1
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Tagua VG, Molina‐Henares MA, Travieso ML, Nisa‐Martínez R, Quesada JM, Espinosa‐Urgel M, Ramos‐González MI. C‐di‐GMP
and biofilm are regulated in
Pseudomonas putida
by the
CfcA
/
CfcR
two‐component system in response to salts. Environ Microbiol 2022; 24:158-178. [DOI: 10.1111/1462-2920.15891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 12/14/2021] [Accepted: 12/26/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Víctor G. Tagua
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | | | - María L. Travieso
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | - Rafael Nisa‐Martínez
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | - José Miguel Quesada
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | - Manuel Espinosa‐Urgel
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
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2
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Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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3
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Gorgel M, Bøggild A, Ulstrup JJ, Weiss MS, Müller U, Nissen P, Boesen T. Against the odds? De novo structure determination of a pilin with two cysteine residues by sulfur SAD. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1095-101. [PMID: 25945575 DOI: 10.1107/s1399004715003272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/16/2015] [Indexed: 11/11/2022]
Abstract
Exploiting the anomalous signal of the intrinsic S atoms to phase a protein structure is advantageous, as ideally only a single well diffracting native crystal is required. However, sulfur is a weak anomalous scatterer at the typical wavelengths used for X-ray diffraction experiments, and therefore sulfur SAD data sets need to be recorded with a high multiplicity. In this study, the structure of a small pilin protein was determined by sulfur SAD despite several obstacles such as a low anomalous signal (a theoretical Bijvoet ratio of 0.9% at a wavelength of 1.8 Å), radiation damage-induced reduction of the cysteines and a multiplicity of only 5.5. The anomalous signal was improved by merging three data sets from different volumes of a single crystal, yielding a multiplicity of 17.5, and a sodium ion was added to the substructure of anomalous scatterers. In general, all data sets were balanced around the threshold values for a successful phasing strategy. In addition, a collection of statistics on structures from the PDB that were solved by sulfur SAD are presented and compared with the data. Looking at the quality indicator R(anom)/R(p.i.m.), an inconsistency in the documentation of the anomalous R factor is noted and reported.
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Affiliation(s)
- Manuela Gorgel
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Andreas Bøggild
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Jakob Jensen Ulstrup
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Uwe Müller
- Macromolecular Crystallography (HZB-MX), Helmholtz Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
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4
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Graves JL, Tajkarimi M, Cunningham Q, Campbell A, Nonga H, Harrison SH, Barrick JE. Rapid evolution of silver nanoparticle resistance in Escherichia coli. Front Genet 2015; 6:42. [PMID: 25741363 PMCID: PMC4330922 DOI: 10.3389/fgene.2015.00042] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/29/2015] [Indexed: 11/16/2022] Open
Abstract
The recent exponential increase in the use of engineered nanoparticles (eNPs) means both greater intentional and unintentional exposure of eNPs to microbes. Intentional use includes the use of eNPs as biocides. Unintentional exposure results from the fact that eNPs are included in a variety of commercial products (paints, sunscreens, cosmetics). Many of these eNPs are composed of heavy metals or metal oxides such as silver, gold, zinc, titanium dioxide, and zinc oxide. It is thought that since metallic/metallic oxide NPs impact so many aspects of bacterial physiology that it will difficult for bacteria to evolve resistance to them. This study utilized laboratory experimental evolution to evolve silver nanoparticle (AgNP) resistance in the bacterium Escherichia coli (K-12 MG1655), a bacterium that does not harbor any known silver resistance elements. After 225 generations of exposure to the AgNP environment, the treatment populations demonstrated greater fitness vs. control strains as measured by optical density (OD) and colony forming units (CFU) in the presence of varying concentrations of 10 nm citrate-coated silver nanoparticles (AgNP) or silver nitrate (AgNO3). Genomic analysis shows that changes associated with AgNP resistance were already accumulating within the treatment populations by generation 100, and by generation 200 three mutations had swept to high frequency in the AgNP resistance stocks. This study indicates that despite previous claims to the contrary bacteria can easily evolve resistance to AgNPs, and this occurs by relatively simple genomic changes. These results indicate that care should be taken with regards to the use of eNPs as biocides as well as with regards to unintentional exposure of microbial communities to eNPs in waste products.
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Affiliation(s)
- Joseph L. Graves
- Department of Nanoengineering, Joint School for Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University/University of North CarolinaGreensboro, NC, USA
| | - Mehrdad Tajkarimi
- Department of Nanoscience, Joint School for Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University/University of North CarolinaGreensboro, NC, USA
| | - Quincy Cunningham
- Department of Biology, North Carolina Agricultural and Technical State UniversityGreensboro, NC, USA
| | - Adero Campbell
- Department of Biology, Bennett CollegeGreensboro, NC, USA
| | - Herve Nonga
- Student Research Opportunity Program, Michigan State UniversityEast Lansing, MI, USA
| | - Scott H. Harrison
- Department of Biology, North Carolina Agricultural and Technical State UniversityGreensboro, NC, USA
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, The University of Texas at AustinAustin, TX, USA
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5
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Zhu JY, Fu ZQ, Chen L, Xu H, Chrzas J, Rose J, Wang BC. Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1242-52. [PMID: 22948926 PMCID: PMC3489105 DOI: 10.1107/s0907444912026212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/09/2012] [Indexed: 12/22/2022]
Abstract
The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent a novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF(anom)/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R(free) = 26.8%) to 2.3 Å resolution (PDB entry 3o3k). High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R(free) = 21.4%) to 1.85 Å resolution (PDB entry 3ov8). AF1382 has a winged-helix-turn-helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1-82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.
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Affiliation(s)
- Jin-Yi Zhu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Qing Fu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Lirong Chen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Hao Xu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - John Chrzas
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - John Rose
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
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6
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Ru H, Zhao L, Ding W, Jiao L, Shaw N, Liang W, Zhang L, Hung LW, Matsugaki N, Wakatsuki S, Liu ZJ. S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:521-30. [PMID: 22525750 PMCID: PMC3335285 DOI: 10.1107/s0907444912004490] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 02/02/2012] [Indexed: 12/17/2022]
Abstract
A subset of tumour necrosis factor receptor (TNFR) superfamily members contain death domains in their cytoplasmic tails. Death receptor 6 (DR6) is one such member and can trigger apoptosis upon the binding of a ligand by its cysteine-rich domains (CRDs). The crystal structure of the ectodomain (amino acids 1-348) of human death receptor 6 (DR6) encompassing the CRD region was phased using the anomalous signal from S atoms. In order to explore the feasibility of S-SAD phasing at longer wavelengths (beyond 2.5 Å), a comparative study was performed on data collected at wavelengths of 2.0 and 2.7 Å. In spite of sub-optimal experimental conditions, the 2.7 Å wavelength used for data collection showed potential for S-SAD phasing. The results showed that the R(ano)/R(p.i.m.) ratio is a good indicator for monitoring the anomalous data quality when the anomalous signal is relatively strong, while d''/sig(d'') calculated by SHELXC is a more sensitive and stable indicator applicable for grading a wider range of anomalous data qualities. The use of the `parameter-space screening method' for S-SAD phasing resulted in solutions for data sets that failed during manual attempts. SAXS measurements on the ectodomain suggested that a dimer defines the minimal physical unit of an unliganded DR6 molecule in solution.
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Affiliation(s)
- Heng Ru
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100 049, People’s Republic of China
| | - Lixia Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Wei Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Lianying Jiao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Neil Shaw
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, People’s Republic of China
| | - Wenguang Liang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Liguo Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Li-Wei Hung
- Physics Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Naohiro Matsugaki
- Structure Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Soichi Wakatsuki
- Structure Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, People’s Republic of China
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7
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Genetic Encoding of 3-Iodo-l-Tyrosine in Escherichia coli for Single-Wavelength Anomalous Dispersion Phasing in Protein Crystallography. Structure 2009; 17:335-44. [DOI: 10.1016/j.str.2009.01.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 01/15/2009] [Accepted: 01/15/2009] [Indexed: 11/21/2022]
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