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Rasor BJ, Chirania P, Rybnicky GA, Giannone RJ, Engle NL, Tschaplinski TJ, Karim AS, Hettich RL, Jewett MC. Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods. ACS Synth Biol 2023; 12:405-418. [PMID: 36700560 DOI: 10.1021/acssynbio.2c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ70 promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.
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Affiliation(s)
- Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Payal Chirania
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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2
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Choi J, Salvail H, Groisman EA. RNA chaperone activates Salmonella virulence program during infection. Nucleic Acids Res 2021; 49:11614-11628. [PMID: 34751407 PMCID: PMC8599858 DOI: 10.1093/nar/gkab992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 11/17/2022] Open
Abstract
Organisms often harbor seemingly redundant proteins. In the bacterium Salmonella enterica serovar Typhimurium (S. Typhimurium), the RNA chaperones CspC and CspE appear to play redundant virulence roles because a mutant lacking both chaperones is attenuated, whereas mutants lacking only one exhibit wild-type virulence. We now report that CspC—but not CspE—is necessary to activate the master virulence regulator PhoP when S. Typhimurium experiences mildly acidic pH, such as inside macrophages. This CspC-dependent PhoP activation is specific to mildly acidic pH because a cspC mutant behaves like wild-type S. Typhimurium under other PhoP-activating conditions. Moreover, it is mediated by ugtL, a virulence gene required for PhoP activation inside macrophages. Purified CspC promotes ugtL translation by disrupting a secondary structure in the ugtL mRNA that occludes ugtL’s ribosome binding site. Our findings demonstrate that proteins that are seemingly redundant actually confer distinct and critical functions to the lifestyle of an organism.
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Affiliation(s)
- Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Hubert Salvail
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
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3
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Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 2021; 12:182-218. [PMID: 34499567 PMCID: PMC8632127 DOI: 10.1080/21541264.2021.1973865] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles - xenogeneic silencers and developmental regulators - and that many unrecognized potential NAPs exist in each bacterial species examined.
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Affiliation(s)
- Haley M. Amemiya
- University of Michigan Medical School, Ann Arbor, MI, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L. Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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4
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Cheng-Guang H, Gualerzi CO. The Ribosome as a Switchboard for Bacterial Stress Response. Front Microbiol 2021; 11:619038. [PMID: 33584583 PMCID: PMC7873864 DOI: 10.3389/fmicb.2020.619038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/03/2020] [Indexed: 12/29/2022] Open
Abstract
As free-living organisms, bacteria are subject to continuous, numerous and occasionally drastic environmental changes to which they respond with various mechanisms which enable them to adapt to the new conditions so as to survive. Here we describe three situations in which the ribosome and its functions represent the sensor or the target of the stress and play a key role in the subsequent cellular response. The three stress conditions which are described are those ensuing upon: a) zinc starvation; b) nutritional deprivation, and c) temperature downshift.
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5
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von König K, Kachel N, Kalbitzer HR, Kremer W. RNA and DNA Binding Epitopes of the Cold Shock Protein TmCsp from the Hyperthermophile Thermotoga maritima. Protein J 2020; 39:487-500. [PMID: 33094361 PMCID: PMC7704496 DOI: 10.1007/s10930-020-09929-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2020] [Indexed: 11/29/2022]
Abstract
Prokaryotic cold shock proteins (CSPs) are considered to play an important role in the transcriptional and translational regulation of gene expression, possibly by acting as transcription anti-terminators and “RNA chaperones”. They bind with high affinity to single-stranded nucleic acids. Here we report the binding epitope of TmCsp from Thermotoga maritima for both single-stranded DNA and RNA, using heteronuclear 2D NMR spectroscopy. At “physiological” growth temperatures of TmCsp (≥ 343 K), all oligonucleotides studied have dissociation constants between 1.6 ((dT)7) and 25.2 ((dA)7) μM as determined by tryptophan fluorescence quenching. Reduction of the temperature to 303 K leads to a pronounced increase of affinity for thymidylate (dT)7 and uridylate (rU)7 heptamers with dissociation constants of 4.0 and 10.8 nM, respectively, whereas the weak binding of TmCsp to cytidylate, adenylate, and guanylate heptamers (dC)7, (dA)7, and (dT)7 is almost unaffected by temperature. The change of affinities of TmCsp for (dT)7 and (rU)7 by approximately 3 orders of magnitude shows that it represents a cold chock sensor that switches on the cold shock reaction of the cell. A temperature dependent conformational switch of the protein is required for this action. The binding epitope on TmCsp for the ssDNA and RNA heptamers is very similar and comprises β-strands 1 and 2, the loop β1–β2 as well as the loops connecting β3 with β4 and β4 with β5. Besides the loop regions, surprisingly, mainly the RNA-binding motif RNP1 is involved in ssDNA and RNA binding, while only two amino acids, H28 and W29, of the postulated RNA-binding motif RNP2 interact with the uridylate and thymidylate homonucleotides, although a high affinity in the nanomolar range is achieved. This is in contrast to the binding properties of other CSPs or cold shock domains, where RNP1 as well as RNP2 are involved in binding. TmCsp takes up a unique position since it is the only one which possesses a tryptophan residue instead of a usually highly conserved phenylalanine or tyrosine residue at the end of RNP2. NMR titrations suggest that neither (dT)7 nor (rU)7 represent the full binding motif and that non-optimal intercalation of W29 into these oligonucleotides blocks the access of the RNP2 site to the DNA or RNA. NMR-experiments with (dA)7 suggest an interaction of W29 with the adenine ring. Full binding seems to require at least one single purine base well-positioned within a thymine- or uracil-rich stretch of nucleic acids.
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Affiliation(s)
- Konstanze von König
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany
| | - Norman Kachel
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany
| | - Hans Robert Kalbitzer
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany.
| | - Werner Kremer
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, 93040, Regensburg, Germany.
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6
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Higuchi K, Yabuki T, Ito M, Kigawa T. Cold shock proteins improve
E. coli
cell‐free synthesis in terms of soluble yields of aggregation‐prone proteins. Biotechnol Bioeng 2020; 117:1628-1639. [DOI: 10.1002/bit.27326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/05/2020] [Accepted: 03/08/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Kae Higuchi
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
| | - Takashi Yabuki
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
- SI Innovation Center, Taiyo Nippon Sanso Corporation Tama‐shi Tokyo Japan
| | - Masahiro Ito
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
| | - Takanori Kigawa
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
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7
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Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. The art of adapting to extreme environments: The model system Pseudoalteromonas. Phys Life Rev 2019; 36:137-161. [PMID: 31072789 DOI: 10.1016/j.plrev.2019.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/10/2023]
Abstract
Extremophilic microbes have adapted to thrive in ecological niches characterized by harsh chemical/physical conditions such as, for example, very low/high temperature. Living organisms inhabiting these environments have developed peculiar mechanisms to cope with extreme conditions, in such a way that they mark the chemical-physical boundaries of life on Earth. Studying such mechanisms is stimulating from a basic research viewpoint and because of biotechnological applications. Pseudoalteromonas species are a group of marine gamma-proteobacteria frequently isolated from a range of extreme environments, including cold habitats and deep-sea sediments. Since deep-sea floors constitute almost 60% of the Earth's surface and cold temperatures represent the most common of the extreme conditions, the genus Pseudoalteromonas can be considered one of the most important model systems for studying microbial adaptation. Particularly, among all Pseudoalteromonas representatives, P. haloplanktis TAC125 has recently gained a central role. This bacterium was isolated from seawater sampled along the Antarctic ice-shell and is considered one of the model organisms of cold-adapted bacteria. It is capable of thriving in a wide temperature range and it has been suggested as an alternative host for the soluble overproduction of heterologous proteins, given its ability to rapidly multiply at low temperatures. In this review, we will present an overview of the recent advances in the characterization of Pseudoalteromonas strains and, more importantly, in the understanding of their evolutionary and chemical-physical strategies to face such a broad array of extreme conditions. A particular attention will be given to systems-biology approaches in the study of the above-mentioned topics, as genome-scale datasets (e.g. genomics, proteomics, phenomics) are beginning to expand for this group of organisms. In this context, a specific section dedicated to P. haloplanktis TAC125 will be presented to address the recent efforts in the elucidation of the metabolic rewiring of the organisms in its natural environment (Antarctica).
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Affiliation(s)
- Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Pietro Tedesco
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | | | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Napoli, Italy, Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Napoli, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
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8
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Wu L, Ma L, Li X, Huang Z, Gao X. Contribution of the cold shock protein CspA to virulence in Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT PATHOLOGY 2019; 20:382-391. [PMID: 30372574 PMCID: PMC6637868 DOI: 10.1111/mpp.12763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes a damaging bacterial leaf blight disease in rice. Cold shock proteins (Csps) are highly conserved nucleic acid-binding proteins present in various bacterial genera, but relatively little is known about their functions in Xanthomonas. Herein, we identified four Csps (CspA-CspD) in the Xoo PXO99A strain. Deletion of cspA decreased cold adaptation and a few known pathogenic factors, including bacterial pathogenicity, biofilm formation and polysaccharide production. Furthermore, we performed transcriptomic and chromosome immunoprecipitation (ChIP) experiments to identify direct targets of CspA and to determine its DNA-binding sequence. Integrative data analysis revealed that CspA directly regulates two genes, PXO_RS11830 and PXO_RS01060, by binding to a conserved CCAAT sequence in the promoter region. We generated single-deletion mutants of each gene and the results indicate that both are responsible for Xanthomonas pathogenicity. In addition, quantitative real-time polymerase chain reaction and western blotting showed that CspA suppressed the expression of its direct targets. In summary, our study clarifies the characteristics of Csps in Xanthomonas and greatly advances our understanding of the mechanisms underlying the contribution of CspA to bacterial virulence.
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Affiliation(s)
- Liming Wu
- College of Plant ProtectionNanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of EducationNanjing210095China
| | - Liumin Ma
- College of Plant ProtectionNanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of EducationNanjing210095China
| | - Xi Li
- College of Plant ProtectionNanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of EducationNanjing210095China
| | - Ziyang Huang
- College of Plant ProtectionNanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of EducationNanjing210095China
| | - Xuewen Gao
- College of Plant ProtectionNanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of EducationNanjing210095China
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9
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Nemali KS, Bonin C, Dohleman FG, Stephens M, Reeves WR, Nelson DE, Castiglioni P, Whitsel JE, Sammons B, Silady RA, Anstrom D, Sharp RE, Patharkar OR, Clay D, Coffin M, Nemeth MA, Leibman ME, Luethy M, Lawson M. Physiological responses related to increased grain yield under drought in the first biotechnology-derived drought-tolerant maize. PLANT, CELL & ENVIRONMENT 2015; 38:1866-80. [PMID: 25210866 DOI: 10.1111/pce.12446] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/08/2014] [Accepted: 08/25/2014] [Indexed: 05/21/2023]
Abstract
Maize (Zea mays ssp. mays L.) is highly susceptible to drought stress. This work focused on whole-plant physiological mechanisms by which a biotechnology-derived maize event expressing bacterial cold shock protein B (CspB), MON 87460, increased grain yield under drought. Plants of MON 87460 and a conventional control (hereafter 'control') were tested in the field under well-watered (WW) and water-limited (WL) treatments imposed during mid-vegetative to mid-reproductive stages during 2009-2011. Across years, average grain yield increased by 6% in MON 87460 compared with control under WL conditions. This was associated with higher soil water content at 0.5 m depth during the treatment phase, increased ear growth, decreased leaf area, leaf dry weight and sap flow rate during silking, increased kernel number and harvest index in MON 87460 than the control. No consistent differences were observed under WW conditions. This indicates that MON 87460 acclimated better under WL conditions than the control by lowering leaf growth which decreased water use during silking, thereby eliciting lower stress under WL conditions. These physiological responses in MON 87460 under WL conditions resulted in increased ear growth during silking, which subsequently increased the kernel number, harvest index and grain yield compared to the control.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rebecca A Silady
- Biology Department, Southern Connecticut State University, New Haven, CT, 06515, USA
| | | | - Robert E Sharp
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - Osric R Patharkar
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - David Clay
- Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
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10
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Freischmidt A, Liss M, Wagner R, Kalbitzer HR, Horn G. RNA secondary structure and in vitro translation efficiency. Protein Expr Purif 2012; 82:26-31. [DOI: 10.1016/j.pep.2011.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 01/01/2023]
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11
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Expression of Escherichia coli cspA during early exponential growth at 37°C. Gene 2012; 492:382-8. [DOI: 10.1016/j.gene.2011.10.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 10/13/2011] [Accepted: 10/27/2011] [Indexed: 11/24/2022]
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12
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Sachs R, Max KE, Heinemann U, Balbach J. RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution. RNA (NEW YORK, N.Y.) 2012; 18:65-76. [PMID: 22128343 PMCID: PMC3261745 DOI: 10.1261/rna.02809212] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 08/29/2011] [Indexed: 05/26/2023]
Abstract
Bacterial cold shock proteins (CSPs) regulate the cellular response to temperature downshift. Their general principle of function involves RNA chaperoning and transcriptional antitermination. Here we present two crystal structures of cold shock protein B from Bacillus subtilis (Bs-CspB) in complex with either a hexanucleotide (5'-UUUUUU-3') or heptanucleotide (5'-GUCUUUA-3') single-stranded RNA (ssRNA). Hydrogen bonds and stacking interactions between RNA bases and aromatic sidechains characterize individual binding subsites. Additional binding subsites which are not occupied by the ligand in the crystal structure were revealed by NMR spectroscopy in solution on Bs-CspB·RNA complexes. Binding studies demonstrate that Bs-CspB associates with ssDNA as well as ssRNA with moderate sequence specificity. Varying affinities of oligonucleotides are reflected mainly in changes of the dissociation rates. The generally lower binding affinity of ssRNA compared to its ssDNA analog is attributed solely to the substitution of thymine by uracil bases in RNA.
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Affiliation(s)
- Rolf Sachs
- Fachgruppe Biophysik Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Klaas E.A. Max
- Max-Delbrück-Centrum für Molekulare Medizin Berlin-Buch, 13125 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin Berlin-Buch, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Jochen Balbach
- Fachgruppe Biophysik Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
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13
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Söderholm H, Lindström M, Somervuo P, Heap J, Minton N, Lindén J, Korkeala H. cspB encodes a major cold shock protein in Clostridium botulinum ATCC 3502. Int J Food Microbiol 2011; 146:23-30. [PMID: 21367479 DOI: 10.1016/j.ijfoodmicro.2011.01.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 12/13/2010] [Accepted: 01/23/2011] [Indexed: 11/27/2022]
Abstract
The relative expression of three cold shock protein coding genes (cspA, cspB and cspC) of Clostridium botulinum ATCC 3502 was studied with quantitative RT-PCR analysis following a cold shock shift from 37 °C to 15 °C. A significant increase in the relative expression of all three genes was observed upon the temperature downshift. To validate these findings, single-gene insertional inactivation of cspA, cspB and cspC was undertaken with the ClosTron gene knock-out system. In growth experiments, mutations in cspB or cspC, but not cspA, resulted in a cold-sensitive phenotype. No growth of the cspB mutant was observed at 15°C over a ten day period, whereas at 20 °C the growth rate was 70% lower than that of wild type strain. The growth rate of cspC mutant was 70% and 80% lower than the growth rate of the wild type strain at 15 °C and 20 °C, respectively. At 37 °C the growth of cspB mutant did not differ from, but the growth rate of cspC mutant was 30% lower than, that of the wild type strain. The cspA mutant grew somewhat faster than the wild type strain at all studied temperatures. Since the inactivation of cspB resulted in the most prominent defect in growth at low temperatures, we suggest that cspB encodes the major cold shock protein of C. botulinum ATCC 3502. Understanding the mechanisms behind cold tolerance of C. botulinum helps to evaluate the safety risks this foodborne pathogen poses in the modern food industry.
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Affiliation(s)
- H Söderholm
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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14
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Smith DP, Kitner JB, Norbeck AD, Clauss TR, Lipton MS, Schwalbach MS, Steindler L, Nicora CD, Smith RD, Giovannoni SJ. Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique. PLoS One 2010; 5:e10487. [PMID: 20463970 PMCID: PMC2864753 DOI: 10.1371/journal.pone.0010487] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/11/2010] [Indexed: 11/19/2022] Open
Abstract
Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Thus, we propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. We propose a model in which the RNA-binding activity of CspE and CspL selectively enables protein synthesis of the iron acquisition protein SfuC during transient growth-limiting episodes of iron scarcity.
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Affiliation(s)
- Daniel P. Smith
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Joshua B. Kitner
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Therese R. Clauss
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mary S. Lipton
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Michael S. Schwalbach
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Laura Steindler
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Carrie D. Nicora
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Richard D. Smith
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Stephen J. Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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15
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Morgan HP, Estibeiro P, Wear MA, Max KE, Heinemann U, Cubeddu L, Gallagher MP, Sadler PJ, Walkinshaw MD. Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach. Nucleic Acids Res 2007; 35:e75. [PMID: 17488853 PMCID: PMC1904285 DOI: 10.1093/nar/gkm040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have developed a novel DNA microarray-based approach for identification of the sequence-specificity of single-stranded nucleic-acid-binding proteins (SNABPs). For verification, we have shown that the major cold shock protein (CspB) from Bacillus subtilis binds with high affinity to pyrimidine-rich sequences, with a binding preference for the consensus sequence, 5′-GTCTTTG/T-3′. The sequence was modelled onto the known structure of CspB and a cytosine-binding pocket was identified, which explains the strong preference for a cytosine base at position 3. This microarray method offers a rapid high-throughput approach for determining the specificity and strength of ss DNA–protein interactions. Further screening of this newly emerging family of transcription factors will help provide an insight into their cellular function.
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Affiliation(s)
- Hugh P. Morgan
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Peter Estibeiro
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Martin A. Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Klaas E.A. Max
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Udo Heinemann
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Liza Cubeddu
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Maurice P. Gallagher
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Peter J. Sadler
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
- *To whom correspondence should be addressed. Tel:+44 (0) 131 650 7056; Fax: +44 (0) 131 650 7055;
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16
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Zeeb M, Max KE, Weininger U, Löw C, Sticht H, Balbach J. Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution. Nucleic Acids Res 2006; 34:4561-71. [PMID: 16956971 PMCID: PMC1636342 DOI: 10.1093/nar/gkl376] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cold shock proteins (CSP) belong to the family of single-stranded nucleic acid binding proteins with OB-fold. CSP are believed to function as 'RNA chaperones' and during anti-termination. We determined the solution structure of Bs-CspB bound to the single-stranded DNA (ssDNA) fragment heptathymidine (dT7) by NMR spectroscopy. Bs-CspB reveals an almost invariant conformation when bound to dT7 with only minor reorientations in loop beta1-beta2 and beta3-beta4 and of few aromatic side chains involved in base stacking. Binding studies of protein variants and mutated ssDNA demonstrated that Bs-CspB associates with ssDNA at almost diffusion controlled rates and low sequence specificity consistent with its biological function. A variation of the ssDNA affinity is accomplished solely by changes of the dissociation rate. 15N NMR relaxation and H/D exchange experiments revealed that binding of dT7 increases the stability of Bs-CspB and reduces the sub-nanosecond dynamics of the entire protein and especially of loop beta3-beta4.
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Affiliation(s)
| | - Klaas E.A. Max
- Max-Delbrück-Centrum für Molekulare Medizin13125 Berlin, Germany
| | | | | | - Heinrich Sticht
- Institut für Biochemie, Emil-Fischer-Zentrum, Universität Erlangen–Nürnberg91054 Erlangen, Germany
| | - Jochen Balbach
- To whom correspondence should be addressed. Tel: +49 345 55 25353; Fax: +49 345 55 27383;
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