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Jian P, Liu J, Li L, Song Q, Zhang D, Zhang S, Chai C, Zhao H, Zhao G, Zhu H, Qiao J. AcrR1, a novel TetR/AcrR family repressor, mediates acid and antibiotic resistance and nisin biosynthesis in Lactococcus lactis F44. J Dairy Sci 2024:S0022-0302(24)00806-3. [PMID: 38762103 DOI: 10.3168/jds.2024-24754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/31/2024] [Indexed: 05/20/2024]
Abstract
Lactococcus lactis, widely used in the manufacture of dairy products, encounters various environmental stresses both in natural habitats and during industrial processes. It has evolved intricate machinery of stress sensing and defense to survive harsh stress conditions. Here, we identified a novel TetR/AcrR family transcription regulator, designated AcrR1, to be a repressor for acid and antibiotic tolerance that was derepressed in the presence of vancomycin or under acid stress. The survival rates of acrR1 deletion strain ΔAcrR1 under acid and vancomycin stresses were about 28.7-fold (pH 3.0, HCl), 8.57-fold (pH 4.0, lactic acid) and 2.73-fold (300 ng/mL vancomycin) as that of original strain F44. We also demonstrated that ΔAcrR1 was better able to maintain intracellular pH homeostasis and had a lower affinity to vancomycin. No evident effects of AcrR1 deletion on the growth and morphology of strain F44 were observed. Subsequently, we characterized that the transcription level of genes associated with amino acids biosynthesis, carbohydrate transport and metabolism, multiple drug resistance and DNA repair proteins significantly upregulated in ΔAcrR1 using transcriptome analysis and quantitative reverse transcription-PCR (qRT-PCR) assays. Additionally, AcrR1 could repress the transcription of nisin post-translational modification gene, nisC, leading to a 16.3% increase in nisin yield after AcrR1 deletion. Our results not only refined the knowledge of the regulatory mechanism of TetR/AcrR family regulator in L. lactis, but presented a potential strategy to enhance industrial production of nisin.
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Affiliation(s)
- Pingqiu Jian
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Jiaheng Liu
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China.
| | - Li Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Qianqian Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Di Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Shenyi Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Chaofan Chai
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Hui Zhao
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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The Impact of Single-Stranded DNA-Binding Protein SSB and Putative SSB-Interacting Proteins on Genome Integrity in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Int J Mol Sci 2023; 24:ijms24054558. [PMID: 36901989 PMCID: PMC10003305 DOI: 10.3390/ijms24054558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The study of DNA repair in hyperthermophiles has the potential to elucidate the mechanisms of genome integrity maintenance systems under extreme conditions. Previous biochemical studies have suggested that the single-stranded DNA-binding protein (SSB) from the hyperthermophilic crenarchaeon Sulfolobus is involved in the maintenance of genome integrity, namely, in mutation avoidance, homologous recombination (HR), and the repair of helix-distorting DNA lesions. However, no genetic study has been reported that elucidates whether SSB actually maintains genome integrity in Sulfolobus in vivo. Here, we characterized mutant phenotypes of the ssb-deleted strain Δssb in the thermophilic crenarchaeon S. acidocaldarius. Notably, an increase (29-fold) in mutation rate and a defect in HR frequency was observed in Δssb, indicating that SSB was involved in mutation avoidance and HR in vivo. We characterized the sensitivities of Δssb, in parallel with putative SSB-interacting protein-encoding gene-deleted strains, to DNA-damaging agents. The results showed that not only Δssb but also Δalhr1 and ΔSaci_0790 were markedly sensitive to a wide variety of helix-distorting DNA-damaging agents, indicating that SSB, a novel helicase SacaLhr1, and a hypothetical protein Saci_0790, were involved in the repair of helix-distorting DNA lesions. This study expands our knowledge of the impact of SSB on genome integrity and identifies novel and key proteins for genome integrity in hyperthermophilic archaea in vivo.
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Pcal_2031, a RecA/Rad51 homologue from Pyrobaculum calidifontis, complements the ultraviolet light sensitivity of Escherichia coli. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01187-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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4
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De Falco M, De Felice M. Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea. Int J Mol Sci 2021; 22:ijms222413296. [PMID: 34948099 PMCID: PMC8708640 DOI: 10.3390/ijms222413296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers SV. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerization and interaction with ArlI, the motor ATPase of the archaellum. Mol Microbiol 2021; 116:943-956. [PMID: 34219289 DOI: 10.1111/mmi.14781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Since autophosphorylation and dephosphorylation of KaiC are central properties for the function of KaiC, we asked whether autophosphorylation is also a property of ArlH proteins. We observed that both ArlH from the euryarchaeon Pyrococcus furiosus (PfArlH) and from the crenarchaeon Sulfolobus acidocaldarius (SaArlH) have autophosphorylation activity. Using a combination of single-molecule fluorescence measurements and biochemical assays, we show that autophosphorylation of ArlH is closely linked to its oligomeric state when bound to hexameric ArlI. These experiments also strongly suggest that ArlH is a hexamer in its ArlI-bound state. Mutagenesis of the putative catalytic residue (Glu-57 in SaArlH) in ArlH results in a reduced autophosphorylation activity and abolished archaellation and motility in S. acidocaldarius, indicating that optimum phosphorylation activity of ArlH is essential for archaellation and motility.
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Affiliation(s)
- J Nuno de Sousa Machado
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Leonie Vollmar
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Julia Schimpf
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Rashmi Kumariya
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital. Chin Med J (Engl) 2021; 133:2573-2585. [PMID: 32969865 PMCID: PMC7722564 DOI: 10.1097/cm9.0000000000001101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) poses distinct clinical challenges due to extensively drug resistant (XDR) phenotype, and sequence type (ST) 11 is the most dominant blaKPC-2-bearing CP-Kp clone in China. The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit (ICU) of a Chinese tertiary hospital. Methods Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination, polymerase chain reaction, and pyrosequencing. The six ST11 XDR CP-Kp, as well as three multi-drug resistant (MDR) and four susceptible strains, were sequenced using single-molecule real-time method. Comprehensively structural and functional analysis based on comparative genomics was performed to identify genomic characteristics of the XDR ST11 CP-Kp strains. Results We found that ST11 XDR blaKPC-2-bearing CP-Kp strains isolated from inpatients spread in the ICU of the hospital. Functionally, genes associated with information storage and processing of the ST11 XDR CP-Kp strains were more abundant than those of MDR and susceptible strains, especially genes correlative with mobile genetic elements (MGEs) such as transposons and prophages. Structurally, eleven large-scale genetic regions taken for the unique genome in these ST11 XDR CP-Kp strains were identified as MGEs including transposons, integrons, prophages, genomic islands, and integrative and conjugative elements. Three of them were located on plasmids and eight on chromosomes; five of them were with antimicrobial resistance genes and eight with adaptation associated genes. Notably, a new blaKPC-2-bearing ΔΔTn1721-blaKPC-2 transposon, probably transposed and truncated from ΔTn1721-blaKPC-2 by IS903D and ISKpn8, was identified in all six ST11 XDR CP-Kp strains. Conclusion Our findings suggested that together with clonal spread, MGEs identified uniquely in the ST11 XDR CP-Kp strains might contribute to their formidable adaptability, which facilitated their widespread dissemination in hospital.
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers S. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerisation and interaction with ArlI, the motor ATPase of the archaellum.. [DOI: 10.1101/2021.03.19.436134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Similar to KaiC, ArlH exhibits autophosphorylation activity, which was observed for both ArlH of the euryarchaeonPyrococcus furiosus (PfArlH)and the crenarchaeonSulfolobus acidocaldarius(SaArlH). Using a combination of single molecule fluorescence measurements and biochemical assays, it is shown that autophosphorylation of ArlH is closely linked to the oligomeric state of ArlH bound to ArlI. These experiments also strongly suggest that ArlH is a hexamer in its functional ArlI bound state. Mutagenesis of the putative catalytic residue Glu-57 inSaArlH results in a reduced autophosphorylation activity and abolished archaellation and motility, suggesting that optimum phosphorylation activity of ArlH is essential for both archaellation and motility.
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8
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Knadler C, Rolfsmeier M, Vallejo A, Haseltine C. Characterization of an archaeal recombinase paralog that exhibits novel anti-recombinase activity. Mutat Res 2020; 821:111703. [PMID: 32416400 DOI: 10.1016/j.mrfmmm.2020.111703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/01/2020] [Indexed: 01/31/2023]
Abstract
The process of homologous recombination is heavily dependent on the RecA family of recombinases for repair of DNA double-strand breaks. These recombinases are responsible for identifying homologies and forming heteroduplex DNA between substrate ssDNA and dsDNA templates, activities that are modified by various accessory factors. In this work we describe the biochemical functions of the SsoRal2 recombinase paralog from the crenarchaeon Sulfolobus solfataricus. We found that the SsoRal2 protein is a DNA-independent ATPase that, unlike the other S. solfataricus paralogs, does not bind either ss- or dsDNA. Instead, SsoRal2 alters the ssDNA binding activity of the SsoRadA recombinase in conjunction with another paralog, SsoRal1. In the presence of SsoRal1, SsoRal2 has a modest effect on strand invasion but effectively abrogates strand exchange activity. Taken together, these results indicate that SsoRal2 assists in nucleoprotein filament modulation and control of strand exchange in S. solfataricus.
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Affiliation(s)
- Corey Knadler
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States
| | - Michael Rolfsmeier
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States
| | - Antonia Vallejo
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States
| | - Cynthia Haseltine
- Washington State University, Biotech/LifeSciences Rm 137, Pullman, 99164, United States.
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Huang Q, Mayaka JB, Zhong Q, Zhang C, Hou G, Ni J, Shen Y. Phosphorylation of the Archaeal Holliday Junction Resolvase Hjc Inhibits Its Catalytic Activity and Facilitates DNA Repair in Sulfolobus islandicus REY15A. Front Microbiol 2019; 10:1214. [PMID: 31214148 PMCID: PMC6555300 DOI: 10.3389/fmicb.2019.01214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/15/2019] [Indexed: 11/18/2022] Open
Abstract
Protein phosphorylation is one of the main protein post-translational modifications and regulates DNA repair in eukaryotes. Archaeal genomes encode eukaryotic-like DNA repair proteins and protein kinases (ePKs), and several proteins involved in homologous recombination repair (HRR) including Hjc, a conserved Holliday junction (HJ) resolvase in Archaea, undergo phosphorylation, indicating that phosphorylation plays important roles in HRR. Herein, we performed phosphorylation analysis of Hjc by various ePKs from Sulfolobus islandicus. It was shown that SiRe_0171, SiRe_2030, and SiRe_2056, were able to phosphorylate Hjc in vitro. These ePKs phosphorylated Hjc at different Ser/Thr residues: SiRe_0171 on S34, SiRe_2030 on both S9 and T138, and SiRe_2056 on T138. The HJ cleavage activity of the phosphorylation-mimic mutants was analyzed and the results showed that the cleavage activity of S34E was completely lost and that of S9E had greatly reduced. S. islandicus strain expressing S34E in replacement of the wild type Hjc was resistant to higher doses of DNA damaging agents. Furthermore, SiRe_0171 deletion mutant exhibited higher sensitivity to DNA damaging agents, suggesting that Hjc phosphorylation by SiRe_0171 enhanced the DNA repair capability. Our results revealed that HJ resolvase is regulated by protein phosphorylation, reminiscent of the regulation of eukaryotic HJ resolvases GEN1 and Yen1.
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Affiliation(s)
- Qihong Huang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Joseph Badys Mayaka
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qing Zhong
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Chao Zhang
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guihua Hou
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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White MF, Allers T. DNA repair in the archaea-an emerging picture. FEMS Microbiol Rev 2018; 42:514-526. [PMID: 29741625 DOI: 10.1093/femsre/fuy020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/02/2018] [Indexed: 12/12/2022] Open
Abstract
There has long been a fascination in the DNA repair pathways of archaea, for two main reasons. Firstly, many archaea inhabit extreme environments where the rate of physical damage to DNA is accelerated. These archaea might reasonably be expected to have particularly robust or novel DNA repair pathways to cope with this. Secondly, the archaea have long been understood to be a lineage distinct from the bacteria, and to share a close relationship with the eukarya, particularly in their information processing systems. Recent discoveries suggest the eukarya arose from within the archaeal domain, and in particular from lineages related to the TACK superphylum and Lokiarchaea. Thus, archaeal DNA repair proteins and pathways can represent a useful model system. This review focuses on recent advances in our understanding of archaeal DNA repair processes including base excision repair, nucleotide excision repair, mismatch repair and double-strand break repair. These advances are discussed in the context of the emerging picture of the evolution and relationship of the three domains of life.
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Affiliation(s)
- Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, Fife KY16 9ST, UK
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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Iguchi H, Yoshida Y, Fujisawa K, Taga H, Yurimoto H, Oyama T, Sakai Y. KaiC family proteins integratively control temperature-dependent UV resistance in Methylobacterium extorquens AM1. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:634-643. [PMID: 29901260 DOI: 10.1111/1758-2229.12662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
KaiC protein is the pivotal component of the circadian clock in cyanobacteria. While KaiC family proteins are well-conserved throughout divergent phylogenetic lineages, studies of the physiological roles of KaiC proteins from other microorganisms have been limited. We examined the role of the KaiC proteins, KaiC1 and KaiC2, in the methanol-utilizing bacterium Methylobacterium extorquens AM1. Wild-type M. extorquens AM1 cells exhibited temperature-dependent UV resistance (TDR) under permissive growth temperatures (24 °C -32 °C). Both the phosphorylation of KaiC2 and the intracellular levels of KaiC1 were temperature-dependent, and the TDR phenotype was positively regulated by KaiC1 and negatively regulated by KaiC2. Taken together with biochemical and functional analogies to the KaiC protein of cyanobacteria, our present results suggest that KaiC family proteins function to integrate environmental cues, that is, temperature and UV light, and output appropriate cellular responses to allow cells to adapt to changing environmental conditions.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Affiliation(s)
- Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
- Faculty of Bioenvironmental Science, Department of Agriculture and Food Technology, Kyoto Gakuen University, 1-1 Nanjo-Ohtani, Sogabe, Kameoka, 621-8555, Japan
| | - Yusuke Yoshida
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kento Fujisawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroki Taga
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
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De Falco M, Massa F, Rossi M, De Felice M. The Sulfolobus solfataricus RecQ-like DNA helicase Hel112 inhibits the NurA/HerA complex exonuclease activity. Extremophiles 2018; 22:581-589. [PMID: 29488113 DOI: 10.1007/s00792-018-1018-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/21/2018] [Indexed: 02/03/2023]
Abstract
ATPase/Helicases and nucleases play important roles in DNA end-resection, a critical step during homologous recombination repair in all organisms. In hyperthermophilic archaea the exo-endonuclease NurA and the ATPase HerA cooperate with the highly conserved Mre11-Rad50 complex in 3' single-stranded DNA (ssDNA) end processing to coordinate repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA complex. In this study we demonstrate that the NurA exonuclease activity is inhibited by the Sulfolobus solfataricus RecQ-like Hel112 helicase. Inhibition occurs both in the presence and in the absence of HerA, but is much stronger when NurA is in complex with HerA. In contrast, the endonuclease activity of NurA is not affected by the presence of Hel112. Taken together these results suggest that the functional interaction between NurA/HerA and Hel112 is important for DNA end-resection in archaeal homologous recombination.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy.
| | - Federica Massa
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy
| | - Mariarita De Felice
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy.
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13
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The RadA Recombinase and Paralogs of the Hyperthermophilic Archaeon Sulfolobus solfataricus. Methods Enzymol 2018; 600:255-284. [PMID: 29458762 DOI: 10.1016/bs.mie.2017.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Repair of DNA double-strand breaks is a critical function shared by organisms in all three domains of life. The majority of mechanistic understanding of this process has come from characterization of bacterial and eukaryotic proteins, while significantly less is known about analogous activities in the third, archaeal domain. Despite the physical resemblance of archaea to bacteria, archaeal proteins involved in break repair are remarkably similar to those used by eukaryotes. Investigating the function of the archaeal version of these proteins is, in many cases, simpler than working with eukaryotic homologs owing to their robust nature and ease of purification. In this chapter, we describe methods for purification and activity analysis for the RadA recombinase and its paralogs from the hyperthermophilic acidophilic archaeon Sulfolobus solfataricus.
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14
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Liew LP, Lim ZY, Cohen M, Kong Z, Marjavaara L, Chabes A, Bell SD. Hydroxyurea-Mediated Cytotoxicity Without Inhibition of Ribonucleotide Reductase. Cell Rep 2017; 17:1657-1670. [PMID: 27806303 PMCID: PMC5134839 DOI: 10.1016/j.celrep.2016.10.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/29/2016] [Accepted: 10/07/2016] [Indexed: 11/30/2022] Open
Abstract
In many organisms, hydroxyurea (HU) inhibits class I ribonucleotide reductase, leading to lowered cellular pools of deoxyribonucleoside triphosphates. The reduced levels for DNA precursors is believed to cause replication fork stalling. Upon treatment of the hyperthermophilic archaeon Sulfolobus solfataricus with HU, we observe dose-dependent cell cycle arrest, accumulation of DNA double-strand breaks, stalled replication forks, and elevated levels of recombination structures. However, Sulfolobus has a HU-insensitive class II ribonucleotide reductase, and we reveal that HU treatment does not significantly impact cellular DNA precursor pools. Profiling of protein and transcript levels reveals modulation of a specific subset of replication initiation and cell division genes. Notably, the selective loss of the regulatory subunit of the primase correlates with cessation of replication initiation and stalling of replication forks. Furthermore, we find evidence for a detoxification response induced by HU treatment. Sulfolobus has a HU-insensitive class II ribonucleotide reductase HU impairs DNA replication and is toxic to Sulfolobus cells HU treatment leads to selective loss of the regulatory subunit of DNA primase
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Affiliation(s)
- Li Phing Liew
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Zun Yi Lim
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Matan Cohen
- Department of Biology, Indiana University, Simon Hall MSB, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, SE 90197 Umeå, Sweden
| | - Lisette Marjavaara
- Department of Medical Biochemistry and Biophysics, Umeå University, SE 90197 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE 90197 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden, Umeå University, SE 90197 Umeå, Sweden
| | - Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 South Hawthorne Drive, Bloomington, IN 47405, USA; Department of Biology, Indiana University, Simon Hall MSB, 212 South Hawthorne Drive, Bloomington, IN 47405, USA.
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15
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Wang B, Zhang H, Liang D, Hao P, Li Y, Qiao J. Acid or erythromycin stress significantly improves transformation efficiency through regulating expression of DNA binding proteins in Lactococcus lactis F44. J Dairy Sci 2017; 100:9532-9538. [PMID: 28987584 DOI: 10.3168/jds.2017-13101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 07/22/2017] [Indexed: 11/19/2022]
Abstract
Lactococcus lactis is a gram-positive bacterium used extensively in the dairy industry and food fermentation, and its biological characteristics are usually improved through genetic manipulation. However, poor transformation efficiency was the main restriction factor for the construction of engineered strains. In this study, the transformation efficiency of L. lactis F44 showed a 56.1-fold increase in acid condition (pH 5.0); meanwhile, erythromycin stress (0.04 μg/mL) promoted the transformation efficiency more significantly (76.9-fold). Notably, the transformation efficiency of F44e (L. lactis F44 harboring empty pLEB124) increased up to 149.1-fold under the synergistic stresses of acid and erythromycin. In addition, the gene expression of some DNA binding proteins (DprA, RadA, RadC, RecA, RecQ, and SsbA) changed correspondingly. Especially for radA, 25.1-fold improvement was detected when F44e was exposed to pH 5.0. Overexpression of some DNA binding proteins could improve the transformation efficiency. The results suggested that acid or erythromycin stress could improve the transformation efficiency of L. lactis through regulating gene expression of DNA binding proteins. We have proposed a simple but promising strategy for improving the transformation efficiency of L. lactis and other hard-transformed microorganisms.
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Affiliation(s)
- Binbin Wang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education Tianjin, 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Huawei Zhang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education Tianjin, 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Dongmei Liang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education Tianjin, 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Panlong Hao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education Tianjin, 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Yanni Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education Tianjin, 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education Tianjin, 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China.
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16
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Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea. SCIENCE CHINA-LIFE SCIENCES 2017; 60:370-385. [DOI: 10.1007/s11427-016-0355-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/18/2016] [Indexed: 12/26/2022]
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17
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De Falco M, Catalano F, Rossi M, Ciaramella M, De Felice M. NurA Is Endowed with Endo- and Exonuclease Activities that Are Modulated by HerA: New Insight into Their Role in DNA-End Processing. PLoS One 2015; 10:e0142345. [PMID: 26560692 PMCID: PMC4641729 DOI: 10.1371/journal.pone.0142345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/20/2015] [Indexed: 11/18/2022] Open
Abstract
The nuclease NurA and the ATPase HerA are present in all known thermophilic archaea and cooperate with the highly conserved MRE11/RAD50 proteins to facilitate efficient DNA double-strand break end processing during homologous recombinational repair. However, contradictory results have been reported on the exact activities and mutual dependence of these two enzymes. To understand the functional relationship between these two enzymes we deeply characterized Sulfolobus solfataricus NurA and HerA proteins. We found that NurA is endowed with exo- and endonuclease activities on various DNA substrates, including linear (single-stranded and double stranded) as well as circular molecules (single stranded and supercoiled double-stranded). All these activities are not strictly dependent on the presence of HerA, require divalent ions (preferably Mn2+), and are inhibited by the presence of ATP. The endo- and exonculease activities have distinct requirements: whereas the exonuclease activity on linear DNA fragments is stimulated by HerA and depends on the catalytic D58 residue, the endonuclease activity on circular double-stranded DNA is HerA-independent and is not affected by the D58A mutation. On the basis of our results we propose a mechanism of action of NurA/HerA complex during DNA end processing.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
- * E-mail: (M. De Falco); (M. De Felice)
| | - Federico Catalano
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Mariarita De Felice
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
- * E-mail: (M. De Falco); (M. De Felice)
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18
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Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:942605. [PMID: 26146487 PMCID: PMC4471258 DOI: 10.1155/2015/942605] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/21/2015] [Indexed: 11/17/2022]
Abstract
Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity.
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19
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Huang Q, Liu L, Liu J, Ni J, She Q, Shen Y. Efficient 5'-3' DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus. BMC Mol Biol 2015; 16:2. [PMID: 25880130 PMCID: PMC4351679 DOI: 10.1186/s12867-015-0030-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/26/2015] [Indexed: 12/31/2022] Open
Abstract
Background ATPase/Helicases and nucleases play important roles in homologous recombination repair (HRR). Many of the mechanistic details relating to these enzymes and their function in this fundamental and complicated DNA repair process remain poorly understood in archaea. Here we employed Sulfolobus islandicus, a hyperthermophilic archaeon, as a model to investigate the in vivo functions of the ATPase/helicase HerA, the nuclease NurA, and their associated proteins Mre11 and Rad50. Results We revealed that each of the four genes in the same operon, mre11, rad50, herA, and nurA, are essential for cell viability by a mutant propagation assay. A genetic complementation assay with mutant proteins was combined with biochemical characterization demonstrating that the ATPase activity of HerA, the interaction between HerA and NurA, and the efficient 5′-3′ DNA end resection activity of the HerA-NurA complex are essential for cell viability. NurA and two other putative HRR proteins: a PIN (PilT N-terminal)-domain containing ATPase and the Holliday junction resolvase Hjc, were co-purified with a chromosomally encoded N-His-HerA in vivo. The interactions of HerA with the ATPase and Hjc were further confirmed by in vitro pull down. Conclusion Efficient 5′-3′ DNA end resection activity of the HerA-NurA complex contributes to necessity of HerA and NurA in Sulfolobus, which is crucial to yield a 3′-overhang in HRR. HerA may have additional binding partners in cells besides NurA. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0030-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qihong Huang
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, 250100, P. R. China. .,Archaea Centre, Department of Biology, University of Copenhagen, Ole MaaløesVej 5, Copenhagen N, DK-2200, Denmark.
| | - Linlin Liu
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, 250100, P. R. China.
| | - Junfeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, 250100, P. R. China.
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, 250100, P. R. China.
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole MaaløesVej 5, Copenhagen N, DK-2200, Denmark.
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Rd., Jinan, 250100, P. R. China.
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20
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Abstract
Homologous DNA pairing and strand exchange are at the core of homologous recombination. These reactions are promoted by a DNA-strand-exchange protein assembled into a nucleoprotein filament comprising the DNA-pairing protein, ATP, and single-stranded DNA. The catalytic activity of this molecular machine depends on control of its dynamic instability by accessory factors. Here we discuss proteins known as recombination mediators that facilitate formation and functional activation of the DNA-strand-exchange protein filament. Although the basics of homologous pairing and DNA-strand exchange are highly conserved in evolution, differences in mediator function are required to cope with differences in how single-stranded DNA is packaged by the single-stranded DNA-binding protein in different species, and the biochemical details of how the different DNA-strand-exchange proteins nucleate and extend into a nucleoprotein filament. The set of (potential) mediator proteins has apparently expanded greatly in evolution, raising interesting questions about the need for additional control and coordination of homologous recombination in more complex organisms.
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Affiliation(s)
- Alex Zelensky
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands Department of Radiation Oncology, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Claire Wyman
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands Department of Radiation Oncology, Erasmus Medical Center Cancer Institute, 3000 CA, Rotterdam, The Netherlands
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21
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Han W, Shen Y, She Q. Nanobiomotors of archaeal DNA repair machineries: current research status and application potential. Cell Biosci 2014; 4:32. [PMID: 24995126 PMCID: PMC4080772 DOI: 10.1186/2045-3701-4-32] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 06/13/2014] [Indexed: 11/10/2022] Open
Abstract
Nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. These proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Several archaeal nucleic acid nanobiomotors, such as DNA helicases that unwind double-stranded DNA molecules during DNA damage repair, have been characterized in details. XPB, XPD and Hjm are SF2 family helicases, each of which employs two ATPase domains for ATP binding and hydrolysis to drive DNA unwinding. They also carry additional specific domains for substrate binding and regulation. Another helicase, HerA, forms a hexameric ring that may act as a DNA-pumping enzyme at the end processing of double-stranded DNA breaks. Common for all these nanobiomotors is that they contain ATPase domain that adopts RecA fold structure. This structure is characteristic for RecA/RadA family proteins and has been studied in great details. Here we review the structural analyses of these archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion. The application potential of archaeal nanobiomotors in drug delivery has been discussed.
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Affiliation(s)
- Wenyuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China ; Archaeal Centre, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Copenhagen, Denmark
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| | - Qunxin She
- Archaeal Centre, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Copenhagen, Denmark
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