1
|
Bohmer M, Bhullar AS, Weitao T, Zhang L, Lee JH, Guo P. Revolving hexameric ATPases as asymmetric motors to translocate double-stranded DNA genome along one strand. iScience 2023; 26:106922. [PMID: 37305704 PMCID: PMC10250835 DOI: 10.1016/j.isci.2023.106922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023] Open
Abstract
DsDNA translocation through nanoscale pores is generally accomplished by ATPase biomotors. The discovery of the revolving dsDNA translocation mechanism, as opposed to rotation, in bacteriophage phi29 elucidated how ATPase motors move dsDNA. Revolution-driven, hexameric dsDNA motors have been reported in herpesvirus, bacterial FtsK, Streptomyces TraB, and T7 phage. This review explores the common relationship between their structure and mechanisms. Commonalities include moving along the 5'→3' strand, inchworm sequential action leading to an asymmetrical structure, channel chirality, channel size, and 3-step channel gating for controlling motion direction. The revolving mechanism and contact with one of the dsDNA strands addresses the historic controversy of dsDNA packaging using nicked, gapped, hybrid, or chemically modified DNA. These controversies surrounding dsDNA packaging activity using modified materials can be answered by whether the modification was introduced into the 3'→5' or 5'→3' strand. Perspectives concerning solutions to the controversy of motor structure and stoichiometry are also discussed.
Collapse
Affiliation(s)
- Margaret Bohmer
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Abhjeet S. Bhullar
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, USA
| | - Tao Weitao
- Center for the Genetics of Host Defense UT Southwestern Medical Center, Dallas, TX, USA
| | - Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jing-Huei Lee
- Department of Biomedical Engineering, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
2
|
Chitosan-based nanodelivery systems for cancer therapy: Recent advances. Carbohydr Polym 2021; 272:118464. [PMID: 34420724 DOI: 10.1016/j.carbpol.2021.118464] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/11/2021] [Accepted: 07/18/2021] [Indexed: 02/06/2023]
Abstract
Nowadays, cancer is one of the most prominent issues related to human health since it causes more than one-tenth of death cases throughout the world. On the other hand, routine therapeutic approaches in cancer suppression such as radiation therapy, chemotherapy, surgery, etc. due to their undesirable therapeutic outputs, including low efficiency in cancer inhibition, non-targeted drug delivery, nonselective distribution, and enormous side effects, have been indicated inefficient potency in cancer therapy or at least its growth inhibition. As a result, the development of novel and practical therapeutic methods such as nanoparticle-based drug delivery systems can be outstandingly beneficial in cancer suppression. Among various nanoparticles used in the delivery of bioactive to the tumor site, chitosan (CS) nanoparticles have received high attention. CS, poly [β-(1-4)-linked-2-amino-2-deoxy-d-glucose], is a natural linear amino polysaccharide derived from chitin which is made of irregularly distributed d-glucosamine and N-acetyl-d-glucosamine units. CS nanoparticles owing to their appropriate aspects, including nanometric size, great drug loading efficacy, ease of manipulation, non-toxicity, excellent availability and biocompatibility, good serum stability, long-term circulation time, suitable pharmacokinetic and pharmacodynamics, non-immunogenicity, and enhanced drug solubility in the human body, have been designated as an efficient candidate for drug delivery systems. They can be involved in both passive (based on the enhanced permeability and retention effect cancer targeting) and active (receptor-mediated or stimuli-responsive cancer targeting) drug delivery systems for potential cancer therapy. This review presents the properties, preparation, modification, and numerous pharmaceutical applications of CS-based drug nanodelivery systems in the diagnosis and therapy of cancer.
Collapse
|
3
|
A spiral path to unfolding. Nat Struct Mol Biol 2020; 26:763-765. [PMID: 31427794 DOI: 10.1038/s41594-019-0284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
4
|
Guo P, Driver D, Zhao Z, Zheng Z, Chan C, Cheng X. Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality. ACS NANO 2019; 13:6207-6223. [PMID: 31067030 PMCID: PMC6595433 DOI: 10.1021/acsnano.8b08849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nanomotors in nanotechnology are as important as engines in daily life. Many ATPases are nanoscale biomotors classified into three categories based on the motion mechanisms in transporting substrates: linear, rotating, and the recently discovered revolving motion. Most biomotors adopt a multisubunit ring-shaped structure that hydrolyzes ATP to generate force. How these biomotors control the motion direction and regulate the sequential action of their multiple subunits is intriguing. Many ATPases are hexameric with each monomer containing a conserved arginine finger. This review focuses on recent findings on how the arginine finger controls motion direction and coordinates adjacent subunit interactions in both revolving and rotating biomotors. Mechanisms of intersubunit interactions and sequential movements of individual subunits are evidenced by the asymmetrical appearance of one dimer and four monomers in high-resolution structural complexes. The arginine finger is situated at the interface of two subunits and extends into the ATP binding pocket of the downstream subunit. An arginine finger mutation results in deficiency in ATP binding/hydrolysis, substrate binding, and transport, highlighting the importance of the arginine finger in regulating energy transduction and motor function. Additionally, the roles of channel chirality and channel size are discussed as related to controlling one-way trafficking and differentiating the revolving and rotating mechanisms. Finally, the review concludes by discussing the conformational changes and entropy conversion triggered by ATP binding/hydrolysis, offering a view different from the traditional concept of ATP-mediated mechanochemical energy coupling. The elucidation of the motion mechanism and direction control in ATPases could facilitate nanomotor fabrication in nanotechnology.
Collapse
Affiliation(s)
- Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
- E-mail:
| | - Dana Driver
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhengyi Zhao
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhen Zheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Chun Chan
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Xiaolin Cheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| |
Collapse
|
5
|
Li L, Hu X, Zhang M, Ma S, Yu F, Zhao S, Liu N, Wang Z, Wang Y, Guan H, Pan X, Gao Y, Zhang Y, Liu Y, Yang Y, Tang X, Li M, Liu C, Li Z, Mei X. Dual Tumor-Targeting Nanocarrier System for siRNA Delivery Based on pRNA and Modified Chitosan. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 8:169-183. [PMID: 28918019 PMCID: PMC5503097 DOI: 10.1016/j.omtn.2017.06.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 02/07/2023]
Abstract
Highly specific and efficient delivery of siRNA is still unsatisfactory. Herein, a dual tumor-targeting siRNA delivery system combining pRNA dimers with chitosan nanoparticles (CNPPs) was designed to improve the specificity and efficiency of siRNA delivery. In this dual delivery system, folate-conjugated and PEGylated chitosan nanoparticles encapsulating pRNA dimers were used as the first class of delivery system and would selectively deliver intact pRNA dimers near or into target cells. pRNA dimers simultaneously carrying siRNA and targeting aptamer, the second class of delivery system, would specifically deliver siRNA into the target cells via aptamer-mediated endocytosis or proper particle size. To certify the delivering efficiency of this dual system, CNPPs, pRNA dimers alone, chitosan nanoparticles containing siRNA with folate conjugation and PEGylation (CNPS), and chitosan nanoparticles containing pRNA dimers alone (CN) were first prepared. Then, we observed that treatment with CNPPs resulted in increased cellular uptake, higher cell apoptosis, stronger cell cytotoxicity, and more efficacious gene silencing compared to the other three formulations. Higher accumulation of siRNA in the tumor site, stronger tumor inhibition, and longer circulating time were also observed with CNPPs compared to other formulations. In conclusion, this dual nanocarrier system showed high targeting and favorable therapeutic efficacy both in vitro and in vivo. Thereby, a new approach is provided in this study for specific and efficient delivery of siRNA, which lays a foundation for the development of pRNA hexamers, which can simultaneously carry six different substances.
Collapse
Affiliation(s)
- Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xiaoqin Hu
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Min Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Siyu Ma
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Fanglin Yu
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Shiqing Zhao
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Nan Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Zhiyuan Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yu Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hua Guan
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiujie Pan
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yue Gao
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Yue Zhang
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Yan Liu
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Yang Yang
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Xuemei Tang
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Mingyuan Li
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Cheng Liu
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Zhiping Li
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Xingguo Mei
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| |
Collapse
|
6
|
Gu X, Park SY, Tonelli M, Cornilescu G, Xia T, Zhong D, Schroeder SJ. NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions. J Phys Chem Lett 2016; 7:3841-3846. [PMID: 27631837 PMCID: PMC5762182 DOI: 10.1021/acs.jpclett.6b01465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Metal ions are critical for RNA structure and enzymatic activity. We present the structure of an asymmetric RNA loop that binds metal ions and has an essential function in a bacteriophage packaging motor. Prohead RNA is a noncoding RNA that is required for genome packaging activity in phi29-like bacteriophage. The loops in GA1 and phi29 bacteriophage share a conserved adenine that forms a base triple, although the structural context for the base triple differs. NMR relaxation studies and femtosecond time-resolved fluorescence spectroscopy reveal the dynamic behavior of the loop in the metal ion bound and unbound forms. The mechanism of metal ion binding appears to be an induced conformational change between two dynamic ensembles rather than a conformational capture mechanism. These results provide experimental benchmarks for computational models of RNA-metal ion interactions.
Collapse
Affiliation(s)
- Xiaobo Gu
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sun-Young Park
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Marco Tonelli
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Tianbing Xia
- Department of Molecular and Cell Biology, University of Texas, Dallas, Texas 75080, United States
| | - Dongping Zhong
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Susan J. Schroeder
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Corresponding Author.
| |
Collapse
|
7
|
Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism. J Virol 2016; 90:8036-46. [PMID: 27356896 DOI: 10.1128/jvi.00508-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.
Collapse
|
8
|
Specific Delivery of MiRNA for High Efficient Inhibition of Prostate Cancer by RNA Nanotechnology. Mol Ther 2016; 24:1267-77. [PMID: 27125502 DOI: 10.1038/mt.2016.85] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/07/2016] [Indexed: 12/19/2022] Open
Abstract
Both siRNA and miRNA can serve as powerful gene-silencing reagents but their specific delivery to cancer cells in vivo without collateral damage to healthy cells remains challenging. We report here the application of RNA nanotechnology for specific and efficient delivery of anti-miRNA seed-targeting sequence to block the growth of prostate cancer in mouse models. Utilizing the thermodynamically ultra-stable three-way junction of the pRNA of phi29 DNA packaging motor, RNA nanoparticles were constructed by bottom-up self-assembly containing the anti-prostate-specific membrane antigen (PSMA) RNA aptamer as a targeting ligand and anti-miR17 or anti-miR21 as therapeutic modules. The 16 nm RNase-resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection in mice and strongly bound to tumors with little or no accumulation in healthy organs 8 hours postinjection, and subsequently repressed tumor growth at low doses with high efficiency.
Collapse
|
9
|
Kumar R, Grubmüller H. Elastic properties and heterogeneous stiffness of the phi29 motor connector channel. Biophys J 2014; 106:1338-48. [PMID: 24655509 DOI: 10.1016/j.bpj.2014.01.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 01/08/2014] [Accepted: 01/23/2014] [Indexed: 12/31/2022] Open
Abstract
The DNA packaging motor of the bacteriophage ϕ29, comprising head-tail connector, ATPase, and pRNA, transports the viral DNA inside the procapsid against pressure differences of up to ∼60 atm during replication. Several models for the DNA packaging mechanism have been proposed, which attribute different roles to the connector, and require specific mechanical properties of the connector. To characterize these properties at the atomic level, and to understand how the connector withstands this large pressure, we have carried out molecular dynamics simulations of the whole connector both in equilibrium and under mechanical stress. The simulations revealed a quite heterogeneous distribution of stiff and soft regions, resembling that of typical composite materials that are also optimized to resist mechanical stress. In particular, the conserved middle α-helical region is found to be remarkably stiff, similar only to structural proteins forming viral shell, silk, or collagen. In contrast, large parts of the peripheral interface to the ϕ29 procapsid turned out to be rather soft. Force probe and umbrella sampling simulations showed that large connector deformations are remarkably reversible, and served to calculate the free energies required for these deformations. In particular, for an untwisting deformation by 12°, as postulated by the untwist-twist model, more than four times' larger energy is required than is available from hydrolysis of one ATP molecule. Combined with previous experiments, this result is incompatible with the untwist-twist model. In contrast, our simulations support the recently proposed one-way revolution model and suggest in structural terms how the connector blocks DNA leakage. In particular, conserved loops at the rim of the central channel, which are in direct contact with the DNA, are found to be rather flexible and tightly anchored to the rigid central region. These findings suggest a check-valve mechanism, with the flexible loops obstructing the channel by interacting with the viral DNA.
Collapse
Affiliation(s)
- Rajendra Kumar
- Max-Planck-Institute for Biophysical Chemistry, Department of Theoretical and Computational Biophysics, Göttingen, Germany
| | - Helmut Grubmüller
- Max-Planck-Institute for Biophysical Chemistry, Department of Theoretical and Computational Biophysics, Göttingen, Germany.
| |
Collapse
|
10
|
Happonen LJ, Erdmann S, Garrett RA, Butcher SJ. Adenosine triphosphatases of thermophilic archaeal double-stranded DNA viruses. Cell Biosci 2014; 4:37. [PMID: 25105011 PMCID: PMC4124505 DOI: 10.1186/2045-3701-4-37] [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: 09/04/2013] [Accepted: 06/13/2014] [Indexed: 12/02/2022] Open
Abstract
Adenosine triphosphatases (ATPases) of double-stranded (ds) DNA archaeal viruses are structurally related to the AAA+ hexameric helicases and translocases. These ATPases have been implicated in viral life cycle functions such as DNA entry into the host, and viral genome packaging into preformed procapsids. We summarize bioinformatical analyses of a wide range of archaeal ATPases, and review the biochemical and structural properties of those archaeal ATPases that have measurable ATPase activity. We discuss their potential roles in genome delivery into the host, virus assembly and genome packaging in comparison to hexameric helicases and packaging motors from bacteriophages.
Collapse
Affiliation(s)
- Lotta J Happonen
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Susanne Erdmann
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Roger A Garrett
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Sarah J Butcher
- Institute of Biotechnology, University of Helsinki, (Viikinkaari 1), P.O. Box 65, FI-00014 Helsinki, Finland
| |
Collapse
|
11
|
Wolfe A, Phipps K, Weitao T. Viral and cellular SOS-regulated motor proteins: dsDNA translocation mechanisms with divergent functions. Cell Biosci 2014; 4:31. [PMID: 24995125 PMCID: PMC4080785 DOI: 10.1186/2045-3701-4-31] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/13/2014] [Indexed: 01/15/2023] Open
Abstract
DNA damage attacks on bacterial cells have been known to activate the SOS response, a transcriptional response affecting chromosome replication, DNA recombination and repair, cell division and prophage induction. All these functions require double-stranded (ds) DNA translocation by ASCE hexameric motors. This review seeks to delineate the structural and functional characteristics of the SOS response and the SOS-regulated DNA translocases FtsK and RuvB with the phi29 bacteriophage packaging motor gp16 ATPase as a prototype to study bacterial motors. While gp16 ATPase, cellular FtsK and RuvB are similarly comprised of hexameric rings encircling dsDNA and functioning as ATP-driven DNA translocases, they utilize different mechanisms to accomplish separate functions, suggesting a convergent evolution of these motors. The gp16 ATPase and FtsK use a novel revolution mechanism, generating a power stroke between subunits through an entropy-DNA affinity switch and pushing dsDNA inward without rotation of DNA and the motor, whereas RuvB seems to employ a rotation mechanism that remains to be further characterized. While FtsK and RuvB perform essential tasks during the SOS response, their roles may be far more significant as SOS response is involved in antibiotic-inducible bacterial vesiculation and biofilm formation as well as the perspective of the bacteria-cancer evolutionary interaction.
Collapse
Affiliation(s)
- Annie Wolfe
- Biology Department, College of Science and Mathematics, Southwest Baptist University, 1600 University Ave, Bolivar, Missouri 65613, USA
| | - Kara Phipps
- Biology Department, College of Science and Mathematics, Southwest Baptist University, 1600 University Ave, Bolivar, Missouri 65613, USA
| | - Tao Weitao
- Biology Department, College of Science and Mathematics, Southwest Baptist University, 1600 University Ave, Bolivar, Missouri 65613, USA
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|