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Nerber HN, Baloh M, Brehm JN, Sorg JA. The small acid-soluble proteins of Clostridioides difficile regulate sporulation in a SpoIVB2-dependent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.17.541253. [PMID: 37292792 PMCID: PMC10245694 DOI: 10.1101/2023.05.17.541253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clostridioides difficile is a pathogen whose transmission relies on the formation of dormant endospores. Spores are highly resilient forms of bacteria that resist environmental and chemical insults. In recent work, we found that C. difficile SspA and SspB, two small acid-soluble proteins (SASPs), protect spores from UV damage and, interestingly, are necessary for the formation of mature spores. Here, we build upon this finding and show that C. difficile sspA and sspB are required for the formation of the spore cortex layer. Moreover, using an EMS mutagenesis selection strategy, we identified mutations that suppressed the defect in sporulation of C. difficile SASP mutants. Many of these strains contained mutations in CDR20291_0714 (spoIVB2) revealing a connection between the SpoIVB2 protease and the SASPs in the sporulation pathway. This work builds upon the hypothesis that the small acid-soluble proteins can regulate gene expression.
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Affiliation(s)
- Hailee N Nerber
- Department of Biology, Texas A&M University, College Station, TX 77845
| | - Marko Baloh
- Department of Biology, Texas A&M University, College Station, TX 77845
| | - Joshua N Brehm
- Department of Biology, Texas A&M University, College Station, TX 77845
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station, TX 77845
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2
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Nerber HN, Sorg JA. The small acid-soluble proteins of spore-forming organisms: similarities and differences in function. Anaerobe 2024; 87:102844. [PMID: 38582142 DOI: 10.1016/j.anaerobe.2024.102844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
The small acid-soluble proteins are found in all endospore-forming organisms and are a major component of spores. Through their DNA binding capabilities, the SASPs shield the DNA from outside insults (e.g., UV and genotoxic chemicals). The absence of the major SASPs results in spores with reduced viability when exposed to UV light and, in at least one case, the inability to complete sporulation. While the SASPs have been characterized for decades, some evidence suggests that using newer technologies to revisit the roles of the SASPs could reveal novel functions in spore regulation.
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Affiliation(s)
- Hailee N Nerber
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station, TX, United States.
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3
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Yang X, Liu C, Ren P. Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning. J Chem Theory Comput 2024; 20:4065-4075. [PMID: 38742922 PMCID: PMC11187603 DOI: 10.1021/acs.jctc.4c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Conformational dynamics play a crucial role in determining the behavior of the biomolecules. Polarizable force fields, such as AMOEBA, can accurately capture electrostatic interactions underlying the conformational space. However, applying a polarizable force field in molecular dynamics (MD) simulations can be computationally expensive, especially in studying long-time-scale dynamics. To overcome this challenge, we incorporated the AMOEBA potential with Milestoning, an enhanced sampling method in this work. This integration allows us to efficiently sample the rare and important conformational states of a biomolecule by using many short and independent molecular dynamics trajectories with the AMOEBA force field. We applied this method to investigate the conformational dynamics of alanine dipeptide, DNA, and RNA A-B form conversion. Well-converged thermodynamic and kinetic properties were obtained, including the free energy difference, mean first passage time, and critical transitions between states. Our results demonstrate the power of integrating polarizable force fields with enhanced sampling methods in quantifying the thermodynamic and kinetic properties of biomolecules at the atomic level.
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Affiliation(s)
- Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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4
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Smirnov E, Molínová P, Chmúrčiaková N, Vacík T, Cmarko D. Non-canonical DNA structures in the human ribosomal DNA. Histochem Cell Biol 2023; 160:499-515. [PMID: 37750997 DOI: 10.1007/s00418-023-02233-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
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Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic.
| | - Pavla Molínová
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Nikola Chmúrčiaková
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Tomáš Vacík
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
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5
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Setlow P, Christie G. New Thoughts on an Old Topic: Secrets of Bacterial Spore Resistance Slowly Being Revealed. Microbiol Mol Biol Rev 2023; 87:e0008022. [PMID: 36927044 PMCID: PMC10304885 DOI: 10.1128/mmbr.00080-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
The quest for bacterial survival is exemplified by spores formed by some Firmicutes members. They turn up everywhere one looks, and their ubiquity reflects adaptations to the stresses bacteria face. Spores are impactful in public health, food safety, and biowarfare. Heat resistance is the hallmark of spores and is countered principally by a mineralized gel-like protoplast, termed the spore core, with reduced water which minimizes macromolecular movement/denaturation/aggregation. Dry heat, however, introduces mutations into spore DNA. Spores have countermeasures to extreme conditions that are multifactorial, but the fact that spore DNA is in a crystalline-like nucleoid in the spore core, likely due to DNA saturation with small acid-soluble spore proteins (SASPs), suggests that reduced macromolecular motion is also critical in spore dry heat resistance. SASPs are also central in the radiation resistance characteristic of spores, where the contributions of four spore features-SASP; Ca2+, with pyridine-2,6-dicarboxylic acid (CaDPA); photoproduct lyase; and low water content-minimize DNA damage. Notably, the spore environment steers UV photochemistry toward a product that germinated spores can repair without significant mutagenesis. This resistance extends to chemicals and macromolecules that could damage spores. Macromolecules are excluded by the spore coat which impedes the passage of moieties of ≥10 kDa. Additionally, damaging chemicals may be degraded or neutralized by coat enzymes/proteins. However, the principal protective mechanism here is the inner membrane, a compressed structure lacking lipid fluidity and presenting a barrier to the diffusion of chemicals into the spore core; SASP saturation of DNA also protects against genotoxic chemicals. Spores are also resistant to other stresses, including high pressure and abrasion. Regardless, overarching mechanisms associated with resistance seem to revolve around reduced molecular motion, a fine balance between rigidity and flexibility, and perhaps efficient repair.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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6
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Heydenreich R, Delbrück AI, Mathys A. Post-high-pressure temperature and time - Overlooked parameters in high pressure treatment of bacterial spores. Int J Food Microbiol 2023; 402:110279. [PMID: 37331115 DOI: 10.1016/j.ijfoodmicro.2023.110279] [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: 02/01/2023] [Revised: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/20/2023]
Abstract
High pressure (HP) processing has high potential for bacterial spore inactivation with minimal thermal input. To advance HP germination and subsequent inactivation of spores, this study explored the physiological state of HP-treated spores using flow cytometry (FCM). Bacillus subtilis spores were treated at 550 MPa and 60 °C (very HP (vHP)) in buffer, incubated after the HP treatment, and stained for FCM analysis with SYTO16 indicating germination and propidium iodide (PI) indicating membrane damage. FCM subpopulations were analyzed depending on the HP dwell time (≤20 min), post-HP temperature (ice, 37 °C, 60 °C) and time (≤4 h), germination-relevant cortex-lytic enzymes (CLEs) and small-acid-soluble-proteins-(SASP)-degrading enzymes by using deletion strains. The effect of post-HP temperatures (ice, 37 °C) was additionally studied for moderate HP (150 MPa, 38 °C, 10 min). Post-HP incubation conditions strongly influenced the prevalence of five observed FCM subpopulations. Post-HP incubation on ice did not or only slowly shifted SYTO16-positive spores to higher SYTO16 levels. At 37 °C post-HP, this shift accelerated, and a shift to high PI intensities occurred depending on the HP dwell time. At 60 °C post-HP, the main shift was from SYTO16-positive to PI-positive subpopulations. The enzymes CwlJ and SleB, which are CLEs, seemed both necessary for PI or SYTO16 uptake, and to have different sensitivities to 550 MPa and 60 °C. Different extents of SASP degradation might explain the existence of two SYTO16-positive subpopulations. Shifts to higher SYTO16 intensities during post-HP incubation on ice or at 37 °C might rely on the activity and recovery of CLEs, SASP-degrading enzymes or their associated proteins from reversible HP-induced structural changes. These enzymes seemingly become active only during decompression or after vHP treatments (550 MPa, 60 °C). Based on our results, we provide a refined model of HP germination-inactivation of B. subtilis spores and an optimized FCM method for quantification of the safety-relevant subpopulation, i.e., vHP (550 MPa, 60 °C) superdormant spores. This study contributes to the development of mild spore inactivation processes by shedding light on overlooked parameters: post-HP incubation conditions. Post-HP conditions significantly influenced the physiological state of spores, likely due to varying enzymatic activity. This finding may explain inconsistencies in previous research and shows the importance of reporting post-HP conditions in future research. Furthermore, the addition of post-HP conditions as HP process parameter may open up new possibilities to optimize HP-based inactivation of spores for potential industrial applications in the food industry.
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Affiliation(s)
- Rosa Heydenreich
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Alessia I Delbrück
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Alexander Mathys
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland.
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7
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Sun J, Cai W, Wang Y, Niu H, Chen X, Han X. The Effect of Decreased Ca ++/Mg ++ ATPase Activity on Lactobacillus delbrueckii subsp. bulgaricus sp1.1 Survival during Spray Drying. Foods 2023; 12:foods12040787. [PMID: 36832862 PMCID: PMC9955740 DOI: 10.3390/foods12040787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/29/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Compared with the commonly used technique of freeze-drying, spray drying has lower energy costs. However, spray drying also has a fatal disadvantage: a lower survival rate. In this study, the survival of bacteria in a spray-drying tower decreased as the water content was reduced. The water content of 21.10% was the critical point for spray drying Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) sp1.1 based on sampling in the tower. Based on the relationship between the moisture content of spray drying and the survival rate, the water content of 21.10% was also the critical point for the change in the survival rate during spray drying. Proteomic analysis was used to investigate the reasons for L. bulgaricus sp1.1 inactivation during and after spray drying. Gene Ontology (GO) enrichment revealed that differentially expressed proteins were mainly associated with the cell membrane and transport. In particular, proteins related to metal ion transport included those involved in the transport of potassium, calcium and magnesium ions. The protein-protein interaction (PPI) network revealed that Ca++/Mg++ adenosine triphosphatase (ATPase) may be a key protein. Ca++/Mg++ ATPase activity decreased substantially during spray drying (p < 0.05). Supplementation with Ca++ and Mg++ significantly increased the expression of ATPase-related genes and enzyme activity (p < 0.05). The Ca++/Mg++ ATPase activity of L. bulgaricus sp1.1 was enhanced by increasing the intracellular Ca++ or Mg++ concentration, thus increasing the survival of spray-dried LAB. Bacterial survival rates were increased to 43.06% with the addition of Ca++ and to 42.64% with the addition of Mg++, respectively. Ca++/Mg++ ATPase may be the key to the damage observed in spray-dried bacteria. Furthermore, the addition of Ca++ or Mg++ also reduced bacterial injury during spray drying by enhancing the activity of Ca++/Mg++ ATPase.
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Affiliation(s)
| | | | | | | | | | - Xue Han
- Correspondence: ; Tel.: +86-133-1365-9156
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8
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Floccari VA, Dragoš A. Host control by SPβ phage regulatory switch as potential manipulation strategy. Curr Opin Microbiol 2023; 71:102260. [PMID: 36580707 DOI: 10.1016/j.mib.2022.102260] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022]
Abstract
The interaction between temperate phages and their bacterial hosts has always been one of the most controversial in nature. As genetic parasites, phages need their hosts to propagate, while the host may take advantage of the genetic arsenal carried in the phage genome. This intriguing host-parasite interplay with an evident mutualistic implication could be challenged by recent discoveries of alternative phage lifestyles and regulatory systems that seem to support a manipulative strategy pursued by the phage. Through two fascinating novel mechanisms concerning the active lysogeny and a phage-encoded quorum sensing system, referred as 'Arbitrium', employed by SPβ-like phages of Bacilli, we propose the parasite manipulation as ecological relationship between certain temperate phages and bacteria.
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Affiliation(s)
- Valentina A Floccari
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Anna Dragoš
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia.
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9
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Butala M, Dragoš A. Unique relationships between phages and endospore-forming hosts. Trends Microbiol 2022; 31:498-510. [PMID: 36535834 DOI: 10.1016/j.tim.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
As part of their survival strategy under harsh environmental conditions, endospore-forming bacteria can trigger a sporulation developmental program. Although the regulatory cascades that precisely control the transformation of vegetative bacteria into mother cells and resilient spores have been described in detail, less is known about how bacteriophages that prey on endospore-formers exploit sporulation. Herein, we argue that phages infecting these bacteria have evolved several specific molecular mechanisms, not yet known in other bacteria, that manifest from the phage-driven alliance to negative effects on the host. We anticipate that the relationships between phages and endospore-formers outlined here will inspire studies on phage ecology and evolution, and could facilitate important advances in the development of phage therapies against pathogenic spore-formers.
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Affiliation(s)
- Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anna Dragoš
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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10
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Liu F, Li J, Zhang T, Chen J, Ho CL. Engineered Spore-Forming Bacillus as a Microbial Vessel for Long-Term DNA Data Storage. ACS Synth Biol 2022; 11:3583-3591. [PMID: 36150134 DOI: 10.1021/acssynbio.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA data storage technology may supersede conventional chip or magnetic data storage medium, providing long-term stability, high density, and sustainable storage. Due to its error-correcting capability, DNA data stored in living organisms exhibits high fidelity in information replication. Here we report the development of a Bacillus chassis integrated with an inducible artificially assembled bacterial chromosome to facilitate random data access. We generated three sets of data in the form of DNA sequences using a rudimentary coding system accessible by the regulatory promoter. Sporulated Bacillus harboring the genes were used for long-term storage, where viability assays of spores were subjected to harsh environmental stresses to evaluate the data storage stability. The data accuracy remained above 99% after high temperature and oxidative stress treatment, whereas UV irradiation treatment provided above 96% accuracy. The developed Bacillus chassis and artificial chromosome facilitate the long-term storage of larger datum volume by using other DNA digital encoding and decoding programs.
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Affiliation(s)
- Feng Liu
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China
| | - Jiashu Li
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China
| | - Tongzhou Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China
| | - Jun Chen
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen518055, China
| | - Chun Loong Ho
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen518055, China
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11
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Kim JM. Molecular Link between DNA Damage Response and Microtubule Dynamics. Int J Mol Sci 2022; 23:ijms23136986. [PMID: 35805981 PMCID: PMC9266319 DOI: 10.3390/ijms23136986] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Microtubules are major components of the cytoskeleton that play important roles in cellular processes such as intracellular transport and cell division. In recent years, it has become evident that microtubule networks play a role in genome maintenance during interphase. In this review, we highlight recent advances in understanding the role of microtubule dynamics in DNA damage response and repair. We first describe how DNA damage checkpoints regulate microtubule organization and stability. We then highlight how microtubule networks are involved in the nuclear remodeling following DNA damage, which leads to changes in chromosome organization. Lastly, we discuss how microtubule dynamics participate in the mobility of damaged DNA and promote consequent DNA repair. Together, the literature indicates the importance of microtubule dynamics in genome organization and stability during interphase.
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Affiliation(s)
- Jung Min Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju 58128, Korea
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12
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Lezcano MÁ, Sánchez-García L, Quesada A, Carrizo D, Fernández-Martínez MÁ, Cavalcante-Silva E, Parro V. Comprehensive Metabolic and Taxonomic Reconstruction of an Ancient Microbial Mat From the McMurdo Ice Shelf (Antarctica) by Integrating Genetic, Metaproteomic and Lipid Biomarker Analyses. Front Microbiol 2022; 13:799360. [PMID: 35928160 PMCID: PMC9345047 DOI: 10.3389/fmicb.2022.799360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Paleobiological reconstructions based on molecular fossils may be limited by degradation processes causing differential preservation of biomolecules, the distinct taxonomic specificity of each biomolecule type, and analytical biases. Here, we combined the analysis of DNA, proteins and lipid biomarkers using 16S and 18S rRNA gene metabarcoding, metaproteomics and lipid analysis to reconstruct the taxonomic composition and metabolisms of a desiccated microbial mat from the McMurdo Ice Shelf (MIS) (Antarctica) dated ~1,000 years BP. The different lability, taxonomic resolution and analytical bias of each biomolecule type led to a distinct microbial community profile. DNA analysis showed selective preservation of DNA remnants from the most resistant taxa (e.g., spore-formers). In contrast, the proteins profile revealed microorganisms missed by DNA sequencing, such as Cyanobacteria, and showed a microbial composition similar to fresh microbial mats in the MIS. Lipid hydrocarbons also confirmed Cyanobacteria and suggested the presence of mosses or vascular plant remnants from a period in Antarctica when the climate was warmer (e.g., Mid-Miocene or Eocene). The combined analysis of the three biomolecule types also revealed diverse metabolisms that operated in the microbial mat before desiccation: oxygenic and anoxygenic photosynthesis, nitrogen fixation, nitrification, denitrification, sulfur reduction and oxidation, and methanogenesis. Therefore, the joint analysis of DNA, proteins and lipids resulted in a powerful approach that improved taxonomic and metabolic reconstructions overcoming information gaps derived from using individual biomolecules types.
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Affiliation(s)
- María Ángeles Lezcano
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- *Correspondence: María Ángeles Lezcano,
| | | | - Antonio Quesada
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- Departamento de Biología, C. Darwin 2, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
| | | | | | - Víctor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
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13
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Small Prokaryotic DNA-Binding Proteins Protect Genome Integrity throughout the Life Cycle. Int J Mol Sci 2022; 23:ijms23074008. [PMID: 35409369 PMCID: PMC8999374 DOI: 10.3390/ijms23074008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/27/2022] [Accepted: 04/01/2022] [Indexed: 12/17/2022] Open
Abstract
Genomes of all organisms are persistently threatened by endogenous and exogenous assaults. Bacterial mechanisms of genome maintenance must provide protection throughout the physiologically distinct phases of the life cycle. Spore-forming bacteria must also maintain genome integrity within the dormant endospore. The nucleoid-associated proteins (NAPs) influence nucleoid organization and may alter DNA topology to protect DNA or to alter gene expression patterns. NAPs are characteristically multifunctional; nevertheless, Dps, HU and CbpA are most strongly associated with DNA protection. Archaea display great variety in genome organization and many inhabit extreme environments. As of yet, only MC1, an archaeal NAP, has been shown to protect DNA against thermal denaturation and radiolysis. ssDNA are intermediates in vital cellular processes, such as DNA replication and recombination. Single-stranded binding proteins (SSBs) prevent the formation of secondary structures but also protect the hypersensitive ssDNA against chemical and nuclease degradation. Ionizing radiation upregulates SSBs in the extremophile Deinococcus radiodurans.
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14
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Engineered Bacteriophage as a Delivery Vehicle for Antibacterial Protein, SASP. Pharmaceuticals (Basel) 2021; 14:ph14101038. [PMID: 34681262 PMCID: PMC8538823 DOI: 10.3390/ph14101038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
The difficulties in developing novel classes of antibacterials is leading to a resurgence of interest in bacteriophages as therapeutic agents, and in particular engineered phages that can be optimally designed. Here, pre-clinical microbiology assessment is presented of a Staphylococcus aureus phage engineered to deliver a gene encoding an antibacterial small acid soluble spore protein (SASP) and further, rendered non-lytic to give product SASPject PT1.2. PT1.2 has been developed initially for nasal decolonisation of S. aureus, including methicillin-resistant S. aureus. Time-kill curve assays were conducted with PT1.2 against a range of staphylococcal species, and serial passaging experiments were conducted to investigate the potential for resistance to develop. SASPject PT1.2 demonstrates activity against 100% of 225 geographically diverse S. aureus isolates, exquisite specificity for S. aureus, and a rapid speed of kill. The kinetics of S. aureus/PT1.2 interaction is examined together with demonstrating that PT1.2 activity is unaffected by the presence of human serum albumin. SASPject PT1.2 shows a low propensity for resistance to develop with no consistent shift in sensitivity in S. aureus cells passaged for up to 42 days. SASPject PT1.2 shows promise as a novel first-in-class antibacterial agent and demonstrates potential for the SASPject platform.
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15
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Nerber HN, Sorg JA. The small acid-soluble proteins of Clostridioides difficile are important for UV resistance and serve as a check point for sporulation. PLoS Pathog 2021; 17:e1009516. [PMID: 34496003 PMCID: PMC8452069 DOI: 10.1371/journal.ppat.1009516] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/20/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile is a nosocomial pathogen which causes severe diarrhea and colonic inflammation. C. difficile causes disease in susceptible patients when endospores germinate into the toxin-producing vegetative form. The action of these toxins results in diarrhea and the spread of spores into the hospital and healthcare environments. Thus, the destruction of spores is imperative to prevent disease transmission between patients. However, spores are resilient and survive extreme temperatures, chemical exposure, and UV treatment. This makes their elimination from the environment difficult and perpetuates their spread between patients. In the model spore-forming organism, Bacillus subtilis, the small acid-soluble proteins (SASPs) contribute to these resistances. The SASPs are a family of small proteins found in all endospore-forming organisms, C. difficile included. Although these proteins have high sequence similarity between organisms, the role(s) of the proteins differ. Here, we investigated the role of the main α/β SASPs, SspA and SspB, and two annotated putative SASPs, CDR20291_1130 and CDR20291_3080, in protecting C. difficile spores from environmental insults. We found that SspA is necessary for conferring spore UV resistance, SspB minorly contributes, and the annotated putative SASPs do not contribute to UV resistance. In addition, the SASPs minorly contribute to the resistance of nitrous acid. Surprisingly, the combined deletion of sspA and sspB prevented spore formation. Overall, our data indicate that UV resistance of C. difficile spores is dependent on SspA and that SspA and SspB regulate/serve as a checkpoint for spore formation, a previously unreported function of SASPs.
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Affiliation(s)
- Hailee N. Nerber
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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What's new and notable in bacterial spore killing! World J Microbiol Biotechnol 2021; 37:144. [PMID: 34351499 PMCID: PMC8342367 DOI: 10.1007/s11274-021-03108-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/05/2021] [Indexed: 02/08/2023]
Abstract
Spores of many species of the orders Bacillales and Clostridiales can be vectors for food spoilage, human diseases and intoxications, and biological warfare. Many agents are used for spore killing, including moist heat in an autoclave, dry heat at elevated temperatures, UV radiation at 254 and more recently 222 and 400 nm, ionizing radiation of various types, high hydrostatic pressures and a host of chemical decontaminants. An alternative strategy is to trigger spore germination, as germinated spores are much easier to kill than the highly resistant dormant spores—the so called “germinate to eradicate” strategy. Factors important to consider in choosing methods for spore killing include the: (1) cost; (2) killing efficacy and kinetics; (3) ability to decontaminate large areas in buildings or outside; and (4) compatibility of killing regimens with the: (i) presence of people; (ii) food quality; (iii) presence of significant amounts of organic matter; and (iv) minimal damage to equipment in the decontamination zone. This review will summarize research on spore killing and point out some common flaws which can make results from spore killing research questionable.
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17
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Liu T, Yu T, Zhang S, Wang Y, Zhang W. Thermodynamic and kinetic properties of a single base pair in A-DNA and B-DNA. Phys Rev E 2021; 103:042409. [PMID: 34005973 DOI: 10.1103/physreve.103.042409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
Abstract
Double stranded DNA can adopt different forms, the so-called A-, B-, and Z-DNA, which play different biological roles. In this work, the thermodynamic and the kinetic parameters for the base-pair closing and opening in A-DNA and B-DNA were calculated by all-atom molecular dynamics simulations at different temperatures. The thermodynamic parameters of the base pair in B-DNA were in good agreement with the experimental results. The free energy barrier of breaking a single base stack results from the enthalpy increase ΔH caused by the disruption of hydrogen bonding and base-stacking interactions, as well as water and base interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss ΔS caused by the restriction of torsional angles and hydration. It was found that the enthalpy change ΔH and the entropy change ΔS for the base pair in A-DNA are much larger than those in B-DNA, and the transition rates between the opening and the closing state for the base pair in A-DNA are much slower than those in B-DNA. The large difference of the enthalpy and entropy change for forming the base pair in A-DNA and B-DNA results from different hydration in A-DNA and B-DNA. The hydration pattern observed around DNA is an accompanying process for forming the base pair, rather than a follow-up of the conformation.
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Affiliation(s)
- Taigang Liu
- Department of Physics Wuhan University, Wuhan 430072, China.,School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China
| | - Ting Yu
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Shuhao Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Yujie Wang
- Department of Physics Wuhan University, Wuhan 430072, China.,Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China
| | - Wenbing Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
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Dragoš A, Priyadarshini B, Hasan Z, Strube ML, Kempen PJ, Maróti G, Kaspar C, Bose B, Burton BM, Bischofs IB, Kovács ÁT. Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. ISME JOURNAL 2020; 15:1344-1358. [PMID: 33343000 DOI: 10.1038/s41396-020-00854-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - B Priyadarshini
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zahraa Hasan
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Paul J Kempen
- Department of Health Technology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6701, Hungary
| | - Charlotte Kaspar
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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Francés-Monerris A, Hognon C, Douki T, Monari A. Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics*. Chemistry 2020; 26:14236-14241. [PMID: 32597544 DOI: 10.1002/chem.202002484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 11/07/2022]
Abstract
Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid-soluble proteins that drastically modify the structure and photoreactivity of the nucleic acid. Herein, multiscale molecular dynamics simulations, including extended classical molecular dynamics and quantum mechanics/molecular mechanics based dynamics, are used to elucidate the coupling of electronic and structural factors that lead to this photochemical outcome. In particular, the well-described impact of the peculiar DNA environment found in spores on the favored formation of the spore photoproduct, given the small free energy barrier found for this path, is rationalized. Meanwhile, the specific organization of spore DNA precludes the photochemical path that leads to cyclobutane pyrimidine dimer formation.
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Affiliation(s)
- Antonio Francés-Monerris
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Departament de Química Física, Universitat de València, 46100, Burjassot, Spain
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Université de Lorraine and CNRS, CRAN UMR 7039, 54000, Nancy, France
| | - Thierry Douki
- SyMMES, CEA, CNRS, IRIG, University Grenoble Alpes, 38000, Grenoble, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments. Proc Natl Acad Sci U S A 2020; 117:19643-19652. [PMID: 32759221 DOI: 10.1073/pnas.2011125117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.
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21
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Taylor W, Camilleri E, Craft DL, Korza G, Granados MR, Peterson J, Szczpaniak R, Weller SK, Moeller R, Douki T, Mok WWK, Setlow P. DNA Damage Kills Bacterial Spores and Cells Exposed to 222-Nanometer UV Radiation. Appl Environ Microbiol 2020; 86:AEM.03039-19. [PMID: 32033948 PMCID: PMC7117916 DOI: 10.1128/aem.03039-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 01/16/2023] Open
Abstract
This study examined the microbicidal activity of 222-nm UV radiation (UV222), which is potentially a safer alternative to the 254-nm UV radiation (UV254) that is often used for surface decontamination. Spores and/or growing and stationary-phase cells of Bacillus cereus, Bacillus subtilis, Bacillus thuringiensis, Staphylococcus aureus, and Clostridioides difficile and a herpesvirus were all killed or inactivated by UV222 and at lower fluences than with UV254B. subtilis spores and cells lacking the major DNA repair protein RecA were more sensitive to UV222, as were spores lacking their DNA-protective proteins, the α/β-type small, acid-soluble spore proteins. The spore cores' large amount of Ca2+-dipicolinic acid (∼25% of the core dry weight) also protected B. subtilis and C. difficile spores against UV222, while spores' proteinaceous coat may have given some slight protection against UV222 Survivors among B. subtilis spores treated with UV222 acquired a large number of mutations, and this radiation generated known mutagenic photoproducts in spore and cell DNA, primarily cyclobutane-type pyrimidine dimers in growing cells and an α-thyminyl-thymine adduct termed the spore photoproduct (SP) in spores. Notably, the loss of a key SP repair protein markedly decreased spore UV222 resistance. UV222-treated B. subtilis spores germinated relatively normally, and the generation of colonies from these germinated spores was not salt sensitive. The latter two findings suggest that UV222 does not kill spores by general protein damage, and thus, the new results are consistent with the notion that DNA damage is responsible for the killing of spores and cells by UV222IMPORTANCE Spores of a variety of bacteria are resistant to common decontamination agents, and many of them are major causes of food spoilage and some serious human diseases, including anthrax caused by spores of Bacillus anthracis Consequently, there is an ongoing need for efficient methods for spore eradication, in particular methods that have minimal deleterious effects on people or the environment. UV radiation at 254 nm (UV254) is sporicidal and commonly used for surface decontamination but can cause deleterious effects in humans. Recent work, however, suggests that 222-nm UV (UV222) may be less harmful to people than UV254 yet may still kill bacteria and at lower fluences than UV254 The present work has identified the damage by UV222 that leads to the killing of growing cells and spores of some bacteria, many of which are human pathogens, and UV222 also inactivates a herpesvirus.
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Affiliation(s)
- Willie Taylor
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Emily Camilleri
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - D Levi Craft
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Maria Rocha Granados
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Jaliyah Peterson
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Renata Szczpaniak
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Sandra K Weller
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Ralf Moeller
- Space Microbiology Research Group, Radiation Biology Department, Institute for Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Thierry Douki
- Universite Grenoble Alpes, CEA, CNRS, INAC-SYMMBEST, Grenoble, France
| | - Wendy W K Mok
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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Travers A, Muskhelishvili G. Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0016-2019. [PMID: 32056535 PMCID: PMC11168577 DOI: 10.1128/ecosalplus.esp-0016-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/22/2022]
Abstract
In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.
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Affiliation(s)
- Andrew Travers
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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23
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Evaluation of methods for DNA extraction from Clostridium tyrobutyricum spores and its detection by qPCR. J Microbiol Methods 2019; 169:105818. [PMID: 31881287 DOI: 10.1016/j.mimet.2019.105818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 12/18/2022]
Abstract
Clostridium tyrobutyricum is the major agent that causes the blowing defect in cheese due to the germination of its dormant spores during the ripening stage. As a result, many of the affected cheeses show cavities and cracks, which cause the product loss in most cases. Nowadays, there is not a fast method capable of detecting milk contaminated with C. tyrobutyricum spores. The aim of this study has been to develop a fast and reliable method based on real time PCR (qPCR) to detect C. tyrobutyricum spores in raw milk. One of the main limitations has been to find a good procedure for the spore disruption to extract the DNA due to its high resistance. For this reason, different disruption methods have been tested, including chemical agents, bead beating, enzymatic and microwave treatment. Furthermore, an enzymatic treatment with subtilisin was applied for milk clarification and recovery of spores. The comparison of the assayed methods has been made using sterile milk spiked with C. tyrobutyricum spores, obtained in solid or liquid medium. The results showed that microwave treatment followed by a standard DNA purification step was found to be the best disruption method. The Ct values obtained for spores were higher than those found for vegetative cells by qPCR, for the same quantity of DNA. This difference could be due to the action of the Small Acid Soluble Proteins (SASP) in the DNA packaging of spores. Moreover, spores obtained in agar plate were found more resistant to disruption than those obtained in liquid medium. Subtilisin and microwave treatments were found to be successful for DNA extraction from C. tyrobutyricum spores in milk and subsequent identification by qPCR. However, the differences observed between the amplification of DNA from spores obtained in different media and from vegetative cells have to be taken into account to optimize a method for C. tyrobutyricum detection.
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Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111580. [DOI: 10.1016/j.jphotobiol.2019.111580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 07/07/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023]
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25
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Gong P, Sun J, Lin K, Di W, Zhang L, Han X. Changes process in the cellular structures and constituents of Lactobacillus bulgaricus sp1.1 during spray drying. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Zgarbová M, Jurečka P, Šponer J, Otyepka M. A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker. J Chem Theory Comput 2017; 14:319-328. [DOI: 10.1021/acs.jctc.7b00926] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
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Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:63-73. [DOI: 10.1016/j.pbiomolbio.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 04/16/2017] [Accepted: 05/23/2017] [Indexed: 01/19/2023]
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Butler RR, Schill KM, Wang Y, Pombert JF. Genetic Characterization of the Exceptionally High Heat Resistance of the Non-toxic Surrogate Clostridium sporogenes PA 3679. Front Microbiol 2017; 8:545. [PMID: 28421047 PMCID: PMC5376575 DOI: 10.3389/fmicb.2017.00545] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 03/15/2017] [Indexed: 01/01/2023] Open
Abstract
Clostridium sporogenes PA 3679 is a non-toxic endospore former that is widely used as a surrogate for Clostridium botulinum by the food processing industry to validate thermal processing strategies. PA 3679 produces spores of exceptionally high heat resistance without botulinum neurotoxins, permitting the use of PA 3679 in inoculated pack studies while ensuring the safety of food processing facilities. To identify genes associated with this heat resistance, the genomes of C. sporogenes PA 3679 isolates were compared to several other C. sporogenes strains. The most significant difference was the acquisition of a second spoVA operon, spoVA2, which is responsible for transport of dipicolinic acid into the spore core during sporulation. Interestingly, spoVA2 was also found in some C. botulinum species which phylogenetically cluster with PA 3679. Most other C. sporogenes strains examined both lack the spoVA2 locus and are phylogenetically distant within the group I Clostridium, adding to the understanding that C. sporogenes are dispersed C. botulinum strains which lack toxin genes. C. sporogenes strains are thus a very eclectic group, and few strains possess the characteristic heat resistance of PA 3679.
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Affiliation(s)
- Robert R Butler
- Department of Biology, Illinois Institute of TechnologyChicago, IL, USA
| | - Kristin M Schill
- United States Food and Drug Administration, Center for Food Safety and Applied NutritionBedford Park, IL, USA
| | - Yun Wang
- United States Food and Drug Administration, Center for Food Safety and Applied NutritionBedford Park, IL, USA
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30
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Myintzu Hlaing M, Wood B, McNaughton D, Ying D, Augustin MA. Raman spectroscopic analysis of Lactobacillus rhamnosus GG in response to dehydration reveals DNA conformation changes. JOURNAL OF BIOPHOTONICS 2017; 10:589-597. [PMID: 27244082 DOI: 10.1002/jbio.201600046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/19/2016] [Accepted: 03/23/2016] [Indexed: 06/05/2023]
Abstract
Dehydration of bacterial cells elicits cellular stress responses in bacteria. Microencapsulation has been used to protect cells against the environmental stress. In this study, Confocal Raman Spectroscopy was used to examine DNA changes in the chemical composition of non-encapsulated and microencapsulated Lactobacillus rhamnosus GG and the reversibility of these changes upon freeze drying and rehydration. The viability of cells upon freeze drying was also enumerated using culture methods and membrane integrity was measured using BacLight Live/Dead staining. Raman analyses show changes in the spectral features associated with various biochemical compounds, which are interpreted as the result of detrimental freeze drying effects on the bacterial cells. Specifically, analyses based on Principal Components Analysis (PCA) of Raman spectra, confirm that microencapsulation protects cells from environmental stress. The results also reveal a B- to A-like DNA conformation change in dormant cells that provided insights into the extent of reversibility of this transition upon rehydration. The extent of this reversibility is less in non-encapsulated than in microencapsulated cells. These findings indicate the potential application of Raman spectroscopy in rapid sensing of microbial dehydration stress responses.
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Affiliation(s)
- Mya Myintzu Hlaing
- CSIRO Food and Nutrition, 671 Sneydes Road, Werribee, Victoria, 3030, Australia
| | - Bayden Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria, 3800, Australia
| | - Don McNaughton
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria, 3800, Australia
| | - DanYan Ying
- CSIRO Food and Nutrition, 671 Sneydes Road, Werribee, Victoria, 3030, Australia
| | - Mary Ann Augustin
- CSIRO Food and Nutrition, 671 Sneydes Road, Werribee, Victoria, 3030, Australia
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Lebre PH, De Maayer P, Cowan DA. Xerotolerant bacteria: surviving through a dry spell. Nat Rev Microbiol 2017; 15:285-296. [DOI: 10.1038/nrmicro.2017.16] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Yang L, Jian Y, Setlow P, Li L. Spore photoproduct within DNA is a surprisingly poor substrate for its designated repair enzyme-The spore photoproduct lyase. DNA Repair (Amst) 2017; 53:31-42. [PMID: 28320593 DOI: 10.1016/j.dnarep.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/23/2016] [Accepted: 11/15/2016] [Indexed: 12/15/2022]
Abstract
DNA repair enzymes typically recognize their substrate lesions with high affinity to ensure efficient lesion repair. In UV irradiated endospores, a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, termed the spore photoproduct (SP), is the dominant DNA photolesion, which is rapidly repaired during spore outgrowth mainly by spore photoproduct lyase (SPL) using an unprecedented protein-harbored radical transfer process. Surprisingly, our in vitro studies using SP-containing short oligonucleotides, pUC 18 plasmid DNA, and E. coli genomic DNA found that they are all poor substrates for SPL in general, exhibiting turnover numbers of 0.01-0.2min-1. The faster turnover numbers are reached under single turnover conditions, and SPL activity is low with oligonucleotide substrates at higher concentrations. Moreover, SP-containing oligonucleotides do not go past one turnover. In contrast, the dinucleotide SP TpT exhibits a turnover number of 0.3-0.4min-1, and the reaction may reach up to 10 turnovers. These observations distinguish SPL from other specialized DNA repair enzymes. To the best of our knowledge, SPL represents an unprecedented example of a major DNA repair enzyme that cannot effectively repair its substrate lesion within the normal DNA conformation adopted in growing cells. Factors such as other DNA binding proteins, helicases or an altered DNA conformation may cooperate with SPL to enable efficient SP repair in germinating spores. Therefore, both SP formation and SP repair are likely to be tightly controlled by the unique cellular environment in dormant and outgrowing spore-forming bacteria, and thus SP repair may be extremely slow in non-spore-forming organisms.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, United States
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States; Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
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Hlaing MM, Wood BR, McNaughton D, Ying D, Dumsday G, Augustin MA. Effect of Drying Methods on Protein and DNA Conformation Changes in Lactobacillus rhamnosus GG Cells by Fourier Transform Infrared Spectroscopy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1724-1731. [PMID: 28132503 DOI: 10.1021/acs.jafc.6b05508] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microencapsulation protects cells against environmental stress encountered during the production of probiotics, which are used as live microbial food ingredients. Freeze-drying and spray-drying are used in the preparation of powdered microencapsulated probiotics. This study examines the ability of Fourier transform infrared (FTIR) spectroscopy to detect differences in cells exposed to freeze-drying and spray-drying of encapsulated Lactobacillus rhamnosus GG cells. The FTIR analysis clearly demonstrated there were more significant molecular changes in lipid, fatty acid content, protein, and DNA conformation of nonencapsulated compared to encapsulated bacterial cells. The technique was also able to differentiate between spray-dried and freeze-dried cells. The results also revealed the extent of protection from a protein-carbohydrate-based encapsulant matrix on the cells depending on the type drying process. The extent of this protection to the dehydration stress was shown to be less in spray-dried cells than in freeze-dried cells. This suggests that FTIR could be used as a rapid, noninvasive, and real-time measurement technique to detect detrimental drying effects on cells.
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Affiliation(s)
- Mya M Hlaing
- CSIRO Agriculture and Food , 671 Sneydes Road, Werribee, Victoria 3030, Australia
| | - Bayden R Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University , Clayton, Victoria 3800, Australia
| | - Don McNaughton
- Centre for Biospectroscopy, School of Chemistry, Monash University , Clayton, Victoria 3800, Australia
| | - DanYang Ying
- CSIRO Agriculture and Food , 671 Sneydes Road, Werribee, Victoria 3030, Australia
| | - Geoff Dumsday
- CSIRO Agriculture and Food , 671 Sneydes Road, Werribee, Victoria 3030, Australia
| | - Mary Ann Augustin
- CSIRO Agriculture and Food , 671 Sneydes Road, Werribee, Victoria 3030, Australia
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Bumah VV, Aboualizadeh E, Masson-Meyers DS, Eells JT, Enwemeka CS, Hirschmugl CJ. Spectrally resolved infrared microscopy and chemometric tools to reveal the interaction between blue light (470nm) and methicillin-resistant Staphylococcus aureus. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 167:150-157. [DOI: 10.1016/j.jphotobiol.2016.12.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/08/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
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Berteau O, Benjdia A. DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From Biochemistry to Structural Investigations. Photochem Photobiol 2017; 93:67-77. [DOI: 10.1111/php.12702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Olivier Berteau
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Alhosna Benjdia
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
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Jamroskovic J, Chromikova Z, List C, Bartova B, Barak I, Bernier-Latmani R. Variability in DPA and Calcium Content in the Spores of Clostridium Species. Front Microbiol 2016; 7:1791. [PMID: 27891119 PMCID: PMC5104732 DOI: 10.3389/fmicb.2016.01791] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/25/2016] [Indexed: 01/31/2023] Open
Abstract
Spores of a number of clostridial species, and their resistance to thermal treatment is a major concern for the food industry. Spore resistance to wet heat is related to the level of spore hydration, which is inversely correlated with the content of calcium and dipicolinic acid (DPA) in the spore core. It is widely believed that the accumulation of DPA and calcium in the spore core is a fundamental component of the sporulation process for all endospore forming species. We have noticed heterogeneity in the heat resistance capacity and overall DPA/calcium content among the spores of several species belonging to Clostridium sensu stricto group: two C. acetobutylicum strains (DSM 792 and 1731), two C. beijerinckii strains (DSM 791 and NCIMB 8052), and a C. collagenovorans strain (DSM 3089). A C. beijerinckii strain (DSM 791) and a C. acetobutylicum strain (DSM 792) display low Ca and DPA levels. In addition, these two species, with the lowest average Ca/DPA content amongst the strains considered, also exhibit minimal heat resistance. There appears to be no correlation between the Ca/DPA content and the phylogenetic distribution of the C. acetobutylicum and C. beijerinckii species based either on the 16S rRNA or the spoVA gene. This finding suggests that a subset of Clostridium sensu stricto species produce spores with low resistance to wet heat. Additionally, analysis of individual spores using STEM-EDS and STXM revealed that DPA and calcium levels can also vary amongst individual spores in a single spore population.
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Affiliation(s)
- Jan Jamroskovic
- Swiss Federal Institute of Technology in Lausanne (EPFL)Lausanne, Switzerland; Institute of Molecular Biology, Slovak Academy of SciencesBratislava, Slovakia
| | - Zuzana Chromikova
- Institute of Molecular Biology, Slovak Academy of Sciences Bratislava, Slovakia
| | - Cornelia List
- Swiss Federal Institute of Technology in Lausanne (EPFL) Lausanne, Switzerland
| | - Barbora Bartova
- Swiss Federal Institute of Technology in Lausanne (EPFL) Lausanne, Switzerland
| | - Imrich Barak
- Institute of Molecular Biology, Slovak Academy of Sciences Bratislava, Slovakia
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Deiana M, Pokladek Z, Olesiak-Banska J, Młynarz P, Samoc M, Matczyszyn K. Photochromic switching of the DNA helicity induced by azobenzene derivatives. Sci Rep 2016; 6:28605. [PMID: 27339811 PMCID: PMC4919647 DOI: 10.1038/srep28605] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (Azo-2N and Azo-3N) with double stranded DNA and demonstrate that the photoisomerization of Azo-3N leads to changes in DNA structure. In particular, we show that stabilization and destabilization of the B-DNA secondary structure can be photochemically induced in situ by light. This photo-triggered process is fully reversible and could be an alternative pathway to control a broad range of biological processes. Moreover, we found that the bicationic Azo-3N exhibited a higher DNA-binding constant than the monocationic Azo-2N pointing out that the number of positive charges along the photosensitive polyamines chain plays a pivotal role in stabilizing the photochrome-DNA complex.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ziemowit Pokladek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Piotr Młynarz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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Abstract
Spores of various Bacillus and Clostridium species are among the most resistant life forms known. Since the spores of some species are causative agents of much food spoilage, food poisoning, and human disease, and the spores of Bacillus anthracis are a major bioweapon, there is much interest in the mechanisms of spore resistance and how these spores can be killed. This article will discuss the factors involved in spore resistance to agents such as wet and dry heat, desiccation, UV and γ-radiation, enzymes that hydrolyze bacterial cell walls, and a variety of toxic chemicals, including genotoxic agents, oxidizing agents, aldehydes, acid, and alkali. These resistance factors include the outer layers of the spore, such as the thick proteinaceous coat that detoxifies reactive chemicals; the relatively impermeable inner spore membrane that restricts access of toxic chemicals to the spore core containing the spore's DNA and most enzymes; the low water content and high level of dipicolinic acid in the spore core that protect core macromolecules from the effects of heat and desiccation; the saturation of spore DNA with a novel group of proteins that protect the DNA against heat, genotoxic chemicals, and radiation; and the repair of radiation damage to DNA when spores germinate and return to life. Despite their extreme resistance, spores can be killed, including by damage to DNA, crucial spore proteins, the spore's inner membrane, and one or more components of the spore germination apparatus.
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Kulkarni M, Mukherjee A. Computational Approach to Explore the B/A Junction Free Energy in DNA. Chemphyschem 2016; 17:147-54. [PMID: 26538133 DOI: 10.1002/cphc.201500690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 11/07/2022]
Abstract
Protein-DNA interactions induce conformational changes in DNA such as B- to A-form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B-A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol(-1) for the A-philic GG step and 1.59 kcal mol(-1) for the B-philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B- to A-form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA.
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Affiliation(s)
- Mandar Kulkarni
- Department of Chemistry, Indian Institute of Science Education and Research, Pune-, 411008, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune-, 411008, India.
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Setlow P, Li L. Photochemistry and Photobiology of the Spore Photoproduct: A 50-Year Journey. Photochem Photobiol 2015; 91:1263-90. [PMID: 26265564 PMCID: PMC4631623 DOI: 10.1111/php.12506] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/21/2015] [Indexed: 02/06/2023]
Abstract
Fifty years ago, a new thymine dimer was discovered as the dominant DNA photolesion in UV-irradiated bacterial spores [Donnellan, J. E. & Setlow R. B. (1965) Science, 149, 308-310], which was later named the spore photoproduct (SP). Formation of SP is due to the unique environment in the spore core that features low hydration levels favoring an A-DNA conformation, high levels of calcium dipicolinate that acts as a photosensitizer, and DNA saturation with small, acid-soluble proteins that alters DNA structure and reduces side reactions. In vitro studies reveal that any of these factors alone can promote SP formation; however, SP formation is usually accompanied by the production of other DNA photolesions. Therefore, the nearly exclusive SP formation in spores is due to the combined effects of these three factors. Spore photoproduct photoreaction is proved to occur via a unique H-atom transfer mechanism between the two involved thymine residues. Successful incorporation of SP into an oligonucleotide has been achieved via organic synthesis, which enables structural studies that reveal minor conformational changes in the SP-containing DNA. Here, we review the progress on SP photochemistry and photobiology in the past 50 years, which indicates a very rich SP photobiology that may exist beyond endospores.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
- Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana 46202
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41
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DiMaio F, Yu X, Rensen E, Krupovic M, Prangishvili D, Egelman EH. Virology. A virus that infects a hyperthermophile encapsidates A-form DNA. Science 2015; 348:914-7. [PMID: 25999507 DOI: 10.1126/science.aaa4181] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus SIRV2 (Sulfolobus islandicus rod-shaped virus 2) infects the hyperthermophilic acidophile Sulfolobus islandicus, which lives at 80°C and pH 3. We have used cryo-electron microscopy to generate a three-dimensional reconstruction of the SIRV2 virion at ~4 angstrom resolution, which revealed a previously unknown form of virion organization. Although almost half of the capsid protein is unstructured in solution, this unstructured region folds in the virion into a single extended α helix that wraps around the DNA. The DNA is entirely in the A-form, which suggests a common mechanism with bacterial spores for protecting DNA in the most adverse environments.
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Affiliation(s)
- Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Xiong Yu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Elena Rensen
- Institut Pasteur, Department of Microbiology, 25 rue du Dr. Roux, Paris 75015, France
| | - Mart Krupovic
- Institut Pasteur, Department of Microbiology, 25 rue du Dr. Roux, Paris 75015, France
| | - David Prangishvili
- Institut Pasteur, Department of Microbiology, 25 rue du Dr. Roux, Paris 75015, France.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
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Rosenberg A, Soufi B, Ravikumar V, Soares NC, Krug K, Smith Y, Macek B, Ben-Yehuda S. Phosphoproteome dynamics mediate revival of bacterial spores. BMC Biol 2015; 13:76. [PMID: 26381121 PMCID: PMC4574613 DOI: 10.1186/s12915-015-0184-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/27/2015] [Indexed: 12/19/2022] Open
Abstract
Background Bacterial spores can remain dormant for decades, yet harbor the exceptional capacity to rapidly resume metabolic activity and recommence life. Although germinants and their corresponding receptors have been known for more than 30 years, the molecular events underlying this remarkable cellular transition from dormancy to full metabolic activity are only partially defined. Results Here, we examined whether protein phospho-modifications occur during germination, the first step of exiting dormancy, thereby facilitating spore revival. Utilizing Bacillus subtilis as a model organism, we performed phosphoproteomic analysis to define the Ser/Thr/Tyr phosphoproteome of a reviving spore. The phosphoproteome was found to chiefly comprise newly identified phosphorylation sites located within proteins involved in basic biological functions, such as transcription, translation, carbon metabolism, and spore-specific determinants. Quantitative comparison of dormant and germinating spore phosphoproteomes revealed phosphorylation dynamics, indicating that phospho-modifications could modulate protein activity during this cellular transition. Furthermore, by mutating select phosphorylation sites located within proteins representative of key biological processes, we established a functional connection between phosphorylation and the progression of spore revival. Conclusions Herein, we provide, for the first time, a phosphoproteomic view of a germinating bacterial spore. We further show that the spore phosphoproteome is dynamic and present evidence that phosphorylation events play an integral role in facilitating spore revival. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0184-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alex Rosenberg
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, POB 12272, 91120, Jerusalem, Israel
| | - Boumediene Soufi
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Vaishnavi Ravikumar
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Nelson C Soares
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Karsten Krug
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University - Hadassah Medical School, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Boris Macek
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany.
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, POB 12272, 91120, Jerusalem, Israel.
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Wetzel D, Fischer RJ. Small acid-soluble spore proteins of Clostridium acetobutylicum are able to protect DNA in vitro and are specifically cleaved by germination protease GPR and spore protease YyaC. MICROBIOLOGY-SGM 2015; 161:2098-109. [PMID: 26362088 DOI: 10.1099/mic.0.000162] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Small acid-soluble proteins (SASPs) play an important role in protection of DNA in dormant bacterial endospores against damage by heat, UV radiation or enzymic degradation. In the genome of the strict anaerobe Clostridium acetobutylicum, five genes encoding SASPs have been annotated and here a further sixth candidate is suggested. The ssp genes are expressed in parallel dependent upon Spo0A, a master regulator of sporulation. Analysis of the transcription start points revealed a σG or a σF consensus promoter upstream of each ssp gene, confirming a forespore-specific gene expression. SASPs were termed SspA (Cac2365), SspB (Cac1522), SspD (Cac1620), SspF (Cac2372), SspH (Cac1663) and Tlp (Cac1487). Here it is shown that with the exception of Tlp, every purified recombinant SASP is able to bind DNA in vitro thereby protecting it against enzymic degradation by DNase I. Moreover, SspB and SspD were specifically cleaved by the two germination-specific proteases GPR (Cac1275) and YyaC (Cac2857), which were overexpressed in Escherichia coli and activated by an autocleavage reaction. Thus, for the first time to our knowledge, GPR-like activity and SASP specificity could be demonstrated for a YyaC-like protein. Collectively, the results assign SspA, SspB, SspD, SspF and SspH of C. acetobutylicum as members of α/β-type SASPs, whereas Tlp seems to be a non-DNA-binding spore protein of unknown function. In acetic acid-extracted proteins of dormant spores of C. acetobutylicum, SspA was identified almost exclusively, indicating its dominant biological role as a major α/β-type SASP in vivo.
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Affiliation(s)
- Daniela Wetzel
- Abteilung für Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, D-18051 Rostock, Germany
| | - Ralf-Jörg Fischer
- Abteilung für Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, D-18051 Rostock, Germany
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Doona CJ, Feeherry FE, Kustin K, Olinger GG, Setlow P, Malkin AJ, Leighton T. Fighting Ebola with novel spore decontamination technologies for the military. Front Microbiol 2015; 6:663. [PMID: 26322021 PMCID: PMC4533522 DOI: 10.3389/fmicb.2015.00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/17/2015] [Indexed: 11/13/2022] Open
Abstract
Recently, global public health organizations such as Doctors without Borders (MSF), the World Health Organization (WHO), Public Health Canada, National Institutes of Health (NIH), and the U.S. government developed and deployed Field Decontamination Kits (FDKs), a novel, lightweight, compact, reusable decontamination technology to sterilize Ebola-contaminated medical devices at remote clinical sites lacking infra-structure in crisis-stricken regions of West Africa (medical waste materials are placed in bags and burned). The basis for effectuating sterilization with FDKs is chlorine dioxide (ClO2) produced from a patented invention developed by researchers at the US Army Natick Soldier RD&E Center (NSRDEC) and commercialized as a dry mixed-chemical for bacterial spore decontamination. In fact, the NSRDEC research scientists developed an ensemble of ClO2 technologies designed for different applications in decontaminating fresh produce; food contact and handling surfaces; personal protective equipment; textiles used in clothing, uniforms, tents, and shelters; graywater recycling; airplanes; surgical instruments; and hard surfaces in latrines, laundries, and deployable medical facilities. These examples demonstrate the far-reaching impact, adaptability, and versatility of these innovative technologies. We present herein the unique attributes of NSRDEC's novel decontamination technologies and a Case Study of the development of FDKs that were deployed in West Africa by international public health organizations to sterilize Ebola-contaminated medical equipment. FDKs use bacterial spores as indicators of sterility. We review the properties and structures of spores and the mechanisms of bacterial spore inactivation by ClO2. We also review mechanisms of bacterial spore inactivation by novel, emerging, and established non-thermal technologies for food preservation, such as high pressure processing, irradiation, cold plasma, and chemical sanitizers, using an array of Bacillus subtilis mutants to probe mechanisms of spore germination and inactivation. We employ techniques of high-resolution atomic force microscopy and phase contrast microscopy to examine the effects of γ-irradiation on bacterial spores of Bacillus anthracis, Bacillus thuringiensis, and Bacillus atrophaeus spp. and of ClO2 on B. subtilis spores, and present in detail assays using spore bio-indicators to ensure sterility when decontaminating with ClO2.
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Affiliation(s)
- Christopher J Doona
- U.S. Army Natick - Soldier RD&E Center, Warfighter Directorate, Natick, MA USA
| | - Florence E Feeherry
- U.S. Army Natick - Soldier RD&E Center, Warfighter Directorate, Natick, MA USA
| | - Kenneth Kustin
- Department of Chemistry, Emeritus, Brandeis University, Waltham, MA USA
| | - Gene G Olinger
- National Institute of Allergy and Infectious Diseases, Integrated Research Facility - Division of Clinical Research, Fort Detrick, MD USA
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT USA
| | - Alexander J Malkin
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Terrance Leighton
- Children's Hospital - Oakland Research Institute, University of California San Francisco - Benioff, Oakland, CA USA
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Dittmann C, Han HM, Grabenbauer M, Laue M. Dormant Bacillus spores protect their DNA in crystalline nucleoids against environmental stress. J Struct Biol 2015; 191:156-64. [DOI: 10.1016/j.jsb.2015.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 06/10/2015] [Accepted: 06/18/2015] [Indexed: 12/23/2022]
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Reineke K, Langer K, Hertwig C, Ehlbeck J, Schlüter O. The impact of different process gas compositions on the inactivation effect of an atmospheric pressure plasma jet on Bacillus spores. INNOV FOOD SCI EMERG 2015. [DOI: 10.1016/j.ifset.2015.03.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Arias-Gonzalez JR. Single-molecule portrait of DNA and RNA double helices. Integr Biol (Camb) 2015; 6:904-25. [PMID: 25174412 DOI: 10.1039/c4ib00163j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The composition and geometry of the genetic information carriers were described as double-stranded right helices sixty years ago. The flexibility of their sugar-phosphate backbones and the chemistry of their nucleotide subunits, which give rise to the RNA and DNA polymers, were soon reported to generate two main structural duplex states with biological relevance: the so-called A and B forms. Double-stranded (ds) RNA adopts the former whereas dsDNA is stable in the latter. The presence of flexural and torsional stresses in combination with environmental conditions in the cell or in the event of specific sequences in the genome can, however, stabilize other conformations. Single-molecule manipulation, besides affording the investigation of the elastic response of these polymers, can test the stability of their structural states and transition models. This approach is uniquely suited to understanding the basic features of protein binding molecules, the dynamics of molecular motors and to shedding more light on the biological relevance of the information blocks of life. Here, we provide a comprehensive single-molecule analysis of DNA and RNA double helices in the context of their structural polymorphism to set a rigorous interpretation of their material response both inside and outside the cell. From early knowledge of static structures to current dynamic investigations, we review their phase transitions and mechanochemical behaviour and harness this fundamental knowledge not only through biological sciences, but also for Nanotechnology and Nanomedicine.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Calle Faraday no. 9, Cantoblanco, 28049 Madrid, Spain.
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Jian Y, Ames DM, Ouyang H, Li L. Photochemical reactions of microcrystalline thymidine. Org Lett 2015; 17:824-7. [PMID: 25668312 DOI: 10.1021/ol5036276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleoside/nucleotide/oligonucleotide photoreactions usually result in a number of products simultaneously due to a wide range of conformers existing at a given time. Such a complicated reaction pattern makes it difficult for one to focus on a single DNA photoproduct and elucidate the requirements for its formation. A rare example of thymidine photoreaction in microcrystals is reported, where 5-thyminyl-5,6-dihydrothymine, e.g., the spore photoproduct (SP), is produced as the dominant species in ∼85% yield. This unprecedented high yield clears the major obstacle for future SP photochemistry studies in detail.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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Zhuo S, Ni M. Label-free and real-time imaging of dehydration-induced DNA conformational changes in cellular nucleus using second harmonic microscopy. Sci Rep 2014; 4:7416. [PMID: 25491759 PMCID: PMC4261177 DOI: 10.1038/srep07416] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/21/2014] [Indexed: 12/03/2022] Open
Abstract
Dehydration-induced DNA conformational changes have been probed for the first time with the use of second harmonic microscopy. Unlike conventional approaches, second harmonic microscopy provides a label-free and real-time approach to detect DNA conformational changes. Upon dehydration, cellular DNA undergoes a transition from B- to A-form, whereas cellular nuclei change from invisible to visible under second harmonic microscopy. These results showed that DNA is a second order nonlinear optical material. We further confirmed this by characterizing the nonlinear optical properties of extracted DNA from human cells. Our findings open a new path for SHG imaging. DNA can change its conformations under many circumstances. For example: normal cells turning into cancerous cells and drug molecules binding with DNA. Therefore, the detection of DNA conformational changes with second harmonic microscopy will be a useful tool in cancer therapy and new drug discovery.
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Affiliation(s)
- Shuangmu Zhuo
- Fujian Provincial Key Laboratory for Photonics Technology, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Ming Ni
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
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Abstract
Spore photoproduct lyase (SPL) repairs 5-thyminyl-5,6-dihydrothymine, a thymine dimer that is also called the spore photoproduct (SP), in germinating endospores. SPL is a radical S-adenosylmethionine (SAM) enzyme, utilizing the 5'-deoxyadenosyl radical generated by SAM reductive cleavage reaction to revert SP to two thymine residues. Here we review the current progress in SPL mechanistic studies. Protein radicals are known to be involved in SPL catalysis; however, how these radicals are quenched to close the catalytic cycle is under debate.
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Affiliation(s)
- Linlin Yang
- From the Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202 and
| | - Lei Li
- From the Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202 and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), Indianapolis, Indiana 46202
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