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Mercier C, Thies D, Zhong L, Raftery MJ, Erdmann S. Characterization of an archaeal virus-host system reveals massive genomic rearrangements in a laboratory strain. Front Microbiol 2023; 14:1274068. [PMID: 37789858 PMCID: PMC10544981 DOI: 10.3389/fmicb.2023.1274068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Halophilic archaea (haloarchaea) are known to exhibit multiple chromosomes, with one main chromosome and one or several smaller secondary chromosomes or megaplasmids. Halorubrum lacusprofundi, a model organism for studying cold adaptation, exhibits one secondary chromosome and one megaplasmid that include a large arsenal of virus defense mechanisms. We isolated a virus (Halorubrum tailed virus DL1, HRTV-DL1) infecting Hrr. lacusprofundi, and present an in-depth characterization of the virus and its interactions with Hrr. lacusprofundi. While studying virus-host interactions between Hrr. lacusprofundi and HRTV-DL1, we uncover that the strain in use (ACAM34_UNSW) lost the entire megaplasmid and about 38% of the secondary chromosome. The loss included the majority of virus defense mechanisms, making the strain sensitive to HRTV-DL1 infection, while the type strain (ACAM34_DSMZ) appears to prevent virus replication. Comparing infection of the type strain ACAM34_DSMZ with infection of the laboratory derived strain ACAM34_UNSW allowed us to identify host responses to virus infection that were only activated in ACAM34_UNSW upon the loss of virus defense mechanisms. We identify one of two S-layer proteins as primary receptor for HRTV-DL1 and conclude that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Additionally, we identify archaeal homologs to eukaryotic proteins potentially being involved in the defense against virus infection.
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Affiliation(s)
- Coraline Mercier
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Daniela Thies
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Susanne Erdmann
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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2
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Reconstruction of pathway modification induced by nicotinamide using multi-omic network analyses in triple negative breast cancer. Sci Rep 2017; 7:3466. [PMID: 28615672 PMCID: PMC5471278 DOI: 10.1038/s41598-017-03322-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/26/2017] [Indexed: 11/08/2022] Open
Abstract
Triple negative breast cancer (TNBC) is characterized by an aggressive biological behavior in the absence of a specific target agent. Nicotinamide has recently been proven to be a novel therapeutic agent for skin tumors in an ONTRAC trial. We performed combinatory transcriptomic and in-depth proteomic analyses to characterize the network of molecular interactions in TNBC cells treated with nicotinamide. The multi-omic profiles revealed that nicotinamide drives significant functional alterations related to major cellular pathways, including the cell cycle, DNA replication, apoptosis and DNA damage repair. We further elaborated the global interaction networks of molecular events via nicotinamide-inducible expression changes at the mRNA and functional protein levels. This approach indicated that nicotinamide treatment rewires interaction networks toward dysfunction in DNA damage repair and away from a pro-growth state in TNBC. To our knowledge, the high-resolution network interactions identified in the present study provide the first evidence to comprehensively support the hypothesis of nicotinamide as a novel therapeutic agent in TNBC.
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3
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van Kempen LC, Redpath M, Robert C, Spatz A. Molecular pathology of cutaneous melanoma. Melanoma Manag 2014; 1:151-164. [PMID: 30190820 DOI: 10.2217/mmt.14.23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cutaneous melanoma is associated with strong prognostic phenotypic features, such as gender, Breslow's thickness and ulceration, although the biological significance of these variables is largely unknown. It is likely that these features are surrogates of important biological events rather than directly promoting cutaneous melanoma progression. In this article, we address the molecular mechanisms that drive these phenotypic changes. Furthermore, we present a comprehensive overview of recurrent genetic abnormalities, both germline and somatic, in relation to cutaneous melanoma subtypes, ultraviolet exposure and anatomical localization, as well as pre-existing and targeted therapy-induced mutations that may contribute to resistance. The increasing knowledge of critically important oncogenes and tumor-suppressor genes is promoting a transition in melanoma diagnosis, in which single-gene testing will be replaced by multiplex and multidimensional analyses that combine classical histopathological characteristics with the molecular profile for the prognostication and selection of melanoma therapy.
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Affiliation(s)
- Léon C van Kempen
- McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada.,McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Margaret Redpath
- McGill University, Montreal, QC, Canada.,McGill University, Montreal, QC, Canada
| | - Caroline Robert
- Gustave Roussy Cancer Institute, Villejuif, Paris, France.,Gustave Roussy Cancer Institute, Villejuif, Paris, France
| | - Alan Spatz
- McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Department of Pathology, Jewish General Hospital, 3755 Cote Ste Catherine, Montreal, QC, H3T 1E2, Canada.,McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Department of Pathology, Jewish General Hospital, 3755 Cote Ste Catherine, Montreal, QC, H3T 1E2, Canada
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Matthews LA, Guarné A. Dbf4: the whole is greater than the sum of its parts. Cell Cycle 2013; 12:1180-8. [PMID: 23549174 PMCID: PMC3674083 DOI: 10.4161/cc.24416] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 03/22/2013] [Indexed: 12/29/2022] Open
Abstract
Together with cyclin-dependent kinases, the Dbf4-dependent kinase (DDK) is essential to activate the Mcm2-7 helicase and, hence, initiate DNA replication in eukaryotes. Beyond its role as the regulatory subunit of the DDK complex, the Dbf4 protein also regulates the activity of other cell cycle kinases to mediate the checkpoint response and prevent premature mitotic exit under stress. Two features that are unusual in DNA replication proteins characterize Dbf4. The first is its evolutionary divergence; the second is how its conserved motifs are combined to form distinct functional units. This structural plasticity appears to be at odds with the conserved functions of Dbf4. In this review, we summarize recent genetic, biochemical and structural work delineating the multiple interactions mediated by Dbf4 and its various functions during the cell cycle. We also discuss how the limited sequence conservation of Dbf4 may be an advantage to regulate the activities of multiple cell cycle kinases.
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Affiliation(s)
- Lindsay A Matthews
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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5
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Hubbi ME, Kshitiz, Gilkes DM, Rey S, Wong CC, Luo W, Kim DH, Dang CV, Levchenko A, Semenza GL. A nontranscriptional role for HIF-1α as a direct inhibitor of DNA replication. Sci Signal 2013; 6:ra10. [PMID: 23405012 PMCID: PMC4124626 DOI: 10.1126/scisignal.2003417] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Cell cycle arrest in response to hypoxia is a fundamental physiological mechanism to maintain a balance between O(2) supply and demand. Many of the cellular responses to reduced O(2) availability are mediated through the transcriptional activity of hypoxia-inducible factor 1 (HIF-1). We report a role for the isolated HIF-1α subunit as an inhibitor of DNA replication, and this role was independent of HIF-1β and transcriptional regulation. In response to hypoxia, HIF-1α bound to Cdc6, a protein that is essential for loading of the minichromosome maintenance (MCM) complex (which has DNA helicase activity) onto DNA, and promoted the interaction between Cdc6 and the MCM complex. Although the interaction between Cdc6 and the MCM complex increased the association of the MCM proteins with chromatin, the binding of HIF-1α to the complex decreased phosphorylation and activation of the MCM complex by the kinase Cdc7. As a result, HIF-1α inhibited firing of replication origins, decreased DNA replication, and induced cell cycle arrest in various cell types. These findings establish a transcription-independent mechanism by which the stabilization of HIF-1α leads to cell cycle arrest in response to hypoxia.
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Affiliation(s)
- Maimon E. Hubbi
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kshitiz
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Bioengineering, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Daniele M. Gilkes
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sergio Rey
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Carmen C. Wong
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Weibo Luo
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Deok-Ho Kim
- Department of Bioengineering, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Chi V. Dang
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andre Levchenko
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregg L. Semenza
- Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Pediatrics and Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Feng CJ, Lu XW, Luo DY, Li HJ, Guo JB. Knockdown of Cdc6 inhibits proliferation of tongue squamous cell carcinoma Tca8113 cells. Technol Cancer Res Treat 2012; 12:173-81. [PMID: 22974333 DOI: 10.7785/tcrt.2012.500302] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The present study aimed at evaluating the effects of Cdc6 downregulation on the proliferation of Tca8113 cells. Two lentiviral vectors (KD1 and KD2) expression cdc6 siRNA were constructed and then infected into Tca8113 cells. Real-time PCR and Western blot analysis were performed to detect the mRNA and protein expression of Cdc6. MTT assays were employed to delineate the growth curves, and flow cytometry was performed to assess cell-cycle progression and apoptosis in Tca8113 cells. Following infection with the lentiviral vectors, real-time PCR and Western blot analysis revealed that Cdc6 expression was markedly suppressed in Tca8113 cells. When compared with the negative control group, the mRNA expression of Cdc6 was reduced by 50% and 65% and the protein expression by 65.87% and 79.38% in cells harboring KD1 or KD2, respectively. Cell growth was slowed, and the growth inhibition rate was 25.84% and 30.34% in Tca8113 cells following infection with KD1 or KD2, respectively. In addition, cell-cycle progression was altered. In KD- infected Tca8113 cells, the proportion of cells in the S phase was markedly reduced, but the proportion in the G1 phase was significantly increased; this was accompanied by an increase in cell apoptosis. Downregulation of Cdc6 effectively inhibited the proliferation of Tca8113 cells.
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Affiliation(s)
- Chong-Jin Feng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China, 510080.
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Kundu LR, Seki M, Watanabe N, Murofushi H, Furukohri A, Waga S, Score AJ, Blow JJ, Horikoshi M, Enomoto T, Tada S. Biphasic chromatin binding of histone chaperone FACT during eukaryotic chromatin DNA replication. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:1129-36. [PMID: 21232560 DOI: 10.1016/j.bbamcr.2011.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 12/13/2010] [Accepted: 01/03/2011] [Indexed: 11/17/2022]
Abstract
The facilitates chromatin transcription (FACT) complex affects nuclear DNA transactions in a chromatin context. Though the involvement of FACT in eukaryotic DNA replication has been revealed, a clear understanding of its biochemical behavior during DNA replication still remains elusive. Here, we analyzed the chromatin-binding dynamics of FACT using Xenopus egg extract cell-free system. We found that FACT has at least two distinct chromatin-binding phases: (1) a rapid chromatin-binding phase at the onset of DNA replication that did not involve origin licensing and (2) a second phase of chromatin binding that initiated after origin licensing. Intriguingly, early-binding FACT dissociated from chromatin when DNA replication was blocked by the addition of Cdc6 in the licensed state before origin firing. Cdc6-induced removal of FACT was blocked by the inhibition of origin licensing with geminin, but not by suppressing the activity of DNA polymerases, CDK, or Cdc7. Furthermore, chromatin transfer experiments revealed that impairing the later binding of FACT severely compromises DNA replication activity. Taken together, we propose that even though FACT has rapid chromatin-binding activity, the binding pattern of FACT on chromatin changes after origin licensing, which may contribute to the establishment of its functional link to the DNA replication machinery.
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Affiliation(s)
- Lena R Kundu
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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