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Hackley RK, Hwang S, Herb JT, Bhanap P, Lam K, Vreugdenhil A, Darnell CL, Pastor MM, Martin JH, Maupin-Furlow JA, Schmid AK. TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii. Mol Microbiol 2024; 121:742-766. [PMID: 38204420 PMCID: PMC11023807 DOI: 10.1111/mmi.15225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/09/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.
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Affiliation(s)
- Rylee K. Hackley
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Sungmin Hwang
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Jake T. Herb
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Preeti Bhanap
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Katie Lam
- Biology Department, Duke University, Durham, North Carolina, USA
| | | | | | | | - Johnathan H. Martin
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Amy K. Schmid
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
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2
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Hackley RK, Vreugdenhil-Hayslette A, Darnell CL, Schmid AK. A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities. PLoS Genet 2024; 20:e1011115. [PMID: 38227606 PMCID: PMC10817205 DOI: 10.1371/journal.pgen.1011115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/26/2024] [Accepted: 12/22/2023] [Indexed: 01/18/2024] Open
Abstract
Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica, to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica, TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum, activation of ppsA and repression of pykA, is absent in Har. hispanica. Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica. Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.
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Affiliation(s)
- Rylee K. Hackley
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | | | - Cynthia L. Darnell
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Amy K. Schmid
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, United States of America
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3
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Johnson CW, Schmid AK, Mankos M, Röpke R, Kerker N, Wong EK, Ogletree DF, Minor AM, Stibor A. Near-Monochromatic Tuneable Cryogenic Niobium Electron Field Emitter. Phys Rev Lett 2022; 129:244802. [PMID: 36563244 DOI: 10.1103/physrevlett.129.244802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/29/2022] [Indexed: 06/17/2023]
Abstract
Creating, manipulating, and detecting coherent electrons is at the heart of future quantum microscopy and spectroscopy technologies. Leveraging and specifically altering the quantum features of an electron beam source at low temperatures can enhance its emission properties. Here, we describe electron field emission from a monocrystalline, superconducting niobium nanotip at a temperature of 5.9 K. The emitted electron energy spectrum reveals an ultranarrow distribution down to 16 meV due to tunable resonant tunneling field emission via localized band states at a nanoprotrusion's apex and a cutoff at the sharp low-temperature Fermi edge. This is an order of magnitude lower than for conventional field emission electron sources. The self-focusing geometry of the tip leads to emission in an angle of 3.7°, a reduced brightness of 3.8×10^{8} A/(m^{2} sr V), and a stability of hours at 4.1 nA beam current and 69 meV energy width. This source will decrease the impact of lens aberration and enable new modes in low-energy electron microscopy, electron energy loss spectroscopy, and high-resolution vibrational spectroscopy.
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Affiliation(s)
- C W Johnson
- Lawrence Berkeley National Lab, Molecular Foundry, Berkeley, California 94720, USA
| | - A K Schmid
- Lawrence Berkeley National Lab, Molecular Foundry, Berkeley, California 94720, USA
| | - M Mankos
- Electron Optica Inc., Palo Alto, California 94303, USA
| | - R Röpke
- Institute of Physics and LISA+, University of Tübingen, Tübingen 72076, Germany
| | - N Kerker
- Institute of Physics and LISA+, University of Tübingen, Tübingen 72076, Germany
| | - E K Wong
- Lawrence Berkeley National Lab, Molecular Foundry, Berkeley, California 94720, USA
| | - D F Ogletree
- Lawrence Berkeley National Lab, Molecular Foundry, Berkeley, California 94720, USA
| | - A M Minor
- Lawrence Berkeley National Lab, Molecular Foundry, Berkeley, California 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
| | - A Stibor
- Lawrence Berkeley National Lab, Molecular Foundry, Berkeley, California 94720, USA
- Electron Optica Inc., Palo Alto, California 94303, USA
- Institute of Physics and LISA+, University of Tübingen, Tübingen 72076, Germany
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4
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Pastor MM, Sakrikar S, Rodriguez DN, Schmid AK. Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea. Biomolecules 2022; 12:biom12050682. [PMID: 35625610 PMCID: PMC9138242 DOI: 10.3390/biom12050682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022] Open
Abstract
Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80–90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.
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Affiliation(s)
- Mar Martinez Pastor
- Biology Department, Duke University, Durham, NC 27708, USA; (M.M.P.); (S.S.)
| | - Saaz Sakrikar
- Biology Department, Duke University, Durham, NC 27708, USA; (M.M.P.); (S.S.)
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | | | - Amy K. Schmid
- Biology Department, Duke University, Durham, NC 27708, USA; (M.M.P.); (S.S.)
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
- Correspondence: ; Tel.: +919-613-4464
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5
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Tonner PD, Darnell CL, Bushell FML, Lund PA, Schmid AK, Schmidler SC. A Bayesian non-parametric mixed-effects model of microbial growth curves. PLoS Comput Biol 2020; 16:e1008366. [PMID: 33104703 PMCID: PMC7644099 DOI: 10.1371/journal.pcbi.1008366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 11/05/2020] [Accepted: 08/30/2020] [Indexed: 11/19/2022] Open
Abstract
Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety. Traditional parametric growth curve models capture the population growth behavior through a set of summarizing parameters. However, estimation of these parameters from data is confounded by random effects such as experimental variability, batch effects or differences in experimental material. A systematic statistical method to identify and correct for such confounding effects in population growth data is not currently available. Further, our previous work has demonstrated that parametric models are insufficient to explain and predict microbial response under non-standard growth conditions. Here we develop a hierarchical Bayesian non-parametric model of population growth that identifies the latent growth behavior and response to perturbation, while simultaneously correcting for random effects in the data. This model enables more accurate estimates of the biological effect of interest, while better accounting for the uncertainty due to technical variation. Additionally, modeling hierarchical variation provides estimates of the relative impact of various confounding effects on measured population growth.
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Affiliation(s)
- Peter D. Tonner
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Biology Department, Duke University, Durham, NC, USA
| | | | - Francesca M. L. Bushell
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter A. Lund
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Amy K. Schmid
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Biology Department, Duke University, Durham, NC, USA
- Center for Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Scott C. Schmidler
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Department of Statistical Science, Duke University, Durham, USA
- Department of Computer Science, Duke University, Durham, USA
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6
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Kwon HY, Yoon HG, Lee C, Chen G, Liu K, Schmid AK, Wu YZ, Choi JW, Won C. Magnetic Hamiltonian parameter estimation using deep learning techniques. Sci Adv 2020; 6:6/39/eabb0872. [PMID: 32978161 PMCID: PMC7518863 DOI: 10.1126/sciadv.abb0872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/10/2020] [Indexed: 05/16/2023]
Abstract
Understanding spin textures in magnetic systems is extremely important to the spintronics and it is vital to extrapolate the magnetic Hamiltonian parameters through the experimentally determined spin. It can provide a better complementary link between theories and experimental results. We demonstrate deep learning can quantify the magnetic Hamiltonian from magnetic domain images. To train the deep neural network, we generated domain configurations with Monte Carlo method. The errors from the estimations was analyzed with statistical methods and confirmed the network was successfully trained to relate the Hamiltonian parameters with magnetic structure characteristics. The network was applied to estimate experimentally observed domain images. The results are consistent with the reported results, which verifies the effectiveness of our methods. On the basis of our study, we anticipate that the deep learning techniques make a bridge to connect the experimental and theoretical approaches not only in magnetism but also throughout any scientific research.
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Affiliation(s)
- H Y Kwon
- Center for Spintronics, Korea Institute of Science and Technology, Seoul 02792, South Korea.
| | - H G Yoon
- Department of Physics, Kyung Hee University, Seoul 02447, South Korea
| | - C Lee
- Department of Physics, Kyung Hee University, Seoul 02447, South Korea
| | - G Chen
- Department of Physics, University of California, Davis, Davis, CA 95616, USA
| | - K Liu
- Department of Physics, University of California, Davis, Davis, CA 95616, USA
- Physics Department, Georgetown University, Washington, DC 20057, USA
| | - A K Schmid
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Y Z Wu
- Department of Physics, State Key Laboratory of Surface Physics and Advanced Materials Laboratory, Fudan University, Shanghai 200433, China
| | - J W Choi
- Center for Spintronics, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - C Won
- Department of Physics, Kyung Hee University, Seoul 02447, South Korea.
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7
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Darnell CL, Zheng J, Wilson S, Bertoli RM, Bisson-Filho AW, Garner EC, Schmid AK. The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea. mBio 2020; 11:e01007-20. [PMID: 32788376 PMCID: PMC7439475 DOI: 10.1128/mbio.01007-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 11/24/2022] Open
Abstract
Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. Here, we use genetics, functional genomics, and quantitative imaging to identify and characterize the novel CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division through specific transcriptional control of the gene encoding FtsZ2, a putative tubulin homolog. Using time-lapse fluorescence microscopy in live cells cultivated in microfluidics devices, we further demonstrate that FtsZ2 is required for cell division but not elongation. The cdrS-ftsZ2 locus is highly conserved throughout the archaeal domain, and the central function of CdrS in regulating cell division is conserved across hypersaline adapted archaea. We propose that the CdrSL-FtsZ2 transcriptional network coordinates cell division timing with cell growth in archaea.IMPORTANCE Healthy cell growth and division are critical for individual organism survival and species long-term viability. However, it remains unknown how cells of the domain Archaea maintain a healthy cell cycle. Understanding the archaeal cell cycle is of paramount evolutionary importance given that an archaeal cell was the host of the endosymbiotic event that gave rise to eukaryotes. Here, we identify and characterize novel molecular players needed for regulating cell division in archaea. These molecules dictate the timing of cell septation but are dispensable for growth between divisions. Timing is accomplished through transcriptional control of the cell division ring. Our results shed light on mechanisms underlying the archaeal cell cycle, which has thus far remained elusive.
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Affiliation(s)
| | - Jenny Zheng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan M Bertoli
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Alexandre W Bisson-Filho
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amy K Schmid
- Biology Department, Duke University, Durham, North Carolina, USA
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
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8
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9
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Hwang S, Chavarria NE, Hackley RK, Schmid AK, Maupin-Furlow JA. Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. Int J Mol Sci 2019; 20:ijms20194784. [PMID: 31561502 PMCID: PMC6801745 DOI: 10.3390/ijms20194784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H. volcanii grown on ammonium as an abundant source of fixed nitrogen compared to l-alanine, the latter of which exemplifies an intermediate source of nitrogen that can be obtained from dead cells in natural habitats. By comparing the two growth conditions, 30 genes were found to be differentially expressed, including 16 genes associated with amino acid metabolism and transport. The gene expression profiles contributed to mapping ammonium and l-alanine usage with respect to transporters and metabolic pathways. In addition, conserved DNA motifs were identified in the putative promoter regions and transcription factors were found to be in synteny with the differentially expressed genes, leading us to propose regulons of transcriptionally co-regulated operons. This study provides insight to how H. volcanii responds to and utilizes intermediate vs. abundant sources of fixed nitrogen for growth, with implications for conserved functions in related halophilic archaea.
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Affiliation(s)
- Sungmin Hwang
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | - Nikita E Chavarria
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
- Center for Genomics and Computational Biology, Duke University, Duke University, Durham, NC 27708, USA.
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
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10
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Hackley RK, Schmid AK. Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. J Mol Biol 2019; 431:4147-4166. [PMID: 31437442 PMCID: PMC7419163 DOI: 10.1016/j.jmb.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Abstract
The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.
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Affiliation(s)
- Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA.
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11
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Zaretsky M, Darnell CL, Schmid AK, Eichler J. N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility. Front Microbiol 2019; 10:1367. [PMID: 31275283 PMCID: PMC6591318 DOI: 10.3389/fmicb.2019.01367] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022] Open
Abstract
Halobacterium salinarum are halophilic archaea that display directional swimming in response to various environmental signals, including light, chemicals and oxygen. In Hbt. salinarum, the building blocks (archaellins) of the archaeal swimming apparatus (the archaellum) are N-glycosylated. However, the physiological importance of archaellin N-glycosylation remains unclear. Here, a tetrasaccharide comprising a hexose and three hexuronic acids decorating the five archaellins was characterized by mass spectrometry. Such analysis failed to detect sulfation of the hexuronic acids, in contrast to earlier reports. To better understand the physiological significance of Hbt. salinarum archaellin N-glycosylation, a strain deleted of aglB, encoding the archaeal oligosaccharyltransferase, was generated. In this ΔaglB strain, archaella were not detected and only low levels of archaellins were released into the medium, in contrast to what occurs with the parent strain. Mass spectrometry analysis of the archaellins in ΔaglB cultures did not detect N-glycosylation. ΔaglB cells also showed a slight growth defect and were impaired for motility. Quantitative real-time PCR analysis revealed dramatically reduced transcript levels of archaellin-encoding genes in the mutant strain, suggesting that N-glycosylation is important for archaellin transcription, with downstream effects on archaellum assembly and function. Control of AglB-dependent post-translational modification of archaellins could thus reflect a previously unrecognized route for regulating Hbt. salinarum motility.
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Affiliation(s)
- Marianna Zaretsky
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheba, Israel
| | | | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC, United States.,Center for Genomics and Computational Biology, Duke University, Durham, NC, United States
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheba, Israel
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Bushell FML, Tonner PD, Jabbari S, Schmid AK, Lund PA. Synergistic Impacts of Organic Acids and pH on Growth of Pseudomonas aeruginosa: A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth. Front Microbiol 2019; 9:3196. [PMID: 30671033 PMCID: PMC6331447 DOI: 10.3389/fmicb.2018.03196] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/10/2018] [Indexed: 01/05/2023] Open
Abstract
Different weak organic acids have significant potential as topical treatments for wounds infected by opportunistic pathogens that are recalcitrant to standard treatments. These acids have long been used as bacteriostatic compounds in the food industry, and in some cases are already being used in the clinic. The effects of different organic acids vary with pH, concentration, and the specific organic acid used, but no studies to date on any opportunistic pathogens have examined the detailed interactions between these key variables in a controlled and systematic way. We have therefore comprehensively evaluated the effects of several different weak organic acids on growth of the opportunistic pathogen Pseudomonas aeruginosa. We used a semi-automated plate reader to generate growth profiles for two different strains (model laboratory strain PAO1 and clinical isolate PA1054 from a hospital burns unit) in a range of organic acids at different concentrations and pH, with a high level of replication for a total of 162,960 data points. We then compared two different modeling approaches for the interpretation of this time-resolved dataset: parametric logistic regression (with or without a component to include lag phase) vs. non-parametric Gaussian process (GP) regression. Because GP makes no prior assumptions about the nature of the growth, this method proved to be superior in cases where growth did not follow a standard sigmoid functional form, as is common when bacteria grow under stress. Acetic, propionic and butyric acids were all more detrimental to growth than the other acids tested, and although PA1054 grew better than PAO1 under non-stress conditions, this difference largely disappeared as the levels of stress increased. As expected from knowledge of how organic acids behave, their effect was significantly enhanced in combination with low pH, with this interaction being greatest in the case of propionic acid. Our approach lends itself to the characterization of combinatorial interactions between stressors, especially in cases where their impacts on growth render logistic growth models unsuitable.
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Affiliation(s)
- Francesca M. L. Bushell
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Peter D. Tonner
- Department of Biology, Duke University, Durham, NC, United States
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, United States
| | - Sara Jabbari
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- School of Mathematics, University of Birmingham, Birmingham, United Kingdom
| | - Amy K. Schmid
- Department of Biology, Duke University, Durham, NC, United States
- Center for Genomics and Computational Biology, Duke University, Durham, NC, United States
| | - Peter A. Lund
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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13
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Abstract
Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantification experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known insertion sequence (IS) elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments.
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Affiliation(s)
- Keely A Dulmage
- 1University Program in Genetics and Genomics, Duke University, Durham, NC, USA.,2Biology Department, Duke University, Durham, NC, USA
| | | | | | - Amy K Schmid
- 1University Program in Genetics and Genomics, Duke University, Durham, NC, USA.,2Biology Department, Duke University, Durham, NC, USA.,3Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
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14
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Abstract
Archaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of transcription factor proteins and their target genes. Recent developments in genetics, genomics, and computational methods used with archaeal model organisms have enabled the mapping and prediction of global GRN structures. Experimental tests of these predictions have revealed the dynamical function of GRNs in response to environmental variation. Here, we review recent progress made in this area, from investigating the mechanisms of transcriptional regulation of individual genes to small-scale subnetworks and genome-wide global networks. At each level, archaeal GRNs consist of a hybrid of bacterial, eukaryotic, and uniquely archaeal mechanisms. We discuss this theme from the perspective of the role of individual transcription factors in genome-wide regulation, how these proteins interact to compile GRN topological structures, and how these topologies lead to emergent, high-level GRN functions. We conclude by discussing how systems biology approaches are a fruitful avenue for addressing remaining challenges, such as discovering gene function and the evolution of GRNs.
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Affiliation(s)
| | - Peter D Tonner
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.,Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
| | - Cynthia L Darnell
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.,Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
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15
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McDowell IC, Manandhar D, Vockley CM, Schmid AK, Reddy TE, Engelhardt BE. Clustering gene expression time series data using an infinite Gaussian process mixture model. PLoS Comput Biol 2018; 14:e1005896. [PMID: 29337990 PMCID: PMC5786324 DOI: 10.1371/journal.pcbi.1005896] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 01/26/2018] [Accepted: 11/25/2017] [Indexed: 12/24/2022] Open
Abstract
Transcriptome-wide time series expression profiling is used to characterize the cellular response to environmental perturbations. The first step to analyzing transcriptional response data is often to cluster genes with similar responses. Here, we present a nonparametric model-based method, Dirichlet process Gaussian process mixture model (DPGP), which jointly models data clusters with a Dirichlet process and temporal dependencies with Gaussian processes. We demonstrate the accuracy of DPGP in comparison to state-of-the-art approaches using hundreds of simulated data sets. To further test our method, we apply DPGP to published microarray data from a microbial model organism exposed to stress and to novel RNA-seq data from a human cell line exposed to the glucocorticoid dexamethasone. We validate our clusters by examining local transcription factor binding and histone modifications. Our results demonstrate that jointly modeling cluster number and temporal dependencies can reveal shared regulatory mechanisms. DPGP software is freely available online at https://github.com/PrincetonUniversity/DP_GP_cluster.
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Affiliation(s)
- Ian C. McDowell
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Dinesh Manandhar
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Christopher M. Vockley
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics & Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Amy K. Schmid
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Timothy E. Reddy
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics & Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Barbara E. Engelhardt
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey, United States of America
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16
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Martinez-Pastor M, Lancaster WA, Tonner PD, Adams MWW, Schmid AK. A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea. Nucleic Acids Res 2017; 45:9990-10001. [PMID: 28973467 PMCID: PMC5737653 DOI: 10.1093/nar/gkx662] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023] Open
Abstract
Iron is required for key metabolic processes but is toxic in excess. This circumstance forces organisms across the tree of life to tightly regulate iron homeostasis. In hypersaline lakes dominated by archaeal species, iron levels are extremely low and subject to environmental change; however, mechanisms regulating iron homeostasis in archaea remain unclear. In previous work, we demonstrated that two transcription factors (TFs), Idr1 and Idr2, collaboratively regulate aspects of iron homeostasis in the model species Halobacterium salinarum. Here we show that Idr1 and Idr2 are part of an extended regulatory network of four TFs of the bacterial DtxR family that maintains intracellular iron balance. We demonstrate that each TF directly regulates at least one of the other DtxR TFs at the level of transcription. Dynamical modeling revealed interlocking positive feedback loop architecture, which exhibits bistable or oscillatory network dynamics depending on iron availability. TF knockout mutant phenotypes are consistent with model predictions. Together, our results support that this network regulates iron homeostasis despite variation in extracellular iron levels, consistent with dynamical properties of interlocking feedback architecture in eukaryotes. These results suggest that archaea use bacterial-type TFs in a eukaryotic regulatory network topology to adapt to harsh environments.
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Affiliation(s)
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Peter D Tonner
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA.,Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
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17
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Tonner PD, Darnell CL, Engelhardt BE, Schmid AK. Detecting differential growth of microbial populations with Gaussian process regression. Genome Res 2017; 27:320-333. [PMID: 27864351 PMCID: PMC5287237 DOI: 10.1101/gr.210286.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/15/2016] [Indexed: 02/06/2023]
Abstract
Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist to capture microbial population growth measurements. However, current models are designed to quantify growth under conditions for which growth has a specific functional form. Extensions to these models are required to quantify the effects of perturbations, which often exhibit nonstandard growth curves. Rather than assume specific functional forms for experimental perturbations, we developed a general and robust model of microbial population growth curves using Gaussian process (GP) regression. GP regression modeling of high-resolution time-series growth data enables accurate quantification of population growth and allows explicit control of effects from other covariates such as genetic background. This framework substantially outperforms commonly used microbial population growth models, particularly when modeling growth data from environmentally stressed populations. We apply the GP growth model and develop statistical tests to quantify the differential effects of environmental perturbations on microbial growth across a large compendium of genotypes in archaea and yeast. This method accurately identifies known transcriptional regulators and implicates novel regulators of growth under standard and stress conditions in the model archaeal organism Halobacterium salinarum For yeast, our method correctly identifies known phenotypes for a diversity of genetic backgrounds under cyclohexamide stress and also detects previously unidentified oxidative stress sensitivity across a subset of strains. Together, these results demonstrate that the GP models are interpretable, recapitulating biological knowledge of growth response while providing new insights into the relevant parameters affecting microbial population growth.
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Affiliation(s)
- Peter D Tonner
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
- Biology Department, Duke University, Durham, North Carolina 27708, USA
| | - Cynthia L Darnell
- Biology Department, Duke University, Durham, North Carolina 27708, USA
| | - Barbara E Engelhardt
- Computer Science Department, Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey 08540, USA
| | - Amy K Schmid
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
- Biology Department, Duke University, Durham, North Carolina 27708, USA
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18
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Vu AD, Coraux J, Chen G, N'Diaye AT, Schmid AK, Rougemaille N. Unconventional magnetisation texture in graphene/cobalt hybrids. Sci Rep 2016; 6:24783. [PMID: 27114039 PMCID: PMC4844999 DOI: 10.1038/srep24783] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 04/06/2016] [Indexed: 11/15/2022] Open
Abstract
Magnetic domain structure and spin-dependent reflectivity measurements on cobalt thin films intercalated at the graphene/Ir(111) interface are investigated using spin-polarised low-energy electron microscopy. We find that graphene-covered cobalt films have surprising magnetic properties. Vectorial imaging of magnetic domains reveals an unusually gradual thickness-dependent spin reorientation transition, in which magnetisation rotates from out-of-the-film plane to the in-plane direction by less than 10° per cobalt monolayer. During this transition, cobalt films have a meandering spin texture, characterised by a complex, three-dimensional, wavy magnetisation pattern. In addition, spectroscopy measurements suggest that the electronic band structure of the unoccupied states is essentially spin-independent already a few electron-Volts above the vacuum level. These properties strikingly differ from those of pristine cobalt films and could open new prospects in surface magnetism.
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Affiliation(s)
- A D Vu
- CNRS, Inst NEEL, F-38000 Grenoble, France.,Univ. Grenoble Alpes, Inst NEEL, F-38000 Grenoble, France
| | - J Coraux
- CNRS, Inst NEEL, F-38000 Grenoble, France.,Univ. Grenoble Alpes, Inst NEEL, F-38000 Grenoble, France
| | - G Chen
- NCEM, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - A T N'Diaye
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - A K Schmid
- NCEM, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - N Rougemaille
- CNRS, Inst NEEL, F-38000 Grenoble, France.,Univ. Grenoble Alpes, Inst NEEL, F-38000 Grenoble, France
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19
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Kulp AJ, Sun B, Ai T, Manning AJ, Orench-Rivera N, Schmid AK, Kuehn MJ. Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli. PLoS One 2015; 10:e0139200. [PMID: 26406465 PMCID: PMC4583269 DOI: 10.1371/journal.pone.0139200] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/10/2015] [Indexed: 12/31/2022] Open
Abstract
The production of outer membrane vesicles by Gram-negative bacteria has been well documented; however, the mechanism behind the biogenesis of these vesicles remains unclear. Here a high-throughput experimental method and systems-scale analysis was conducted to determine vesiculation values for the whole genome knockout library of Escherichia coli mutant strains (Keio collection). The resultant dataset quantitatively recapitulates previously observed phenotypes and implicates nearly 150 new genes in the process of vesiculation. Gene functional and biochemical pathway analyses suggest that mutations that truncate outer membrane structures such as lipopolysaccharide and enterobacterial common antigen lead to hypervesiculation, whereas mutants in oxidative stress response pathways result in lower levels. This study expands and refines the current knowledge regarding the cellular pathways required for outer membrane vesiculation in E. coli.
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Affiliation(s)
- Adam J. Kulp
- Dept. of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, United States of America
| | - Bo Sun
- Dept. of Biology, Duke University, Durham, NC, 27708, United States of America
| | - Teresa Ai
- Dept. of Biology, Duke University, Durham, NC, 27708, United States of America
| | - Andrew J. Manning
- Dept. of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States of America
| | - Nichole Orench-Rivera
- Dept. of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States of America
| | - Amy K. Schmid
- Dept. of Biology, Duke University, Durham, NC, 27708, United States of America
- Duke Center for Systems Biology, Duke University, Durham, NC, 27708, United States of America
- * E-mail:
| | - Meta J. Kuehn
- Dept. of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, United States of America
- Dept. of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States of America
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20
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Todor H, Gooding J, Ilkayeva OR, Schmid AK. Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences. PLoS One 2015; 10:e0135693. [PMID: 26284786 PMCID: PMC4540570 DOI: 10.1371/journal.pone.0135693] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/24/2015] [Indexed: 02/04/2023] Open
Abstract
Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in their promoters. This interaction is abolished in the presence of glucose. Although much is known about the effects of TrmB at the transcriptional level, it remains unclear whether and to what extent changes in mRNA levels directly affect metabolite levels. In order to address this question, here we performed a high-resolution metabolite profiling time course during a change in nutrients using a combination of targeted and untargeted methods in wild-type and ΔtrmB strain backgrounds. We found that TrmB-mediated transcriptional changes resulted in widespread and significant changes to metabolite levels across the metabolic network. Additionally, the pattern of growth complementation using various purines suggests that the mis-regulation of gluconeogenesis in the ΔtrmB mutant strain in the absence of glucose results in low phosphoribosylpyrophosphate (PRPP) levels. We confirmed these low PRPP levels using a quantitative mass spectrometric technique and found that they are associated with a metabolic block in de novo purine synthesis, which is partially responsible for the growth defect of the ΔtrmB mutant strain in the absence of glucose. In conclusion, we show how transcriptional regulation of metabolism affects metabolite levels and ultimately, phenotypes.
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Affiliation(s)
- Horia Todor
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Jessica Gooding
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Olga R. Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Amy K. Schmid
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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21
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Darnell CL, Schmid AK. Systems biology approaches to defining transcription regulatory networks in halophilic archaea. Methods 2015; 86:102-14. [PMID: 25976837 DOI: 10.1016/j.ymeth.2015.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 12/31/2022] Open
Abstract
To survive complex and changing environmental conditions, microorganisms use gene regulatory networks (GRNs) composed of interacting regulatory transcription factors (TFs) to control the timing and magnitude of gene expression. Genome-wide datasets; such as transcriptomics and protein-DNA interactions; and experiments such as high throughput growth curves; facilitate the construction of GRNs and provide insight into TF interactions occurring under stress. Systems biology approaches integrate these datasets into models of GRN architecture as well as statistical and/or dynamical models to understand the function of networks occurring in cells. Previously, these types of studies have focused on traditional model organisms (e.g. Escherichia coli, yeast). However, recent advances in archaeal genetics and other tools have enabled a systems approach to understanding GRNs in these relatively less studied archaeal model organisms. In this report, we outline a systems biology workflow for generating and integrating data focusing on the TF regulator. We discuss experimental design, outline the process of data collection, and provide the tools required to produce high confidence regulons for the TFs of interest. We provide a case study as an example of this workflow, describing the construction of a GRN centered on multi-TF coordinate control of gene expression governing the oxidative stress response in the hypersaline-adapted archaeon Halobacterium salinarum.
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Affiliation(s)
| | - Amy K Schmid
- Biology Department, Duke University, Durham, NC 27708, USA; Center for Systems Biology, Duke University, Durham, NC 27708, USA.
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22
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Tonner PD, Pittman AMC, Gulli JG, Sharma K, Schmid AK. A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea. PLoS Genet 2015; 11:e1004912. [PMID: 25569531 PMCID: PMC4287449 DOI: 10.1371/journal.pgen.1004912] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/20/2014] [Indexed: 12/21/2022] Open
Abstract
Networks of interacting transcription factors are central to the regulation of cellular responses to abiotic stress. Although the architecture of many such networks has been mapped, their dynamic function remains unclear. Here we address this challenge in archaea, microorganisms possessing transcription factors that resemble those of both eukaryotes and bacteria. Using genome-wide DNA binding location analysis integrated with gene expression and cell physiological data, we demonstrate that a bacterial-type transcription factor (TF), called RosR, and five TFIIB proteins, homologs of eukaryotic TFs, combinatorially regulate over 100 target genes important for the response to extremely high levels of peroxide. These genes include 20 other transcription factors and oxidative damage repair genes. RosR promoter occupancy is surprisingly dynamic, with the pattern of target gene expression during the transition from rapid growth to stress correlating strongly with the pattern of dynamic binding. We conclude that a hierarchical regulatory network orchestrated by TFs of hybrid lineage enables dynamic response and survival under extreme stress in archaea. This raises questions regarding the evolutionary trajectory of gene networks in response to stress. Complex circuits of genes rather than a single gene underlie many important processes such as disease, development, and cellular damage repair. Although the wiring of many of these circuits has been mapped, how circuits operate in real time to carry out their functions is poorly understood. Here we address these questions by investigating the function of a gene circuit that responds to reactive oxygen species damage in archaea, microorganisms that represent the third domain of life. Members of this domain of life are excellent models for investigating the function and evolution of gene circuits. Components of archaeal regulatory machinery driving gene circuits resemble those of both bacteria and eukaryotes. Here we demonstrate that regulatory proteins of hybrid ancestry collaborate to control the expression of over 100 genes whose products repair cellular damage. Among these are other regulatory proteins, setting up a stepwise hierarchical circuit that controls damage repair. Regulation is dynamic, with gene targets showing immediate response to damage and restoring normal cellular functions soon thereafter. This study demonstrates how strong environmental forces such as stress may have shaped the wiring and dynamic function of gene circuits, raising important questions regarding how circuits originated over evolutionary time.
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Affiliation(s)
- Peter D. Tonner
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | | | - Jordan G. Gulli
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Kriti Sharma
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Amy K. Schmid
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina, United States of America
- Biology Department, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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23
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Todor H, Dulmage K, Gillum N, Bain JR, Muehlbauer MJ, Schmid AK. A transcription factor links growth rate and metabolism in the hypersaline adapted archaeon
H
alobacterium salinarum. Mol Microbiol 2014; 93:1172-82. [DOI: 10.1111/mmi.12726] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Horia Todor
- Department of Biology Duke University Durham NC 27708 USA
| | - Keely Dulmage
- Department of Biology Duke University Durham NC 27708 USA
- University Program in Genetics and Genomics Duke University Durham NC 27708 USA
| | | | - James R. Bain
- Sarah W. Stedman Nutrition and Metabolism Center Duke Molecular Physiology Institute Durham NC 27710 USA
| | - Michael J. Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center Duke Molecular Physiology Institute Durham NC 27710 USA
| | - Amy K. Schmid
- Department of Biology Duke University Durham NC 27708 USA
- University Program in Genetics and Genomics Duke University Durham NC 27708 USA
- Center for Systems Biology Duke University Durham NC 27708 USA
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24
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Mankos M, Shadman K, Persson HHJ, N'Diaye AT, Schmid AK, Davis RW. A novel low energy electron microscope for DNA sequencing and surface analysis. Ultramicroscopy 2014; 145:36-49. [PMID: 24524867 DOI: 10.1016/j.ultramic.2014.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/09/2013] [Accepted: 01/08/2014] [Indexed: 11/28/2022]
Abstract
Monochromatic, aberration-corrected, dual-beam low energy electron microscopy (MAD-LEEM) is a novel technique that is directed towards imaging nanostructures and surfaces with sub-nanometer resolution. The technique combines a monochromator, a mirror aberration corrector, an energy filter, and dual beam illumination in a single instrument. The monochromator reduces the energy spread of the illuminating electron beam, which significantly improves spectroscopic and spatial resolution. Simulation results predict that the novel aberration corrector design will eliminate the second rank chromatic and third and fifth order spherical aberrations, thereby improving the resolution into the sub-nanometer regime at landing energies as low as one hundred electron-Volts. The energy filter produces a beam that can extract detailed information about the chemical composition and local electronic states of non-periodic objects such as nanoparticles, interfaces, defects, and macromolecules. The dual flood illumination eliminates charging effects that are generated when a conventional LEEM is used to image insulating specimens. A potential application for MAD-LEEM is in DNA sequencing, which requires high resolution to distinguish the individual bases and high speed to reduce the cost. The MAD-LEEM approach images the DNA with low electron impact energies, which provides nucleobase contrast mechanisms without organometallic labels. Furthermore, the micron-size field of view when combined with imaging on the fly provides long read lengths, thereby reducing the demand on assembling the sequence. Experimental results from bulk specimens with immobilized single-base oligonucleotides demonstrate that base specific contrast is available with reflected, photo-emitted, and Auger electrons. Image contrast simulations of model rectangular features mimicking the individual nucleotides in a DNA strand have been developed to translate measurements of contrast on bulk DNA to the detectability of individual DNA bases in a sequence.
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Affiliation(s)
- M Mankos
- Electron Optica Inc., 1000 Elwell Court ♯110, Palo Alto, CA 94303, USA.
| | - K Shadman
- Electron Optica Inc., 1000 Elwell Court ♯110, Palo Alto, CA 94303, USA
| | - H H J Persson
- Stanford Genome Technology Center, Stanford University School of Medicine, 855 California Avenue, Palo Alto, CA 94304, USA
| | - A T N'Diaye
- Electron Optica Inc., 1000 Elwell Court ♯110, Palo Alto, CA 94303, USA; NCEM, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - A K Schmid
- NCEM, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - R W Davis
- Stanford Genome Technology Center, Stanford University School of Medicine, 855 California Avenue, Palo Alto, CA 94304, USA
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25
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Abstract
Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challenge in systems biology. Previous work characterized TrmB as a global metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ∼100 metabolic enzyme-coding gene targets. Using a dynamic perturbation approach, we elucidate the topology of the TrmB metabolic GRN in the model archaeon Halobacterium salinarum. Clustering of dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes but cooperates with various regulators to control peripheral metabolic pathways. Using a dynamical model, we predict gene expression patterns for some TrmB-dependent promoters and infer secondary regulators for others. Our data suggest feed-forward gene regulatory topology for cobalamin biosynthesis. In contrast, purine biosynthesis appears to require TrmB-independent regulators. We conclude that TrmB is an important component for mediating metabolic modularity, integrating nutrient status and regulating gene expression dynamics alone and in concert with secondary regulators.
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Affiliation(s)
- Horia Todor
- Department of Biology, Duke University, Durham, NC 27708, USA and Center for Systems Biology, Institute for Genome Science and Policy, Duke University, Durham, NC 27708, USA
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26
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Chen G, Zhu J, Quesada A, Li J, N'Diaye AT, Huo Y, Ma TP, Chen Y, Kwon HY, Won C, Qiu ZQ, Schmid AK, Wu YZ. Novel chiral magnetic domain wall structure in Fe/Ni/Cu(001) films. Phys Rev Lett 2013; 110:177204. [PMID: 23679766 DOI: 10.1103/physrevlett.110.177204] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Indexed: 06/02/2023]
Abstract
Using spin-polarized low energy electron microscopy, we discovered a new type of domain wall structure in perpendicularly magnetized Fe/Ni bilayers grown epitaxially on Cu(100). Specifically, we observed unexpected Néel-type walls with fixed chirality in the magnetic stripe phase. Furthermore, we find that the chirality of the domain walls is determined by the film growth order with the chirality being right handed in Fe/Ni bilayers and left handed in Ni/Fe bilayers, suggesting that the underlying mechanism is the Dzyaloshinskii-Moriya interaction at the film interfaces. Our observations may open a new route to control chiral spin structures using interfacial engineering in transition metal heterostructures.
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Affiliation(s)
- G Chen
- Department of Physics, State Key Laboratory of Surface Physics, Center for Spintronic Devices and Applications, Fudan University, Shanghai 200433, People's Republic of China
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Aldous JD, Burrows CW, Maskery I, Brewer MS, Hase TPA, Duffy JA, Lees MR, Sánchez-Hanke C, Decoster T, Theis W, Quesada A, Schmid AK, Bell GR. Depth-dependent magnetism in epitaxial MnSb thin films: effects of surface passivation and cleaning. J Phys Condens Matter 2012; 24:146002. [PMID: 22418020 DOI: 10.1088/0953-8984/24/14/146002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Depth-dependent magnetism in MnSb(0001) epitaxial films has been studied by combining experimental methods with different surface specificities: polarized neutron reflectivity, x-ray magnetic circular dichroism (XMCD), x-ray resonant magnetic scattering and spin-polarized low energy electron microscopy (SPLEEM). A native oxide ∼4.5 nm thick covers air-exposed samples which increases the film's coercivity. HCl etching efficiently removes this oxide and in situ surface treatment of etched samples enables surface magnetic contrast to be observed in SPLEEM. A thin Sb capping layer prevents oxidation and preserves ferromagnetism throughout the MnSb film. The interpretation of Mn L(3,2) edge XMCD data is discussed.
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Affiliation(s)
- J D Aldous
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
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Abstract
Because iron toxicity and deficiency are equally life threatening, maintaining intracellular iron levels within a narrow optimal range is critical for nearly all known organisms. However, regulatory mechanisms that establish homeostasis are not well understood in organisms that dwell in environments at the extremes of pH, temperature, and salinity. Under conditions of limited iron, the extremophile Halobacterium salinarum, a salt-loving archaeon, mounts a specific response to scavenge iron for growth. We have identified and characterized the role of two transcription factors (TFs), Idr1 and Idr2, in regulating this important response. An integrated systems analysis of TF knockout gene expression profiles and genome-wide binding locations in the presence and absence of iron has revealed that these TFs operate collaboratively to maintain iron homeostasis. In the presence of iron, Idr1 and Idr2 bind near each other at 24 loci in the genome, where they are both required to repress some genes. By contrast, Idr1 and Idr2 are both necessary to activate other genes in a putative a feed forward loop. Even at loci bound independently, the two TFs target different genes with similar functions in iron homeostasis. We discuss conserved and unique features of the Idr1-Idr2 system in the context of similar systems in organisms from other domains of life.
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Affiliation(s)
- Amy K Schmid
- Duke University, Department of Biology and Institute for Genome Sciences and Policy, Center for Systems Biology, Durham, NC 27708, USA.
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Jozwiak C, Graf J, Lebedev G, Andresen N, Schmid AK, Fedorov AV, El Gabaly F, Wan W, Lanzara A, Hussain Z. A high-efficiency spin-resolved photoemission spectrometer combining time-of-flight spectroscopy with exchange-scattering polarimetry. Rev Sci Instrum 2010; 81:053904. [PMID: 20515152 DOI: 10.1063/1.3427223] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We describe a spin-resolved electron spectrometer capable of uniquely efficient and high energy resolution measurements. Spin analysis is obtained through polarimetry based on low-energy exchange scattering from a ferromagnetic thin-film target. This approach can achieve a similar analyzing power (Sherman function) as state-of-the-art Mott scattering polarimeters, but with as much as 100 times improved efficiency due to increased reflectivity. Performance is further enhanced by integrating the polarimeter into a time-of-flight (TOF) based energy analysis scheme with a precise and flexible electrostatic lens system. The parallel acquisition of a range of electron kinetic energies afforded by the TOF approach results in an order of magnitude (or more) increase in efficiency compared to hemispherical analyzers. The lens system additionally features a 90 degrees bandpass filter, which by removing unwanted parts of the photoelectron distribution allows the TOF technique to be performed at low electron drift energy and high energy resolution within a wide range of experimental parameters. The spectrometer is ideally suited for high-resolution spin- and angle-resolved photoemission spectroscopy (spin-ARPES), and initial results are shown. The TOF approach makes the spectrometer especially ideal for time-resolved spin-ARPES experiments.
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Affiliation(s)
- C Jozwiak
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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Santos B, Loginova E, Mascaraque A, Schmid AK, McCarty KF, de la Figuera J. Structure and magnetism in ultrathin iron oxides characterized by low energy electron microscopy. J Phys Condens Matter 2009; 21:314011. [PMID: 21828572 DOI: 10.1088/0953-8984/21/31/314011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have grown epitaxial films a few atomic layers thick of iron oxides on ruthenium. We characterize the growth by low energy electron microscopy. Using selected-area diffraction and intensity-versus-voltage spectroscopy, we detect two distinct phases which are assigned as wüstite and magnetite. Spin-polarized low energy electron microscopy reveals magnetic domain patterns in the magnetite phase at room temperature.
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Affiliation(s)
- B Santos
- Universidad Autónoma de Madrid, Madrid 28049, Spain. Instituto de Química-Física 'Rocasolano', CSIC, Madrid 28006, Spain
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El Gabaly F, Bartelt NC, Schmid AK. Preparing arrays of large atomically flat regions on single crystal substrates. J Phys Condens Matter 2009; 21:314019. [PMID: 21828580 DOI: 10.1088/0953-8984/21/31/314019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report a simple and general procedure to create arrays of atomically flat terraces on single crystal surfaces. Facets of three-dimensional (3D) metal islands formed after hetero-epitaxial growth are often flat and, through annealing or growth at elevated temperature, the formation of rather large (micron-scale) atomically flat-top facets can be promoted. We find that the step-free nature of top facets on such islands can be transferred to the substrate surface through room-temperature ion-sputter etching, followed by an annealing step. We use low-energy electron microscopy (LEEM) and Auger electron spectroscopy (AES) for in situ monitoring of the process steps while fabricating arrays of step-free surface regions on W(110), Ru(0001), Cu(100), and Fe(100) single crystals.
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Affiliation(s)
- F El Gabaly
- Sandia National Laboratories, Livermore, CA 94550, USA. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol 2009; 5:282. [PMID: 19536205 PMCID: PMC2710871 DOI: 10.1038/msb.2009.40] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 05/15/2009] [Indexed: 01/02/2023] Open
Abstract
During evolution, enzyme-coding genes are acquired and/or replaced through lateral gene transfer and compiled into metabolic pathways. Gene regulatory networks evolve to fine tune biochemical fluxes through such metabolic pathways, enabling organisms to acclimate to nutrient fluctuations in a competitive environment. Here, we demonstrate that a single TrmB family transcription factor in Halobacterium salinarum NRC-1 globally coordinates functionally linked enzymes of diverse phylogeny in response to changes in carbon source availability. Specifically, during nutritional limitation, TrmB binds a cis-regulatory element to activate or repress 113 promoters of genes encoding enzymes in diverse metabolic pathways. By this mechanism, TrmB coordinates the expression of glycolysis, TCA cycle, and amino-acid biosynthesis pathways with the biosynthesis of their cognate cofactors (e.g. purine and thiamine). Notably, the TrmB-regulated metabolic network includes enzyme-coding genes that are uniquely archaeal as well as those that are conserved across all three domains of life. Simultaneous analysis of metabolic and gene regulatory network architectures suggests an ongoing process of co-evolution in which TrmB integrates the expression of metabolic enzyme-coding genes of diverse origins.
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Affiliation(s)
- Amy K Schmid
- Institute for Systems Biology, Seattle, WA 98103-8904, USA
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Kisielowski C, Freitag B, Bischoff M, van Lin H, Lazar S, Knippels G, Tiemeijer P, van der Stam M, von Harrach S, Stekelenburg M, Haider M, Uhlemann S, Müller H, Hartel P, Kabius B, Miller D, Petrov I, Olson EA, Donchev T, Kenik EA, Lupini AR, Bentley J, Pennycook SJ, Anderson IM, Minor AM, Schmid AK, Duden T, Radmilovic V, Ramasse QM, Watanabe M, Erni R, Stach EA, Denes P, Dahmen U. Detection of single atoms and buried defects in three dimensions by aberration-corrected electron microscope with 0.5-A information limit. Microsc Microanal 2008; 14:469-477. [PMID: 18793491 DOI: 10.1017/s1431927608080902] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability of electron microscopes to analyze all the atoms in individual nanostructures is limited by lens aberrations. However, recent advances in aberration-correcting electron optics have led to greatly enhanced instrument performance and new techniques of electron microscopy. The development of an ultrastable electron microscope with aberration-correcting optics and a monochromated high-brightness source has significantly improved instrument resolution and contrast. In the present work, we report information transfer beyond 50 pm and show images of single gold atoms with a signal-to-noise ratio as large as 10. The instrument's new capabilities were exploited to detect a buried Sigma3 {112} grain boundary and observe the dynamic arrangements of single atoms and atom pairs with sub-angstrom resolution. These results mark an important step toward meeting the challenge of determining the three-dimensional atomic-scale structure of nanomaterials.
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Affiliation(s)
- C Kisielowski
- National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, One Cyclotron Rd., Berkeley, CA 94720, USA
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Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res 2008; 7:3755-64. [PMID: 18652504 DOI: 10.1021/pr800031f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.
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Affiliation(s)
- Phu T Van
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
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Bare JC, Shannon PT, Schmid AK, Baliga NS. The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics 2007; 8:456. [PMID: 18021453 PMCID: PMC2211326 DOI: 10.1186/1471-2105-8-456] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2007] [Accepted: 11/19/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. RESULTS The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. CONCLUSION The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.
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Affiliation(s)
- J Christopher Bare
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA.
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36
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Rougemaille N, El Gabaly F, Stumpf R, Schmid AK, Thürmer K, Bartelt NC, de la Figuera J. Labyrinthine island growth during Pd/Ru(0001) heteroepitaxy. Phys Rev Lett 2007; 99:106101. [PMID: 17930397 DOI: 10.1103/physrevlett.99.106101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2007] [Indexed: 05/25/2023]
Abstract
Using low energy electron microscopy we observe that Pd deposited on Ru only attaches to small sections of the atomic step edges surrounding Pd islands. This causes a novel epitaxial growth mode in which islands advance in a snakelike motion, giving rise to labyrinthine patterns. Based on density functional theory together with scanning tunneling microscopy and low energy electron microscopy we propose that this growth mode is caused by a surface alloy forming around growing islands. This alloy gradually reduces step attachment rates, resulting in an instability that favors adatom attachment at fast advancing step sections.
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Affiliation(s)
- N Rougemaille
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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37
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Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS. The anatomy of microbial cell state transitions in response to oxygen. Genome Res 2007; 17:1399-413. [PMID: 17785531 PMCID: PMC1987344 DOI: 10.1101/gr.6728007] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Adjustment of physiology in response to changes in oxygen availability is critical for the survival of all organisms. However, the chronology of events and the regulatory processes that determine how and when changes in environmental oxygen tension result in an appropriate cellular response is not well understood at a systems level. Therefore, transcriptome, proteome, ATP, and growth changes were analyzed in a halophilic archaeon to generate a temporal model that describes the cellular events that drive the transition between the organism's two opposing cell states of anoxic quiescence and aerobic growth. According to this model, upon oxygen influx, an initial burst of protein synthesis precedes ATP and transcription induction, rapidly driving the cell out of anoxic quiescence, culminating in the resumption of growth. This model also suggests that quiescent cells appear to remain actively poised for energy production from a variety of different sources. Dynamic temporal analysis of relationships between transcription and translation of key genes suggests several important mechanisms for cellular sustenance under anoxia as well as specific instances of post-transcriptional regulation.
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Affiliation(s)
- Amy K. Schmid
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | - David J. Reiss
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | - Amardeep Kaur
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | - Min Pan
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | - Nichole King
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | - Phu T. Van
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | - Laura Hohmann
- Institute for Systems Biology, Seattle, Washington 98103, USA
| | - Daniel B. Martin
- Institute for Systems Biology, Seattle, Washington 98103, USA
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington 98103, USA
- Corresponding author.E-mail ; fax (206) 732-1299
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Wu YZ, Schmid AK, Qiu ZQ. Spin-dependent quantum interference from epitaxial MgO thin films on Fe(001). Phys Rev Lett 2006; 97:217205. [PMID: 17155772 DOI: 10.1103/physrevlett.97.217205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Indexed: 05/12/2023]
Abstract
Spin-dependent electron reflection from MgO thin films grown on Fe(001) was measured using spin-polarized low energy electron microscopy. The electron reflectivity exhibits quantum interference from which two MgO energy bands with Delta1 symmetry were determined in experiment. We found that a bulklike MgO energy gap is fully established for MgO film thicker than 3 atomic monolayers and that the electron reflectivity from the MgO/Fe interface exhibits a spin-dependent amplitude and a spin-independent phase change.
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Affiliation(s)
- Y Z Wu
- Surface Physics Laboratory (National Key Laboratory), Fudan University, Shanghai 200433, China.
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Rothfuss H, Lara JC, Schmid AK, Lidstrom ME. Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1. Microbiology (Reading) 2006; 152:2779-2787. [PMID: 16946272 DOI: 10.1099/mic.0.28971-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The potential functions have been investigated of two proteins in Deinococcus radiodurans R1 predicted to be involved in the maintenance and integrity of the S layer: the hexagonally packed intermediate (Hpi) protein, and SlpA (DR2577), a homologue of an S-layer SlpA protein in Thermus thermophilus. Deletion of the hpi gene had little effect on the structure of the cell envelope or on shear- or solvent-induced stress responses. However, deletion of the slpA gene caused substantial alterations in cell envelope structure, and a significant defect in resistance to solvent and shear stresses compared to the wild-type. Ultrastructural analysis of slpA mutant cells indicated loss of much of the outer Hpi protein carbohydrate coat, the ‘pink envelope’, and the membrane-like backing layer. Together these results suggest that the SlpA protein may be involved in attachment of the Hpi surface layer to the inner cell envelope, and that SlpA may play an important role in the maintenance of cell envelope integrity in D. radiodurans.
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Affiliation(s)
- Heather Rothfuss
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jimmie C Lara
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Mary E Lidstrom
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
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Spiecker E, Schmid AK, Minor AM, Dahmen U, Hollensteiner S, Jäger W. Self-assembled nanofold network formation on layered crystal surfaces during metal intercalation. Phys Rev Lett 2006; 96:086401. [PMID: 16606202 DOI: 10.1103/physrevlett.96.086401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Indexed: 05/08/2023]
Abstract
We study the formation of planar network nanostructures, which develop during metal deposition on initially smooth surfaces of layered compounds. Using in situ low-energy electron microscopy for dynamic observation and high-resolution transmission electron microscopy for structure analysis, we have observed the rapid formation of hexagonal networks of linear "nanofolds" with prismatic cavities on top of layered VSe2 crystals. Their formation results from relaxation of compressive strains which build up during Cu intercalation into a thin surface layer.
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Affiliation(s)
- E Spiecker
- National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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Rougemaille N, Drouhin HJ, Richard S, Fishman G, Schmid AK. Spin-induced forbidden evanescent states in III-V semiconductors. Phys Rev Lett 2005; 95:186406. [PMID: 16383929 DOI: 10.1103/physrevlett.95.186406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Indexed: 05/05/2023]
Abstract
Within the band gap of a semiconductor no electronic propagating states are allowed, but there exist evanescent states which govern charge transport such as tunneling. In this Letter, we address the issue of their spin dependence in III-V semiconductors. Taking into account the spin-orbit interaction, we treat the problem using a k . p 14 x 14 Hamiltonian that we numerically compute for GaAs. Our results show that the removed spin degeneracy in the band gap can lead to giant energy splittings and induces forbidden zones in space where evanescent states are suppressed.
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Affiliation(s)
- N Rougemaille
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Schmid AK, Lipton MS, Mottaz H, Monroe ME, Smith RD, Lidstrom ME. Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans. J Proteome Res 2005; 4:709-18. [PMID: 15952717 DOI: 10.1021/pr049815n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The results of previous studies indicated that D. radiodurans mounts a regulated protective response to heat shock, and that expression of more than 130 genes, including classical chaperones such as the groESL and dnaKJ operons and proteases such as clpB are induced in response to elevated temperature. In addition, previous qualitative whole-cell mass spectrometric studies conducted under heat shock conditions indicated global changes in the D. radiodurans proteome. To enable the discovery of novel heat shock inducible proteins as well as gain greater biological insight into the classical heat shock response at the protein level, we undertook the global whole-cell FTICR mass spectrometric proteomics study reported here. We have greatly increased the power of this approach by conducting a large number of replicate experiments in addition to taking a semiquantitative approach to data analysis, finding good reproducibility between replicates. Through this analysis, we have identified with high confidence a core set of classical heat shock proteins whose expression increases dramatically and reproducibly in response to elevated temperature. In addition, we have found that the heat shock proteome includes a large number of induced proteins that have not been identified previously as heat responsive, and have therefore been designated as candidate responders. Finally, our results are consistent with the hypothesis that elevated temperature stress could lead to cross-protection against other related stresses.
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Affiliation(s)
- Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195-2125, USA.
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Schmid AK, Howell HA, Battista JR, Peterson SN, Lidstrom ME. HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans. Mol Microbiol 2005; 55:1579-90. [PMID: 15720562 DOI: 10.1111/j.1365-2958.2005.04494.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The HspR protein functions as a negative regulator of chaperone and protease gene expression in a diversity of bacteria. Here we have identified, cloned and deleted the Deinococcus radiodurans HspR homologue, DR0934. Delta hspR mutants exhibit moderate growth defects when shifted to mild heat shock temperatures, but are severely impaired for survival at 48 degrees C. Using quantitative reverse transcription polymerase chain reaction and global transcriptional analysis, we have identified 14 genes that are derepressed in the absence of stress in the delta hspR background, 11 of which encode predicted chaperones and proteases, including dnaKJgrpE, ftsH, lonB, hsp20 and clpB. Promoter mapping indicated that the transcription of these genes initiates from a promoter bearing a sigma70-type consensus, and that putative HspR binding sites (HAIR) were present in the 5'-untranslated regions. Electrophoretic mobility shift assays indicated that HspR binds to these promoters at the HAIR site in vitro. These results strongly suggest that DR0934 encodes the HspR-like global negative regulator of D. radiodurans that directly represses chaperone and protease gene expression by binding to the HAIR site in close proximity to promoter regions.
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Affiliation(s)
- Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195-2180, USA
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Schmid AK, Howell HA, Battista JR, Peterson SN, Lidstrom ME. Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans. J Bacteriol 2005; 187:3339-51. [PMID: 15866918 PMCID: PMC1111999 DOI: 10.1128/jb.187.10.3339-3351.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sig1 gene, predicted to encode an extracytoplasmic function-type heat shock sigma factor of Deinococcus radiodurans, has been shown to play a central role in the positive regulation of the heat shock operons groESL and dnaKJ. To determine if Sig1 is required for the regulation of additional heat shock genes, we monitored the global transcriptional and proteomic profiles of a D. radiodurans R1 sig1 mutant and wild-type cells in response to elevated temperature stress. Thirty-one gene products were identified that showed heat shock induction in the wild type but not in the sig1 mutant. Quantitative real-time PCR experiments verified the transcriptional requirement of Sig1 for the heat shock induction of the mRNA of five of these genes-dnaK, groES, DR1314, pspA, and hsp20. hsp20 appears to encode a new member of the small heat shock protein superfamily, DR1314 is predicted to encode a hypothetical protein with no recognizable orthologs, and pspA is predicted to encode a protein involved in maintenance of membrane integrity. Deletion mutation analysis demonstrated the importance in heat shock protection of hsp20 and DR1314. The promoters of dnaKJE, groESL, DR1314, pspA, and hsp20 were mapped and, combined with computer-based pattern searches of the upstream regions of the 26 other Sig1 regulon members, these results suggested that Sig1 might recognize both sigma70-type and sigma(W)-type promoter consensus sequences. These results expand the D. radiodurans Sig1 heat shock regulon to include 31 potential new members, including not only factors with cytoplasmic functions, such as groES and dnaK, but also those with extracytoplasmic functions, like pspA.
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Affiliation(s)
- Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195-2180, USA.
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Ding HF, Schmid AK, Li D, Guslienko KY, Bader SD. Magnetic bistability of Co nanodots. Phys Rev Lett 2005; 94:157202. [PMID: 15904180 DOI: 10.1103/physrevlett.94.157202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Revised: 11/30/2004] [Indexed: 05/02/2023]
Abstract
Size-dependent magnetic single-domain versus vortex state stability of Co/Ru(0001) nanodots is explored with spin-polarized low-energy electron microscopy, analytical modeling, and micromagnetic simulations. We show that both single-domain and vortex states can be stabilized in a broad region near the phase boundary. The calculated width of the bistability region and temperature dependent heights of the energy barriers between both states agree well with our experimental findings.
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Affiliation(s)
- H F Ding
- Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
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Wu YZ, Schmid AK, Altman MS, Jin XF, Qiu ZQ. Spin-dependent Fabry-Pérot interference from a Cu thin film grown on fcc Co(001). Phys Rev Lett 2005; 94:027201. [PMID: 15698221 DOI: 10.1103/physrevlett.94.027201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Indexed: 05/24/2023]
Abstract
Spin-dependent electron reflection from a Cu thin film grown on Co/Cu(001) was investigated using spin-polarized low-energy electron microscopy (SPLEEM). Fabry-Pe rot type interference was observed and is explained using the phase accumulation model. SPLEEM images of the Cu overlayer reveal magnetic domains in the Co underlayer, with the domain contrast oscillating with electron energy and Cu film thickness. This behavior is attributed to the spin-dependent electron reflectivity at the Cu/Co interface which leads to spin-dependent Fabry-Pe rot electron interference in the Cu film.
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Affiliation(s)
- Y Z Wu
- Department of Physics, University of California, Berkeley, California 94720, USA
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Ling WL, de la Figuera J, Bartelt NC, Hwang RQ, Schmid AK, Thayer GE, Hamilton JC. Strain relief through heterophase interface reconstruction: Ag(111)/Ru(0001). Phys Rev Lett 2004; 92:116102. [PMID: 15089153 DOI: 10.1103/physrevlett.92.116102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Indexed: 05/24/2023]
Abstract
We report an experimental (scanning tunneling microscopy) and theoretical (embedded atom method) study of a heterophase interface reconstruction between Ag(111) and Ru(0001). Despite the large 7% mismatch, the second layer of Ag from the Ru exhibits a hexagonal structure with Ag bulk spacing, providing a close match to bulk Ag. The first layer of Ag (next to Ru) is reconstructed in a highly symmetrical and regular structure containing monolayer long threading dislocations. We argue that this structure may generally occur to relieve strain in a certain class of heterophase interfaces.
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Affiliation(s)
- W L Ling
- Sandia National Laboratories, Livermore, California 94550, USA
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Schmid AK, Lidstrom ME. Involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium Deinococcus radiodurans. J Bacteriol 2002; 184:6182-9. [PMID: 12399488 PMCID: PMC151957 DOI: 10.1128/jb.184.22.6182-6189.2002] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2002] [Accepted: 08/22/2002] [Indexed: 11/20/2022] Open
Abstract
Two genes bearing similarity to alternative sigma factors were identified in the Deinococcus radiodurans genome sequence and designated sig1 and sig2. These genes were cloned and inactivated, and both were found to be important for survival during heat and ethanol stress, although the sig1 mutants displayed a more severe phenotype than the sig2 mutants. Reporter gene fusions to the groESL and dnaKJ operons transformed into these mutant backgrounds indicated that sig1 is required for the heat shock induction of groESL and dnaKJ, whereas sig2 mutants show a more moderate defect in dnaKJ induction and are not impaired for groESL induction. Essentiality tests suggested that neither sig1 nor sig2 is essential under all conditions. Sequence comparisons demonstrated that the sig1 gene product is classed distinctly with extracytoplasmic function (ECF) sigma factors, whereas Sig2 appears to be a more divergent sigma factor ortholog. These results suggest that sig1 encodes the major ECF-derived heat shock sigma factor in D. radiodurans and that it plays a central role in the positive regulation of heat shock genes. sig2, in contrast, appears to play a more minor role in heat shock protection and may serve to modulate the expression of some heat protective genes.
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Affiliation(s)
- Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle 98195-1750, USA
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Thayer GE, Bartelt NC, Ozolins V, Schmid AK, Chiang S, Hwang RQ. Linking surface stress to surface structure: measurement of atomic strain in a surface alloy using scanning tunneling microscopy. Phys Rev Lett 2002; 89:036101. [PMID: 12144406 DOI: 10.1103/physrevlett.89.036101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2001] [Indexed: 05/23/2023]
Abstract
Annealed submonolayer CoAg/Ru(0001) films form an alloy with a structure that contains droplets of Ag surrounded by Co [G. E. Thayer, V. Ozolins, A. K. Schmid, N. C. Bartelt, M. Asta, J. J. Hoyt, S. Chiang, and R. Q. Hwang, Phys. Rev. Lett. 86, 660 (2001)]. To understand how surface stress contributes to the formation of this structure, we use scanning tunneling microscopy to extract atomic displacements at the boundaries between regions of Co and Ag. Comparing our measurements to Frenkel-Kontorova model calculations, we show how stress due to lattice mismatch contributes to the formation of the alloy droplet structure. In particular, we quantitatively evaluate how competing strain and chemical energy contributions determine surface structure.
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Affiliation(s)
- G E Thayer
- Sandia National Laboratories, Livermore, California 94551, USA
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de La Figuera J, Pohl K, de La Fuente OR, Schmid AK, Bartelt NC, Carter CB, Hwang RQ. Direct observation of misfit dislocation glide on surfaces. Phys Rev Lett 2001; 86:3819-3822. [PMID: 11329332 DOI: 10.1103/physrevlett.86.3819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2000] [Indexed: 05/23/2023]
Abstract
Using scanning tunneling microscopy we have observed thermally induced dislocation glide in monolayer Cu films on Ru(0001) at room temperature. The motion is governed by a Peierls barrier that depends on the detailed structure of the dislocations, in particular upon whether the threading dislocations that terminate them are dissociated or not. Calculations based on the Frenkel-Kontorova model reproduce the threading dislocation structure and provide estimates of the Peierls barrier and dislocation stiffness which are consistent with experiment.
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Affiliation(s)
- J de La Figuera
- Sandia National Laboratories, Livermore, California 94550, USA
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