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Liu J, Cai L, Sun W, Cheng R, Wang N, Jin L, Rozovsky S, Seiple IB, Wang L. Photocaged Quinone Methide Crosslinkers for Light‐Controlled Chemical Crosslinking of Protein–Protein and Protein–DNA Complexes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jun Liu
- University of California, San Francisco Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute 555 Mission Bay Blvd. South San Francisco CA 94158 USA
| | - Lingchao Cai
- University of California, San Francisco Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute 555 Mission Bay Blvd. South San Francisco CA 94158 USA
| | - Wei Sun
- University of California, San Francisco Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute 555 Mission Bay Blvd. South San Francisco CA 94158 USA
| | - Rujin Cheng
- University of Delaware Department of Chemistry and Biochemistry Newark DE 19716 USA
| | - Nanxi Wang
- University of California, San Francisco Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute 555 Mission Bay Blvd. South San Francisco CA 94158 USA
| | - Ling Jin
- University of Florida Department of Microbiology and Cell Science Gainesville FL 32611 USA
| | - Sharon Rozovsky
- University of Delaware Department of Chemistry and Biochemistry Newark DE 19716 USA
| | - Ian B. Seiple
- University of California, San Francisco Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute 555 Mission Bay Blvd. South San Francisco CA 94158 USA
| | - Lei Wang
- University of California, San Francisco Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute 555 Mission Bay Blvd. South San Francisco CA 94158 USA
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Liu J, Cai L, Sun W, Cheng R, Wang N, Jin L, Rozovsky S, Seiple IB, Wang L. Photocaged Quinone Methide Crosslinkers for Light-Controlled Chemical Crosslinking of Protein-Protein and Protein-DNA Complexes. Angew Chem Int Ed Engl 2019; 58:18839-18843. [PMID: 31644827 DOI: 10.1002/anie.201910135] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/14/2019] [Indexed: 01/24/2023]
Abstract
Small-molecule crosslinkers are invaluable for probing biomolecular interactions and for crosslinking mass spectrometry. Existing chemical crosslinkers target only a small selection of amino acids, while conventional photo-crosslinkers target almost all residues non-specifically, complicating data analysis. Herein, we report photocaged quinone methide (PQM)-based crosslinkers that target nine nucleophilic residues through Michael addition, including Gln, Arg, and Asn, which are inaccessible to existing chemical crosslinkers. PQM crosslinkers were used in vitro, in Escherichia coli, and in mammalian cells to crosslink dimeric proteins and endogenous membrane receptors. The heterobifunctional crosslinker NHQM could crosslink proteins to DNA, for which few crosslinkers exist. The photoactivatable reactivity of these crosslinkers and their ability to target multiple amino acids will enhance the use of chemical crosslinking for studies of protein-protein and protein-DNA networks and for structural biology.
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Affiliation(s)
- Jun Liu
- University of California, San Francisco, Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Lingchao Cai
- University of California, San Francisco, Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Wei Sun
- University of California, San Francisco, Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Rujin Cheng
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716, USA
| | - Nanxi Wang
- University of California, San Francisco, Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Ling Jin
- University of Florida, Department of Microbiology and Cell Science, Gainesville, FL, 32611, USA
| | - Sharon Rozovsky
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716, USA
| | - Ian B Seiple
- University of California, San Francisco, Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Lei Wang
- University of California, San Francisco, Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
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C-terminal domain swapping of SSB changes the size of the ssDNA binding site. BIOMED RESEARCH INTERNATIONAL 2014; 2014:573936. [PMID: 25162017 PMCID: PMC4137731 DOI: 10.1155/2014/573936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/09/2014] [Indexed: 01/29/2023]
Abstract
Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.
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Li BS, Goh MC. Direct evidence of the role of ATPγS in the binding of single-stranded binding protein (Escherichia coli) and RecA to single-stranded DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14755-14758. [PMID: 20722443 DOI: 10.1021/la102347b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
To gain insight into the influence of ATPγS on the competitive binding of RecA and single-stranded binding protein (SSB) on single-stranded DNA (ssDNA), AFM imaging was used to examine the three-dimensional structures of the different complexes formed by the binding of the two proteins on ssDNA in the presence and absence of ATPγS. In the presence of ATPγS, RecA attaches to ssDNA, displacing SSB, to form continuous binding regions that caused considerable elongation of the strand. When ATPγS is absent, RecA could not compete with SSB and only binds at a few sites that correspond to the vacancy in ssDNA left when SSB unbinds. These results provide direct evidence that, while SSB binding affinity to DNA is substantially higher than that of RecA, the presence of ATPγS is sufficient to alter the events and enable RecA coating of DNA.
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Affiliation(s)
- Bing Shi Li
- Department of Chemistry and Institute for Optical Sciences, University of Toronto, Toronto, Ontario, M5S 3H6 Canada.
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George T, Wen Q, Griffiths R, Ganesh A, Meuth M, Sanders CM. Human Pif1 helicase unwinds synthetic DNA structures resembling stalled DNA replication forks. Nucleic Acids Res 2009; 37:6491-502. [PMID: 19700773 PMCID: PMC2770657 DOI: 10.1093/nar/gkp671] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Pif-1 proteins are 5′→3′ superfamily 1 (SF1) helicases that in yeast have roles in the maintenance of mitochondrial and nuclear genome stability. The functions and activities of the human enzyme (hPif1) are unclear, but here we describe its DNA binding and DNA remodeling activities. We demonstrate that hPif1 specifically recognizes and unwinds DNA structures resembling putative stalled replication forks. Notably, the enzyme requires both arms of the replication fork-like structure to initiate efficient unwinding of the putative leading replication strand of such substrates. This DNA structure-specific mode of initiation of unwinding is intrinsic to the conserved core helicase domain (hPifHD) that also possesses a strand annealing activity as has been demonstrated for the RecQ family of helicases. The result of hPif1 helicase action at stalled DNA replication forks would generate free 3′ ends and ssDNA that could potentially be used to assist replication restart in conjunction with its strand annealing activity.
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Affiliation(s)
- Tresa George
- Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
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Carter RH, Demidenko AA, Hattingh-Willis S, Rothman-Denes LB. Phage N4 RNA polymerase II recruitment to DNA by a single-stranded DNA-binding protein. Genes Dev 2003; 17:2334-45. [PMID: 12975320 PMCID: PMC196469 DOI: 10.1101/gad.1121403] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcription of bacteriophage N4 middle genes is carried out by a phage-coded, heterodimeric RNA polymerase (N4 RNAPII), which belongs to the family of T7-like RNA polymerases. In contrast to phage T7-RNAP, N4 RNAPII displays no activity on double-stranded templates and low activity on single-stranded templates. In vivo, at least one additional N4-coded protein (p17) is required for N4 middle transcription. We show that N4 ORF2 encodes p17 (gp2). Characterization of purified gp2revealed that it is a single-stranded DNA-binding protein that activates N4 RNAPII transcription on single-stranded DNA templates through specific interaction with N4 RNAPII. On the basis of the properties of the proteins involved in N4 RNAPII transcription and of middle promoters, we propose a model for N4 RNAPII promoter recognition, in which gp2plays two roles, stabilization of a single-stranded region at the promoter and recruitment of N4 RNAPII through gp2-N4 RNAPII interactions. Furthermore, we discuss our results in the context of transcription initiation by mitochondrial RNA polymerases.
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Affiliation(s)
- Richard H Carter
- Departments of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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Kamma H, Fujimoto M, Fujiwara M, Matsui M, Horiguchi H, Hamasaki M, Satoh H. Interaction of hnRNP A2/B1 isoforms with telomeric ssDNA and the in vitro function. Biochem Biophys Res Commun 2001; 280:625-30. [PMID: 11162566 DOI: 10.1006/bbrc.2000.4173] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Overexpression of heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1, especially of B1 has been reported as a useful marker to detect cancers in early stage, although the biological reason is not clear. A2/B1 proteins were previously reported to bind telomeric DNA repeats. Alternative splicing of A2/B1 gene produces abundant A2, less abundant B1, and testis-specific minor isoforms B0a and B0b. In this study, B1 and B0b that have the N-terminal 12 amino acid insertion were suggested to have higher affinities to telomeric single-stranded DNA (ssDNA) than A2 and B0a. Kinetic analyses using purified B1 and B0b indicated that they interact dynamically with a single array of telomeric repeats. Furthermore, functional assays demonstrated that B1 and B0b bind with telomeric repeats in a tandem fashion and protect them from a nuclease and promote telomerase activity. A2/B1 proteins, especially B1 and B0b, may function as telomeric ssDNA-binding proteins in cancer and reproductive cells.
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Affiliation(s)
- H Kamma
- Institute of Basic Medical Sciences, University of Tsukuba, Ibaraki 305-8575, Japan.
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Revers F, Cario M, Cao TL, Cazenave C. Detection of proteins binding to short RNA.DNA hybrids or short antisense oligonucleotides in Xenopus laevis oocytes and human macrophage cell extracts by photoaffinity radiolabeling. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1999; 9:317-31. [PMID: 10463076 DOI: 10.1089/oli.1.1999.9.317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Using a 12 base pair RNA.DNA hybrid, substituted with bromouracil on either the RNA or DNA strand, we have detected by photoaffinity radiolabeling a limited set of proteins able to bind to RNA.DNA hybrids in both Xenopus oocyte extracts and human macrophage extracts. Resulting patterns of crosslinked proteins were highly dependent on the strand (DNA or RNA) that was substituted. With one exception, none of the proteins investigated in competition experiments was found to be absolutely specific for RNA.DNA hybrids, as at least one other nucleic acid, either single-stranded DNA or single-stranded RNA, was found to compete efficiently. None of the proteins detected in this assay correspond to the size expected for RNases H. Using the same methodology, we have detected proteins that bind to short oligodeoxyribonucleotides. Although we have essentially detected in Xenopus oocytes one prominent protein of approximately 75 kDa, corresponding to replication protein A (RPA) whatever the oligonucleotide used, the patterns obtained with extracts of human macrophages were more complex and dependent on the oligonucleotide used. If a protein corresponding to RPA was observed most of the time, other crosslinks of similar or sometimes higher intensity were also detected. Interestingly, among these, one protein of 35 kDa appears paradoxically to bind and crosslink to a dodecamer but not to an octadecamer containing the same sequence placed either at its 3'-end or 5'-end.
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Affiliation(s)
- F Revers
- Laboratoire de Biophysique Moléculaire, INSERM U386, Université Victor Segalen Bordeaux II, France
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Abstract
Replication of the two template strands at eukaryotic cell DNA replication forks is a highly coordinated process that ensures accurate and efficient genome duplication. Biochemical studies, principally of plasmid DNAs containing the Simian Virus 40 origin of DNA replication, and yeast genetic studies have uncovered the fundamental mechanisms of replication fork progression. At least two different DNA polymerases, a single-stranded DNA-binding protein, a clamp-loading complex, and a polymerase clamp combine to replicate DNA. Okazaki fragment synthesis involves a DNA polymerase-switching mechanism, and maturation occurs by the recruitment of specific nucleases, a helicase, and a ligase. The process of DNA replication is also coupled to cell-cycle progression and to DNA repair to maintain genome integrity.
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Affiliation(s)
- S Waga
- Cold Spring Harbor Laboratory, New York 11724, USA
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