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Yuan Y, Li H, Leite W, Zhang Q, Bonnesen PV, Labbé JL, Weiss KL, Pingali SV, Hong K, Urban VS, Salmon S, O'Neill H. Biosynthesis and characterization of deuterated chitosan in filamentous fungus and yeast. Carbohydr Polym 2021; 257:117637. [PMID: 33541662 DOI: 10.1016/j.carbpol.2021.117637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/29/2020] [Accepted: 01/09/2021] [Indexed: 10/22/2022]
Abstract
Deuterated chitosan was produced from the filamentous fungus Rhizopus oryzae, cultivated with deuterated glucose in H2O medium, without the need for conventional chemical deacetylation. After extraction and purification, the chemical composition and structure were determined by Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and small-angle neutron scattering (SANS). 13C NMR experiments provided additional information about the position of the deuterons in the glucoseamine backbone. The NMR spectra indicated that the deuterium incorporation at the non-exchangeable hydrogen positions of the aminoglucopyranosyl ring in the C3 - C5 positions was at least 60-80 %. However, the C2 position was deuterated at a much lower level (6%). Also, SANS showed that the structure of deuterated chitosan was very similar compared to the non-deuterated counterpart. The most abundant radii of the protiated and deuterated chitosan fibers were 54 Å and 60 Å, respectively, but there is a broader distribution of fiber radii in the protiated chitosan sample. The highly deuterated, soluble fungal chitosan described here can be used as a model material for studying chitosan-enzyme complexes for future neutron scattering studies. Because the physical behavior of non-deuterated fungal chitosan mimicked that of shrimp shell chitosan, the methods presented here represent a new approach to producing a high quality deuterated non-animal-derived aminopolysaccharide for studying the structure-function association of biocomposite materials in drug delivery, tissue engineering and other bioactive chitosan-based composites.
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Affiliation(s)
- Yue Yuan
- Department of Textile Engineering, Chemistry and Science, Wilson College of Textiles, North Carolina State University, Raleigh, NC, 27606, USA
| | - Hui Li
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Leite
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Qiu Zhang
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Peter V Bonnesen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jessy L Labbé
- Fungal Systems Genetics and Biology Lab, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L Weiss
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sai Venkatesh Pingali
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kunlun Hong
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Volker S Urban
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sonja Salmon
- Department of Textile Engineering, Chemistry and Science, Wilson College of Textiles, North Carolina State University, Raleigh, NC, 27606, USA.
| | - Hugh O'Neill
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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Yu X, Wu Y, Huang F, Ulrich J, Wang J. Purification of RecombinantL-Asparaginase II Using Solvent-Freeze-Out Technology. Chem Eng Technol 2018. [DOI: 10.1002/ceat.201700569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xiaoxi Yu
- China University of Petroleum (East China); College of Chemical Engineering; No. 66 Changjiang West Road 266580 Qingdao China
| | - Yining Wu
- China University of Petroleum (East China); College of Petroleum Engineering; No. 66 Changjiang West Road 266580 Qingdao China
| | - Fang Huang
- China University of Petroleum (East China); College of Chemical Engineering; No. 66 Changjiang West Road 266580 Qingdao China
| | - Joachim Ulrich
- Martin Luther University Halle-Wittenberg; Thermal Process Engineering, Center for Engineering Science; Hoherweg 7 06120 Halle (Saale) Germany
| | - Jingkang Wang
- Tianjin University; School of Chemical Engineering and Technology; State Key Laboratory for Chemical Engineering; No. 92 Weijin Road 300072 Tianjin China
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3
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Chaudhuri BN. Emerging applications of small angle solution scattering in structural biology. Protein Sci 2015; 24:267-76. [PMID: 25516491 PMCID: PMC4353354 DOI: 10.1002/pro.2624] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/05/2014] [Indexed: 12/12/2022]
Abstract
Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu.
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Affiliation(s)
- Barnali N Chaudhuri
- Faculty of Life Sciences and Biotechnology, South Asian UniversityAkbar Bhawan, Chanakyapuri, New Delhi, India
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4
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Qian S, Dean R, Urban VS, Chaudhuri BN. The internal organization of mycobacterial partition assembly: does the DNA wrap a protein core? PLoS One 2012; 7:e52690. [PMID: 23285150 PMCID: PMC3527565 DOI: 10.1371/journal.pone.0052690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/20/2012] [Indexed: 11/18/2022] Open
Abstract
Before cell division in many bacteria, the ParBs spread on a large segment of DNA encompassing the origin-proximal parS site(s) to form the partition assembly that participates in chromosome segregation. Little is known about the structural organization of chromosomal partition assembly. We report solution X-ray and neutron scattering data characterizing the size parameters and internal organization of a nucleoprotein assembly formed by the mycobacterial chromosomal ParB and a 120-meric DNA containing a parS-encompassing region from the mycobacterial genome. The cross-sectional radii of gyration and linear mass density describing the rod-like ParB-DNA assembly were determined from solution scattering. A "DNA outside, protein inside" mode of partition assembly organization consistent with the neutron scattering hydrogen/deuterium contrast variation data is discussed. In this organization, the high scattering DNA is positioned towards the outer region of the partition assembly. The new results presented here provide a basis for understanding how ParBs organize the parS-proximal chromosome, thus setting the stage for further interactions with the DNA condensins, the origin tethering factors and the ParA.
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Affiliation(s)
- Shuo Qian
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Rebecca Dean
- Hauptman Woodward Institute, Buffalo, New York, United States of America
| | - Volker S. Urban
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Barnali N. Chaudhuri
- Hauptman Woodward Institute, Buffalo, New York, United States of America
- Department of Structural Biology, State University of New York, Buffalo, New York, United States of America
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5
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Lee HJ, Wark AW, Goodrich TT, Fang S, Corn RM. Surface enzyme kinetics for biopolymer microarrays: a combination of Langmuir and Michaelis-Menten concepts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:4050-4057. [PMID: 15835973 DOI: 10.1021/la046822h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis-Menten concepts and three rate constants: enzyme adsorption (k(a)), enzyme desorption (k(d)) and enzyme catalysis (k(cat)). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme-substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where k(a)[E] >> k(cat). Experiments using the 3' --> 5' exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.
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Affiliation(s)
- Hye Jin Lee
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
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6
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Adamczyk M, Mattingly PG, Moore JA, Pan Y. Synthesis of a chemiluminescent acridinium hydroxylamine (AHA) for the direct detection of abasic sites in DNA. Org Lett 1999; 1:779-81. [PMID: 10823204 DOI: 10.1021/ol990141+] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] The synthesis of a chemiluminescent acridinium hydroxylamine (AHA) for the direct detection of abasic sites in damaged nucleic acids is described. The reagent reacts readily with abasic sites of damaged calf thymus DNA generated in a time-dependent manner under acid/heat depurination conditions. Preliminary results indicate the sensitivity of the direct chemiluminescent detection format is approximately 0.1 abasic sites detected per 10(6) nucleotides using as little as 200 ng of DNA.
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Affiliation(s)
- M Adamczyk
- Department of Chemistry, Diagnostics Division, Abbott Laboratories, 100 Abbott Park Road, Department 09NM, Bldg. AP20, Abbott Park, Illinois 60064-6016, USA.
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7
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Affiliation(s)
- J. A. Cowan
- The Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
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8
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Kurumizaka H, Aihara H, Ikawa S, Kashima T, Bazemore LR, Kawasaki K, Sarai A, Radding CM, Shibata T. A possible role of the C-terminal domain of the RecA protein. A gateway model for double-stranded DNA binding. J Biol Chem 1996; 271:33515-24. [PMID: 8969216 DOI: 10.1074/jbc.271.52.33515] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
According to the crystal structure, the RecA protein has a domain near the C terminus consisting of amino acid residues 270-328 (from the N terminus). Our model building pointed out the possibility that this domain is a part of "gateway" through which double-stranded DNA finds a path for direct contact with single-stranded DNA within a presynaptic RecA filament in the search for homology. To test this possible function of the domain, we made mutant RecA proteins by site-directed single (or double, in one case) replacement of 2 conserved basic amino acid residues and 5 among 9 nonconserved basic amino acid residues in the domain. Replacement of either of the 2 conserved amino acid residues caused deficiencies in repair of UV-damaged DNA, an in vivo function of RecA protein, whereas the replacement of most (except one) of the tested nonconserved ones gave little or no effect. Purified mutant RecA proteins showed no (or only slight) deficiencies in the formation of presynaptic filaments as assessed by various assays. However, presynaptic filaments of both proteins that had replacement of a conserved amino acid residue had significant defects in binding to and pairing with duplex DNA (secondary binding). These results are consistent with our model that the conserved amino acid residues in the C-terminal domain have a direct role in double-stranded DNA binding and that they constitute a part of a gateway for homologous recognition.
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Affiliation(s)
- H Kurumizaka
- Laboratory of Cellular and Molecular Biology, The Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama 351-01, Japan. tshibata.postman.riken.go.jp
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9
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Takahashi M, Maraboeuf F, Nordén B. Locations of functional domains in the RecA protein. Overlap of domains and regulation of activities. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:20-8. [PMID: 8954148 DOI: 10.1111/j.1432-1033.1996.0020r.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We review the locations of various functional domains of the RecA protein of Escherichia coli, including how they have been assigned, and discuss the potential regulatory roles of spatial overlap between different domains. RecA is a multifunctional and ubiquitous protein involved both in general genetic recombination and in DNA repair: it regulates the synthesis and activity of DNA repair enzymes (SOS induction) and catalyses homologous recombination and mutagenesis. For these activities RecA interacts with a nucleotide cofactor, single-stranded and double-stranded DNAs, the LexA repressor, UmuD protein, the UmuD'2C complex as well as with RecA itself in forming the catalytically active nucleofilament. Attempts to locate the respective interaction sites have been advanced in order to understand the various functions of RecA. An intriguing question is how these numerous functional sites are contained within this rather small protein (38 kDa). To assess more clearly the roles of the respective sites and to what extent the sites may be interacting with each other, we review and compare the results obtained from various biological, biochemical and physico-chemical approaches. From a three-dimensional model it is concluded that all sites are concentrated to one part of the protein. As a consequence there are significant overlaps between the sites and it is speculated that corresponding interactions may play important roles in regulating RecA activities.
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Affiliation(s)
- M Takahashi
- Groupe d'Etude Mutagénèse et Cancérogénèse, UMR 216 CNRS, Orsay, France
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10
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Rehrauer WM, Kowalczykowski SC. The DNA binding site(s) of the Escherichia coli RecA protein. J Biol Chem 1996; 271:11996-2002. [PMID: 8662640 DOI: 10.1074/jbc.271.20.11996] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Photochemical cross-linking has been used to identify residues in the Escherichia coli RecA protein that are proximal to and may directly mediate binding of DNA. Ultraviolet irradiation promotes specific and efficient cross-linking of the RecA protein to poly(deoxythymidylic) acid. Cross-linked peptides remaining covalently attached to the polynucleotide following proteolytic digestion with trypsin correspond to amino acids 61-72, 178-183, and 233-243 of the RecA protein primary sequence. Their location and surface accessibility in the crystal structure, along with the behavior of various recA mutants, support the assignment of the cross-linked regions to the DNA binding site(s) of the RecA protein. Functional overlap of amino acids 61-72 with an element of the ATP binding site suggests a structural mechanism by which nucleotide cofactors allosterically affect the RecA nucleoprotein filament.
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Affiliation(s)
- W M Rehrauer
- Department of Molecular Biology, Northwestern University Medical School, Chicago, Illinois 60611, USA
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11
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Marais A, Bové JM, Renaudin J. Spiroplasma citri virus SpV1-derived cloning vector: deletion formation by illegitimate and homologous recombination in a spiroplasmal host strain which probably lacks a functional recA gene. J Bacteriol 1996; 178:862-70. [PMID: 8550524 PMCID: PMC177736 DOI: 10.1128/jb.178.3.862-870.1996] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have previously described the use of the replicative form (RF) of Spiroplasma citri virus SpV1 as a vector for expressing an epitope of the P1 adhesin protein from Mycoplasma pneumoniae in S. citri (A. Marais, J. M. Bové, S.F. Dallo, J. B. Baseman, and J. Renaudin, J. Bacteriol. 175:2783-2787, 1993). We have now studied the structural instability of the recombinant RF leading to loss of the DNA insert. Analyses of viral clones with deletions have shown that both illegitimate and homologous recombination were involved in deletion formation. For one such clone, deletion has occurred via a double crossing-over exchange between the circular free viral RF and SpV1 viral sequences present in the S. citri host chromosome. The homologous recombination process usually requires the RecA protein. However, characterization of the recA gene of the S. citri R8A2 host strain revealed that over two-thirds of the open reading frame of the recA gene was deleted from the C-terminal part, indicating that this particular strain is probably RecA deficient.
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Affiliation(s)
- A Marais
- Laboratoire de Biologie Cellulaire et Moléculaire Institut National de la Recherche Agronomique, Domaine de la Grande Ferrade, Villenave d'Omon, France
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12
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Morimatsu K, Horii T. The DNA-Binding Site of the Reca Protein. Photochemical Cross-Linking of Tyrl03 to Single-Stranded DNA. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.tb20322.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Wittung P, Nordén B, Takahashi M. Secondary structure of RecA in solution. The effects of cofactor, DNA and ionic conditions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 228:149-54. [PMID: 7882996 DOI: 10.1111/j.1432-1033.1995.tb20243.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The interactions of RecA with double-stranded DNA and with cofactor adenosine 5'-[3-thio]triphosphate (ATP[S] an analog of ATP) have been characterized by circular dichroism (CD) spectroscopy in a search for conformational changes associated with the formation of helical RecA . ATP . DNA fibers. Upon interaction with the RecA protein the cofactor is found to be structurally perturbed, possibly towards the syn ribose form of ATP[S], while the secondary structure of RecA remains unaffected. By contrast, when the ATP[S] . RecA . DNA complex is formed, a distinct change of the protein CD spectrum near 200 nm is observed as a result of interaction of RecA with DNA. The main change occurs upon the binding of the first DNA molecule [RecA can bind up to three DNA molecules simultaneously; Takahashi, M., Kubista, M. & Nordén, B. (1991) Biochimie (Paris) 73, 219-226] and the effect appears to be independent of DNA sequence, suggesting a general change of protein conformation upon DNA binding. The CD of DNA is changed, indicating an alteration of the DNA structure, possibly related to stretching and unwinding. A small, reversible, decrease in the CD amplitude of RecA was observed when raising the temperature from 4 degrees C to 30 degrees C. The CD of RecA increases slightly with pH (up to 7.8) but is constant between pH 6.0 and 6.8. At pH below 6.0 or higher temperature (40 degrees C) slow irreversible denaturation of RecA occurs. The CD signal is effectively independent of salt, even in 2.2 M NaCl or 1 M sodium acetate, which is relevant regarding reported ATPase and coprotease activities promoted by salt. For high concentrations of magnesium (10 mM) at 30 degrees C the CD of RecA changes markedly and the appearance of light scattering indicates aggregation.
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Affiliation(s)
- P Wittung
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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Morimatsu K, Horii T. Analysis of the DNA binding site of Escherichia coli RecA protein. ADVANCES IN BIOPHYSICS 1995; 31:23-48. [PMID: 7625276 DOI: 10.1016/0065-227x(95)99381-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To investigate the DNA binding site of RecA protein, we constructed 15 recA mutants having alterations in the regions homologous to the other ssDNA binding proteins. The in vivo analyses showed that the mutational change at Arg243, Lys248, Tyr264, or simultaneously at Lys6 and Lys19, or Lys6 and Lys23 caused severe defects in the recA functions, while other mutational changes did not. Purified RecA-K6A-K23A (Lys6 and Lys23 changed to Ala and Ala, respectively) protein was indistinguishable from the wild-type RecA protein in its binding to DNA. However, the RecA-R243A (Arg243 changed to Ala) and RecA-Y264A (Tyr264 changed to Ala) proteins were defective in binding to both ss- and ds-DNA. In self-oligomerization property, RecA-R243A was proficient but RecA-Y264A was deficient, suggesting that the RecA-R243A protein had a defect in DNA binding site and the RecA-Y264A protein was defective in its interaction with the adjacent RecA molecule. The region of residues 243-257 including the Arg243 is highly homologous to the DNA binding motif in the ssDNA binding proteins, while the eukaryotic RecA homologues have a similar structure at the amino-terminal side proximal to the nucleotide binding core. The region of residues 243-257 would be a part of the DNA binding site. The other parts of this site would be the Tyr103 and the region of residues 178-183, which were cross-linked to ssDNA. These three regions lie in a line in the crystal structure.
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Affiliation(s)
- K Morimatsu
- Department of Molecular Protozoology, Osaka University, Japan
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15
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Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 1994; 58:401-65. [PMID: 7968921 PMCID: PMC372975 DOI: 10.1128/mr.58.3.401-465.1994] [Citation(s) in RCA: 778] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.
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Affiliation(s)
- S C Kowalczykowski
- Division of Biological Sciences, University of California, Davis 95616-8665
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16
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Kim S, Nordén B, Takahashi M. Role of DNA intercalators in the binding of RecA to double-stranded DNA. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)82404-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Jonsson M, Jacobsson U, Takahashi M, Nordén B. Orientation of large DNA during free solution electrophoresis studied by linear dichroism. ACTA ACUST UNITED AC 1993. [DOI: 10.1039/ft9938902791] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Egelman E, Stasiak A. Electron microscopy of RecA-DNA complexes: Two different states, their functional significance and relation to the solved crystal structure. Micron 1993. [DOI: 10.1016/0968-4328(93)90056-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Nordén B, Elvingson C, Kubista M, Sjöberg B, Ryberg H, Ryberg M, Mortensen K, Takahashi M. Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples. J Mol Biol 1992; 226:1175-91. [PMID: 1518050 DOI: 10.1016/0022-2836(92)91060-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
By combining anisotropy of small-angle neutron scattering (SANS) and optical anisotropy (linear dichroism, l.d.) on flow-oriented RecA-DNA complexes, the average DNA-base orientation has been determined in RecA complexes with double-stranded (ds) as well as single-stranded (ss) DNA. From the anisotropy of the two-dimensional SANS intensity representation, the second moment orientation function S is obtained. Knowledge of S is crucial for the interpretation of l.d. spectra in terms of orientation of the DNA bases and the aromatic amino acid residues. The DNA-base planes are essentially perpendicular to the fibre axis of the complex between RecA and dsDNA in the presence of cofactor ATP gamma S. A somewhat tilted base geometry is found for the RecA-ATP gamma S complexes with single-stranded poly(dT) and poly(d epsilon A). This behaviour contrasts the RecA-ssDNA complex formed without cofactor which displays a poor orientation of the bases. Well-ordered bases in the ssDNA-RecA complex is possibly reflecting the role of RecA in preparing a nucleotide strand for base-pairing in the search-for-homology process. While the central SANS intensity is essentially independent of the pitch of the helical complex, a secondary intensity maximum, which becomes focused upon flow orientation, is found to be a sensitive measure of the pitch. The pitch values for the complexes compare well with cryo-electron microscopy results but are slightly larger than those seen for uranyl-stained samples.
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Affiliation(s)
- B Nordén
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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20
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Timmins PA, Ruigrok RW, DiCapua E. The solution structure of recA filaments by small angle neutron scattering. Biochimie 1991; 73:227-30. [PMID: 1883884 DOI: 10.1016/0300-9084(91)90206-g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The technique of small angle neutron scattering has been applied to study the structure in solution of recA self-polymers and various recA-DNA complexes. These results are compared with those recently obtained by other physical techniques.
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Horii T. Head to head dimer model; an alternative model for the strand exchange reaction by RecA protein of Escherichia coli. Biochimie 1991; 73:177-85. [PMID: 1883880 DOI: 10.1016/0300-9084(91)90200-k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The RecA protein of E coli promotes a strand exchange reaction in vitro which appears to be similar to homologous genetic recombination in vivo. A model for the mechanism of strand transfer reaction by RecA protein has been proposed by Howard-Flanders et al based on the assumption that the RecA monomer has two distinctive DNA binding sites both of which can bind to ssDNA as well as dsDNA. Here, I propose an alternative model based on the assumption that RecA monomer has a single domain for binding to a polynucleotide chain with a unique polarity. In addition, the model is based on a few mechanical assumptions that, in the presence of ATP, two RecA molecules form a head to head dimer as the basic binding unit to DNA, and that the binding of RecA protein to a polynucleotide chain induces a structural change of RecA protein that causes a higher state of affinity for another RecA molecule that is expressed as cooperativy. The model explains many of the biochemical capabilities of RecA protein including the polar polymerization of RecA protein on single stranded DNA and polar strand transfer of DNA by the protein as well as the formation of a joint DNA molecule in a paranemic configuration. The model also presents the energetics in the strand transfer reaction.
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Affiliation(s)
- T Horii
- Laboratory of Genetics, Department of Biology, Faculty of Science, Osaka University, Japan
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22
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Nordén B, Elvingson C, Eriksson T, Kubista M, Sjöberg B, Takahashi M, Mortensen K. Structure of a RecA-DNA complex from linear dichroism and small-angle neutron-scattering in flow-oriented solution. J Mol Biol 1990; 216:223-8. [PMID: 2254923 DOI: 10.1016/s0022-2836(05)80311-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Small-angle neutron-scattering (SANS) and ultraviolet linear dichroism (l.d.) were measured on identical samples of a RecA-double-stranded (ds) DNA complex, including cofactor adenosine 5'-O-thiotriphosphate, which were aligned by flow in two equivalent Couette devices made of niobium and silica, transparent to neutrons and to ultraviolet light, respectively. The SANS anisotropy indicates a modest orientation of the RecA-dsDNA fiber with the helix axis parallel to the flow field. By correlation with the corresponding l.d. of the DNA at the same orientation conditions, it is inferred that the DNA bases have a local orientation that is approximately perpendicular to the helix axis. By comparison with the worse orientation in single-stranded DNA-RecA, this conclusion suggests that the dsDNA in its complex with RecA is not strand separated, and may be accommodated as an essentially unperturbed, straight double helix running along the RecA polymer fiber. The SANS anisotropy is also found to support the assignment of a subsidiary intensity maximum as originating from the pitch of a helical fiber.
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Affiliation(s)
- B Nordén
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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23
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DiCapua E, Schnarr M, Ruigrok RW, Lindner P, Timmins PA. Complexes of RecA protein in solution. A study by small angle neutron scattering. J Mol Biol 1990; 214:557-70. [PMID: 2380987 DOI: 10.1016/0022-2836(90)90198-u] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RecA complexes on DNA and self-polymers were analysed by small-angle neutron scattering in solution. By Guinier analysis at small angles and by model analysis of a subsidiary peak at wider angles, we find that the filaments fall into two groups: the DNA complex in the presence of ATP gamma S, an open helix with pitch 95 A, a cross-sectional radius of gyration of 33 A and a mass per length of about six RecA units per turn, which corresponds to the state of active enzyme; and the compact form (bound to single-stranded DNA in the absence of ATP, or binding ATP gamma S in the absence of DNA, or just the protein on its own), a helical structure with pitch 70 A, cross-sectional radius of gyration 40 A and mass per length about five RecA units per turn, which corresponds to the conditions of inactive enzyme. The results are discussed in the perspective of unifying previous conflicting structural results obtained by electron microscopy.
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Affiliation(s)
- E DiCapua
- Institut Laue-Langevin, Grenoble, France
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24
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DiCapua E, Ruigrok RW, Timmins PA. Activation of recA protein: the salt-induced structural transition. J Struct Biol 1990; 104:91-6. [PMID: 2150915 DOI: 10.1016/1047-8477(90)90062-h] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Purified recA protein is induced by high salt concentrations to hydrolyse ATP even in the absence of DNA. By small angle neutron scattering we show that this salt activation results from a structural transition of the protein filament in the presence of ATP gamma S from the inactive, compact form (a helical polymer of pitch 70 A and cross-sectional radius of gyration Rc 40 A) to the open form (a helical filament of pitch 95 A and Rc 35 A, which are the same structural parameters as in the ATPase active complex with DNA and ATP), without detectable change in the degree of association. We conclude that activation of recA is due to the same structural change whether induced by the binding of DNA or by salt. Indeed, the other enzymatic activity of recA, the proteolytic cleavage of the lexA repressor, is found to be inducible by the same salt concentrations as those of the structural transition.
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Affiliation(s)
- E DiCapua
- Department of Molecular Biology, University of Edinburgh, United Kingdom
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25
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Takahashi M, Schnarr M. Investigation of RecA--polynucleotide interactions from the measurement of LexA repressor cleavage kinetics. Presence of different types of complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 183:617-22. [PMID: 2776755 DOI: 10.1111/j.1432-1033.1989.tb21091.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The proteolysis of the LexA repressor in the presence of RecA and various polynucleotides was studied by measuring the fluorescence decrease of LexA upon cleavage. The results were compared with the DNA binding of RecA to investigate the presence of multiple DNA-RecA complexes. All single-stranded polydeoxyribonucleotides (DNA) efficiently stimulated the proteolysis and the maximum activation was reached in the presence of three or four nucleotides of polynucleotide per monomer of RecA. The stimulative effect was decreased in the presence of larger amounts of poly(dA), poly(dT) or heat-denatured DNA, whereas the excess of single-stranded DNAs chemically modified with chloroacetaldehyde did not present such an inhibitory effect, despite the fact that a second DNA molecule is likely to interact with RecA as monitored by the intrinsic fluorescence of these DNA species. The complicated cleavage promotion and inhibition pattern is tentatively explained by a three-state model assuming that RecA may interact with three single-stranded DNA molecules. According to this model, occupation of the first site would be necessary and sufficient for cleavage promotion, the second site would be neutral with respect to cleavage and the occupation of the third site would inhibit LexA cleavage at least partially. Double-stranded natural DNA did not stimulate cleavage, even under conditions where RecA binds quantitatively to the DNA. No polyribonucleotides (RNA) examined showed a significant stimulative effect either, nor did they appear to interact with RecA.
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Affiliation(s)
- M Takahashi
- Institut de Biologie Moléculaire et Cellulaire du CNRS et Université Louis Pasteur, Strasbourg, France
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