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  • 1
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    DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-05-02
    Description: DNA interstrand cross-links (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. We devised a technique called chromatin mass spectrometry (CHROMASS) to study protein recruitment dynamics during perturbed DNA replication in Xenopus egg extracts. Using CHROMASS, we systematically monitored protein assembly and disassembly on ICL-containing chromatin. Among numerous prospective DNA repair factors, we identified SLF1 and SLF2, which form a complex with RAD18 and together define a pathway that suppresses genome instability by recruiting the SMC5/6 cohesion complex to DNA lesions. Our study provides a global analysis of an entire DNA repair pathway and reveals the mechanism of SMC5/6 relocalization to damaged DNA in vertebrate cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raschle, Markus -- Smeenk, Godelieve -- Hansen, Rebecca K -- Temu, Tikira -- Oka, Yasuyoshi -- Hein, Marco Y -- Nagaraj, Nagarjuna -- Long, David T -- Walter, Johannes C -- Hofmann, Kay -- Storchova, Zuzana -- Cox, Jurgen -- Bekker-Jensen, Simon -- Mailand, Niels -- Mann, Matthias -- HL098316/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 May 1;348(6234):1253671. doi: 10.1126/science.1253671. Epub 2015 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. ; Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark. ; Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. ; Institute of Genetics, University of Cologne, 50674 Cologne, Germany. ; Maintenance of Genome Stability Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. ; Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark. simon.bekker-jensen@cpr.ku.dk niels.mailand@cpr.ku.dk mmann@biochem.mpg.de. ; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. Novo Nordisk Foundation Center for Protein Research, Proteomics Program, University of Copenhagen, DK-2200 Copenhagen, Denmark. simon.bekker-jensen@cpr.ku.dk niels.mailand@cpr.ku.dk mmann@biochem.mpg.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25931565" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/chemistry/metabolism ; *DNA Damage ; *DNA Repair ; DNA Repair Enzymes/*metabolism ; *DNA Replication ; DNA-Binding Proteins/metabolism ; Mass Spectrometry/methods ; Proteomics/methods ; RNA-Binding Proteins/metabolism ; Xenopus
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-10-28
    Description: DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions that trigger non-proteolytic ubiquitylation of adjacent chromatin areas to generate binding sites for DNA repair factors. This depends on the sequential actions of the E3 ubiquitin ligases RNF8 and RNF168 (refs 1-6), and UBC13 (also known as UBE2N), an E2 ubiquitin-conjugating enzyme that specifically generates K63-linked ubiquitin chains. Whereas RNF168 is known to catalyse ubiquitylation of H2A-type histones, leading to the recruitment of repair factors such as 53BP1 (refs 8-10), the critical substrates of RNF8 and K63-linked ubiquitylation remain elusive. Here we elucidate how RNF8 and UBC13 promote recruitment of RNF168 and downstream factors to DSB sites in human cells. We establish that UBC13-dependent K63-linked ubiquitylation at DSB sites is predominantly mediated by RNF8 but not RNF168, and that H1-type linker histones, but not core histones, represent major chromatin-associated targets of this modification. The RNF168 module (UDM1) recognizing RNF8-generated ubiquitylations is a high-affinity reader of K63-ubiquitylated H1, mechanistically explaining the essential roles of RNF8 and UBC13 in recruiting RNF168 to DSBs. Consistently, reduced expression or chromatin association of linker histones impair accumulation of K63-linked ubiquitin conjugates and repair factors at DSB-flanking chromatin. These results identify histone H1 as a key target of RNF8-UBC13 in DSB signalling and expand the concept of the histone code by showing that posttranslational modifications of linker histones can serve as important marks for recognition by factors involved in genome stability maintenance, and possibly beyond.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thorslund, Tina -- Ripplinger, Anita -- Hoffmann, Saskia -- Wild, Thomas -- Uckelmann, Michael -- Villumsen, Bine -- Narita, Takeo -- Sixma, Titia K -- Choudhary, Chunaram -- Bekker-Jensen, Simon -- Mailand, Niels -- England -- Nature. 2015 Nov 19;527(7578):389-93. doi: 10.1038/nature15401. Epub 2015 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark. ; Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark. ; Division of Biochemistry, Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26503038" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin/metabolism ; DNA Breaks, Double-Stranded ; *DNA Damage ; DNA Repair ; DNA-Binding Proteins/metabolism ; Histones/chemistry/*metabolism ; Humans ; Lysine/metabolism ; Protein Structure, Tertiary ; *Signal Transduction ; Ubiquitin/*metabolism ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitin-Protein Ligases/chemistry/metabolism ; Ubiquitination
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Trace elements at the intersection of marine biological and geochemical evolution (2017)
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Earth-Science Reviews 163 (2016): 323-348, doi:10.1016/j.earscirev.2016.10.013.
    Description: Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages have yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth’s ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.
    Description: LJR gratefully acknowledges the support of a Vanier Canada Graduate Scholarship. Discovery Grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) to CAP, BK, DSA, SAC, and KOK supported this work. This material is based upon work supported by the National Aeronautics and Space Administration through the NASA Astrobiology Institute under Cooperative Agreement No. NNA15BB03A issued through the Science Mission Directorate. NJP receives support from the Alternative Earths NASA Astrobiology Institute. Funding from the NASA Astrobiology Institute, and the NSF FESD and ELT programs to TWL, and the Region of Brittany and LabexMER funding to SVL are also gratefully acknowledged. AB thanks the Society of Independent Thinkers.
    Keywords: Iron formations ; Black shales ; Eukaryotes ; Prokaryotes ; Evolution ; Trace elements ; Biolimitation ; Precambrian
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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