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Fusco S, Aulitto M, Iacobucci I, Crocamo G, Pucci P, Bartolucci S, Monti M, Contursi P. The interaction between the F55 virus-encoded transcription regulator and the RadA host recombinase reveals a common strategy in Archaea and Bacteria to sense the UV-induced damage to the host DNA. Biochim Biophys Acta Gene Regul Mech 2020; 1863:194493. [PMID: 32014611 DOI: 10.1016/j.bbagrm.2020.194493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/09/2020] [Accepted: 01/29/2020] [Indexed: 01/28/2023]
Abstract
Sulfolobus spindle-shaped virus 1 is the only UV-inducible member of the virus family Fuselloviridae. Originally isolated from Saccharolobus shibatae B12, it can also infect Saccharolobus solfataricus. Like the CI repressor of the bacteriophage λ, the SSV1-encoded F55 transcription repressor acts as a key regulator for the maintenance of the SSV1 carrier state. In particular, F55 binds to tandem repeat sequences located within the promoters of the early and UV-inducible transcripts. Upon exposure to UV light, a temporally coordinated pattern of gene expression is triggered. In the case of the better characterized bacteriophage λ, the switch from lysogenic to lytic development is regulated by a crosstalk between the virus encoded CI repressor and the host RecA, which regulates also the SOS response. For SSV1, instead, the regulatory mechanisms governing the switch from the carrier to the induced state have not been completely unravelled. In this study we have applied an integrated biochemical approach based on a variant of the EMSA assay coupled to mass spectrometry analyses to identify the proteins associated with F55 when bound to its specific DNA promoter sequences. Among the putative F55 interactors, we identified RadA and showed that the archaeal molecular components F55 and RadA are functional homologs of bacteriophage λ (factor CI) and Escherichia coli (RecA) system.
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Affiliation(s)
- Salvatore Fusco
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145 Naples, Italy
| | - Giulio Crocamo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Pietro Pucci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145 Naples, Italy
| | | | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145 Naples, Italy.
| | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy.
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Stuart MK, Hudman DA, Nachtrab SN, Hiatt JL, Seo J, Pullen SJ, Sargentini NJ. Fine Epitope Mapping of Monoclonal Antibodies to the DNA Repair Protein, RadA. Monoclon Antib Immunodiagn Immunother 2017; 36:83-94. [PMID: 28581365 DOI: 10.1089/mab.2017.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Repair of DNA damage is vital to the health and survival of all organisms. In Escherichia coli, a protein known as RadA (or Sms) participates in recombinational repair, a process that uses an undamaged DNA strand in one DNA duplex to fill a gap in a homologous DNA strand in a sister DNA duplex. In a prior report, we described the production of monoclonal antibodies (MAbs) specific for RadA. Here, we investigated the epitopes recognized by two of the antibodies, MAbs 6F5 and 2A2. Premature stop codons (ochre mutations) were introduced into the radA gene at selected sites, and the truncated RadA proteins were probed by western blotting. Deletion of as few as four amino acids (457-460) from the C-terminus of RadA significantly increased the sensitivity of E. coli to ultraviolet (UV) radiation and abolished recognition of RadA by MAb 6F5. Single alanine substitutions made between positions 443-460 also adversely affected the ability of MAb 6F5 to bind to RadA, further supporting the idea that MAb 6F5 is specific for the RadA C-terminus. An ochre mutation at position 258 abolished the recognition of RadA by MAb 2A2, whereas an ochre mutation at position 279 did not, suggesting that MAb 2A2 binds to an epitope between residues 258 and 279. MAb 2A2 recognition of RadA was destroyed by endoproteinase glu-C cleavage of RadA at position 266, and by a single alanine substitution at position 265. In a competitive enzyme-linked immunosorbent assay (ELISA), a synthetic peptide comprising residues 263-273 of RadA blocked MAb 2A2 recognition of immobilized full-length RadA by more than 97%. We infer from our results that MAb 6F5 binds to the extreme C-terminus of RadA and that MAb 2A2 is specific for an epitope within positions 263-273.
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Affiliation(s)
- Melissa K Stuart
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Deborah A Hudman
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Stephanie N Nachtrab
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
| | - Jacob L Hiatt
- 2 Lakeland Regional Medical Center , Saint Joseph, Michigan
| | - Jin Seo
- 3 Truman State University , Kirksville, Missouri
| | | | - Neil J Sargentini
- 1 Department of Microbiology/Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University , Kirksville, Missouri
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Inoue M, Fukui K, Fujii Y, Nakagawa N, Yano T, Kuramitsu S, Masui R. The Lon protease-like domain in the bacterial RecA paralog RadA is required for DNA binding and repair. J Biol Chem 2017; 292:9801-9814. [PMID: 28432121 DOI: 10.1074/jbc.m116.770180] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/16/2017] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination (HR) plays an essential role in the maintenance of genome integrity. RecA/Rad51 paralogs have been recognized as an important factor of HR. Among them, only one bacterial RecA/Rad51 paralog, RadA, is involved in HR as an accessory factor of RecA recombinase. RadA has a unique Lon protease-like domain (LonC) at its C terminus, in addition to a RecA-like ATPase domain. Unlike Lon protease, RadA's LonC domain does not show protease activity but is still essential for RadA-mediated DNA repair. Reconciling these two facts has been difficult because RadA's tertiary structure and molecular function are unknown. Here, we describe the hexameric ring structure of RadA's LonC domain, as determined by X-ray crystallography. The structure revealed the two positively charged regions unique to the LonC domain of RadA are located at the intersubunit cleft and the central hole of a hexameric ring. Surprisingly, a functional domain analysis demonstrated the LonC domain of RadA binds DNA, with site-directed mutagenesis showing that the two positively charged regions are critical for this DNA-binding activity. Interestingly, only the intersubunit cleft was required for the DNA-dependent stimulation of ATPase activity of RadA, and at least the central hole was essential for DNA repair function. Our data provide the structural and functional features of the LonC domain and their function in RadA-mediated DNA repair.
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Affiliation(s)
- Masao Inoue
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043
| | - Kenji Fukui
- the Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686
| | - Yuki Fujii
- the Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, and
| | - Noriko Nakagawa
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043
| | - Takato Yano
- the Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686
| | - Seiki Kuramitsu
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043
| | - Ryoji Masui
- the Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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Abstract
In this study, Lennon et al. provide new insights into the role of inteins (or protein introns), which are known to autocatalytically excise themselves through protein splicing. They show that intein splicing can be stimulated by a substrate of the invaded host protein, suggesting a new form of post-translational control. Inteins (or protein introns) autocatalytically excise themselves through protein splicing. We challenge the long-considered notion that inteins are merely molecular parasites and posit that some inteins evolved to regulate host protein function. Here we show substrate-induced and DNA damage-induced splicing, in which an archaeal recombinase RadA intein splices dramatically faster and more accurately when provided with ssDNA. This unprecedented example of intein splicing stimulation by the substrate of the invaded host protein provides compelling support in favor of inteins acting as pause buttons to arrest protein function until needed; then, an immediate activity switch is triggered, representing a new form of post-translational control.
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Affiliation(s)
- Christopher W Lennon
- Department of Biological Sciences, RNA Institute, University at Albany, Albany, New York 12222, USA
| | - Matthew Stanger
- Department of Biological Sciences, RNA Institute, University at Albany, Albany, New York 12222, USA
| | - Marlene Belfort
- Department of Biological Sciences, RNA Institute, University at Albany, Albany, New York 12222, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York 12201, USA
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Marsh ME, Scott DE, Ehebauer MT, Abell C, Blundell TL, Hyvönen M. ATP half-sites in RadA and RAD51 recombinases bind nucleotides. FEBS Open Bio 2016; 6:372-85. [PMID: 27419043 PMCID: PMC4856416 DOI: 10.1002/2211-5463.12052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022] Open
Abstract
Homologous recombination is essential for repair of DNA double-strand breaks. Central to this process is a family of recombinases, including archeal RadA and human RAD51, which form nucleoprotein filaments on damaged single-stranded DNA ends and facilitate their ATP-dependent repair. ATP binding and hydrolysis are dependent on the formation of a nucleoprotein filament comprising RadA/RAD51 and single-stranded DNA, with ATP bound between adjacent protomers. We demonstrate that truncated, monomeric Pyrococcus furiosus RadA and monomerised human RAD51 retain the ability to bind ATP and other nucleotides with high affinity. We present crystal structures of both apo and nucleotide-bound forms of monomeric RadA. These structures reveal that while phosphate groups are tightly bound, RadA presents a shallow, poorly defined binding surface for the nitrogenous bases of nucleotides. We suggest that RadA monomers would be constitutively bound to nucleotides in the cell and that the bound nucleotide might play a structural role in filament assembly.
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Affiliation(s)
- May E Marsh
- Department of Biochemistry University of Cambridge UK; Present address: Paul Scherrer Institut Villingen Switzerland
| | | | - Matthias T Ehebauer
- Department of Biochemistry University of Cambridge UK; Present address: Target Discovery Institute Nuffield Department of Medicine University of Oxford UK
| | - Chris Abell
- Department of Chemistry University of Cambridge UK
| | | | - Marko Hyvönen
- Department of Biochemistry University of Cambridge UK
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Gándara C, Alonso JC. DisA and c-di-AMP act at the intersection between DNA-damage response and stress homeostasis in exponentially growing Bacillus subtilis cells. DNA Repair (Amst) 2015; 27:1-8. [PMID: 25616256 DOI: 10.1016/j.dnarep.2014.12.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/24/2014] [Accepted: 12/27/2014] [Indexed: 12/18/2022]
Abstract
Bacillus subtilis contains two vegetative diadenylate cyclases, DisA and CdaA, which produce cyclic di-AMP (c-di-AMP), and one phosphodiesterase, GdpP, that degrades it into a linear di-AMP. We report here that DisA and CdaA contribute to elicit repair of DNA damage generated by alkyl groups and H2O2, respectively, during vegetative growth. disA forms an operon with radA (also termed sms) that encodes a protein distantly related to RecA. Among different DNA damage agents tested, only methyl methane sulfonate (MMS) affected disA null strain viability, while radA showed sensitivity to all of them. A strain lacking both disA and radA was as sensitive to MMS as the most sensitive single parent (epistasis). Low c-di-AMP levels (e.g. by over-expressing GdpP) decreased the ability of cells to repair DNA damage caused by MMS and in less extent by H2O2, while high levels of c-di-AMP (absence of GdpP or expression of sporulation-specific diadenylate cyclase, CdaS) increased cell survival. Taken together, our results support the idea that c-di-AMP is a crucial signalling molecule involved in DNA repair with DisA and CdaA contributing to modulate different DNA damage responses during exponential growth.
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Affiliation(s)
- Carolina Gándara
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Juan C Alonso
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
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