1
|
Yang MJ, Kim J, Lee Y, Lee W, Park CJ. NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus. Int J Mol Sci 2022; 23:ijms23063099. [PMID: 35328522 PMCID: PMC8954794 DOI: 10.3390/ijms23063099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.
Collapse
Affiliation(s)
- Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
| |
Collapse
|
2
|
Caldwell CC, Spies M. Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol 2020; 55:482-507. [PMID: 32856505 PMCID: PMC7821911 DOI: 10.1080/10409238.2020.1813070] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023]
Abstract
The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.
Collapse
Affiliation(s)
- Colleen C. Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| |
Collapse
|
3
|
Japrung D, Bahrami A, Nadzeyka A, Peto L, Bauerdick S, Edel JB, Albrecht T. SSB binding to single-stranded DNA probed using solid-state nanopore sensors. J Phys Chem B 2014; 118:11605-12. [PMID: 25222770 DOI: 10.1021/jp506832u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Single-stranded DNA (ssDNA) binding protein plays an important role in the DNA replication process in a wide range of organisms. It binds to ssDNA to prevent premature reannealing and to protect it from degradation. Current understanding of SSB/ssDNA interaction points to a complex mechanism, including SSB motion along the DNA strand. We report on the first characterization of this interaction at the single-molecule level using solid-state nanopore sensors, namely without any labeling or surface immobilization. Our results show that the presence of SSB on the ssDNA can control the speed of nanopore translocation, presumably due to strong interactions between SSB and the nanopore surface. This enables nanopore-based detection of ssDNA fragments as short as 37 nt, which is normally very difficult with solid-state nanopore sensors, due to constraints in noise and bandwidth. Notably, this fragment is considerably shorter than the 65 nt binding motif, typically required for SSB binding at high salt concentrations. The nonspecificity of SSB binding to ssDNA further suggests that this approach could be used for fragment sizing of short ssDNA.
Collapse
Affiliation(s)
- Deanpen Japrung
- Department of Chemistry, Imperial College London , Exhibition Road, South Kensington Campus, London SW7 2AZ, U.K
| | | | | | | | | | | | | |
Collapse
|
4
|
Diversity of the DNA replication system in the Archaea domain. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:675946. [PMID: 24790526 PMCID: PMC3984812 DOI: 10.1155/2014/675946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/16/2014] [Indexed: 12/11/2022]
Abstract
The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.
Collapse
|
5
|
Zhang J, Zhou R, Inoue J, Mikawa T, Ha T. Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA. Nucleic Acids Res 2013; 42:3821-32. [PMID: 24371279 PMCID: PMC3973332 DOI: 10.1093/nar/gkt1316] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus–Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20–500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.
Collapse
Affiliation(s)
- Jichuan Zhang
- Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana, IL 61801, USA, Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801, USA, RIKEN, Cellular and Molecular Biology Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | | |
Collapse
|
6
|
Wu J, Kodzius R, Cao W, Wen W. Extraction, amplification and detection of DNA in microfluidic chip-based assays. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1140-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
7
|
Olszewski M, Nowak M, Cyranka-Czaja A, Kur J. Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis. Microbiol Res 2013; 169:139-47. [PMID: 23953921 DOI: 10.1016/j.micres.2013.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/09/2013] [Accepted: 07/16/2013] [Indexed: 11/18/2022]
Abstract
Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNA replication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-like gene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoalteromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism. PhaSSB possesses a high sequence similarity to Escherichia coli SSB (48% identity and 57% similarity) and has the longest amino acid sequence (244 amino acid residues) of all the known bacterial SSBs with one OB-fold per monomer. An analysis of purified PhaSSB by means of chemical cross-linking experiments, sedimentation analysis and size exclusion chromatography revealed a stable tetramer in solution. Using EMSA, we characterized the stoichiometry of PhaSSB complexed with a series of ssDNA homopolymers, and the size of the binding site was determined as being approximately 35 nucleotides long. In fluorescence titrations, the occluded site size of PhaSSB on poly(dT) is 34 nucleotides per tetramer under low-salt conditions (2mM NaCl), but increases to 54-64 nucleotides at higher-salt conditions (100-300mM NaCl). This suggests that PhaSSB undergoes a transition between ssDNA binding modes, which is observed for EcoSSB. The binding properties of PhaSSB investigated using SPR technology revealed that the affinity of PhaSSB to ssDNA is typical of SSB proteins. The only difference in the binding mode of PhaSSB to ssDNA is a faster association phase, when compared to EcoSSB, though compensated by faster dissociation rate. When analyzed by differential scanning calorimetry (DSC), the melting temperature (Tm) was determined as 63 °C, which is only a few degrees lower than for EcoSSB.
Collapse
Affiliation(s)
- Marcin Olszewski
- Department of Microbiology, Chemical Faculty, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Marta Nowak
- Department of Microbiology, Chemical Faculty, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Anna Cyranka-Czaja
- University of Wroclaw, Faculty of Biotechnology, Department of Protein Engineering, ul. Tamka 2, 50-138 Wrocław, Poland
| | - Józef Kur
- Department of Microbiology, Chemical Faculty, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland.
| |
Collapse
|
8
|
George NP, Ngo KV, Chitteni-Pattu S, Norais CA, Battista JR, Cox MM, Keck JL. Structure and cellular dynamics of Deinococcus radiodurans single-stranded DNA (ssDNA)-binding protein (SSB)-DNA complexes. J Biol Chem 2012; 287:22123-32. [PMID: 22570477 DOI: 10.1074/jbc.m112.367573] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The single-stranded DNA (ssDNA)-binding protein from the radiation-resistant bacterium Deinococcus radiodurans (DrSSB) functions as a homodimer in which each monomer contains two oligonucleotide-binding (OB) domains. This arrangement is exceedingly rare among bacterial SSBs, which typically form homotetramers of single-OB domain subunits. To better understand how this unusual structure influences the DNA binding and biological functions of DrSSB in D. radiodurans radiation resistance, we have examined the structure of DrSSB in complex with ssDNA and the DNA damage-dependent cellular dynamics of DrSSB. The x-ray crystal structure of the DrSSB-ssDNA complex shows that ssDNA binds to surfaces of DrSSB that are analogous to those mapped in homotetrameric SSBs, although there are distinct contacts in DrSSB that mediate species-specific ssDNA binding. Observations by electron microscopy reveal two salt-dependent ssDNA-binding modes for DrSSB that strongly resemble those of the homotetrameric Escherichia coli SSB, further supporting a shared overall DNA binding mechanism between the two classes of bacterial SSBs. In vivo, DrSSB levels are heavily induced following exposure to ionizing radiation. This accumulation is accompanied by dramatic time-dependent DrSSB cellular dynamics in which a single nucleoid-centric focus of DrSSB is observed within 1 h of irradiation but is dispersed by 3 h after irradiation. These kinetics parallel those of D. radiodurans postirradiation genome reconstitution, suggesting that DrSSB dynamics could play important organizational roles in DNA repair.
Collapse
Affiliation(s)
- Nicholas P George
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | | | | | | | | | | | | |
Collapse
|
9
|
Falero A, Caballero A, Trigueros S, Pérez C, Campos J, Marrero K, Fando R. Characterization of the single-stranded DNA binding protein pV(VGJΦ) of VGJΦ phage from Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1814:1107-12. [PMID: 21586349 DOI: 10.1016/j.bbapap.2011.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 03/22/2011] [Accepted: 04/21/2011] [Indexed: 01/01/2023]
Abstract
pV(VGJΦ), a single-stranded DNA binding protein of the vibriophage VGJΦ was subject to biochemical analysis. Here, we show that this protein has a general affinity for single-stranded DNA (ssDNA) as documented by Electrophoretic Mobility Shift Assay (EMSA). The apparent molecular weight of the monomer is about 12.7kDa as measured by HPLC-SEC. Moreover, isoelectrofocusing showed an isoelectric point for pV(VGJΦ) of 6.82 pH units. Size exclusion chromatography in 150mM NaCl, 50mM sodium phosphate buffer, pH 7.0 revealed a major protein species of 27.0kDa, suggesting homodimeric protein architecture. Furthermore, pV(VGJΦ) binds ssDNA at extreme temperatures and the complex was stable after extended incubation times. Upon frozen storage at -20°C for a year the protein retained its integrity, biological activity and oligomericity. On the other hand, bioinformatics analysis predicted that pV(VGJΦ) protein has a disordered C-terminal, which might be involved in its functional activity. All the aforementioned features make pV(VGJΦ) interesting for biotechnological applications.
Collapse
Affiliation(s)
- Alina Falero
- Department of Molecular Biology, National Center for Scientific Research, Havana, Cuba.
| | | | | | | | | | | | | |
Collapse
|
10
|
Olszewski M, Grot A, Wojciechowski M, Nowak M, Mickiewicz M, Kur J. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana. BMC Microbiol 2010; 10:260. [PMID: 20950419 PMCID: PMC2964679 DOI: 10.1186/1471-2180-10-260] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 10/15/2010] [Indexed: 11/25/2022] Open
Abstract
Background In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. Results We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively). They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold) in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC) the melting temperature (Tm) was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. Conclusion The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR).
Collapse
Affiliation(s)
- Marcin Olszewski
- Department of Microbiology, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | | | | | | | | | | |
Collapse
|
11
|
Thermus thermophilus as biological model. Extremophiles 2009; 13:213-31. [DOI: 10.1007/s00792-009-0226-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 12/31/2008] [Indexed: 10/21/2022]
|
12
|
Shereda RD, Kozlov AG, Lohman TM, Cox MM, Keck JL. SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 2008; 43:289-318. [PMID: 18937104 PMCID: PMC2583361 DOI: 10.1080/10409230802341296] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When duplex DNA is altered in almost any way (replicated, recombined, or repaired), single strands of DNA are usually intermediates, and single-stranded DNA binding (SSB) proteins are present. These proteins have often been described as inert, protective DNA coatings. Continuing research is demonstrating a far more complex role of SSB that includes the organization and/or mobilization of all aspects of DNA metabolism. Escherichia coli SSB is now known to interact with at least 14 other proteins that include key components of the elaborate systems involved in every aspect of DNA metabolism. Most, if not all, of these interactions are mediated by the amphipathic C-terminus of SSB. In this review, we summarize the extent of the eubacterial SSB interaction network, describe the energetics of interactions with SSB, and highlight the roles of SSB in the process of recombination. Similar themes to those highlighted in this review are evident in all biological systems.
Collapse
Affiliation(s)
- Robert D Shereda
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | | | | | | |
Collapse
|
13
|
Olszewski M, Mickiewicz M, Kur J. Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis. Arch Microbiol 2008; 190:79-87. [DOI: 10.1007/s00203-008-0366-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 03/10/2008] [Accepted: 03/17/2008] [Indexed: 11/29/2022]
|
14
|
Wei D, Zhang X. Identification and characterization of a single-stranded DNA-binding protein from thermophilic bacteriophage GVE2. Virus Genes 2007; 36:273-8. [PMID: 17939025 DOI: 10.1007/s11262-007-0170-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Accepted: 09/28/2007] [Indexed: 11/29/2022]
Abstract
Single-stranded DNA-binding (SSB) proteins are indispensable for survival of almost all known living organisms. Due to their numerous applications in diverse molecular biology and analytical methods, SSB proteins have received increasing research interest. In this investigation, a novel SSB gene was identified from a deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) for the first time. The GVE2 SSB protein shared homologies to known SSB proteins from other species. After recombinant expression in E. coli, the purified SSB protein was used for antibody preparation. The Northern and Western blots showed that the GVE2 SSB gene might be an early viral gene. As revealed by DNA binding assay, the recombinant GVE2 SSB protein had single-stranded DNA binding capacity.
Collapse
Affiliation(s)
- Dahai Wei
- School of Life Sciences, Xiamen University, Xiamen, 361005, PR China
| | | |
Collapse
|
15
|
Filipkowski P, Koziatek M, Kur J. A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans. Extremophiles 2006; 10:607-14. [PMID: 16896528 DOI: 10.1007/s00792-006-0011-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 06/14/2006] [Indexed: 10/24/2022]
Abstract
We report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated molecular weight of 32.45 kDa and pI 5.34. The amino acids sequence exhibits 43, 44, 79 and 18% identity with Thermus aquaticus, Thermus thermophilus, Deinococcus radiodurans and E. coli SSBs, respectively. The DrpSSB includes two OB folds per monomer and functions as a homodimer. In fluorescence titrations with poly(dT), DrpSSB bound 24-31 nt depending on the salt concentration, and fluorescence was quenched by about 80%. In a complementation assay in E. coli, DrpSSB took over the in vivo function of EcoSSB. The half-lives of DrpSSB were 120 min at 90 degrees C, 60 min at 95 degrees C and 30 min at 100 degrees C. These results were surprising in the context of half-life of SSB from thermophilic T. aquaticus, which has only 30 s of half-life at 95 degrees C. DrpSSB is the most thermostable SSB-like protein identified to date, offering an attractive alternative for TaqSSB and TthSSB in their applications for molecular biology methods and analytical purposes.
Collapse
Affiliation(s)
- Paweł Filipkowski
- Department of Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | | | | |
Collapse
|
16
|
Filipkowski P, Duraj-Thatte A, Kur J. Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis. Arch Microbiol 2006; 186:129-37. [PMID: 16802171 DOI: 10.1007/s00203-006-0128-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 05/17/2006] [Accepted: 05/19/2006] [Indexed: 10/24/2022]
Abstract
To study the biochemical properties of single-stranded DNA-binding (SSB) protein from Deinococcus geothermalis (DgeSSB), we have cloned the ssb gene obtained by PCR and developed an overexpression system. The gene consists of an open reading frame of 900 nucleotides encoding a protein of 300 amino acids with a calculated molecular weight of 32.45 kDa. The amino acid sequence exhibits 43, 44 and 75% identity with Thermus aquaticus, Thermus thermophilus and Deinococcus radiodurans SSBs, respectively. We show that DgeSSB is similar to Thermus/Deinococcus SSB in its biochemical properties. DgeSSB includes two oligonucleotide/oligosaccharide-binding folds per monomer and functions as a homodimer. In fluorescence titrations with poly(dT), DgeSSB bound about 30 nt independent of the salt concentration, and the fluorescence was quenched by about 65%. In a complementation assay in Escherichia coli, DgeSSB took over the in vivo function of EcoSSB. DgeSSB is thermostable with half-lives of 50 min at 70 degrees C and 5 min at 90 degrees C. Hence, DgeSSB offers an attractive alternative for TaqSSB and TthSSB in their applications for molecular biology methods and for analytical purposes.
Collapse
Affiliation(s)
- Paweł Filipkowski
- Department of Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, 80952 Gdańsk, Poland
| | | | | |
Collapse
|
17
|
Melissis S, Labrou NE, Clonis YD. Nucleotide-mimetic synthetic ligands for DNA-recognizing enzymes One-step purification of Pfu DNA polymerase. J Chromatogr A 2006; 1122:63-75. [PMID: 16712859 DOI: 10.1016/j.chroma.2006.04.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 04/11/2006] [Accepted: 04/12/2006] [Indexed: 11/25/2022]
Abstract
The commercial availability of DNA polymerases has revolutionized molecular biotechnology and certain sectors of the bio-industry. Therefore, the development of affinity adsorbents for purification of DNA polymerases is of academic interest and practical importance. In the present study we describe the design, synthesis and evaluation of a combinatorial library of novel affinity ligands for the purification of DNA polymerases (Pols). Pyrococcus furiosus DNA polymerase (Pfu Pol) was employed as a proof-of-principle example. Affinity ligand design was based on mimicking the natural interactions between deoxynucleoside-triphosphates (dNTPs) and the B-motif, a conserved structural moiety found in Pol-I and Pol-II family of enzymes. Solid-phase 'structure-guided' combinatorial chemistry was used to construct a library of 26 variants of the B-motif-binding 'lead' ligand X-Trz-Y (X is a purine derivative and Y is an aliphatic/aromatic sulphonate or phosphonate derivative) using 1,3,5-triazine (Trz) as the scaffold for assembly. The 'lead' ligand showed complementarity against a Lys and a Tyr residue of the polymerase B-motif. The ligand library was screened for its ability to bind and purify Pfu Pol from Escherichia coli extract. One immobilized ligand (oABSAd), bearing 9-aminoethyladenine (AEAd) and sulfanilic acid (oABS) linked on the triazine scaffold, displayed the highest purifying ability and binding capacity (0,55 mg Pfu Pol/g wet gel). Adsorption equilibrium studies with this affinity ligand and Pfu Pol determined a dissociation constant (K(D)) of 83 nM for the respective complex. The oABSAd affinity adsorbent was exploited in the development of a facile Pfu Pol purification protocol, affording homogeneous enzyme (>99% purity) in a single chromatography step. Quality control tests showed that Pfu Pol purified on the B-motif-complementing ligand is free of nucleic acids and contaminating nuclease activities, therefore, suitable for experimental use.
Collapse
Affiliation(s)
- S Melissis
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
| | | | | |
Collapse
|
18
|
Inoue J, Shigemori Y, Mikawa T. Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein. Nucleic Acids Res 2006; 34:e69. [PMID: 16707659 PMCID: PMC1463899 DOI: 10.1093/nar/gkl350] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Rolling circle amplification (RCA) of plasmid or genomic DNA using random hexamers and bacteriophage phi29 DNA polymerase has become increasingly popular in the amplification of template DNA in DNA sequencing. We have found that the mutant protein of single-stranded DNA binding protein (SSB) from Thermus thermophilus (Tth) HB8 enhances the efficiency of amplification of DNA templates. In addition, the TthSSB mutant protein increased the specificity of phi29 DNA polymerase. We have overexpressed the native and mutant forms of TthSSB protein in Escherichia coli and purified them to homogeneity. In vitro, these proteins were found to bind specifically to single-stranded DNA. Addition of TthSSB mutant protein to RCA halved the elongation time required for phi29 DNA polymerase to synthesize DNA fragments in RCA. Furthermore, the presence of the TthSSB mutant protein essentially eliminates nonspecific DNA products in RCA reactions.
Collapse
Affiliation(s)
- Jin Inoue
- International Graduate School of Arts and Science, Yokohama City University1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | | | - Tsutomu Mikawa
- RIKEN Harima Institute/SPring-8Mikazuki cho, Hyogo 679-5148, Japan
- RIKEN Discovery Research Institute2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- International Graduate School of Arts and Science, Yokohama City University1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- To whom correspondence should be addressed. Tel: +81 45 508 7224; Fax: +81 45 508 7364;
| |
Collapse
|
19
|
Olszewski M, Rebała K, Szczerkowska Z, Kur J. Application of SSB-like protein from Thermus aquaticus in multiplex PCR of human Y-STR markers identification. Mol Cell Probes 2005; 19:203-5. [PMID: 15797821 DOI: 10.1016/j.mcp.2004.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Revised: 09/16/2004] [Accepted: 11/24/2004] [Indexed: 11/26/2022]
Abstract
Here, we demonstrate the application of SSB-like protein from Thermus aquaticus (TaqSSB) in multiplex PCR of human Y-STR markers identification. The use of thermostable TaqSSB prevents or reduces primer dimmer formation, one of the particular problems known to cause inhibition of primer hybridization to the template and reduction of a number of primers available for annealing in PCR reaction.
Collapse
Affiliation(s)
- Marcin Olszewski
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | | | | | | |
Collapse
|
20
|
Witte G, Urbanke C, Curth U. Single-stranded DNA-binding protein of Deinococcus radiodurans: a biophysical characterization. Nucleic Acids Res 2005; 33:1662-70. [PMID: 15781492 PMCID: PMC1069009 DOI: 10.1093/nar/gki310] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The highly conserved bacterial single-stranded DNA-binding (SSB) proteins play an important role in DNA replication, repair and recombination and are essential for the survival of the cell. They are functional as tetramers, in which four OB(oligonucleotide/oligosaccharide binding)-folds act as DNA-binding domains. The protomer of the SSB protein from the extremely radiation-resistant organism Deinococcus radiodurans (DraSSB) has twice the size of the other bacterial SSB proteins and contains two OB-folds. Using analytical ultracentrifugation, we could show that DraSSB forms globular dimers with some protrusions. These DraSSB dimers can interact with two molecules of E.coli DNA polymerase III chi subunit. In fluorescence titrations with poly(dT) DraSSB bound 47-54 nt depending on the salt concentration, and fluorescence was quenched by more than 75%. A distinct low salt binding mode as for EcoSSB was not observed for DraSSB. Nucleic acid binding affinity, rate constant and association mechanism are quite similar for EcoSSB and DraSSB. In a complementation assay in E.coli, DraSSB took over the in vivo function of EcoSSB. With DraSSB behaving almost identical to EcoSSB the question remains open as to why dimeric SSB proteins have evolved in the Thermus group of bacteria.
Collapse
Affiliation(s)
| | | | - Ute Curth
- To whom correspondence should be addressed at Medizinische Hochschule Hannover, Zentrale Einrichtung für biophysikalisch-biochemische Verfahren, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany. Tel: +49 511 532 3707; Fax: +49 511 532 5966;
| |
Collapse
|
21
|
Bernstein DA, Eggington JM, Killoran MP, Misic AM, Cox MM, Keck JL. Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage. Proc Natl Acad Sci U S A 2004; 101:8575-80. [PMID: 15159541 PMCID: PMC423236 DOI: 10.1073/pnas.0401331101] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-stranded DNA (ssDNA)-binding (SSB) proteins are uniformly required to bind and protect single-stranded intermediates in DNA metabolic pathways. All bacterial and eukaryotic SSB proteins studied to date oligomerize to assemble four copies of a conserved domain, called an oligonucleotide/oligosaccharide-binding (OB) fold, that cooperate in nonspecific ssDNA binding. The vast majority of bacterial SSB family members function as homotetramers, with each monomer contributing a single OB fold. However, SSB proteins from the Deinococcus-Thermus genera are exceptions to this rule, because they contain two OB folds per monomer. To investigate the structural consequences of this unusual arrangement, we have determined a 1.8-A-resolution x-ray structure of Deinococcus radiodurans SSB. The structure shows that D. radiodurans SSB comprises two OB domains linked by a beta-hairpin motif. The protein assembles a four-OB-fold arrangement by means of symmetric dimerization. In contrast to homotetrameric SSB proteins, asymmetry exists between the two OB folds of D. radiodurans SSB because of sequence differences between the domains. These differences appear to reflect specialized roles that have evolved for each domain. Extensive crystallographic contacts link D. radiodurans SSB dimers in an arrangement that has important implications for higher-order structures of the protein bound to ssDNA. This assembly utilizes the N-terminal OB domain and the beta-hairpin structure that is unique to Deinococcus and Thermus species SSB proteins. We hypothesize that differences between D. radiodurans SSB and homotetrameric bacterial SSB proteins may confer a selective advantage to D. radiodurans cells that aids viability in environments that challenge genomic stability.
Collapse
Affiliation(s)
- Douglas A Bernstein
- Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | | | | | | | | | | |
Collapse
|
22
|
Perales C, Cava F, Meijer WJJ, Berenguer J. Enhancement of DNA, cDNA synthesis and fidelity at high temperatures by a dimeric single-stranded DNA-binding protein. Nucleic Acids Res 2004; 31:6473-80. [PMID: 14602905 PMCID: PMC275559 DOI: 10.1093/nar/gkg865] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Bacterial single-stranded DNA-binding proteins (SSBs) are required for DNA replication and repair. We have over-expressed and purified the native form and two His-tagged fusions of the SSB from Thermus thermophilus (TthSSB). The three proteins were found as dimers in solution. They bound in vitro to single-stranded DNA specifically over a temperature range of 4-80 degrees C, and the wild-type protein could withstand incubation at 94 degrees C for 2 min. Addition of TthSSB to PCR halved the elongation time required for the DNA polymerases of T.thermophilus (Tth) and Pyrococcus furiosus (Pfu) to synthesise DNA fragments in PCRs. The presence of TthSSB increased the fidelity of the proof- reading-free DNA polymerase of T.thermophilus. TthSSB was also able to bind single-stranded RNA, allowing a dramatic enhancement of the reverse transcription activity of its cognate Tth DNA polymerase during cDNA synthesis.
Collapse
Affiliation(s)
- Celia Perales
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | | | | | | |
Collapse
|