1
|
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.
Collapse
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
| |
Collapse
|
2
|
Nguyen MCT, Nguyen HQ, Jang H, Noh S, Lee SY, Jang KS, Lee J, Sohn Y, Yee K, Jung H, Kim J. Sterilization effects of UV laser irradiation on Bacillus atrophaeus spore viability, structure, and proteins. Analyst 2021; 146:7682-7692. [PMID: 34812439 DOI: 10.1039/d1an01717a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacillus spores are highly resistant to toxic chemicals and extreme environments. Because some Bacillus species threaten public health, spore inactivation techniques have been intensively investigated. We exposed Bacillus atrophaeus spores to a 266 nm Nd:YVO4 laser at a laser power of 1 W and various numbers of scans. As a result, the UV laser reduced the viability of Bacillus atrophaeus spores. Although the outer coat of spores remained intact after UV laser irradiation of 720 scans, damage inside the spores was observed. Spore proteins were identified by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry during the course of UV laser irradiation. Photochemical and photothermal processes are believed to be involved in the UV laser sterilization of Bacillus spores. Our findings suggest that a UV laser is capable of sterilizing Bacillus atrophaeus spores.
Collapse
Affiliation(s)
- My-Chi Thi Nguyen
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Huu-Quang Nguyen
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hanbyeol Jang
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sojung Noh
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seong-Yeon Lee
- Department of Physics and Institute of Quantum Systems, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Center, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jaebeom Lee
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Youngku Sohn
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kiju Yee
- Department of Physics and Institute of Quantum Systems, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Heesoo Jung
- Chem-Bio Technology Center, Agency for Defense Development (ADD), Yuseong P.O. Box 35, Daejeon, 34186, Republic of Korea.
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Republic of Korea.
| |
Collapse
|
3
|
Handler F. Predicting Inactivation of Bacillus subtilis Spores Exposed to Broadband and Solar Ultraviolet Light. ENVIRONMENTAL ENGINEERING SCIENCE 2019; 36:667-680. [PMID: 31236005 PMCID: PMC6588126 DOI: 10.1089/ees.2018.0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/20/2018] [Indexed: 05/12/2023]
Abstract
This study develops general predictive models for the ultraviolet (UV) radiation dose-response behavior of Bacillus subtilis spores to solar UV irradiation that occurs in the environment and broadband UV irradiation used in water disinfection systems. The approach is demonstrated using previously obtained experimental survival rates for B. subtilis spores deposited on dry surfaces as well as in water and exposed to both narrow band UV radiation as well as broadband UV irradiation from solar exposure and disinfectant lamps. Results are modeled to derive predicted survival rates for spores as a function of irradiance intensity and wavelength, capability for repair, and depletion of available sites for UV damage. The essential features of the approach are expression of the inactivation action spectrum in terms of the probability of an incident photon being absorbed and forming a dimer lesion, and expression of the spore survival as a cumulative binomial distribution for damage. The results provide increased accuracy in estimating dispersed biological hazards, and evaluating the effectiveness of UV air and water disinfectant systems. In addition, the approach for the first time explains the observed reduced inactivation rate in a repair-capable strain compared with a sensitive, repair-deficient strain by accounting for the depletion of available lesion-forming sites due to increasing DNA damage.
Collapse
|
4
|
Electrical discharges in water induce spores' DNA damage. PLoS One 2018; 13:e0201448. [PMID: 30102709 PMCID: PMC6089432 DOI: 10.1371/journal.pone.0201448] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 07/15/2018] [Indexed: 11/19/2022] Open
Abstract
Bacterial spores are one of the most resilient life forms on earth and are involved in many human diseases, such as infectious diarrhea, fatal paralytic illnesses and respiratory infections. Here, we investigated the mechanisms involved in the death of Bacillus pumilus spores after exposure to electric arcs in water. Cutting-edge microscopies at the nanoscale did not reveal any structural disorganization of spores exposed to electric arcs. This result suggested the absence of physical destruction by a propagating shock wave or an exposure to an electric field. However, Pulsed-Field Gel Electrophoresis (PFGE) revealed genomic DNA damage induced by UV radiation and Reactive Oxygen Species (ROS). UV induced single-strand DNA breaks and thymine dimers while ROS were mainly involved in base excision. Our findings revealed a correlation between DNA damage and the treatment of spores with electrical discharges.
Collapse
|
5
|
Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments. Appl Microbiol Biotechnol 2018; 102:1869-1887. [DOI: 10.1007/s00253-017-8712-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/09/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
|
6
|
Mundt R, Torres Ziegenbein C, Fröbel S, Weingart O, Gilch P. Femtosecond Spectroscopy of Calcium Dipicolinate—A Major Component of Bacterial Spores. J Phys Chem B 2016; 120:9376-86. [DOI: 10.1021/acs.jpcb.6b06230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramona Mundt
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
| | - Christian Torres Ziegenbein
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
| | - Sascha Fröbel
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
| | - Oliver Weingart
- Institut
für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr. 1, D-40225 Düsseldorf, Germany
| | - Peter Gilch
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
| |
Collapse
|
7
|
Nanomechanical Characterization of Bacillus anthracis Spores by Atomic Force Microscopy. Appl Environ Microbiol 2016; 82:2988-2999. [PMID: 26969703 DOI: 10.1128/aem.00431-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The study of structures and properties of bacterial spores is important to understanding spore formation and biological responses to environmental stresses. While significant progress has been made over the years in elucidating the multilayer architecture of spores, the mechanical properties of the spore interior are not known. Here, we present a thermal atomic force microscopy (AFM) study of the nanomechanical properties of internal structures of Bacillus anthracis spores. We developed a nanosurgical sectioning method in which a stiff diamond AFM tip was used to cut an individual spore, exposing its internal structure, and a soft AFM tip was used to image and characterize the spore interior on the nanometer scale. We observed that the elastic modulus and adhesion force, including their thermal responses at elevated temperatures, varied significantly in different regions of the spore section. Our AFM images indicated that the peptidoglycan (PG) cortex of Bacillus anthracis spores consisted of rod-like nanometer-sized structures that are oriented in the direction perpendicular to the spore surface. Our findings may shed light on the spore architecture and properties. IMPORTANCE A nanosurgical AFM method was developed that can be used to probe the structure and properties of the spore interior. The previously unknown ultrastructure of the PG cortex of Bacillus anthracis spores was observed to consist of nanometer-sized rod-like structures that are oriented in the direction perpendicular to the spore surface. The variations in the nanomechanical properties of the spore section were largely correlated with its chemical composition. Different components of the spore materials showed different thermal responses at elevated temperatures.
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Calle Faraday no. 9, Cantoblanco, 28049 Madrid, Spain.
| |
Collapse
|
9
|
Singh I, Lian Y, Li L, Georgiadis MM. The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:752-9. [PMID: 24598744 PMCID: PMC3949526 DOI: 10.1107/s1399004713032987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/05/2013] [Indexed: 11/12/2022]
Abstract
The spore photoproduct lesion (SP; 5-thymine-5,6-dihydrothymine) is the dominant photoproduct found in UV-irradiated spores of some bacteria such as Bacillus subtilis. Upon spore germination, this lesion is repaired in a light-independent manner by a specific repair enzyme: the spore photoproduct lyase (SP lyase). In this work, a host-guest approach in which the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) serves as the host and DNA as the guest was used to determine the crystal structures of complexes including 16 bp oligonucleotides with and without the SP lesion at 2.14 and 1.72 Å resolution, respectively. In contrast to other types of thymine-thymine lesions, the SP lesion retains normal Watson-Crick hydrogen bonding to the adenine bases of the complementary strand, with shorter hydrogen bonds than found in the structure of the undamaged DNA. However, the lesion induces structural changes in the local conformation of what is otherwise B-form DNA. The region surrounding the lesion differs significantly in helical form from B-DNA, and the minor groove is widened by almost 3 Å compared with that of the undamaged DNA. Thus, these unusual structural features associated with SP lesions may provide a basis for recognition by the SP lyase.
Collapse
Affiliation(s)
- Isha Singh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yajun Lian
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
| | - Lei Li
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
| |
Collapse
|
10
|
Li AG, Xing Y, Burggraf LW. Thermal effects on surface structures and properties of Bacillus anthracis spores on nanometer scales. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8343-8354. [PMID: 23742662 DOI: 10.1021/la400992q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial spores, one of the hardiest forms of life known, can survive severe environmental stresses such as high temperature. Using thermal atomic force microscopy (AFM), we show that the surface structures and properties of Bacillus anthracis spores when exposed to elevated temperatures undergo substantial changes on nanometer scales. Thermal-blister-like nanostructures, which grow in size with increasing temperature, are formed on the spore surface when it is heated by a thermal tip. Although thermal damage to the spore surface is persistent upon cooling heat-treated spores to room temperature, thermal effects on surface properties of the spores are complex. The thermally induced nanostructures show a lower surface-tip adhesion and a higher modulus than the surrounding spore surface. The overall trend is for the adhesion to decrease with increasing temperature. However, the adhesion of heat-treated spores may be smaller than, equal to, or larger than that of untreated spores, depending upon the degree of surface damage induced by heat. Although the overall spore dimensions show few changes during and after heat treatment, the size of the spore substructures decreases significantly. In addition, we demonstrate a nanoscratch AFM method for imaging the subsurface structures of spores.
Collapse
Affiliation(s)
- Alex G Li
- Department of Engineering Physics, Air Force Institute of Technology, 2950 Hobson Way, Wright-Patterson AFB Ohio 45433-7765, United States.
| | | | | |
Collapse
|
11
|
Li L. Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL). BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1264-77. [PMID: 22197590 PMCID: PMC3314140 DOI: 10.1016/j.bbapap.2011.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 11/28/2011] [Indexed: 02/06/2023]
Abstract
Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
Collapse
Affiliation(s)
- Lei Li
- Department of Chemistry, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA.
| |
Collapse
|
12
|
Recent advances in cyclonucleosides: C-cyclonucleosides and spore photoproducts in damaged DNA. Molecules 2012; 17:11630-54. [PMID: 23023688 PMCID: PMC6268316 DOI: 10.3390/molecules171011630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 12/04/2022] Open
Abstract
Cyclonucleosides which are fixed in a specific conformation around the glycosyl bond by a carbon and heteroatom chain constitute a unique category of nucleoside derivatives. Because they are structural analogs, cyclonucleosides and oligodeoxynucleotides containing them would be useful tools for investigating the biological functions and conformations of DNA, RNA as well as their steric interactions with proteins. C-Cyclonucleosides bridged by a carbon chain between the base and sugar moieties are the most attractive from the synthetic points of view as well as for use as biological tools. In this review, recent progress of the synthesis of C-cyclonucleosides is surveyed. Among the C-cyclonucleosides, 5′,8-C-cyclodeoxyadenosine is one of the well-known derivatives of which the first practical synthesis was reported over 30 years ago. Recently, 5′,8-C-cyclodeoxyadenosine has attracted considerable interest as a biomarker, since its formation in oxidatively-damaged DNA is considered to be related to various diseases and aging. Another important analogue of cyclonucleosides is a unique thymidine phosphate dimer, a so-called spore photoproduct, which has been found in photo-damaged DNA. Recent advances in the synthesis, mechanism-studies, and stereochemical preference of repairing enzymes related to 5′,8-C-cyclodeoxyadenosine and spore photoproducts are also reviewed.
Collapse
|
13
|
Fessl T, Adamec F, Polívka T, Foldynová-Trantírková S, Vácha F, Trantírek L. Towards characterization of DNA structure under physiological conditions in vivo at the single-molecule level using single-pair FRET. Nucleic Acids Res 2012; 40:e121. [PMID: 22544706 PMCID: PMC3439876 DOI: 10.1093/nar/gks333] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence resonance energy transfer (FRET) under in vivo conditions is a well-established technique for the evaluation of populations of protein bound/unbound nucleic acid (NA) molecules or NA hybridization kinetics. However, in vivo FRET has not been applied to in vivo quantitative conformational analysis of NA thus far. Here we explored parameters critical for characterization of NA structure using single-pair (sp)FRET in the complex cellular environment of a living Escherichia coli cell. Our measurements showed that the fluorophore properties in the cellular environment differed from those acquired under in vitro conditions. The precision for the interprobe distance determination from FRET efficiency values acquired in vivo was found lower (∼31%) compared to that acquired in diluted buffers (13%). Our numerical simulations suggest that despite its low precision, the in-cell FRET measurements can be successfully applied to discriminate among various structural models. The main advantage of the in-cell spFRET setup presented here over other established techniques allowing conformational analysis in vivo is that it allows investigation of NA structure in various cell types and in a native cellular environment, which is not disturbed by either introduced bulk NA or by the use of chemical transfectants.
Collapse
Affiliation(s)
- Tomás Fessl
- Faculty of Sciences, University of South Bohemia, Czech Republic
| | | | | | | | | | | |
Collapse
|
14
|
Hormeño S, Ibarra B, Valpuesta JM, Carrascosa JL, Ricardo Arias-Gonzalez J. Mechanical stability of low-humidity single DNA molecules. Biopolymers 2011; 97:199-208. [DOI: 10.1002/bip.21728] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 10/14/2011] [Indexed: 12/12/2022]
|
15
|
Small acid-soluble proteins with intrinsic disorder are required for UV resistance in Myxococcus xanthus spores. J Bacteriol 2011; 193:3042-8. [PMID: 21515768 DOI: 10.1128/jb.00293-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial sporulation in Gram-positive bacteria results in small acid-soluble proteins called SASPs that bind to DNA and prevent the damaging effects of UV radiation. Orthologs of Bacillus subtilis genes encoding SASPs can be found in many sporulating and nonsporulating bacteria, but they are noticeably absent from spore-forming, Gram-negative Myxococcus xanthus. This is despite the fact that M. xanthus can form UV-resistant spores. Here we report evidence that M. xanthus produces its own unique group of low-molecular-weight, acid-soluble proteins that facilitate UV resistance in spores. These M. xanthus-specific SASPs vary depending upon whether spore formation is induced by starvation inside cell aggregations of fruiting bodies or is induced artificially by glycerol induction. Molecular predictions indicate that M. xanthus SASPs may have some association with the cell walls of M. xanthus spores, which may signify a different mechanism of UV protection than that seen in Gram-positive spores.
Collapse
|
16
|
Macur K, Temporini C, Massolini G, Grzenkowicz-Wydra J, Obuchowski M, Bączek T. Proteomic analysis of small acid soluble proteins in the spore core of Bacillus subtilis ΔprpE and 168 strains with predictions of peptides liquid chromatography retention times as an additional tool in protein identification. Proteome Sci 2010; 8:60. [PMID: 21092197 PMCID: PMC3003637 DOI: 10.1186/1477-5956-8-60] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/22/2010] [Indexed: 12/03/2022] Open
Abstract
Background Sporulation, characteristic for some bacteria such as Bacillus subtilis, has not been entirely defined yet. Protein phosphatase E (PrpE) and small, acid soluble spore proteins (SASPs) influence this process. Nevertheless, direct result of PrpE interaction on SASPs content in spore coat of B. subtilis has not been evidenced so far. As proteomic approach enables global analysis of occurring proteins, therefore it was chosen in this experiment to compare SASPs occurrence in two strains of B. subtilis, standard 168 and ΔprpE, lacking PrpE phosphatase. Proteomic analysis is still a challenge, and despite of big approach in mass spectrometry (MS) field, the identification reliability remains unsatisfactory. Therefore there is a rising interest in new methods, particularly bioinformatic tools that would harden protein identification. Most of currently applied algorithms are based on MS-data. Information from separation steps is not still in routine usage, even though they also provide valuable facts about analyzed structures. The aim of this research was to apply a model for peptides retention times prediction, based on quantitative structure-retention relationships (QSRR) in SASPs analysis, obtained from two strains of B. subtilis proteome digests after separation and identification of the peptides by LC-ESI-MS/MS. The QSRR approach was applied as the additional constraint in proteomic research verifying results of MS/MS ion search and confirming the correctness of the peptides identifications along with the indication of the potential false positives and false negatives. Results In both strains of B. subtilis, peptides characteristic for SASPs were found, however their identification confidence varied. According to the MS identity parameter Xcorr and difference between predicted and experimental retention times (ΔtR) four groups could be distinguished: correctly and incorrectly identified, potential false positives and false negatives. The ΔprpE strain was characterized by much higher amount of SASPs peptides than standard 168 and their identification confidence was, mostly for alpha- and beta-type SASP, satisfactory. Conclusions The QSRR-based model for predicting retention times of the peptides, was a useful additional to MS tool, enhancing protein identification. Higher content of SASPs in strain lacking PrpE phosphatase suggests that this enzyme may influence their occurrence in the spores, lowering levels of these proteins.
Collapse
Affiliation(s)
- Katarzyna Macur
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
| | | | | | | | | | | |
Collapse
|
17
|
Desnous C, Guillaume D, Clivio P. Spore Photoproduct: A Key to Bacterial Eternal Life. Chem Rev 2009; 110:1213-32. [DOI: 10.1021/cr0781972] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Céline Desnous
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
| | - Dominique Guillaume
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
| | - Pascale Clivio
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
| |
Collapse
|
18
|
Iwig JS, Chivers PT. DNA recognition and wrapping by Escherichia coli RcnR. J Mol Biol 2009; 393:514-26. [PMID: 19703465 DOI: 10.1016/j.jmb.2009.08.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 08/14/2009] [Accepted: 08/14/2009] [Indexed: 11/16/2022]
Abstract
Escherichia coli RcnR is a founding member of a recently discovered large and widespread structural family of bacterial transcription factors that are predicted to respond to a variety of environmental stresses. RcnR directly regulates transcription of the gene encoding the RcnA nickel and cobalt efflux protein by coordination of DNA-binding and metal-binding activities. A crystal structure of a Cu(I)-sensing homolog from Mycobacterium tuberculosis did not reveal how the novel all-alpha-helical fold of this protein family interacts with DNA because it lacks a well-characterized DNA-binding motif. In this study, we investigated the biophysical properties of the RcnR-DNA interaction using isothermal titration calorimetry and footprinting techniques. We found that an RcnR tetramer recognizes a TACT-G(6)-N-AGTA motif, of which there are two in the rcnA-rcnR intergenic region. G-tracts are found in many predicted binding sites of other RcnR/CsoR proteins, and here we show that they endow A-form DNA characteristics to the RcnR operator sites. Interestingly, RcnR also interacts nonspecifically with the approximately 50 base pairs flanking the core binding site, resulting in DNA wrapping and the introduction of a single negative supercoil into plasmid DNA. Comparisons with other RcnR/CsoR proteins reveal likely key differences in DNA binding among members of this family that result from variations in the number and sequence of operator sites.
Collapse
Affiliation(s)
- Jeffrey S Iwig
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | |
Collapse
|
19
|
Baker ES, Bowers MT. B-DNA helix stability in a solvent-free environment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1188-95. [PMID: 17434745 DOI: 10.1016/j.jasms.2007.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 02/27/2007] [Accepted: 03/01/2007] [Indexed: 05/11/2023]
Abstract
B-DNA is the most common DNA helix conformation under physiological conditions. However, when the amount of water in a DNA solution is decreased, B-to-A helix transitions have been observed. To understand what type of helix conformations exist in a solvent-free environment, a series of poly d(CG)(n) and mixed sequence DNA duplexes from 18 to 30 bp were examined with circular dichroism (CD), ESI-MS, ion mobility, and molecular dynamics. From the CD spectra, it was observed that all sequences had B-form helices in solution. However, the solvent-free results were more complex. For the poly d(CG)(n) series, the 18 bp duplex had an A-form helix conformation, both A- and B-helices were present for the 22 bp duplex, and only B-helices were observed for the 26 and 30 bp duplexes. Since these sequences were all present as B-DNA in solution, the observed solvent-free structures illustrate that smaller helices with fewer base pairs convert to A-DNA more easily than larger helices in the absence of solvent. A similar trend was observed for the mixed sequence duplexes where both an A- and B-helix were present for the 18 bp duplex, while only B-helices occur for the larger 22, 26, and 30 bp duplexes. Since the solvent-free B-helices appear at smaller sizes for the mixed sequences than for the pure d(CG)(n) duplexes, the pure d(CG)(n) duplexes have a greater A-philicity.
Collapse
Affiliation(s)
- Erin Shammel Baker
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
| | | |
Collapse
|
20
|
Buis JM, Cheek J, Kalliri E, Broderick JB. Characterization of an Active Spore Photoproduct Lyase, a DNA Repair Enzyme in the Radical S-Adenosylmethionine Superfamily. J Biol Chem 2006; 281:25994-6003. [PMID: 16829680 DOI: 10.1074/jbc.m603931200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major photoproduct in UV-irradiated Bacillus spore DNA is a unique thymine dimer called spore photoproduct (SP, 5-thyminyl-5,6-dihydrothymine). The enzyme spore photoproduct lyase (SP lyase) has been found to catalyze the repair of SP dimers to thymine monomers in a reaction that requires S-adenosylmethionine. We present here the first detailed characterization of catalytically active SP lyase, which has been anaerobically purified from overexpressing Escherichia coli. Anaerobically purified SP lyase is monomeric and is red-brown in color. The purified enzyme contains approximately 3.1 iron and 3.0 acid-labile S(2-) per protein and has a UV-visible spectrum characteristic of iron-sulfur proteins (410 nm (11.9 mM(-1) cm(-1)) and 450 nm (10.5 mM(-1) cm(-1))). The X-band EPR spectrum of the purified enzyme shows a nearly isotropic signal (g = 2.02) characteristic of a [3Fe-4S]1+ cluster; reduction of SP lyase with dithionite results in the appearance of a new EPR signal (g = 2.03, 1.93, and 1.89) with temperature dependence and g values consistent with its assignment to a [4Fe-4S]1+ cluster. The reduced purified enzyme is active in SP repair, with a specific activity of 0.33 micromol/min/mg. Only a catalytic amount of S-adenosylmethionine is required for DNA repair, and no irreversible cleavage of S-adenosylmethionine into methionine and 5'-deoxyadenosine is observed during the reaction. Label transfer from [5'-3H]S-adenosylmethionine to repaired thymine is observed, providing evidence to support a mechanism in which a 5'-deoxyadenosyl radical intermediate directly abstracts a hydrogen from SP C-6 to generate a substrate radical, and subsequent to radical-mediated beta-scission, a product thymine radical abstracts a hydrogen from 5'-deoxyadenosine to regenerate the 5'-deoxyadenosyl radical. Together, our results support a mechanism in which S-adenosylmethionine acts as a catalytic cofactor, not a substrate, in the DNA repair reaction.
Collapse
Affiliation(s)
- Jeffrey M Buis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
| | | | | | | |
Collapse
|
21
|
Nejedlý K, Chládková J, Kypr J. Photochemical probing of the B--a conformational transition in a linearized pUC19 DNA and its polylinker region. Biophys Chem 2006; 125:237-46. [PMID: 16962700 DOI: 10.1016/j.bpc.2006.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 08/14/2006] [Accepted: 08/16/2006] [Indexed: 10/24/2022]
Abstract
We induced the B-to-A conformational transition by ethanol in a linearized pUC19 DNA. A primer extension method was used in combination with UV light irradiation to follow the transition, based on pausing of DNA synthesis due to the presence of damaged bases in the template. Primer extension data highly correlated with the results of another method monitoring the B-A transition, i.e. inhibition of restriction endonuclease cleavage of UV light-irradiated DNA. Primer extension enabled us to locate damaged nucleotides within the region of interest. Most damaged nucleotides were located in B-form trimers, exclusively containing both pyrimidine bases (TTC, TCT, CTC, and CTT), and in a cytosine tetramer. The amount of damaged bases decreased in the course of B-A transition. Some of the damage even disappeared in the A-form, which mainly concerns the C(4) and C(3) blocks. The cleavage was nearly restored in the A-form within this region (Eco88I). On the contrary the decrease of damage was less significant with thymine dimers, only dropping to 50-60% of the B-form level. Consequently, the cleavage with EcoRI and HindIII remained mostly as before the transition (75% and 60% of uncleaved DNA preserved). We found significant differences in the B- and A-form pattern of UV light-damaged bases within the same region (polylinker) of DNA embedded within long (plasmid) or short (127 bp fragment) DNA molecules. The B-A transition of the fragment was found less cooperative than with linearized plasmid, which was confirmed by both CD spectroscopy and restriction cleavage inhibition.
Collapse
Affiliation(s)
- Karel Nejedlý
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | | | | |
Collapse
|
22
|
Kejnovský E, Nejedlý K, Kypr J. Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage. Int J Biol Macromol 2005; 34:213-22. [PMID: 15225994 DOI: 10.1016/j.ijbiomac.2004.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
DNA molecules of pUC19, pBR322 and PhiX174 were irradiated by various doses of UV light and the irradiated molecules were cleaved by about two dozen type II restrictases. The irradiation generally blocked the cleavage in a dose-dependent way. In accordance with previous studies, the (A + T)-richness and the (PyPy) dimer content of the restriction site belongs among the factors that on average, cause an increase in the resistance of UV damaged DNA to the restrictase cleavage. However, we observed strong effects of UV irradiation even with (G + C)-rich and (PyPy)-poor sites. In addition, sequences flanking the restriction site influenced the protection in some cases (e.g. HindIII), but not in others (e.g. SalI), whereas neoschizomer couples SmaI and AvaI, or SacI and Ecl136II, cleaved the UV-irradiated DNA similarly. Hence the intrastrand thymine dimers located in the recognition site are not the only photoproduct blocking the restrictases. UV irradiation of the A-form generally made the irradiated DNA less resistant to restrictase cleavage than irradiation in the B-form and in some cases, the A-form completely protected the UV-irradiated DNA against the damage recognized by the restrictases. The present results also demonstrate that the UV irradiation approach used to generate partial digests in genomic DNA studies, can be extended to the (G + C)-rich and (PyPy)-poor restriction sites. The present extensive and quantitative data can be used in genomic applications of UV damage probing by restrictases.
Collapse
Affiliation(s)
- Eduard Kejnovský
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
| | | | | |
Collapse
|
23
|
Nejedlý K, Chládková J, Vorlíčková M, Hrabcová I, Kypr J. Mapping the B-A conformational transition along plasmid DNA. Nucleic Acids Res 2005; 33:e5. [PMID: 15644308 PMCID: PMC546179 DOI: 10.1093/nar/gni008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 12/13/2004] [Accepted: 12/13/2004] [Indexed: 12/26/2022] Open
Abstract
A simple method is presented to monitor conformational isomerizations along genomic DNA. We illustrate properties of the method with the B-A conformational transition induced by ethanol in linearized pUC19 plasmid DNA. At various ethanol concentrations, the DNA was irradiated with ultraviolet light, transferred to a restriction endonuclease buffer and the irradiated DNA was cleaved by 17 restriction endonucleases. The irradiation damaged DNA and the damage blocked the restrictase cleavage. The amount of uncleaved, i.e. damaged, DNA depended on the concentration of ethanol in a characteristic S-shape way typical of the cooperative B-A transition. The transition beginning and midpoint were determined for each restriction endonuclease. These data map the B-A transition along the whole polylinker of pUC19 DNA and six evenly distributed recognition sequences within the rest of the plasmid. The transition midpoints fell within the B-A transition region of the plasmid simultaneously determined by CD spectroscopy. The present method complements the previous methods used to study the B-A transition. It can be employed to analyze multikilobase regions of genomic DNA whose restriction endonuclease cleavage fragments can be separated and quantified on agarose gels.
Collapse
Affiliation(s)
- Karel Nejedlý
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKrálovopolská 135, CZ-61265 Brno, Czech Republic
| | - Jana Chládková
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKrálovopolská 135, CZ-61265 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKrálovopolská 135, CZ-61265 Brno, Czech Republic
| | - Iva Hrabcová
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKrálovopolská 135, CZ-61265 Brno, Czech Republic
| | - Jaroslav Kypr
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKrálovopolská 135, CZ-61265 Brno, Czech Republic
| |
Collapse
|
24
|
Frenkiel-Krispin D, Sack R, Englander J, Shimoni E, Eisenstein M, Bullitt E, Horowitz-Scherer R, Hayes CS, Setlow P, Minsky A, Wolf SG. Structure of the DNA-SspC complex: implications for DNA packaging, protection, and repair in bacterial spores. J Bacteriol 2004; 186:3525-30. [PMID: 15150240 PMCID: PMC415783 DOI: 10.1128/jb.186.11.3525-3530.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial spores have long been recognized as the sturdiest known life forms on earth, revealing extraordinary resistance to a broad range of environmental assaults. A family of highly conserved spore-specific DNA-binding proteins, termed alpha/beta-type small, acid-soluble spore proteins (SASP), plays a major role in mediating spore resistance. The mechanism by which these proteins exert their protective activity remains poorly understood, in part due to the lack of structural data on the DNA-SASP complex. By using cryoelectron microscopy, we have determined the structure of the helical complex formed between DNA and SspC, a characteristic member of the alpha/beta-type SASP family. The protein is found to fully coat the DNA, forming distinct protruding domains, and to modify DNA structure such that it adopts a 3.2-nm pitch. The protruding SspC motifs allow for interdigitation of adjacent DNA-SspC filaments into a tightly packed assembly of nucleoprotein helices. By effectively sequestering DNA molecules, this dense assembly of filaments is proposed to enhance and complement DNA protection obtained by DNA saturation with the alpha/beta-type SASP.
Collapse
|
25
|
Nicholson WL, Setlow B, Setlow P. UV photochemistry of DNA in vitro and in Bacillus subtilis spores at earth-ambient and low atmospheric pressure: implications for spore survival on other planets or moons in the solar system. ASTROBIOLOGY 2002; 2:417-425. [PMID: 12593780 DOI: 10.1089/153110702762470518] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Two major parameters influencing the survival of Bacillus subtilis spores in space and on bodies within the Solar System are UV radiation and vacuum, both of which induce inactivating damage to DNA. To date, however, spore survival and DNA photochemistry have been explored only at the extremes of Earth-normal atmospheric pressure (101.3 kPa) and at simulated space vacuum (10(-3)-10(-6) Pa). In this study, wild-type spores, mutant spores lacking alpha/beta-type small, acid-soluble spore proteins (SASP), naked DNA, and complexes between SASP SspC and DNA were exposed simultaneously to UV (254 nm) at intermediate pressure (1-2 Pa), and the UV photoproducts cis,syn-thymine-thymine cyclobutane dimer (c,sTT), trans,syn-thymine-thymine cyclobutane dimer (t,sTT), and "spore photoproduct" (SP) were quantified. At 101.3 kPa, UV-treated wild-type spores accumulated only SP, but spores treated with UV radiation at 1-2 Pa exhibited a spectrum of DNA damage similar to that of spores treated at 10(-6) Pa, with accumulation of SP, c,sTT, and t,sTT. The presence or absence of alpha/beta-type SASP in spores was partly responsible for the shift observed between levels of SP and c,sTT, but not t,sTT. The changes observed in spore DNA photochemistry at 1-2 Pa in vivo were not reproduced by irradiation of naked DNA or SspC:DNA complexes in vitro, suggesting that factors other than SASP are involved in spore DNA photochemistry at low pressure.
Collapse
Affiliation(s)
- Wayne L Nicholson
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Arizona 85721, USA.
| | | | | |
Collapse
|
26
|
Hanzálek P, Kypr J. Tertiary structures of the Escherichia coli and human chromosome 21 molecules of DNA. Biochem Biophys Res Commun 2001; 283:219-23. [PMID: 11322791 DOI: 10.1006/bbrc.2001.4755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using the NDB database, we calculated geometrical parameters that were needed to reproduce crystal structures of short DNA fragments in a phosphorus atom representation. The geometrical parameters were included in a software generating tertiary structures of, for example, the Escherichia coli and human chromosome 21 molecules of DNA whose complete nucleotide sequences are deposited in the EMBL and related databases. Both molecules were found to be heavily folded and composed of domains. A more elaborate version of the present approach will make analysis and comparison possible of tertiary structures of genomic DNA molecules of various chromosomes to identify the chromosome evolutionary and functional relationships.
Collapse
Affiliation(s)
- P Hanzálek
- Institute of Biophysics of the Academy of Sciences of the Czech Republic, Královopolská 135, Brno, CZ-61265, Czech Republic
| | | |
Collapse
|
27
|
Setlow P. Resistance of spores of Bacillus species to ultraviolet light. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2001; 38:97-104. [PMID: 11746741 DOI: 10.1002/em.1058] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Dormant spores of the various Bacillus species, including B. subtilis, are 5 to 50 times more resistant to UV radiation than are the corresponding growing cells. This elevated spore UV resistance is due to: a) the photochemistry of DNA within spores, as UV generates few if any cyclobutane dimers, but rather a photoproduct (Fig. 1) called spore photoproduct (SP; 5-thyminyl-5,6-dihydrothymine); and b) DNA repair, in particular SP-specific repair, during spore germination. The novel UV photochemistry of spore DNA is largely due to its saturation with a group of small, acid-soluble proteins (SASP), which are unique to spores and whose binding alters the DNA conformation and thus its photochemistry. SP-specific repair is also unique to spores and is carried out by a light-independent SP-lyase, an iron-sulfur protein that utilizes S-adenosylmethionine to catalyze SP monomerization without DNA backbone cleavage.
Collapse
Affiliation(s)
- P Setlow
- Department of Biochemistry, University of Connecticut Health Center, Farmington, Connecticut 06032, USA.
| |
Collapse
|
28
|
Nicholson WL, Munakata N, Horneck G, Melosh HJ, Setlow P. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol Mol Biol Rev 2000; 64:548-72. [PMID: 10974126 PMCID: PMC99004 DOI: 10.1128/mmbr.64.3.548-572.2000] [Citation(s) in RCA: 1125] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Endospores of Bacillus spp., especially Bacillus subtilis, have served as experimental models for exploring the molecular mechanisms underlying the incredible longevity of spores and their resistance to environmental insults. In this review we summarize the molecular laboratory model of spore resistance mechanisms and attempt to use the model as a basis for exploration of the resistance of spores to environmental extremes both on Earth and during postulated interplanetary transfer through space as a result of natural impact processes.
Collapse
Affiliation(s)
- W L Nicholson
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Arizona 85721, USA.
| | | | | | | | | |
Collapse
|
29
|
Trantírek L, Stefl R, Vorlícková M, Koca J, Sklenár V, Kypr J. An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J Mol Biol 2000; 297:907-22. [PMID: 10736226 DOI: 10.1006/jmbi.2000.3592] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA usually adopts structure B in aqueous solution, while structure A is preferred in mixtures of trifluoroethanol (TFE) with water. However, the octamer d(CCCCGGGG) and other d(C(n)G(n)) fragments of DNA provide CD spectra that suggest that the base-pairs are stacked in an A-like fashion even in aqueous solution. Yet, d(CCCCGGGG) undergoes a cooperative TFE-induced transition into structure A, indicating that an important part of the aqueous duplex retains structure B. NMR spectroscopy shows that puckering of the deoxyribose rings is of the B-type. Hence, combination of the information provided by CD spectroscopy and NMR spectroscopy suggests an unprecedented double helix of DNA in which A-like base stacking is combined with B-type puckering of the deoxyribose rings. In order to determine whether this combination is possible, we used molecular dynamics to simulate the duplex of d(CCCCGGGG). Remarkably, the simulations, completely unrestrained by the experimental data, provided a very stable double helix of DNA, exhibiting just the intermediate B/A features described above. The double helix contained well-stacked guanine bases but almost unstacked cytosine bases. This generated a hole in the double helix center, which is a property characteristic for A-DNA, but absent from B-DNA. The minor groove was narrow at the double helix ends but wide at the central CG step where the Watson-Crick base-pairs were buckled in opposite directions. The base-pairs stacked tightly at the ends but stacking was loose in the duplex center. The present double helix, in which A-like base stacking is combined with B-type sugar puckering, is relevant to replication and transcription because both of these phenomena involve a local B-to-A transition.
Collapse
Affiliation(s)
- L Trantírek
- Institute of Biophysics of the Academy of Sciences of the Czech Republic, Královopolská 135, Brno, CZ-612 65, Czech Republic
| | | | | | | | | | | |
Collapse
|
30
|
Slieman TA, Nicholson WL. Artificial and solar UV radiation induces strand breaks and cyclobutane pyrimidine dimers in Bacillus subtilis spore DNA. Appl Environ Microbiol 2000; 66:199-205. [PMID: 10618224 PMCID: PMC91806 DOI: 10.1128/aem.66.1.199-205.2000] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The loss of stratospheric ozone and the accompanying increase in solar UV flux have led to concerns regarding decreases in global microbial productivity. Central to understanding this process is determining the types and amounts of DNA damage in microbes caused by solar UV irradiation. While UV irradiation of dormant Bacillus subtilis endospores results mainly in formation of the "spore photoproduct" 5-thyminyl-5,6-dihydrothymine, genetic evidence indicates that an additional DNA photoproduct(s) may be formed in spores exposed to solar UV-B and UV-A radiation (Y. Xue and W. L. Nicholson, Appl. Environ. Microbiol. 62:2221-2227, 1996). We examined the occurrence of double-strand breaks, single-strand breaks, cyclobutane pyrimidine dimers, and apurinic-apyrimidinic sites in spore DNA under several UV irradiation conditions by using enzymatic probes and neutral or alkaline agarose gel electrophoresis. DNA from spores irradiated with artificial 254-nm UV-C radiation accumulated single-strand breaks, double-strand breaks, and cyclobutane pyrimidine dimers, while DNA from spores exposed to artificial UV-B radiation (wavelengths, 290 to 310 nm) accumulated only cyclobutane pyrimidine dimers. DNA from spores exposed to full-spectrum sunlight (UV-B and UV-A radiation) accumulated single-strand breaks, double-strand breaks, and cyclobutane pyrimidine dimers, whereas DNA from spores exposed to sunlight from which the UV-B component had been removed with a filter ("UV-A sunlight") accumulated only single-strand breaks and double-strand breaks. Apurinic-apyrimidinic sites were not detected in spore DNA under any of the irradiation conditions used. Our data indicate that there is a complex spectrum of UV photoproducts in DNA of bacterial spores exposed to solar UV irradiation in the environment.
Collapse
Affiliation(s)
- T A Slieman
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Arizona 85721, USA
| | | |
Collapse
|
31
|
Rebeil R, Sun Y, Chooback L, Pedraza-Reyes M, Kinsland C, Begley TP, Nicholson WL. Spore photoproduct lyase from Bacillus subtilis spores is a novel iron-sulfur DNA repair enzyme which shares features with proteins such as class III anaerobic ribonucleotide reductases and pyruvate-formate lyases. J Bacteriol 1998; 180:4879-85. [PMID: 9733691 PMCID: PMC107513 DOI: 10.1128/jb.180.18.4879-4885.1998] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major photoproduct in UV-irradiated spore DNA is the unique thymine dimer 5-thyminyl-5,6-dihydrothymine, commonly referred to as spore photoproduct (SP). An important determinant of the high UV resistance of Bacillus subtilis spores is the accurate in situ reversal of SP during spore germination by the DNA repair enzyme SP lyase. To study the molecular aspects of SP lyase-mediated SP repair, the cloned B. subtilis splB gene was engineered to encode SP lyase with a molecular tag of six histidine residues at its amino terminus. The engineered six-His-tagged SP lyase expressed from the amyE locus restored UV resistance to spores of a UV-sensitive mutant B. subtilis strain carrying a deletion-insertion mutation which removed the entire splAB operon at its natural locus and was shown to repair SP in vivo during spore germination. The engineered SP lyase was purified both from dormant B. subtilis spores and from an Escherichia coli overexpression system by nickel-nitrilotriacetic acid (NTA) agarose affinity chromatography and was shown by Western blotting, UV-visible spectroscopy, and iron and acid-labile sulfide analysis to be a 41-kDa iron-sulfur (Fe-S) protein, consistent with its amino acid sequence homology to the 4Fe-4S clusters in anaerobic ribonucleotide reductases and pyruvate-formate lyases. SP lyase was capable of reversing SP from purified SP-containing DNA in an in vitro reaction either when present in a cell-free extract prepared from dormant spores or after purification on nickel-NTA agarose. SP lyase activity was dependent upon reducing conditions and addition of S-adenosylmethionine as a cofactor.
Collapse
Affiliation(s)
- R Rebeil
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | | | | | | | |
Collapse
|
32
|
Clivio P, Guillaume D, Adeline MT, Hamon J, Riche C, Fourrey JL. Synthesis and Photochemical Behavior of Peptide Nucleic Acid Dimers and Analogues Containing 4-Thiothymine: Unprecedented (5−4) Photoadduct Reversion. J Am Chem Soc 1998. [DOI: 10.1021/ja971983b] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
33
|
|
34
|
Xue Y, Nicholson WL. The two major spore DNA repair pathways, nucleotide excision repair and spore photoproduct lyase, are sufficient for the resistance of Bacillus subtilis spores to artificial UV-C and UV-B but not to solar radiation. Appl Environ Microbiol 1996; 62:2221-7. [PMID: 8779559 PMCID: PMC168002 DOI: 10.1128/aem.62.7.2221-2227.1996] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bacterial endospores are 1 to 2 orders of magnitude more resistant to 254-nm UV (UV-C) radiation than are exponentially growing cells of the same strain. This high UV resistance is due to two related phenomena: (i) DNA of dormant spores irradiated with 254-nm UV accumulates mainly a unique thymine dimer called the spore photoproduct (SP), and (ii) SP is corrected during spore germination by two major DNA repair pathways, nucleotide excision repair (NER) and an SP-specific enzyme called SP lyase. To date, it has been assumed that these two factors also account for resistance of bacterial spores to solar UV in the environment, despite the fact that sunlight at the Earth's surface consists of UV-B, UV-A, visible, and infrared wavelengths of approximately 290 nm and longer. To test this assumption, isogenic strains of Bacillus subtilis lacking either the NER or SP lyase DNA repair pathway were assayed for their relative resistance to radiation at a number of UV wavelengths, including UV-C (254 nm), UV-B (290 to 320 nm), full-spectrum sunlight, and sunlight from which the UV-B portion had been removed. For purposes of direct comparison, spore UV resistance levels were determined with respect to a calibrated biological dosimeter consisting of a mixture of wild-type spores and spores lacking both DNA repair systems. It was observed that the relative contributions of the two pathways to spore UV resistance change depending on the UV wavelengths used in a manner suggesting that spores irradiated with light at environmentally relevant UV wavelengths may accumulate significant amounts of one or more DNA photoproducts in addition to SP. Furthermore, it was noted that upon exposure to increasing wavelengths, wild-type spores decreased in their UV resistance from 33-fold (UV-C) to 12-fold (UV-B plus UV-A sunlight) to 6-fold (UV-A sunlight alone) more resistant than mutants lacking both DNA repair systems, suggesting that at increasing solar UV wavelengths, spores are inactivated either by DNA damage not reparable by the NER or SP lyase system, damage caused to photosensitive molecules other than DNA, or both.
Collapse
Affiliation(s)
- Y Xue
- Department of Microbiology and Immunology, University of North Texas Health Science Center, Fort Worth 76107, USA
| | | |
Collapse
|
35
|
Abstract
Photoreactivation of ultraviolet radiation-induced DNA damage was examined in exponential-phase cells of six mesophilic species of the genus Bacillus. Under the experimental conditions used, it was observed that the laboratory strains B. cereus strain T and B. thuringiensis var. thuringiensis strain NRRL-B4039 exhibited strong photoreactivation (86-fold and 70-fold respectively). Bacillus licheniformis strain ATCC 8480 exhibited moderate (15-fold) photoreactivation. Weak photoreactivation was observed in B. subtilis strain 168 (4-fold) and B. megaterium strain QM B1551 (3.4-fold). Bacillus amyloliquefaciens strain H demonstrated no detectable photoreactivation.
Collapse
Affiliation(s)
- W L Nicholson
- Department of Microbiology and Immunology, University of North Texas Health Science Center, Fort Worth 76107, USA
| |
Collapse
|
36
|
Fajardo-Cavazos P, Nicholson WL. Molecular dissection of mutations in the Bacillus subtilis spore photoproduct lyase gene which affect repair of spore DNA damage caused by UV radiation. J Bacteriol 1995; 177:4402-9. [PMID: 7635825 PMCID: PMC177190 DOI: 10.1128/jb.177.15.4402-4409.1995] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In response to UV irradiation, Bacillus subtilis spore DNA accumulates the unique thymine dimer 5-thyminyl-5,6-dihydrothymine, or spore photoproduct (SP). SP is broken down into monomers during spore germination by the product of the spl gene which has been proposed to encode the enzyme SP lyase. The wild-type spl gene was cloned by complementation of a mutation designated spl-1; the putative spl gene product is a 40-kDa protein whose deduced amino acid sequence contains regions homologous to DNA photolyases. During phenotypic characterization of spl subclones using transformation crosses between the cloned wild-type spl gene and an spl-1 mutant recipient, in addition to the expected transformant classes exhibiting UV-resistant (type I) and UV-sensitive (type III) spores, an additional recombinant class was observed (called type II), spores of which exhibited slower germination kinetics following UV irradiation. The results suggested that the spl-1 allele consisted of at least two separable mutations. The DNA region which could rescue the spl-1 allele was localized to a 511-bp region within the spl coding sequence; this region was amplified from the spl-1 mutant chromosome by PCR and sequenced. The region contained two amino acid substitutions, an Arg replacing Gly-168 (G168R) and an Asp replacing Gly-242 (G242D) in the deduced SP lyase sequence, as well as 18 silent mutations. PCR amplification of chromosomal DNA from a selected type II recombinant and sequence analysis of the amplification product confirmed that recombination had indeed occurred between codons 168 and 242 and further localized the point of crossover by using the 18 silent mutations as molecular markers throughout the region. By in vitro mutagenesis, alleles of spl containing all combinations of single and double amino acid substitutions were introduced into the cloned wild-type spl gene. When integrated into the B. subtilis chromosome at the amyE locus, it was observed that although both amino acid substitutions contribute to the spl-1 phenotype, the G168R mutation exerted a much greater effect than did the G242D mutation.
Collapse
Affiliation(s)
- P Fajardo-Cavazos
- Department of Microbiology and Immunology, University of North Texas Health Science Center, Fort Worth 76107, USA
| | | |
Collapse
|
37
|
Basham B, Schroth GP, Ho PS. An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA. Proc Natl Acad Sci U S A 1995; 92:6464-8. [PMID: 7604014 PMCID: PMC41538 DOI: 10.1073/pnas.92.14.6464] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The ability to predict macromolecular conformations from sequence and thermodynamic principles has long been coveted but generally has not been achieved. We show that differences in the hydration of DNA surfaces can be used to distinguish between sequences that form A- and B-DNA. From this, a "triplet code" of A-DNA propensities was derived as energetic rules for predicting A-DNA formation. This code correctly predicted > 90% of A- and B-DNA sequences in crystals and correlates with A-DNA formation in solution. Thus, with our previous studies on Z-DNA, we now have a single method to predict the relative stability of sequences in the three standard DNA duplex conformations.
Collapse
Affiliation(s)
- B Basham
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA
| | | | | |
Collapse
|
38
|
Pedraza-Reyes M, Gutiérrez-Corona F, Nicholson WL. Temporal regulation and forespore-specific expression of the spore photoproduct lyase gene by sigma-G RNA polymerase during Bacillus subtilis sporulation. J Bacteriol 1994; 176:3983-91. [PMID: 8021181 PMCID: PMC205596 DOI: 10.1128/jb.176.13.3983-3991.1994] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bacterial spores are highly resistant to killing by UV radiation and exhibit unique DNA photochemistry. UV irradiation of spore DNA results in formation of spore photoproduct (SP), the thymine dimer 5-thyminyl-5,6-dihydrothymine. Repair of SP occurs during germination of Bacillus subtilis spores by two distinct routes, either by the general nucleotide excision repair (uvr) pathway or by a novel SP-specific monomerization reaction mediated by the enzyme SP lyase, which is encoded by the spl gene. Repair of SP occurs early in spore germination and is independent of de novo protein synthesis, suggesting that the SP repair enzymes are synthesized during sporulation and are packaged in the dormant spore. To test this hypothesis, the expression of a translational spl-lacZ fusion integrated at the spl locus was monitored during B. subtilis growth and sporulation. beta-Galactosidase expression from the spl-lacZ fusion was silent during vegetative growth and was not DNA damage inducible, but it was activated at morphological stage III of sporulation specifically in the forespore compartment, coincident with activation of expression of the stage III marker enzyme glucose dehydrogenase. Expression of the spl-lacZ fusion was shown to be dependent upon the sporulation-specific RNA polymerase containing the sigma-G factor (E sigma G), as spl-lacZ expression was abolished in a mutant harboring a deletion in the sigG gene and restored by expression of the sigG gene in trans. Primer extension analysis of spl mRNA revealed a major extension product initiating upstream from a small open reading frame of unknown function which precedes spl, and it revealed two other shorter minor extension products. All three extension products were present in higher quantities during sporulation and after sigG induction. The three putative transcripts are all preceded by sequences which share homology with the consensus sigma-G factor-type promoter sequence, but in vitro transcription by purified sigma-G RNA polymerase was detected only from the promoter corresponding to the major extension product. The open reading frame-spl operon therefore appears to be an additional member of the sigma-G regulon, which also includes as members the small, acid-soluble spore proteins which are in large part responsible for spore DNA photochemistry. Therefore, sporulating bacteria appear to coordinately regulate genes whose products not only alter spore DNA photochemistry but also repair the major spore-specific photoproduct during germination
Collapse
Affiliation(s)
- M Pedraza-Reyes
- Institute of Investigation in Experimental Biology, Faculty of Chemistry, University of Guanajuato, Mexico
| | | | | |
Collapse
|
39
|
Abstract
The initiation of sporulation in Bacillus subtilis is regulated by a signal transduction system leading to activation (by phosphorylation) of the Spo0A transcription factor. Activated Spo0A controls the expression of genes encoding different RNA polymerase sigma factors, whose synthesis and activities are related to morphological events and intercompartmental communication between the developing forespore and the mother cell.
Collapse
Affiliation(s)
- M A Strauch
- Department of Molecular and Experimental Medicine, Scripps Research Institute La Jolla, CA 92037
| | | |
Collapse
|
40
|
Fajardo-Cavazos P, Salazar C, Nicholson WL. Molecular cloning and characterization of the Bacillus subtilis spore photoproduct lyase (spl) gene, which is involved in repair of UV radiation-induced DNA damage during spore germination. J Bacteriol 1993; 175:1735-44. [PMID: 8449881 PMCID: PMC203968 DOI: 10.1128/jb.175.6.1735-1744.1993] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Upon UV irradiation, Bacillus subtilis spore DNA accumulates the novel thymine dimer 5-thyminyl-5,6-dihydrothymine. Spores can repair this "spore photoproduct" (SP) upon germination either by the uvr-mediated general excision repair pathway or by the SP-specific spl pathway, which involves in situ monomerization of SP to two thymines by an enzyme named SP lyase. Mutants lacking both repair pathways produce spores that are extremely sensitive to UV. For cloning DNA that can repair a mutation in the spl pathway called spl-1, a library of EcoRI fragments of chromosomal DNA from B. subtilis 168 was constructed in integrative plasmid pJH101 and introduced by transformation into a mutant B. subtilis strain that carries both the uvrA42 and spl-1 mutations, and transformants whose spores exhibited UV resistance were selected by UV irradiation. With a combination of genetic and physical mapping techniques, the DNA responsible for the restoration of UV resistance was shown to be present on a 2.3-kb EcoRI-HindIII fragment that was mapped to a new locus in the metC-pyrD region of the B. subtilis chromosome immediately downstream from the pstI gene. The spl coding sequence was localized on the cloned fragment by analysis of in vitro-generated deletions and by nucleotide sequencing. The spl nucleotide sequence contains an open reading frame capable of encoding a 40-kDa polypeptide that shows regional amino acid sequence homology to DNA photolyases from a number of bacteria and fungi.
Collapse
Affiliation(s)
- P Fajardo-Cavazos
- Department of Microbiology and Immunology, Texas College of Osteopathic Medicine, Fort Worth 76107
| | | | | |
Collapse
|
41
|
Setlow B, Setlow P. Dipicolinic Acid Greatly Enhances Production of Spore Photoproduct in Bacterial Spores upon UV Irradiation. Appl Environ Microbiol 1993; 59:640-3. [PMID: 16348882 PMCID: PMC202161 DOI: 10.1128/aem.59.2.640-643.1993] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Formation of the spore photoproduct (SP) (5-thyminyl-5,6-dihydrothymine) in DNA of dormant spores of
Bacillus subtilis
upon UV irradiation is due to binding of α/β-type small, acid-soluble proteins (SASP). However, the yield of SP as a function of UV fluence is ∼15-fold higher in spores than in an α/β-type-SASP-DNA complex in vitro. The yield of SP as a function of UV fluence in forespore DNA from mutants which make α/β-type SASP but not dipicolinic acid (DPA) was 10 to 20 times lower than that in dormant spores. Furthermore, the yield of SP as a function of UV fluence in an α/β-type-SASP-DNA complex in vitro was increased sixfold by DPA. These data provide further support for the idea that the high DPA level in dormant spores increases the yield of SP as a function of UV fluence and thereby sensitizes spores to UV.
Collapse
Affiliation(s)
- B Setlow
- Department of Biochemistry, University of Connecticut Health Center, Farmington, Connecticut 06030-3305
| | | |
Collapse
|
42
|
Affiliation(s)
- P Setlow
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06030-3305
| |
Collapse
|