ribosome is an organelle for cellular protein biosynthesis. However, little is known about how the ribosome operates as a machine to mediate microbial pathogenesis. Here, we demonstrate that Nop53, a late-acting factor for 60S ribosomal subunit maturation, is crucial for the pathogen's development and virulence. BcNop53 is functionally equivalent to yeast nop53p. Complementation of BcNOP53 completely restored the growth defect of the yeast Δnop53 mutant. BcNop53 is located in nuclei and disruption of BcNOP53 also dramatically impaired pathogen growth. Deletion of BcNOP53 blocked infection structure formation and abolished virulence of the pathogen, possibly due to reduced production of reactive oxygen species. Moreover, loss of BcNOP53 impaired pathogen conidiation and stress adaptation, altered conidial and sclerotial morphology, retarded conidium and sclerotium germination as well as reduced the activities of cell-wall degradation-associated enzymes. Sclerotium production was, however, increased. Complementation with the wild-type BcNOP53 allele rescued defects found in the ΔBcnop53 mutant. Our work establishes a systematic elucidation of Nop53 in regulating microbial development and pathogenesis, provides novel insights into ribosomal processes that regulate fungal pathogenesis, and may open up new targets for addressing fungal diseases.
Collapse
Affiliation(s)
- Sheng-Nan Cao
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Ye Yuan
- College of Plant Sciences, Jilin University, Changchun 130062, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun 130062, China
| | - Yu Haity Qin
- College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ming-Zhe Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, TX 77843, USA.,Norman Borlaug Center, Texas A&M University, College Station, TX 77843, USA.,Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Gui-Hua Li
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Qing-Ming Qin
- College of Plant Sciences, Jilin University, Changchun 130062, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun 130062, China
| |
Collapse
|
10
|
Zheng D, Ye S, Wang X, Zhang Y, Yan D, Cai X, Gao W, Shan H, Gao Y, Chen J, Hu Z, Li H, Li J. Pre-RC Protein MCM7 depletion promotes mitotic exit by Inhibiting CDK1 activity. Sci Rep 2017; 7:2854. [PMID: 28588300 PMCID: PMC5460140 DOI: 10.1038/s41598-017-03148-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
MCM7, a subunit of mini-chromosome maintenance proteins (MCM) complex, plays an important role in initiating DNA replication during the G1 phase and extending DNA strands during the S phase. Here, we demonstrated that MCM7 is not only sustained but maintains association with chromatin during M phase. Remarkably, MCM7 siRNA can accelerate mitotic exit. MCM7 depletion leads to CDK1 inactivation and promotes subsequent cohesin/RAD21 cleavage, which eventually leads to sister chromatin segregation. Moreover, MCM7 is co-localized with tubulin in the mitotic cells and MCM7 depletion results in aberrant mitosis. Our results indicate that MCM7 may exert certain functions on spindle formation to prevent cytokinesis during early mitosis by regulating CDK1 activity.
Collapse
Affiliation(s)
- Dianpeng Zheng
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Sichao Ye
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiuyun Wang
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Yongjun Zhang
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Daoyu Yan
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiangsheng Cai
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Weihong Gao
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongbo Shan
- Department of Endoscopy, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yang Gao
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Juanjuan Chen
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhiming Hu
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongwei Li
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China.
| | - Jinlong Li
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China.
| |
Collapse
|
11
|
Abstract
The eukaryotic replicative DNA helicase, Mcm2-7, is loaded in inactive form as a double hexameric complex around double-stranded DNA. To ensure that replication origins fire no more than once per S phase, activation of the Mcm2-7 helicase is temporally separated from Mcm2-7 loading in the cell cycle. This 2-step mechanism requires that inactive Mcm2-7 complexes be maintained for variable periods of time in a topologically bound state on chromatin, which may create a steric obstacle to other DNA transactions. We have recently found in the budding yeast, Saccharomyces cerevisiae, that Mcm2-7 double hexamers can respond to collisions with transcription complexes by sliding along the DNA template. Importantly, Mcm2-7 double hexamers remain functional after displacement along DNA and support replication initiation from sites distal to the origin. These results reveal a novel mechanism to specify eukaryotic replication origin sites and to maintain replication origin competence without the need for Mcm2-7 reloading.
Collapse
Affiliation(s)
- Charanya Kumar
- a Molecular Biology Program, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| | - Dirk Remus
- a Molecular Biology Program, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| |
Collapse
|
12
|
Aladjem MI, Redon CE. Order from clutter: selective interactions at mammalian replication origins. Nat Rev Genet 2017; 18:101-116. [PMID: 27867195 PMCID: PMC6596300 DOI: 10.1038/nrg.2016.141] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian chromosome duplication progresses in a precise order and is subject to constraints that are often relaxed in developmental disorders and malignancies. Molecular information about the regulation of DNA replication at the chromatin level is lacking because protein complexes that initiate replication seem to bind chromatin indiscriminately. High-throughput sequencing and mathematical modelling have yielded detailed genome-wide replication initiation maps. Combining these maps and models with functional genetic analyses suggests that distinct DNA-protein interactions at subgroups of replication initiation sites (replication origins) modulate the ubiquitous replication machinery and supports an emerging model that delineates how indiscriminate DNA-binding patterns translate into a consistent, organized replication programme.
Collapse
Affiliation(s)
- Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
| |
Collapse
|
13
|
Peng YP, Zhu Y, Yin LD, Zhang JJ, Guo S, Fu Y, Miao Y, Wei JS. The Expression and Prognostic Roles of MCMs in Pancreatic Cancer. PLoS One 2016; 11:e0164150. [PMID: 27695057 PMCID: PMC5047525 DOI: 10.1371/journal.pone.0164150] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Minichromosome maintenance (MCM) proteins play important roles in DNA replication by interacting with other factors which participate in the regulation of DNA synthesis. Abnormal over-expression of MCMs was observed in numerous malignancies, such as colorectal cancer. However, the expression of MCMs in pancreatic cancer (PC) was less investigated so far. This study was designed to analyze the expression and prognostic roles of MCM1-10 in PC based on the data provided by The Cancer Genome Atlas (TCGA). METHODS Pearson χ2 test was applied to evaluate the association of MCMs expression with clinicopathologic indicators, and biomarkers for tumor biological behaviors. Kaplan-Meier plots and log-rank tests were used to assess survival analysis, and univariate and multivariate Cox proportional hazard regression models were used to recognize independent prognostic factors. RESULTS MCM1-10 were generally expressed in PC samples. The levels of some molecules were markedly correlated with that of biomarkers for S phase, proliferation, gemcitabine resistance. And part of these molecules over-expression was significantly associated with indicators of disease progression, such as depth of tumor invasion and lymph node metastasis. Furthermore, MCM2, 4, 6, 8, and 10 over-expression was remarkably associated with shorter disease free survival time, and MCM2, 4,8, and 10 over-expression was associated with shorter overall survival time. Further multivariate analysis suggested that MCM8 was an independent prognostic factor for PC. CONCLUSION MCMs abnormal over-expression was significantly associated with PC progression and prognosis. These molecules could be regarded as prognostic and therapeutic biomarkers for PC. The roles of MCMs may be vitally important and the underlying mechanisms need to be furtherinvestigated.
Collapse
Affiliation(s)
- Yun-Peng Peng
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
| | - Yi Zhu
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
| | - Ling-Di Yin
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
| | - Jing-Jing Zhang
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
| | - Song Guo
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
| | - Yue Fu
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
| | - Yi Miao
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- * E-mail: (MY); (WJ-S)
| | - Ji-Shu Wei
- Pancreas Institute of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- Department of General Surgery, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People’s Republic of China
- * E-mail: (MY); (WJ-S)
| |
Collapse
|
14
|
High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation. G3-GENES GENOMES GENETICS 2016; 6:993-1012. [PMID: 26865697 PMCID: PMC4825667 DOI: 10.1534/g3.116.027904] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid partitioning and suggest underlying biological roles shared by such elements.
Collapse
|
15
|
Gros J, Kumar C, Lynch G, Yadav T, Whitehouse I, Remus D. Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA. Mol Cell 2015; 60:797-807. [PMID: 26656162 DOI: 10.1016/j.molcel.2015.10.022] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/28/2015] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
Eukaryotic genomes are replicated from many origin sites that are licensed by the loading of the replicative DNA helicase, Mcm2-7. How eukaryotic origin positions are specified remains elusive. Here we show that, contrary to the bacterial paradigm, eukaryotic replication origins are not irrevocably defined by selection of the helicase loading site, but can shift in position after helicase loading. Using purified proteins we show that DNA translocases, including RNA polymerase, can push budding yeast Mcm2-7 double hexamers along DNA. Displaced Mcm2-7 double hexamers support DNA replication initiation distal to the loading site in vitro. Similarly, in yeast cells that are defective for transcription termination, collisions with RNA polymerase induce a redistribution of Mcm2-7 complexes along the chromosomes, resulting in a corresponding shift in DNA replication initiation sites. These results reveal a eukaryotic origin specification mechanism that departs from the classical replicon model, helping eukaryotic cells to negotiate transcription-replication conflict.
Collapse
Affiliation(s)
- Julien Gros
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Charanya Kumar
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Gerard Lynch
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Tejas Yadav
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA; Weill-Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
16
|
Newman TJ, Mamun MA, Nieduszynski CA, Blow JJ. Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts. Nucleic Acids Res 2013; 41:9705-18. [PMID: 23963700 PMCID: PMC3834809 DOI: 10.1093/nar/gkt728] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/24/2013] [Accepted: 07/25/2013] [Indexed: 01/21/2023] Open
Abstract
During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication is maximized if replication origins are evenly spaced, the largest inter-origin distances are minimized, and the end-most origins are positioned close to chromosome ends. We show that origin positions in the yeast Saccharomyces cerevisiae genome conform to all three predictions thereby maximizing the probability of complete replication if replication forks stall. Origin positions in four other yeasts-Kluyveromyces lactis, Lachancea kluyveri, Lachancea waltii and Schizosaccharomyces pombe-also conform to these predictions. Equating failure rates at chromosome ends with those in chromosome interiors gives a mean per nucleotide fork stall rate of ∼5 × 10(-8), which is consistent with experimental estimates. Using this value in our theoretical predictions gives replication failure rates that are consistent with data from replication origin knockout experiments. Our theory also predicts that significantly larger genomes, such as those of mammals, will experience a much greater probability of replication failure genome-wide, and therefore will likely require additional compensatory mechanisms.
Collapse
Affiliation(s)
- Timothy J. Newman
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mohammed A. Mamun
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Conrad A. Nieduszynski
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - J. Julian Blow
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| |
Collapse
|
17
|
Hoggard T, Shor E, Müller CA, Nieduszynski CA, Fox CA. A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast. PLoS Genet 2013; 9:e1003798. [PMID: 24068963 PMCID: PMC3772097 DOI: 10.1371/journal.pgen.1003798] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 07/30/2013] [Indexed: 01/19/2023] Open
Abstract
Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal positions and triggers molecular events culminating in the initiation of DNA replication (a.k.a. origin firing) during S-phase. Each chromosome uses multiple origins for its duplication, and each origin fires at a characteristic time during S-phase, creating a cell-type specific genome replication pattern relevant to differentiation and genome stability. It is unclear whether ORC-origin interactions are relevant to origin activation time. We applied a novel genome-wide strategy to classify origins in the model eukaryote Saccharomyces cerevisiae based on the types of molecular interactions used for ORC-origin binding. Specifically, origins were classified as DNA-dependent when the strength of ORC-origin binding in vivo could be explained by the affinity of ORC for origin DNA in vitro, and, conversely, as ‘chromatin-dependent’ when the ORC-DNA interaction in vitro was insufficient to explain the strength of ORC-origin binding in vivo. These two origin classes differed in terms of nucleosome architecture and dependence on origin-flanking sequences in plasmid replication assays, consistent with local features of chromatin promoting ORC binding at ‘chromatin-dependent’ origins. Finally, the ‘chromatin-dependent’ class was enriched for origins that fire early in S-phase, while the DNA-dependent class was enriched for later firing origins. Conversely, the latest firing origins showed a positive association with the ORC-origin DNA paradigm for normal levels of ORC binding, whereas the earliest firing origins did not. These data reveal a novel association between ORC-origin binding mechanisms and the regulation of origin activation time. Cell division requires the duplication of chromosomes, protein-DNA complexes harboring genetic information. Specific chromosomal positions, origins, initiate this duplication. Multiple origins are required for accurate, efficient duplication—an insufficient number leads to mistakes in the genetic material and pathologies such as cancer. Origins are chosen when the origin recognition complex (ORC) binds to them. The molecular interactions controlling this binding remain unclear. Understanding these interactions will lead to new ways to control cell division, which could aid in treatments of disease. Experiments were performed in the eukaryotic microbe budding yeast to define the types of molecular interactions ORC uses to bind origins. Yeasts are useful for these studies because chromosome duplication and structure are well conserved from yeast to humans. While ORC-DNA interactions were important, interactions between ORC and chromosomal proteins played a role. In addition, different origins relied on different types of molecular interactions with ORC. Finally, ORC-protein interactions but not ORC-DNA interactions were associated with enhanced origin function during chromosome-duplication, revealing an unanticipated link between the types of molecular interactions ORC uses to select an origin and the ultimate function of that origin. These results have implications for interfering with ORC-origin interactions to control cell division.
Collapse
Affiliation(s)
- Timothy Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Program in Cellular and Molecular Biology, College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erika Shor
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Carolin A. Müller
- Centre for Genetics and Genomics, University of Nottingham Queen's Medical Centre, Nottingham, United Kingdom
| | - Conrad A. Nieduszynski
- Centre for Genetics and Genomics, University of Nottingham Queen's Medical Centre, Nottingham, United Kingdom
- * E-mail: (CAN); (CAF)
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Program in Cellular and Molecular Biology, College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (CAN); (CAF)
| |
Collapse
|
18
|
Müller CA, Nieduszynski CA. Conservation of replication timing reveals global and local regulation of replication origin activity. Genome Res 2012; 22:1953-62. [PMID: 22767388 PMCID: PMC3460190 DOI: 10.1101/gr.139477.112] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DNA replication initiates from defined locations called replication origins; some origins are highly active, whereas others are dormant and rarely used. Origins also differ in their activation time, resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. paradoxus, S. arboricolus, and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also in activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae/S. bayanus hybrid strain and find that there are both local and global regulators of origin function.
Collapse
Affiliation(s)
- Carolin A Müller
- Centre for Genetics and Genomics, The University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | | |
Collapse
|
19
|
Abstract
In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.
Collapse
|
20
|
Liachko I, Tanaka E, Cox K, Chung SCC, Yang L, Seher A, Hallas L, Cha E, Kang G, Pace H, Barrow J, Inada M, Tye BK, Keich U. Novel features of ARS selection in budding yeast Lachancea kluyveri. BMC Genomics 2011; 12:633. [PMID: 22204614 PMCID: PMC3306766 DOI: 10.1186/1471-2164-12-633] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The characterization of DNA replication origins in yeast has shed much light on the mechanisms of initiation of DNA replication. However, very little is known about the evolution of origins or the evolution of mechanisms through which origins are recognized by the initiation machinery. This lack of understanding is largely due to the vast evolutionary distances between model organisms in which origins have been examined. RESULTS In this study we have isolated and characterized autonomously replicating sequences (ARSs) in Lachancea kluyveri - a pre-whole genome duplication (WGD) budding yeast. Through a combination of experimental work and rigorous computational analysis, we show that L. kluyveri ARSs require a sequence that is similar but much longer than the ARS Consensus Sequence well defined in Saccharomyces cerevisiae. Moreover, compared with S. cerevisiae and K. lactis, the replication licensing machinery in L. kluyveri seems more tolerant to variations in the ARS sequence composition. It is able to initiate replication from almost all S. cerevisiae ARSs tested and most Kluyveromyces lactis ARSs. In contrast, only about half of the L. kluyveri ARSs function in S. cerevisiae and less than 10% function in K. lactis. CONCLUSIONS Our findings demonstrate a replication initiation system with novel features and underscore the functional diversity within the budding yeasts. Furthermore, we have developed new approaches for analyzing biologically functional DNA sequences with ill-defined motifs.
Collapse
Affiliation(s)
- Ivan Liachko
- School of Mathematics and Statistics, University of Sydney, Sydney, Australia.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Siow CC, Nieduszynska SR, Müller CA, Nieduszynski CA. OriDB, the DNA replication origin database updated and extended. Nucleic Acids Res 2011; 40:D682-6. [PMID: 22121216 PMCID: PMC3245157 DOI: 10.1093/nar/gkr1091] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites. The original database collated and curated Saccharomyces cerevisiae origin mapping studies. Here, we report that the OriDB database and web site have been revamped to improve user accessibility to curated data sets, to greatly increase the number of curated origin mapping studies, and to include the collation of replication origin sites in the fission yeast Schizosaccharomyces pombe. The revised database structure underlies these improvements and will facilitate further expansion in the future. The updated OriDB for S. cerevisiae is available at http://cerevisiae.oridb.org/ and for S. pombe at http://pombe.oridb.org/.
Collapse
Affiliation(s)
- Cheuk C Siow
- Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | | | | | | |
Collapse
|
22
|
Lõoke M, Reimand J, Sedman T, Sedman J, Järvinen L, Värv S, Peil K, Kristjuhan K, Vilo J, Kristjuhan A. Relicensing of transcriptionally inactivated replication origins in budding yeast. J Biol Chem 2010; 285:40004-11. [PMID: 20962350 PMCID: PMC3000982 DOI: 10.1074/jbc.m110.148924] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA replication origins are licensed in early G1 phase of the cell cycle where the origin recognition complex (ORC) recruits the minichromosome maintenance (MCM) helicase to origins. These pre-replicative complexes (pre-RCs) remain inactive until replication is initiated in the S phase. However, transcriptional activity in the regions of origins can eliminate their functionality by displacing the components of pre-RC from DNA. We analyzed genome-wide data of mRNA and cryptic unstable transcripts in the context of locations of replication origins in yeast genome and found that at least one-third of the origins are transcribed and therefore might be inactivated by transcription. When investigating the fate of transcriptionally inactivated origins, we found that replication origins were repetitively licensed in G1 to reestablish their functionality after transcription. We propose that reloading of pre-RC components in G1 might be utilized for the maintenance of sufficient number of competent origins for efficient initiation of DNA replication in S phase.
Collapse
Affiliation(s)
- Marko Lõoke
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, Weinreich M, Eaton ML, MacAlpine DM, Fox CA. The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev 2010; 24:1418-33. [PMID: 20595233 PMCID: PMC2895200 DOI: 10.1101/gad.1906410] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 05/11/2010] [Indexed: 12/15/2022]
Abstract
The origin recognition complex (ORC) binds to the specific positions on chromosomes that serve as DNA replication origins. Although ORC is conserved from yeast to humans, the DNA sequence elements that specify ORC binding are not. In particular, metazoan ORC shows no obvious DNA sequence specificity, whereas yeast ORC binds to a specific DNA sequence within all yeast origins. Thus, whereas chromatin must play an important role in metazoan ORC's ability to recognize origins, it is unclear whether chromatin plays a role in yeast ORC's recognition of origins. This study focused on the role of the conserved N-terminal bromo-adjacent homology domain of yeast Orc1 (Orc1BAH). Recent studies indicate that BAH domains are chromatin-binding modules. We show that the Orc1BAH domain was necessary for ORC's stable association with yeast chromosomes, and was physiologically relevant to DNA replication in vivo. This replication role was separable from the Orc1BAH domain's previously defined role in transcriptional silencing. Genome-wide analyses of ORC binding in ORC1 and orc1bahDelta cells revealed that the Orc1BAH domain contributed to ORC's association with most yeast origins, including a class of origins highly dependent on the Orc1BAH domain for ORC association (orc1bahDelta-sensitive origins). Orc1bahDelta-sensitive origins required the Orc1BAH domain for normal activity on chromosomes and plasmids, and were associated with a distinct local nucleosome structure. These data provide molecular insights into how the Orc1BAH domain contributes to ORC's selection of replication origins, as well as new tools for examining conserved mechanisms governing ORC's selection of origins within eukaryotic chromosomes.
Collapse
Affiliation(s)
- Philipp Müller
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sookhee Park
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Erika Shor
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dana J. Huebert
- Program in Cellular and Molecular Biology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Christopher L. Warren
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aseem Z. Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael Weinreich
- Laboratory for Chromosome Replication, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Matthew L. Eaton
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David M. MacAlpine
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Program in Cellular and Molecular Biology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| |
Collapse
|
24
|
Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M. Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem 2010; 79:89-130. [PMID: 20373915 DOI: 10.1146/annurev.biochem.052308.103205] [Citation(s) in RCA: 370] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA replication is central to cell proliferation. Studies in the past six decades since the proposal of a semiconservative mode of DNA replication have confirmed the high degree of conservation of the basic machinery of DNA replication from prokaryotes to eukaryotes. However, the need for replication of a substantially longer segment of DNA in coordination with various internal and external signals in eukaryotic cells has led to more complex and versatile regulatory strategies. The replication program in higher eukaryotes is under a dynamic and plastic regulation within a single cell, or within the cell population, or during development. We review here various regulatory mechanisms that control the replication program in eukaryotes and discuss future directions in this dynamic field.
Collapse
Affiliation(s)
- Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan.
| | | | | | | | | |
Collapse
|
25
|
de Moura APS, Retkute R, Hawkins M, Nieduszynski CA. Mathematical modelling of whole chromosome replication. Nucleic Acids Res 2010; 38:5623-33. [PMID: 20457753 PMCID: PMC2943597 DOI: 10.1093/nar/gkq343] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
All chromosomes must be completely replicated prior to cell division, a requirement that demands the activation of a sufficient number of appropriately distributed DNA replication origins. Here we investigate how the activity of multiple origins on each chromosome is coordinated to ensure successful replication. We present a stochastic model for whole chromosome replication where the dynamics are based upon the parameters of individual origins. Using this model we demonstrate that mean replication time at any given chromosome position is determined collectively by the parameters of all origins. Combining parameter estimation with extensive simulations we show that there is a range of model parameters consistent with mean replication data, emphasising the need for caution in interpreting such data. In contrast, the replicated-fraction at time points through S phase contains more information than mean replication time data and allowed us to use our model to uniquely estimate many origin parameters. These estimated parameters enable us to make a number of predictions that showed agreement with independent experimental data, confirming that our model has predictive power. In summary, we demonstrate that a stochastic model can recapitulate experimental observations, including those that might be interpreted as deterministic such as ordered origin activation times.
Collapse
Affiliation(s)
- Alessandro P S de Moura
- Department of Physics, University of Aberdeen, Aberdeen AB24 3UE and School of Biology, University of Nottingham, Nottingham NG7 2UH, UK
| | | | | | | |
Collapse
|
26
|
Spiesser TW, Diener C, Barberis M, Klipp E. What influences DNA replication rate in budding yeast? PLoS One 2010; 5:e10203. [PMID: 20436919 PMCID: PMC2860512 DOI: 10.1371/journal.pone.0010203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 03/12/2010] [Indexed: 11/18/2022] Open
Abstract
Background DNA replication begins at specific locations called replication origins, where helicase and polymerase act in concert to unwind and process the single DNA filaments. The sites of active DNA synthesis are called replication forks. The density of initiation events is low when replication forks travel fast, and is high when forks travel slowly. Despite the potential involvement of epigenetic factors, transcriptional regulation and nucleotide availability, the causes of differences in replication times during DNA synthesis have not been established satisfactorily, yet. Methodology/Principal Findings Here, we aimed at quantifying to which extent sequence properties contribute to the DNA replication time in budding yeast. We interpreted the movement of the replication machinery along the DNA template as a directed random walk, decomposing influences on DNA replication time into sequence-specific and sequence-independent components. We found that for a large part of the genome the elongation time can be well described by a global average replication rate, thus by a single parameter. However, we also showed that there are regions within the genomic landscape of budding yeast with highly specific replication rates, which cannot be explained by global properties of the replication machinery. Conclusion/Significance Computational models of DNA replication in budding yeast that can predict replication dynamics have rarely been developed yet. We show here that even beyond the level of initiation there are effects governing the replication time that can not be explained by the movement of the polymerase along the DNA template alone. This allows us to characterize genomic regions with significantly altered elongation characteristics, independent of initiation times or sequence composition.
Collapse
Affiliation(s)
- Thomas W. Spiesser
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
| | - Christian Diener
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
| | - Matteo Barberis
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (MB); (EK)
| | - Edda Klipp
- Theoretical Biophysics, Institute for Biology, Humboldt University Berlin, Berlin, Germany
- * E-mail: (MB); (EK)
| |
Collapse
|
27
|
Shor E, Warren CL, Tietjen J, Hou Z, Müller U, Alborelli I, Gohard FH, Yemm AI, Borisov L, Broach JR, Weinreich M, Nieduszynski CA, Ansari AZ, Fox CA. The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication. PLoS Genet 2009; 5:e1000755. [PMID: 19997491 PMCID: PMC2778871 DOI: 10.1371/journal.pgen.1000755] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 11/06/2009] [Indexed: 11/18/2022] Open
Abstract
The origin recognition complex (ORC) marks chromosomal sites as replication origins and is essential for replication initiation. In yeast, ORC also binds to DNA elements called silencers, where its primary function is to recruit silent information regulator (SIR) proteins to establish transcriptional silencing. Indeed, silencers function poorly as chromosomal origins. Several genetic, molecular, and biochemical studies of HMR-E have led to a model proposing that when ORC becomes limiting in the cell (such as in the orc2-1 mutant) only sites that bind ORC tightly (such as HMR-E) remain fully occupied by ORC, while lower affinity sites, including many origins, lose ORC occupancy. Since HMR-E possessed a unique non-replication function, we reasoned that other tight sites might reveal novel functions for ORC on chromosomes. Therefore, we comprehensively determined ORC “affinity” genome-wide by performing an ORC ChIP–on–chip in ORC2 and orc2-1 strains. Here we describe a novel group of orc2-1–resistant ORC–interacting chromosomal sites (ORF–ORC sites) that did not function as replication origins or silencers. Instead, ORF–ORC sites were comprised of protein-coding regions of highly transcribed metabolic genes. In contrast to the ORC–silencer paradigm, transcriptional activation promoted ORC association with these genes. Remarkably, ORF–ORC genes were enriched in proximity to origins of replication and, in several instances, were transcriptionally regulated by these origins. Taken together, these results suggest a surprising connection among ORC, replication origins, and cellular metabolism. Chromosomes must be replicated prior to cell division. The process of duplication of each eukaryotic chromosome starts at discrete sites called origins of replication. An evolutionarily conserved Origin Recognition Complex (ORC) binds origins and helps make them replication-competent. ORC also binds another class of chromosomal sites that primarily function not as origins but as “silencers.” Silencers serve as starting points for the formation of silent chromatin, a special structure that represses local gene transcription in a promoter-independent fashion. One yeast silencer studied in great detail was found to bind ORC in vitro and in vivo with high affinity (“tightly”). On the other hand, several replication origins were found to bind ORC with lower affinity (“loosely”). We performed a genome-wide comparison of ORC affinity and found a novel class of high-affinity ORC–binding sites. Surprisingly, this class consisted neither of origins nor of silencers but of highly expressed genes involved in various metabolic processes. Transcriptional activation helped target ORC to these sites. These genes were frequently found near origins of replication, and in several instances their transcription was affected by deletion of the nearby origin. These results may shed light on a new molecular mechanism connecting nutrient status and cell division.
Collapse
Affiliation(s)
- Erika Shor
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Christopher L. Warren
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Joshua Tietjen
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Zhonggang Hou
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ulrika Müller
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ilaria Alborelli
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Florence H. Gohard
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Adrian I. Yemm
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Lev Borisov
- Department of Mathematics, College of Letters and Science, University of Wisconsin, Madison, Wisconsin, United States of America
| | - James R. Broach
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Michael Weinreich
- Laboratory of Chromosome Replication, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | - Conrad A. Nieduszynski
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Aseem Z. Ansari
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
- The Genome Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|
28
|
Omberg L, Meyerson JR, Kobayashi K, Drury LS, Diffley JFX, Alter O. Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression. Mol Syst Biol 2009; 5:312. [PMID: 19888207 PMCID: PMC2779084 DOI: 10.1038/msb.2009.70] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 08/19/2009] [Indexed: 11/09/2022] Open
Abstract
This report provides a global view of how gene expression is affected by DNA replication. We analyzed synchronized cultures of Saccharomyces cerevisiae under conditions that prevent DNA replication initiation without delaying cell cycle progression. We use a higher-order singular value decomposition to integrate the global mRNA expression measured in the multiple time courses, detect and remove experimental artifacts and identify significant combinations of patterns of expression variation across the genes, time points and conditions. We find that, first, approximately 88% of the global mRNA expression is independent of DNA replication. Second, the requirement of DNA replication for efficient histone gene expression is independent of conditions that elicit DNA damage checkpoint responses. Third, origin licensing decreases the expression of genes with origins near their 3' ends, revealing that downstream origins can regulate the expression of upstream genes. This confirms previous predictions from mathematical modeling of a global causal coordination between DNA replication origin activity and mRNA expression, and shows that mathematical modeling of DNA microarray data can be used to correctly predict previously unknown biological modes of regulation.
Collapse
Affiliation(s)
- Larsson Omberg
- Department of Biomedical Engineering, University of Texas, Austin, TX 78712, USA
| | | | | | | | | | | |
Collapse
|
29
|
Nieduszynski CA, Donaldson AD. Detection of replication origins using comparative genomics and recombinational ARS assay. Methods Mol Biol 2009; 521:295-313. [PMID: 19563113 DOI: 10.1007/978-1-60327-815-7_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Effective experimental techniques are available to identify replication origin regions in eukaryotic cells. Genome-wide identification of the precise sequence elements that direct origin activity is however still not straightforward, even in the yeast Saccharomyces cerevisiae which has the best characterised eukaryotic replication origins. The availability of genome sequences for a series of closely related (sensu stricto) budding yeasts has allowed us to take a 'comparative genomics' approach to this problem. Since they represent functional protein-binding sites, origin sequences are conserved better than the surrounding intergenic sequence within the genomes of closely related yeasts. We describe here how phylogenetic comparison data can be used to identify candidate replication origin sequences in the S. cerevisiae genome, and how large numbers of such candidate sites can simultaneously be assayed for ability to initiate replication. Similar approaches could potentially be used to identify protein-binding sequence elements having other functions, as well as replication origin sites in other species.
Collapse
|
30
|
Keich U, Gao H, Garretson JS, Bhaskar A, Liachko I, Donato J, Tye BK. Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast. BMC Bioinformatics 2008; 9:372. [PMID: 18786274 PMCID: PMC2566582 DOI: 10.1186/1471-2105-9-372] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 09/12/2008] [Indexed: 11/17/2022] Open
Abstract
Background In analyzing the stability of DNA replication origins in Saccharomyces cerevisiae we faced the question whether one set of sequences is significantly enriched in the number and/or the quality of the matches of a particular position weight matrix relative to another set. Results We present SADMAMA, a computational solution to a address this problem. SADMAMA implements two types of statistical tests to answer this question: one type is based on simplified models, while the other relies on bootstrapping, and as such might be preferable to users who are averse to such models. The bootstrap approach incorporates a novel "site-protected" resampling procedure which solves a problem we identify with naive resampling. Conclusion SADMAMA's utility is demonstrated here by offering a plausible explanation to the differential ARS activity observed in our previous mcm1-1 mutant experiments [1], by suggesting the relevance of multiple weak ACS matches to efficient replication origin function in Saccharomyces cerevisiae, and by suggesting an explanation to the observed negative effect FKH2 has on chromatin silencing [2]. SADMAMA is available for download from .
Collapse
Affiliation(s)
- Uri Keich
- Department of Computer Science, Cornell University, Ithaca, NY 14853, USA.
| | | | | | | | | | | | | |
Collapse
|
31
|
Aladjem MI. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 2007; 8:588-600. [PMID: 17621316 DOI: 10.1038/nrg2143] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Replication in eukaryotes initiates from discrete genomic regions according to a strict, often tissue-specific temporal programme. However, the locations of initiation events within initiation regions vary, show sequence disparity and are affected by interactions with distal elements. Increasing evidence suggests that specification of replication sites and the timing of replication are dynamic processes that are regulated by tissue-specific and developmental cues, and are responsive to epigenetic modifications. Dynamic specification of replication patterns might serve to prevent or resolve possible spatial and/or temporal conflicts between replication, transcription and chromatin assembly, and facilitate subtle or extensive changes of gene expression during differentiation and development.
Collapse
Affiliation(s)
- Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Building 37, Room 5056, 37 Convent Drive, Bethesda, Maryland 20892-4255, USA.
| |
Collapse
|
32
|
Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 2006; 7:276. [PMID: 17067396 PMCID: PMC1657020 DOI: 10.1186/1471-2164-7-276] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 10/26/2006] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Eukaryotic replication origins exhibit different initiation efficiencies and activation times within S-phase. Although local chromatin structure and function influences origin activity, the exact mechanisms remain poorly understood. A key to understanding the exact features of chromatin that impinge on replication origin function is to define the precise locations of the DNA sequences that control origin function. In S. cerevisiae, Autonomously Replicating Sequences (ARSs) contain a consensus sequence (ACS) that binds the Origin Recognition Complex (ORC) and is essential for origin function. However, an ACS is not sufficient for origin function and the majority of ACS matches do not function as ORC binding sites, complicating the specific identification of these sites. RESULTS To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen) to map the ORC and Mcm2p binding sites at high resolution. These binding sites define a set of potential Autonomously Replicating Sequences (ARSs), which we term nimARSs. The nimARS set comprises 529 ORC and/or Mcm2p binding sites, which includes 95% of known ARSs, and experimental verification demonstrates that 94% are functional. The resolution of the analysis facilitated identification of potential ACSs (nimACSs) within 370 nimARSs. Cross-validation shows that the nimACS predictions include 58% of known ACSs, and experimental verification indicates that 82% are essential for ARS activity. CONCLUSION These findings provide the most comprehensive, accurate, and detailed mapping of ORC binding sites to date, adding to the emerging picture of the chromatin organization of the budding yeast genome.
Collapse
|
33
|
Nieduszynski CA, Hiraga SI, Ak P, Benham CJ, Donaldson AD. OriDB: a DNA replication origin database. Nucleic Acids Res 2006; 35:D40-6. [PMID: 17065467 PMCID: PMC1781122 DOI: 10.1093/nar/gkl758] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Replication of eukaryotic chromosomes initiates at multiple sites called replication origins. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where several complementary studies have mapped their locations genome-wide. We have collated these datasets, taking account of the resolution of each study, to generate a single list of distinct origin sites. OriDB provides a web-based catalogue of these confirmed and predicted S.cerevisiae DNA replication origin sites. Each proposed or confirmed origin site appears as a record in OriDB, with each record comprising seven pages. These pages provide, in text and graphical formats, the following information: genomic location and chromosome context of the origin site; time of origin replication; DNA sequence of proposed or experimentally confirmed origin elements; free energy required to open the DNA duplex (stress-induced DNA duplex destabilization or SIDD); and phylogenetic conservation of sequence elements. In addition, OriDB encourages community submission of additional information for each origin site through a User Notes facility. Origin sites are linked to several external resources, including the Saccharomyces Genome Database (SGD) and relevant publications at PubMed. Finally, a Chromosome Viewer utility allows users to interactively generate graphical representations of DNA replication data genome-wide. OriDB is available at .
Collapse
Affiliation(s)
- Conrad A Nieduszynski
- Institute of Medical Science, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
| | | | | | | | | |
Collapse
|
34
|
Gibson DG, Bell SP, Aparicio OM. Cell cycle execution point analysis of ORC function and characterization of the checkpoint response to ORC inactivation in Saccharomyces cerevisiae. Genes Cells 2006; 11:557-73. [PMID: 16716188 DOI: 10.1111/j.1365-2443.2006.00967.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chromosomal replication initiates through the assembly of a prereplicative complex (pre-RC) at individual replication origins in the G1-phase, followed by activation of these complexes in the S-phase. In Saccharomyces cerevisiae, the origin recognition complex (ORC) binds replication origins throughout the cell cycle and participates in pre-RC assembly. Whether the ORC plays an additional role subsequent to pre-RC assembly in replication initiation or any other essential cell cycle process is not clear. To study the function of the ORC during defined cell cycle periods, we performed cell cycle execution point analyses with strains containing a conditional mutation in the ORC1, ORC2 or ORC5 subunit of ORC. We found that the ORC is essential for replication initiation, but is dispensable for replication elongation or later cell cycle events. Defective initiation in ORC mutant cells results in incomplete replication and mitotic arrest enforced by the DNA damage and spindle assembly checkpoint pathways. The involvement of the spindle assembly checkpoint implies a defect in kinetochore-spindle attachment or sister chromatid cohesion due to incomplete replication and/or DNA damage. Remarkably, under semipermissive conditions for ORC1 function, the spindle checkpoint alone suffices to block proliferation, suggesting this checkpoint is highly sensitive to replication initiation defects. We discuss the potential significance of these overlapping checkpoints and the impact of our findings on previously postulated role(s) of ORCs in other cell cycle functions.
Collapse
Affiliation(s)
- Daniel G Gibson
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910, USA
| | | | | |
Collapse
|
35
|
Nieduszynski CA, Knox Y, Donaldson AD. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 2006; 20:1874-9. [PMID: 16847347 PMCID: PMC1522085 DOI: 10.1101/gad.385306] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We discovered that sequences essential for replication origin function are frequently conserved in sensu stricto Saccharomyces species. Here we use analysis of phylogenetic conservation to identify replication origin sequences throughout the Saccharomyces cerevisiae genome at base pair resolution. Origin activity was confirmed for each of 228 predicted sites--representing 86% of apparent origin regions. This is the first study to determine the genome-wide location of replication origins at a resolution sufficient to identify the sequence elements bound by replication proteins. Our results demonstrate that phylogenetic conservation can be used to identify the origin sequences responsible for replicating a eukaryotic genome.
Collapse
|
36
|
Donato JJ, Chung SCC, Tye BK. Genome-wide hierarchy of replication origin usage in Saccharomyces cerevisiae. PLoS Genet 2006; 2:e141. [PMID: 16965179 PMCID: PMC1560401 DOI: 10.1371/journal.pgen.0020141] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Accepted: 07/25/2006] [Indexed: 12/02/2022] Open
Abstract
Replication origins in a genome are inherently different in their base sequence and in their response to temporal and cell cycle regulation signals for DNA replication. To investigate the chromosomal determinants that influence the efficiency of initiation of DNA replication genome-wide, we made use of a reverse strategy originally used for the isolation of replication initiation mutants in Saccharomyces cerevisiae. In yeast, replication origins isolated from chromosomes support the autonomous replication of plasmids. These replication origins, whether in the context of a chromosome or a plasmid, will initiate efficiently in wild-type cells but show a dramatically contrasted efficiency of activation in mutants defective in the early steps of replication initiation. Serial passages of a genomic library of autonomously replicating sequences (ARSs) in such a mutant allowed us to select for constitutively active ARSs. We found a hierarchy of preferential initiation of ARSs that correlates with local transcription patterns. This preferential usage is enhanced in mutants defective in the assembly of the prereplication complex (pre-RC) but not in mutants defective in the activation of the pre-RC. Our findings are consistent with an interference of local transcription with the assembly of the pre-RC at a majority of replication origins. The length of S phase regulated by the rate of DNA synthesis varies dramatically during the development of metazoans. Key to this regulation is the number of replication origins utilized in different developmental stages. A fundamental question is whether there is a hierarchy in the usage of replication origins under different conditions and if so, what are the determinants for preferential usage. In Saccharomyces cerevisiae, replication origins isolated in DNA fragments are known as autonomously replicating sequences (ARSs). To gain insight into the determinants that regulate replication origin usage, genomic ARSs that are preferentially used under adverse conditions for replication initiation were identified. One of the determinants appears to be the local transcription pattern. Transcriptional activity directed towards an ARS correlates with reduced efficiency of replication initiation of that ARS. This transcriptional interference appears to be targeted at the assembly of the prereplication complex. These results are consistent with the deregulated initiation patterns observed in early developing Xenopus embryos that are devoid of transcription. Other yet-to-be-identified factors are also important in determining the efficiency of replication origin usage.
Collapse
Affiliation(s)
- Justin J Donato
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Shau Chee C Chung
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Bik K Tye
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
37
|
Abstract
There has been remarkable progress in the last 20 years in defining the molecular mechanisms that regulate initiation of DNA synthesis in eukaryotic cells. Replication origins in the DNA nucleate the ordered assembly of protein factors to form a prereplication complex (preRC) that is poised for DNA synthesis. Transition of the preRC to an active initiation complex is regulated by cyclin-dependent kinases and other signaling molecules, which promote further protein assembly and activate the mini chromosome maintenance helicase. We will review these mechanisms and describe the state of knowledge about the proteins involved. However, we will also consider an additional layer of complexity. The DNA in the cell is packaged with histone proteins into chromatin. Chromatin structure provides an additional layer of heritable information with associated epigenetic modifications. Thus, we will begin by describing chromatin structure, and how the cell generally controls access to the DNA. Access to the DNA requires active chromatin remodeling, specific histone modifications, and regulated histone deposition. Studies in transcription have revealed a variety of mechanisms that regulate DNA access, and some of these are likely to be shared with DNA replication. We will briefly describe heterochromatin as a model for an epigenetically inherited chromatin state. Next, we will describe the mechanisms of replication initiation and how these are affected by constraints of chromatin. Finally, chromatin must be reassembled with appropriate modifications following passage of the replication fork, and our third major topic will be the reassembly of chromatin and its associated epigenetic marks. Thus, in this chapter, we seek to bring together the studies of replication initiation and the studies of chromatin into a single holistic narrative.
Collapse
Affiliation(s)
- Angel P Tabancay
- Molecular and Computational Biology Section University of Southern California Los Angeles, California 90089, USA
| | | |
Collapse
|
38
|
Current awareness on yeast. Yeast 2005; 22:1249-56. [PMID: 16320446 DOI: 10.1002/yea.1170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|