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Godain A, Vogel TM, Monnier JM, Paitier A, Haddour N. Metaproteomic and Metagenomic-Coupled Approach to Investigate Microbial Response to Electrochemical Conditions in Microbial Fuel Cells. Microorganisms 2023; 11:2695. [PMID: 38004707 PMCID: PMC10673480 DOI: 10.3390/microorganisms11112695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
MFCs represent a promising sustainable biotechnology that enables the direct conversion of organic matter from wastewater into electricity using bacterial biofilms as biocatalysts. A crucial aspect of MFCs is how electroactive bacteria (EAB) behave and their associated mechanisms during extracellular electron transfer to the anode. A critical phase in the MFC start-up process is the initial colonization of the anode by EAB. Two MFCs were operated with an external resistance of 1000 ohms, one with an applied electrical voltage of 500 mV during the initial four days of biofilm formation and the other without any additional applied voltage. After stabilization of electricity production, total DNA and protein were extracted and sequenced from both setups. The combined metaproteomic/metagenomic analysis revealed that the application of voltage during the colonization step predominantly increased direct electron transfer via cytochrome c, mediated primarily by Geobacter sp. Conversely, the absence of applied voltage during colonization resulted in a broader diversity of bacteria, including Pseudomonas and Aeromonas, which participated in electricity production via mediated electron transfer involving flavin family members.
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Affiliation(s)
- Alexiane Godain
- Ecole Centrale de Lyon, INSA Lyon, University Lyon, Université Claude Bernard Lyon 1, CNRS, Ampère, UMR5005, 69130 Ecully, France
- Laboratoire d’Ecologie Microbienne, Universite Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France
| | - Timothy M. Vogel
- Laboratoire d’Ecologie Microbienne, Universite Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France
| | - Jean-Michel Monnier
- Ecole Centrale de Lyon, INSA Lyon, University Lyon, Université Claude Bernard Lyon 1, CNRS, Ampère, UMR5005, 69130 Ecully, France
| | - Agathe Paitier
- Ecole Centrale de Lyon, INSA Lyon, University Lyon, Université Claude Bernard Lyon 1, CNRS, Ampère, UMR5005, 69130 Ecully, France
- Laboratoire d’Ecologie Microbienne, Universite Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France
| | - Naoufel Haddour
- Ecole Centrale de Lyon, INSA Lyon, University Lyon, Université Claude Bernard Lyon 1, CNRS, Ampère, UMR5005, 69130 Ecully, France
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2
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Chowdhury NB, Alsiyabi A, Saha R. Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 through a Genome-Scale Metabolic and Expression Model. Microbiol Spectr 2022; 10:e0146322. [PMID: 35730964 PMCID: PMC9431616 DOI: 10.1128/spectrum.01463-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 11/20/2022] Open
Abstract
Rhodopseudomonas palustris CGA009 is a Gram-negative purple nonsulfur bacterium that grows phototrophically by fixing carbon dioxide and nitrogen or chemotrophically by fixing or catabolizing a wide array of substrates, including lignin breakdown products for its carbon and fixing nitrogen for its nitrogen requirements. It can grow aerobically or anaerobically and can use light, inorganic, and organic compounds for energy production. Due to its ability to convert different carbon sources into useful products during anaerobic growth, this study reconstructed a metabolic and expression (ME) model of R. palustris to investigate its anaerobic-photoheterotrophic growth. Unlike metabolic (M) models, ME models include transcription and translation reactions along with macromolecules synthesis and couple these reactions with growth rate. This unique feature of the ME model led to nonlinear growth curve predictions, which matched closely with experimental growth rate data. At the theoretical maximum growth rate, the ME model suggested a diminishing rate of carbon fixation and predicted malate dehydrogenase and glycerol-3 phosphate dehydrogenase as alternate electron sinks. Moreover, the ME model also identified ferredoxin as a key regulator in distributing electrons between major redox balancing pathways. Because ME models include the turnover rate for each metabolic reaction, it was used to successfully capture experimentally observed temperature regulation of different nitrogenases. Overall, these unique features of the ME model demonstrated the influence of nitrogenases and rubiscos on R. palustris growth and predicted a key regulator in distributing electrons between major redox balancing pathways, thus establishing a platform for in silico investigation of R. palustris metabolism from a multiomics perspective. IMPORTANCE In this work, we reconstructed the first ME model for a purple nonsulfur bacterium (PNSB). Using the ME model, different aspects of R. palustris metabolism were examined. First, the ME model was used to analyze how reducing power entering the R. palustris cell through organic carbon sources gets partitioned into biomass, carbon dioxide fixation, and nitrogen fixation. Furthermore, the ME model predicted electron flux through ferredoxin as a major bottleneck in distributing electrons to nitrogenase enzymes. Next, the ME model characterized different nitrogenase enzymes and successfully recapitulated experimentally observed temperature regulations of those enzymes. Identifying the bottleneck responsible for transferring an electron to nitrogenase enzymes and recapitulating the temperature regulation of different nitrogenase enzymes can have profound implications in metabolic engineering, such as hydrogen production from R. palustris. Another interesting application of this ME model can be to take advantage of its redox balancing strategy to gain an understanding of the regulatory mechanism of biodegradable plastic production precursors, such as polyhydroxybutyrate (PHB).
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Affiliation(s)
- Niaz Bahar Chowdhury
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Adil Alsiyabi
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Rajib Saha
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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3
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Grant CR, Amor M, Trujillo HA, Krishnapura S, Iavarone AT, Komeili A. Distinct gene clusters drive formation of ferrosome organelles in bacteria. Nature 2022; 606:160-164. [PMID: 35585231 PMCID: PMC10906721 DOI: 10.1038/s41586-022-04741-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/07/2022] [Indexed: 12/20/2022]
Abstract
Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification1-3. The most common modes of iron storage use proteinaceous compartments, such as ferritins and related proteins4,5. Although lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown6,7. Here we focus on one such compartment, herein named the 'ferrosome', that was previously observed in the anaerobic bacterium Desulfovibrio magneticus6. Using a proteomic approach, we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes in D. magneticus. Fez proteins are encoded in a putative operon and include FezB, a P1B-6-ATPase found in phylogenetically and metabolically diverse species of bacteria and archaea. We show that two other bacterial species, Rhodopseudomonas palustris and Shewanella putrefaciens, make ferrosomes through the action of their six-gene fez operon. Additionally, we find that fez operons are sufficient for ferrosome formation in foreign hosts. Using S. putrefaciens as a model, we show that ferrosomes probably have a role in the anaerobic adaptation to iron starvation. Overall, this work establishes ferrosomes as a new class of iron storage organelles and sets the stage for studying their formation and structure in diverse microorganisms.
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Affiliation(s)
- Carly R Grant
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Matthieu Amor
- Aix-Marseille Université, CEA, CNRS, BIAM, Saint-Paul-lez-Durance, France
| | - Hector A Trujillo
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sunaya Krishnapura
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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4
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Sun J, Yang P, Huang S, Li N, Zhang Y, Yuan Y, Lu X. Enhanced removal of veterinary antibiotic from wastewater by photoelectroactive biofilm of purple anoxygenic phototroph through photosynthetic electron uptake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136605. [PMID: 31951842 DOI: 10.1016/j.scitotenv.2020.136605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/22/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Purple anoxygenic phototrophs have been recently attracted substantial attention for their growing potential in wastewater treatment and their diverse metabolic patterns can be regulated for process control and optimization. In this study, the photoheterotrophic metabolism of Rhodopseudomonas palustris (R. palustris) was modified by photosynthetic electron uptake using a poised electrode which was explored to enhance removal of veterinary antibiotic from aqueous medium. The results showed that R. palustris grown as biofilm on electrode surface had excellent photoelectroactive activity and the photosynthetic electron uptake from the photoelectroactive biofilm significantly enhanced antibiotic florfenicol (FLO) degradation. The specific degradation rate of FLO at the set electrode potential of 0 V was 2.59-fold higher than that without applied potential. Enhanced co-metabolic reductive dehalogenation by use of the photosynthetic electrons extracted from co-substrate was mainly responsible for FLO degradation which eliminated the antibacterial activity of FLO. The electrode potential controlled the processes of photosynthetic electron uptake and its resultant FLO degradation. The fastest degradation of FLO was achieved at 0 V because the electrode poised at this potential stroke a proper balance between the enhancing photosynthetic electron uptake by serving as electron acceptor and minimizing competition with FLO for the photosynthetic electron from co-substrate. The activity of photoelectroactive biofilm was not negatively affected by FLO at environmental relevant concentration, suggesting its great potential for removal of antibiotic contaminants in wastewater. R. palustris could serve as a reservoir for floR resistance gene but its abundance can be diminished by choosing appropriate electrode potential.
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Affiliation(s)
- Jian Sun
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Ping Yang
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Shengzheng Huang
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Nan Li
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Yaping Zhang
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Yong Yuan
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Xingwen Lu
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
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5
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Bacusmo JM, Kuzmishin AB, Cantara WA, Goto Y, Suga H, Musier-Forsyth K. Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid α-aminobutyrate. RNA Biol 2017; 15:576-585. [PMID: 28737471 DOI: 10.1080/15476286.2017.1353846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Accuracy in protein biosynthesis is maintained through multiple pathways, with a critical checkpoint occurring at the tRNA aminoacylation step catalyzed by aminoacyl-tRNA synthetases (ARSs). In addition to the editing functions inherent to some synthetases, single-domain trans-editing factors, which are structurally homologous to ARS editing domains, have evolved as alternative mechanisms to correct mistakes in aminoacyl-tRNA synthesis. To date, ARS-like trans-editing domains have been shown to act on specific tRNAs that are mischarged with genetically encoded amino acids. However, structurally related non-protein amino acids are ubiquitous in cells and threaten the proteome. Here, we show that a previously uncharacterized homolog of the bacterial prolyl-tRNA synthetase (ProRS) editing domain edits a known ProRS aminoacylation error, Ala-tRNAPro, but displays even more robust editing of tRNAs misaminoacylated with the non-protein amino acid α-aminobutyrate (2-aminobutyrate, Abu) in vitro and in vivo. Our results indicate that editing by trans-editing domains such as ProXp-x studied here may offer advantages to cells, especially under environmental conditions where concentrations of non-protein amino acids may challenge the substrate specificity of ARSs.
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Affiliation(s)
- Jo Marie Bacusmo
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - Alexandra B Kuzmishin
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - William A Cantara
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - Yuki Goto
- c Department of Chemistry , Graduate School of Science, The University of Tokyo , Bunkyo , Tokyo , Japan
| | - Hiroaki Suga
- c Department of Chemistry , Graduate School of Science, The University of Tokyo , Bunkyo , Tokyo , Japan
| | - Karin Musier-Forsyth
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
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6
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Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS. Genes essential for phototrophic growth by a purple alphaproteobacterium. Environ Microbiol 2017; 19:3567-3578. [PMID: 28677146 DOI: 10.1111/1462-2920.13852] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/13/2017] [Accepted: 06/28/2017] [Indexed: 12/01/2022]
Abstract
Tn-seq was used to identify genes essential for phototrophic growth by the purple bacterium Rhodopseudomonas palustris. About 167 genes required for anaerobic growth on acetate in light were identified, 35 of which are annotated as photosynthesis genes. The essentiality of many of these genes by analysing the phenotypes of independently generated mutants that had altered pigmentation was verified. Three genes were identified, two possibly involved in biogenesis of the membrane-bound photosynthetic apparatus and one for phosphatidylcholine biosynthesis, that were not known to be essential for phototrophic growth. Site-directed mutagenesis was used to show that the NADH:quinone oxidoreductase complex IE was essential for phototrophic growth under strictly anaerobic conditions and appeared to play a role in reverse electron transport to generate NADH. A homologous NADH:quinone oxidoreductase complex IA likely operates in the opposite direction to oxidize NADH. The operation of the two enzymes in opposition would allow R. palustris to maintain redox balance. As a complement to the genetic data, proteomics experiments were carried out in which it was found that 408 proteins were present in significantly higher amounts in cells grown anaerobically in light compared with aerobically. Among these were proteins encoded by subset of the phototrophic growth-essential genes.
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Affiliation(s)
- Jianming Yang
- Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Liang Yin
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Faith H Lessner
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Samuel H Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kathryn R Fixen
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Larry Gallagher
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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7
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Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A, Singh DP, Prabha R, Sahu PK, Gupta VK, Singh HB, Krishanani KK, Minhas PS. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies. FRONTIERS IN PLANT SCIENCE 2017; 8:172. [PMID: 28232845 PMCID: PMC5299014 DOI: 10.3389/fpls.2017.00172] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.
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Affiliation(s)
- Kamlesh K. Meena
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Ajay M. Sorty
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Utkarsh M. Bitla
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Khushboo Choudhary
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Priyanka Gupta
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Dhananjaya P. Singh
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Ratna Prabha
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Pramod K. Sahu
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Vijai K. Gupta
- Molecular Glyco-Biotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of TechnologyTallinn, Estonia
| | - Harikesh B. Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu UniversityVaranasi, India
| | - Kishor K. Krishanani
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Paramjit S. Minhas
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
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8
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Catazaro J, Lowe AJ, Cerny RL, Powers R. The NMR solution structure and function of RPA3313: a putative ribosomal transport protein from Rhodopseudomonas palustris. Proteins 2016; 85:93-102. [PMID: 27802574 DOI: 10.1002/prot.25201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/12/2016] [Accepted: 10/23/2016] [Indexed: 01/15/2023]
Abstract
Protein function elucidation often relies heavily on amino acid sequence analysis and other bioinformatics approaches. The reliance is extended to structure homology modeling for ligand docking and protein-protein interaction mapping. However, sequence analysis of RPA3313 exposes a large, unannotated class of hypothetical proteins mostly from the Rhizobiales order. In the absence of sequence and structure information, further functional elucidation of this class of proteins has been significantly hindered. A high quality NMR structure of RPA3313 reveals that the protein forms a novel split ββαβ fold with a conserved ligand binding pocket between the first β-strand and the N-terminus of the α-helix. Conserved residue analysis and protein-protein interaction prediction analyses reveal multiple protein binding sites and conserved functional residues. Results of a mass spectrometry proteomic analysis strongly point toward interaction with the ribosome and its subunits. The combined structural and proteomic analyses suggest that RPA3313 by itself or in a larger complex may assist in the transportation of substrates to or from the ribosome for further processing. Proteins 2016; 85:93-102. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jonathan Catazaro
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
| | - Austin J Lowe
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
| | - Ronald L Cerny
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
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9
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Farmer RM, Tabita FR. Phosphoribulokinase mediates nitrogenase-induced carbon dioxide fixation gene repression in Rhodobacter sphaeroides. MICROBIOLOGY-SGM 2015; 161:2184-91. [PMID: 26306848 PMCID: PMC4806589 DOI: 10.1099/mic.0.000160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many organisms there is a balance between carbon and nitrogen metabolism. These observations extend to the nitrogen-fixing, nonsulfur purple bacteria, which have the classic family of P(II) regulators that coordinate signals of carbon and nitrogen status to regulate nitrogen metabolism. Curiously, these organisms also possess a reverse mechanism to regulate carbon metabolism based on cellular nitrogen status. In this work, studies in Rhodobacter sphaeroides firmly established that the activity of the enzyme that catalyses nitrogen fixation, nitrogenase, induces a signal that leads to repression of genes encoding enzymes of the Calvin–Benson–Bassham (CBB) CO2 fixation pathway. Additionally, genetic and metabolomic experiments revealed that NADH-activated phosphoribulokinase is an intermediate in the signalling pathway. Thus, nitrogenase activity appears to be linked to cbb gene repression through phosphoribulokinase.
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Affiliation(s)
- Ryan M Farmer
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292, USA
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292, USA
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10
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Kernan C, Chow PP, Christianson RJ, Huang J. Experimental and Computational Investigation of Biofilm Formation by Rhodopseudomonas palustris Growth under Two Metabolic Modes. PLoS One 2015; 10:e0129354. [PMID: 26087200 PMCID: PMC4472842 DOI: 10.1371/journal.pone.0129354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/08/2015] [Indexed: 11/18/2022] Open
Abstract
We examined biofilms formed by the metabolically versatile bacterium Rhodopseudomonas palustris grown via different metabolic modes. R. palustris was grown in flow cell chambers with identical medium conditions either in the presence or absence of light and oxygen. In the absence of oxygen and the presence of light, R. palustris grew and formed biofilms photoheterotrophically, and in the presence of oxygen and the absence of light, R. palustris grew and formed biofilms heterotrophically. We used confocal laser scanning microscopy and image analysis software to quantitatively analyze and compare R. palustris biofilm formation over time in these two metabolic modes. We describe quantifiable differences in structure between the biofilms formed by the bacterium grown heterotrophically and those grown photoheterotrophically. We developed a computational model to explore ways in which biotic and abiotic parameters could drive the observed biofilm architectures, as well as a random-forest machine-learning algorithm based on structural differences that was able to identify growth conditions from the confocal imaging of the biofilms with 87% accuracy. Insight into the structure of phototrophic biofilms and conditions that influence biofilm formation is relevant for understanding the generation of biofilm structures with different properties, and for optimizing applications with phototrophic bacteria growing in the biofilm state.
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Affiliation(s)
- Chase Kernan
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
| | - Philicia P. Chow
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
| | - Rebecca J. Christianson
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
- * E-mail:
| | - Jean Huang
- Franklin W. Olin College of Engineering, Needham, Massachusetts, United States of America
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11
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Allen MS, Hurst GB, Lu TYS, Perry LM, Pan C, Lankford PK, Pelletier DA. Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response. J Proteome Res 2015; 14:2158-68. [PMID: 25853567 DOI: 10.1021/pr5012558] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. To begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σ(RPA4225) (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the -35 and -10 regions with the consensus sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Taken together, these data suggest that ECF σ(RPA4225) and the three additional genes make up a sigma factor mimicry system in R. palustris.
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Affiliation(s)
- Michael S Allen
- §Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017, United States.,∥Center for Biosafety and Biosecurity Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | | | | | - Leslie M Perry
- §Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017, United States
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Apo-bacteriophytochromes modulate bacterial photosynthesis in response to low light. Proc Natl Acad Sci U S A 2013; 111:E237-44. [PMID: 24379368 DOI: 10.1073/pnas.1322410111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophytochromes (BphPs) are light-sensing regulatory proteins encoded by photosynthetic and nonphotosynthetic bacteria. This protein class has been characterized structurally, but its biological activities remain relatively unexplored. Two BphPs in the anoxygenic photosynthetic bacterium Rhodopseudomonas palustris, designated regulatory proteins RpBphP2 and RpBphP3, are configured as light-regulated histidine kinases, which initiate a signal transduction system that controls expression of genes for the low light harvesting 4 (LH4) antenna complex. In vitro, RpBphP2 and RpBphP3 respond to light quality by reversible photoconversion, a property that requires the light-absorbing chromophore biliverdin. In vivo, RpBphP2 and RpBphP3 are both required for the expression of the LH4 antenna complex under anaerobic conditions, but biliverdin requires oxygen for its synthesis by heme oxygenase. On further investigation, we found that the apo-bacteriophytochrome forms of RpBphP2 and RpBphP3 are necessary and sufficient to control LH4 expression in response to light intensity in conjunction with other signal transduction proteins. One possibility is that the system senses a reduced quinone pool generated when light energy is absorbed by bacteriochlorophyll. The biliverdin-bound forms of the BphPs have the additional property of being able to fine-tune LH4 expression in response to light quality. These observations support the concept that some bacteriophytochromes can function with or without a chromophore and may be involved in regulating physiological processes not directly related to light sensing.
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Dykstra AB, St Brice L, Rodriguez M, Raman B, Izquierdo J, Cook KD, Lynd LR, Hettich RL. Development of a multipoint quantitation method to simultaneously measure enzymatic and structural components of the Clostridium thermocellum cellulosome protein complex. J Proteome Res 2013; 13:692-701. [PMID: 24274857 DOI: 10.1021/pr400788e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clostridium thermocellum has emerged as a leading bioenergy-relevant microbe due to its ability to solubilize cellulose into carbohydrates, mediated by multicomponent membrane-attached complexes termed cellulosomes. To probe microbial cellulose utilization rates, it is desirable to be able to measure the concentrations of saccharolytic enzymes and estimate the total amount of cellulosome present on a mass basis. Current cellulase determination methodologies involve labor-intensive purification procedures and only allow for indirect determination of abundance. We have developed a method using multiple reaction monitoring (MRM-MS) to simultaneously quantitate both enzymatic and structural components of the cellulosome protein complex in samples ranging in complexity from purified cellulosomes to whole cell lysates, as an alternative to a previously developed enzyme-linked immunosorbent assay (ELISA) method of cellulosome quantitation. The precision of the cellulosome mass concentration in technical replicates is better than 5% relative standard deviation for all samples, indicating high precision for determination of the mass concentration of cellulosome components.
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Affiliation(s)
- Andrew B Dykstra
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
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McInnis CE, Blackwell HE. Non-native N-aroyl L-homoserine lactones are potent modulators of the quorum sensing receptor RpaR in Rhodopseudomonas palustris. Chembiochem 2013; 15:87-93. [PMID: 24281952 DOI: 10.1002/cbic.201300570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 12/14/2022]
Abstract
Quorum sensing (QS) is a process by which bacteria use low-molecular-weight signaling molecules (or autoinducers) to assess their local population densities and alter gene expression levels at high cell numbers. Many Gram-negative bacteria use N-acyl L-homoserine lactones (AHLs) with aliphatic acyl groups as signaling molecules for QS. However, bacteria that utilize AHLs with aroyl acyl groups have been recently discovered; they include the metabolically versatile soil bacterium Rhodopseudomonas palustris, which uses p-coumaroyl HL (p-cAHL) as its QS signal. This autoinducer is especially unusual because its acyl group is believed to originate from a monolignol (i.e., p-coumarate) produced exogenously by plants in the R. palustris environment, rather than through the endogenous fatty acid biosynthesis pathway like other native AHLs. As such, p-cAHL could signal not only bacterial density, but also the availability of an exogenous plant-derived substrate and might even constitute an interkingdom signal. Like other Gram-negative bacteria, QS in R. palustris is controlled by the p-cAHL signal binding its cognate LuxR-type receptor, RpaR. We sought to determine if non-native aroyl HLs (ArHLs) could potentially activate or inhibit RpaR in R. palustris, and thereby modulate QS in this bacterium. Herein, we report the testing of a set of synthetic ArHLs for RpaR agonism and antagonism by using a R. palustris reporter strain. Several potent non-native RpaR agonists and antagonists were identified. Additionally, the screening data revealed that lower concentrations of ArHL are required to strongly agonize RpaR than to antagonize it. Structure-activity relationship analyses of the active ArHLs indicated that potent RpaR agonists tend to have sterically small substituents on their aryl groups, most notably in the ortho position. In turn, the most potent RpaR antagonists were based on either the phenylpropionyl HL (PPHL) or the phenoxyacetyl HL (POHL) scaffold, and many contained an electron-withdrawing group at either the meta or para positions of the aryl ring. To our knowledge, the compounds reported herein represent the first abiotic chemical modulators of RpaR, and more generally, the first abiotic ligands capable of intercepting QS in bacteria that utilize native ArHL signals. In view of the origins of the p-cAHL signal in R. palustris, the largely unknown role of QS in this bacterium, and R. palustris' unique environmental lifestyles, we anticipate that these compounds could be valuable as chemical probes to study QS in R. palustris in a range of fundamental and applied contexts.
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Affiliation(s)
- Christine E McInnis
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706 (USA); Current address: Dow Microbial Control, The Dow Chemical Company, 727 Norristown Rd., P. O. Box 904, Spring House, PA 19477 (USA)
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Hettich RL, Pan C, Chourey K, Giannone RJ. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 2013; 85:4203-14. [PMID: 23469896 PMCID: PMC3696428 DOI: 10.1021/ac303053e] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high-performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample.
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Hu CW, Lin MH, Huang HC, Ku WC, Yi TH, Tsai CF, Chen YJ, Sugiyama N, Ishihama Y, Juan HF, Wu SH. Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production. J Proteome Res 2012; 11:5362-75. [PMID: 23030682 DOI: 10.1021/pr300582p] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopseudomonas palustris (R. palustris) is a purple nonsulfur anoxygenic phototrophic bacterium with metabolic versatility and is able to grow under photoheterotrophic and chemoheterotrophic states. It has uses in carbon management, carbon recycling, hydrogen generation, and lipid production; therefore, it has the potential for bioenergy production and biodegradation. This study is the first to identify the phosphoproteome of R. palustris including 100 phosphopeptides from 54 phosphoproteins and 74 phosphopeptides from 42 phosphoproteins in chemoheterotrophic and photoheterotrophic growth conditions, respectively. In the identified phosphoproteome, phosphorylation at the threonine residue, Thr487, of pyruvate phosphate dikinase (PPDK, RPA1051) was found to participate in the regulation of carbon metabolism. Here, we show that PPDK enzyme activity is higher in photoheterotrophic growth, with Thr487 phosphorylation as a possible mediator. Under the same photoheterotrophic conditions, R. palustris with overexpressed wild-type PPDK showed an enhanced accumulation of total lipids than those with mutant PPDK (T487V) form. This study reveals the role of the PPDK in the production of biodiesel material, lipid content, with threonyl-phosphorylation as one of the possible regulatory events during photoheterotrophic growth in R. palustris.
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Affiliation(s)
- Chia-Wei Hu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan
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17
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Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation. Appl Environ Microbiol 2011; 78:1424-36. [PMID: 22179257 DOI: 10.1128/aem.06792-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.
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Cantarel BL, Erickson AR, VerBerkmoes NC, Erickson BK, Carey PA, Pan C, Shah M, Mongodin EF, Jansson JK, Fraser-Liggett CM, Hettich RL. Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. PLoS One 2011; 6:e27173. [PMID: 22132090 PMCID: PMC3223167 DOI: 10.1371/journal.pone.0027173] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 10/11/2011] [Indexed: 11/05/2022] Open
Abstract
Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate protein catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration of mass spectrometry-based proteomics data with computational proteome predictions from environmental metagenomic sequences has been challenging because of the variable overlap between proteomic datasets and corresponding short-read nucleotide sequence data. In this study, we have benchmarked several strategies for increasing microbial peptide spectral matching in metaproteomic datasets using protein predictions generated from matched metagenomic sequences from the same human fecal samples. Additionally, we investigated the impact of mass spectrometry-based filters (high mass accuracy, delta correlation), and de novo peptide sequencing on the number and robustness of peptide-spectrum assignments in these complex datasets. In summary, we find that high mass accuracy peptide measurements searched against non-assembled reads from DNA sequencing of the same samples significantly increased identifiable proteins without sacrificing accuracy.
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Affiliation(s)
- Brandi L. Cantarel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alison R. Erickson
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, United States of America
- Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Nathan C. VerBerkmoes
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Brian K. Erickson
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, United States of America
- Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Patricia A. Carey
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Chongle Pan
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Manesh Shah
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Emmanuel F. Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Janet K. Jansson
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Department of Ecology, Berkeley, California, United States of America
| | - Claire M. Fraser-Liggett
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Robert L. Hettich
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, United States of America
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Abraham P, Adams R, Giannone RJ, Kalluri U, Ranjan P, Erickson B, Shah M, Tuskan GA, Hettich RL. Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J Proteome Res 2011; 11:449-60. [PMID: 22003893 DOI: 10.1021/pr200851y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Current state-of-the-art experimental and computational proteomic approaches were integrated to obtain a comprehensive protein profile of Populus vascular tissue. This featured: (1) a large sample set consisting of two genotypes grown under normal and tension stress conditions, (2) bioinformatics clustering to effectively handle gene duplication, and (3) an informatics approach to track and identify single amino acid polymorphisms (SAAPs). By applying a clustering algorithm to the Populus database, the number of protein entries decreased from 64,689 proteins to a total of 43,069 protein groups, thereby reducing 7505 identified proteins to a total of 4226 protein groups, in which 2016 were singletons. This reduction implies that ∼50% of the measured proteins shared extensive sequence homology. Using conservative search criteria, we were able to identify 1354 peptides containing a SAAP and 201 peptides that become tryptic due to a K or R substitution. These newly identified peptides correspond to 502 proteins, including 97 previously unidentified proteins. In total, the integration of deep proteome measurements on an extensive sample set with protein clustering and peptide sequence variants provided an exceptional level of proteome characterization for Populus, allowing us to spatially resolve the vascular tissue proteome.
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Affiliation(s)
- Paul Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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20
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Simmons SS, Isokpehi RD, Brown SD, McAllister DL, Hall CC, McDuffy WM, Medley TL, Udensi UK, Rajnarayanan RV, Ayensu WK, Cohly HHP. Functional Annotation Analytics of Rhodopseudomonas palustris Genomes. Bioinform Biol Insights 2011; 5:115-29. [PMID: 22084572 PMCID: PMC3201837 DOI: 10.4137/bbi.s7316] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R. palustris genomes.
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Affiliation(s)
- Shaneka S Simmons
- Department of Biology, Center for Bioinformatics & Computational Biology, Department of Biology, Jackson State University, PO Box 18540 Jackson MS 39217 USA
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Jiao Y, D'haeseleer P, Dill BD, Shah M, VerBerkmoes NC, Hettich RL, Banfield JF, Thelen MP. Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol 2011; 77:5230-7. [PMID: 21685158 PMCID: PMC3147463 DOI: 10.1128/aem.03005-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/03/2011] [Indexed: 01/01/2023] Open
Abstract
In microbial communities, extracellular polymeric substances (EPS), also called the extracellular matrix, provide the spatial organization and structural stability during biofilm development. One of the major components of EPS is protein, but it is not clear what specific functions these proteins contribute to the extracellular matrix or to microbial physiology. To investigate this in biofilms from an extremely acidic environment, we used shotgun proteomics analyses to identify proteins associated with EPS in biofilms at two developmental stages, designated DS1 and DS2. The proteome composition of the EPS was significantly different from that of the cell fraction, with more than 80% of the cellular proteins underrepresented or undetectable in EPS. In contrast, predicted periplasmic, outer membrane, and extracellular proteins were overrepresented by 3- to 7-fold in EPS. Also, EPS proteins were more basic by ∼2 pH units on average and about half the length. When categorized by predicted function, proteins involved in motility, defense, cell envelope, and unknown functions were enriched in EPS. Chaperones, such as histone-like DNA binding protein and cold shock protein, were overrepresented in EPS. Enzymes, such as protein peptidases, disulfide-isomerases, and those associated with cell wall and polysaccharide metabolism, were also detected. Two of these enzymes, identified as β-N-acetylhexosaminidase and cellulase, were confirmed in the EPS fraction by enzymatic activity assays. Compared to the differences between EPS and cellular fractions, the relative differences in the EPS proteomes between DS1 and DS2 were smaller and consistent with expected physiological changes during biofilm development.
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Affiliation(s)
| | - Patrik D'haeseleer
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | | | - Manesh Shah
- Biosciences Divisions, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | | | | | - Jillian F. Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720
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Integrative Control of Carbon, Nitrogen, Hydrogen, and Sulfur Metabolism: The Central Role of the Calvin–Benson–Bassham Cycle. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010. [DOI: 10.1007/978-1-4419-1528-3_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. [PMID: 20211023 PMCID: PMC2848648 DOI: 10.1186/1471-2105-11-119] [Citation(s) in RCA: 6254] [Impact Index Per Article: 446.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 03/08/2010] [Indexed: 11/10/2022] Open
Abstract
Background The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. Results With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. Conclusion We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.
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Affiliation(s)
- Doug Hyatt
- Computational Biology and Bioinformatics Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Rey FE, Harwood CS. FixK, a global regulator of microaerobic growth, controls photosynthesis inRhodopseudomonas palustris. Mol Microbiol 2010; 75:1007-20. [DOI: 10.1111/j.1365-2958.2009.07037.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Kalluri UC, Hurst GB, Lankford PK, Ranjan P, Pelletier DA. Shotgun proteome profile of Populus developing xylem. Proteomics 2009; 9:4871-80. [PMID: 19743414 DOI: 10.1002/pmic.200800854] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Understanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here, we report the application of shotgun MS/MS profiling to the proteome of Populus developing xylem. Nearly 6000 different proteins were identified from the xylem proteome. To identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factors and chromatin remodeling proteins were identified using this method, such as NAC domain, CtCP-like and CHB3-SWI/SNF-related proteins. Public databases were mined to obtain information in support of subcellular localization, transcript-level expression and functional categorization of identified proteins. In addition to finding protein-level evidence of candidate cell wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, sucrose synthase and polygalacturonase, several other potentially new candidate genes in the cell wall biosynthesis pathway were discovered. Further application of such proteomics methods will aid in plant systems biology modeling efforts by enhancing the understanding not only of cell wall biosynthesis but also of other plant developmental and physiological pathways.
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Affiliation(s)
- Udaya C Kalluri
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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26
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Thompson MR, Chourey K, Froelich JM, Erickson BK, VerBerkmoes NC, Hettich RL. Experimental approach for deep proteome measurements from small-scale microbial biomass samples. Anal Chem 2009; 80:9517-25. [PMID: 19072265 DOI: 10.1021/ac801707s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many methods of microbial proteome characterizations require large quantities of cellular biomass (>1-2 g) for sample preparation and protein identification. Our experimental approach differs from traditional techniques by providing the ability to identify the proteomic state of a microbe from a few milligrams of starting cellular material. The small-scale, guanidine lysis method minimizes sample loss by achieving cellular lysis and protein digestion in a single-tube experiment. For this experimental approach, the freshwater microbe Shewanella oneidensis MR-1 and the purple non-sulfur bacterium Rhodopseudomonas palustris CGA0010 were used as model organisms for technology development and evaluation. A 2-D LC-MS/MS comparison between a standard sonication lysis method and the small-scale guanidine lysis techniques demonstrates that the guanidine lysis method is more efficient with smaller sample amounts of cell pellet (i.e., down to 1 mg). The described methodology enables deeper proteome measurements from a few milliliters of confluent bacterial cultures. We also report a new protocol for efficient lysis from small amounts of natural biofilm samples for deep proteome measurements, which should greatly enhance the emerging field of environmental microbial community proteomics. This straightforward sample boiling protocol is complementary to the small-scale guanidine lysis technique, is amenable for small sample quantities, and requires no special reagents that might complicate the MS measurements.
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Affiliation(s)
- Melissa R Thompson
- Graduate School of Genome Science and Technology, Oak Ridge National Laboratory-University of Tennessee, Knoxville, Tennessee 37830, USA
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27
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Unell M, Abraham PE, Shah M, Zhang B, Rückert C, VerBerkmoes NC, Jansson JK. Impact of phenolic substrate and growth temperature on the Arthrobacter chlorophenolicus proteome. J Proteome Res 2009; 8:1953-64. [PMID: 19714879 DOI: 10.1021/pr800897c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol, or phenol at 5 and 28 degrees C, both for the wild-type and a mutant strain with mass spectrometry based proteomics. A label-free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol-degradation pathway was confirmed, but not that for phenol.
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Affiliation(s)
- Maria Unell
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden
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Nikodinovic-Runic J, Flanagan M, Hume AR, Cagney G, O'Connor KE. Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions. Microbiology (Reading) 2009; 155:3348-3361. [DOI: 10.1099/mic.0.031153-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas putida CA-3 is a styrene-degrading bacterium capable of accumulating medium-chain-length polyhydroxyalkanoate (mclPHA) when exposed to limiting concentrations of a nitrogen source in the growth medium. Using shotgun proteomics we analysed global proteome expression in P. putida CA-3 supplied with styrene as the sole carbon and energy source under N-limiting (condition permissive for mclPHA synthesis) and non-limiting (condition non-permissive for mclPHA accumulation) growth conditions in order to provide insight into the molecular response of P. putida CA-3 to limitation of nitrogen when grown on styrene. A total of 1761 proteins were identified with high confidence and the detected proteins could be assigned to functional groups including styrene degradation, energy, nucleotide metabolism, protein synthesis, transport, stress response and motility. Proteins involved in the upper and lower styrene degradation pathway were expressed throughout the 48 h growth period under both nitrogen limitation and excess. Proteins involved in polyhydroxyalkanoate (PHA) biosynthesis, nitrogen assimilation and amino acid transport, and outer membrane proteins were upregulated under nitrogen limitation. PHA accumulation and biosynthesis were only expressed under nitrogen limitation. Nitrogen assimilation proteins were detected on average at twofold higher amounts under nitrogen limitation. Expression of the branched-chain amino acid ABC transporter was up to 16-fold higher under nitrogen-limiting conditions. Branched chain amino acid uptake by nitrogen-limited cultures was also higher than that by non-limited cultures. Outer membrane lipoproteins were expressed at twofold higher levels under nitrogen limitation. This was confirmed by Western blotting (immunochemical detection) of cells grown under nitrogen limitation. Our study provides the first global description of protein expression changes during growth of any organism on styrene and accumulating mclPHA (nitrogen-limited growth).
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Affiliation(s)
- Jasmina Nikodinovic-Runic
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michelle Flanagan
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling R. Hume
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gerard Cagney
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin E. O'Connor
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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Kertesz V, Connelly HM, Erickson BK, Hettich RL. PTMSearchPlus: Software Tool for Automated Protein Identification and Post-Translational Modification Characterization by Integrating Accurate Intact Protein Mass and Bottom-Up Mass Spectrometric Data Searches. Anal Chem 2009; 81:8387-95. [DOI: 10.1021/ac901163c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vilmos Kertesz
- Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131, and Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, Tennessee 37830
| | - Heather M. Connelly
- Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131, and Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, Tennessee 37830
| | - Brian K. Erickson
- Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131, and Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, Tennessee 37830
| | - Robert L. Hettich
- Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131, and Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, Tennessee 37830
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Shi L, Ansong C, Smallwood H, Rommereim L, McDermott JE, Brewer HM, Norbeck AD, Taylor RC, Gustin JK, Heffron F, Smith RD, Adkins JN. Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium. ACTA ACUST UNITED AC 2009; 2:388-397. [PMID: 19953200 DOI: 10.4172/jpb.1000099] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To determine the impact of a low Mg(2+)/pH defined growth medium (MgM) on the proteome of Salmonella enterica serotype Typhimurium, we cultured S. Typhimurium cells in the medium under two different conditions termed MgM Shock and MgM Dilution and then comparatively analyzed the bacterial cells harvested from these conditions by a global proteomic approach. Proteomic results showed that MgM Shock and MgM Dilution differentially affected the S. Typhimurium proteome. MgM Shock induced a group of proteins whose induction usually occurred at low O(2) level, while MgM Dilution induced those related to the type III secretion system (T3SS) of Salmonella Pathogenicity Island 2 (SPI2) and those involved in thiamine or biotin biosynthesis. The metabolic state of the S. Typhimurium cells grown under MgM Shock condition also differed significantly from that under MgM Dilution condition. Western blot analysis not only confirmed the proteomic results, but also showed that the abundances of SPI2-T3SS proteins SsaQ and SseE and biotin biosynthesis proteins BioB and BioD increased after S. Typhimurium infection of RAW 264.7 macrophages. Deletion of the gene encoding BioB reduced the bacterial ability to replicate inside the macrophages, suggesting a biotin-limited environment encountered by S. Typhimurium within RAW 264.7 macrophages.
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Affiliation(s)
- Liang Shi
- Pacific Northwest National Laboratory, Richland, Washington 99352
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Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica. Infect Immun 2009; 77:3227-33. [PMID: 19528222 DOI: 10.1128/iai.00063-09] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
To investigate the extent to which macrophages respond to Salmonella infection, we infected RAW 264.7 macrophages with Salmonella enterica serotype Typhimurium and analyzed macrophage proteins at various time points following infection by using a global proteomic approach. A total of 1,006 macrophage and 115 Salmonella proteins were identified with high confidence. Most of the Salmonella proteins were observed in the late stage of the infection time course, which is consistent with the fact that the bacterial cells proliferate inside RAW 264.7 macrophages. The peptide abundances of most of the identified macrophage proteins remained relatively constant over the time course of infection. Compared to those of the control, the peptide abundances of 244 macrophage proteins (i.e., 24% of the total identified macrophage proteins) changed significantly after infection. The functions of these Salmonella-affected macrophage proteins were diverse, including production of antibacterial nitric oxide (i.e., inducible nitric oxide synthase), production of prostaglandin H(2) (i.e., cyclooxygenase 2), and regulation of intracellular traffic (e.g., sorting nexin 5 [SNX5], SNX6, and SNX9). Diverse functions of the Salmonella-affected macrophage proteins demonstrate a global macrophage response to Salmonella infection. Western blot analysis not only confirmed the proteomic results for a selected set of proteins but also revealed that (i) the protein abundance of mitochondrial superoxide dismutase increased following macrophage infection, indicating an infection-induced oxidative stress in mitochondria, and (ii) in contrast to infection of macrophages by wild-type Salmonella, infection by the sopB deletion mutant had no negative impact on the abundance of SNX6, suggesting a role for SopB in regulating the abundance of SNX6.
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Hervey WJ, Khalsa-Moyers G, Lankford PK, Owens ET, McKeown CK, Lu TY, Foote LJ, Asano KG, Morrell-Falvey JL, McDonald WH, Pelletier DA, Hurst GB. Evaluation of Affinity-Tagged Protein Expression Strategies Using Local and Global Isotope Ratio Measurements. J Proteome Res 2009; 8:3675-88. [DOI: 10.1021/pr801088f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- W. Judson Hervey
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Gurusahai Khalsa-Moyers
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Patricia K. Lankford
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Elizabeth T. Owens
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Catherine K. McKeown
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Tse-Yuan Lu
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Linda J. Foote
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Keiji G. Asano
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Jennifer L. Morrell-Falvey
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - W. Hayes McDonald
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Dale A. Pelletier
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
| | - Gregory B. Hurst
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville and Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, Tennessee 37830-8026, Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, and Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131
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Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 2009; 75:4599-615. [PMID: 19429552 DOI: 10.1128/aem.02943-08] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.
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Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 2009; 73:62-70. [PMID: 19258533 DOI: 10.1128/mmbr.00028-08] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It also highlights current publications and describes major scientific findings. The review closes with a discussion of critical improvements in the area of integrating experimental mass spectrometry technologies with bioinformatics as well as improved sample handling.
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Differential accumulation of form I RubisCO in Rhodopseudomonas palustris CGA010 under Photoheterotrophic growth conditions with reduced carbon sources. J Bacteriol 2009; 191:4243-50. [PMID: 19376869 DOI: 10.1128/jb.01795-08] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodopseudomonas palustris is unique among characterized nonsulfur purple bacteria because of its capacity for anaerobic photoheterotrophic growth using aromatic acids. Like growth with other reduced electron donors, this growth typically requires the presence of bicarbonate/CO(2) or some other added electron acceptor in the growth medium. Proteomic studies indicated that there was specific accumulation of form I ribulose 1, 5-bisphosphate carboxylase/oxygenase (RubisCO) subunit proteins (CbbL and CbbS), as well as the CbbX protein, in cells grown on benzoate without added bicarbonate; such cells used the small amounts of dissolved CO(2) in the medium to support growth. These proteins were not observed in extracts from cells grown in the presence of high levels (10 mM) of added bicarbonate. To confirm the results of the proteomics studies, it was shown that the total RubisCO activity levels were significantly higher (five- to sevenfold higher) in wild-type (CGA010) cells grown on benzoate with a low level (0.5 mM) of added bicarbonate. Immunoblots indicated that the increase in RubisCO activity levels was due to a specific increase in the amount of form I RubisCO (CbbLS) and not in the amount of form II RubisCO (CbbM), which was constitutively expressed. Deletion of the main transcriptional regulator gene, cbbR, resulted in impaired growth on benzoate-containing low-bicarbonate media, and it was established that form I RubisCO synthesis was absolutely and specifically dependent on CbbR. To understand the regulatory role of the CbbRRS two-component system, strains with nonpolar deletions of the cbbRRS genes were grown on benzoate. Distinct from the results obtained with photoautotrophic growth conditions, the results of studies with various CbbRRS mutant strains indicated that this two-component system did not affect the observed enhanced synthesis of form I RubisCO under benzoate growth conditions. These studies indicate that diverse growth conditions differentially affect the ability of the CbbRRS two-component system to influence cbb transcription.
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Mastroleo F, Leroy B, Van Houdt R, s’ Heeren C, Mergeay M, Hendrickx L, Wattiez R. Shotgun Proteome Analysis of Rhodospirillum rubrum S1H: Integrating Data from Gel-Free and Gel-Based Peptides Fractionation Methods. J Proteome Res 2009; 8:2530-41. [DOI: 10.1021/pr900007d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Felice Mastroleo
- Department of Proteomics and Protein Biochemistry, University of Mons, Mons, Belgium, and Expert group Molecular and Cellular Biology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Protein Biochemistry, University of Mons, Mons, Belgium, and Expert group Molecular and Cellular Biology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium
| | - Rob Van Houdt
- Department of Proteomics and Protein Biochemistry, University of Mons, Mons, Belgium, and Expert group Molecular and Cellular Biology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium
| | - Catherine s’ Heeren
- Department of Proteomics and Protein Biochemistry, University of Mons, Mons, Belgium, and Expert group Molecular and Cellular Biology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium
| | - Max Mergeay
- Department of Proteomics and Protein Biochemistry, University of Mons, Mons, Belgium, and Expert group Molecular and Cellular Biology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium
| | - Larissa Hendrickx
- Department of Proteomics and Protein Biochemistry, University of Mons, Mons, Belgium, and Expert group Molecular and Cellular Biology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Protein Biochemistry, University of Mons, Mons, Belgium, and Expert group Molecular and Cellular Biology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium
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Lacerda CMR, Reardon KF. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:75-87. [PMID: 19279070 DOI: 10.1093/bfgp/elp005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.
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Affiliation(s)
- Carla M R Lacerda
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA
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VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 2009; 7:196-205. [DOI: 10.1038/nrmicro2080] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Carmona M, Zamarro MT, Blázquez B, Durante-Rodríguez G, Juárez JF, Valderrama JA, Barragán MJL, García JL, Díaz E. Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol Mol Biol Rev 2009; 73:71-133. [PMID: 19258534 PMCID: PMC2650882 DOI: 10.1128/mmbr.00021-08] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.
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Affiliation(s)
- Manuel Carmona
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Karpinets TV, Pelletier DA, Pan C, Uberbacher EC, Melnichenko GV, Hettich RL, Samatova NF. Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris. PLoS One 2009; 4:e4615. [PMID: 19242537 PMCID: PMC2643473 DOI: 10.1371/journal.pone.0004615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 01/07/2009] [Indexed: 11/18/2022] Open
Abstract
Anaerobic degradation of complex organic compounds by microorganisms is crucial for development of innovative biotechnologies for bioethanol production and for efficient degradation of environmental pollutants. In natural environments, the degradation is usually accomplished by syntrophic consortia comprised of different bacterial species. This strategy allows consortium organisms to reduce efforts required for maintenance of the redox homeostasis at each syntrophic level. Cellular mechanisms that maintain the redox homeostasis during the degradation of aromatic compounds by one organism are not fully understood. Here we present a hypothesis that the metabolically versatile phototrophic bacterium Rhodopseudomonas palustris forms its own syntrophic consortia, when it grows anaerobically on p-coumarate or benzoate as a sole carbon source. We have revealed the consortia from large-scale measurements of mRNA and protein expressions under p-coumarate, benzoate and succinate degrading conditions using a novel computational approach referred as phenotype fingerprinting. In this approach, marker genes for known R. palustris phenotypes are employed to determine the relative expression levels of genes and proteins in aromatics versus non-aromatics degrading condition. Subpopulations of the consortia are inferred from the expression of phenotypes and known metabolic modes of the R. palustris growth. We find that p-coumarate degrading conditions may lead to at least three R. palustris subpopulations utilizing p-coumarate, benzoate, and CO2 and H2. Benzoate degrading conditions may also produce at least three subpopulations utilizing benzoate, CO2 and H2, and N2 and formate. Communication among syntrophs and inter-syntrophic dynamics in each consortium are indicated by up-regulation of transporters and genes involved in the curli formation and chemotaxis. The N2-fixing subpopulation in the benzoate degrading consortium has preferential activation of the vanadium nitrogenase over the molybdenum nitrogenase. This subpopulation in the consortium was confirmed in an independent experiment by consumption of dissolved nitrogen gas under the benzoate degrading conditions.
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Affiliation(s)
- Tatiana V Karpinets
- Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
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Organization and Assembly of Light-Harvesting Complexes in the Purple Bacterial Membrane. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4020-8815-5_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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Harwood CS. Degradation of Aromatic Compounds by Purple Nonsulfur Bacteria. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_29] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Savidor A, Donahoo RS, Hurtado-Gonzales O, Land ML, Shah MB, Lamour KH, McDonald WH. Cross-species global proteomics reveals conserved and unique processes in Phytophthora sojae and Phytophthora ramorum. Mol Cell Proteomics 2008; 7:1501-16. [PMID: 18316789 PMCID: PMC2500229 DOI: 10.1074/mcp.m700431-mcp200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 01/23/2008] [Indexed: 11/06/2022] Open
Abstract
Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. P. sojae has a narrow host range, whereas P. ramorum has a wide host range. A global proteomics comparison of the vegetative (mycelium) and infective (germinating cyst) life stages of P. sojae and P. ramorum was conducted to identify candidate proteins involved in host range, early infection, and vegetative growth. Sixty-two candidates for early infection, 26 candidates for vegetative growth, and numerous proteins that may be involved in defining host specificity were identified. In addition, common life stage proteomic trends between the organisms were observed. In mycelia, proteins involved in transport and metabolism of amino acids, carbohydrates, and other small molecules were up-regulated. In the germinating cysts, up-regulated proteins associated with lipid transport and metabolism, cytoskeleton, and protein synthesis were observed. It appears that the germinating cyst catabolizes lipid reserves through the beta-oxidation pathway to drive the extensive protein synthesis necessary to produce the germ tube and initiate infection. Once inside the host, the pathogen switches to vegetative growth in which energy is derived from glycolysis and utilized for synthesis of amino acids and other molecules that assist survival in the plant tissue.
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Affiliation(s)
- Alon Savidor
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory Oak Ridge, Oak Ridge, Tennessee 37830, USA
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Tabb DL, Ma ZQ, Martin DB, Ham AJL, Chambers MC. DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res 2008; 7:3838-46. [PMID: 18630943 DOI: 10.1021/pr800154p] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In shotgun proteomics, tandem mass spectra of peptides are typically identified through database search algorithms such as Sequest. We have developed DirecTag, an open-source algorithm to infer partial sequence tags directly from observed fragment ions. This algorithm is unique in its implementation of three separate scoring systems to evaluate each tag on the basis of peak intensity, m/ z fidelity, and complementarity. In data sets from several types of mass spectrometers, DirecTag reproducibly exceeded the accuracy and speed of InsPecT and GutenTag, two previously published algorithms for this purpose. The source code and binaries for DirecTag are available from http://fenchurch.mc.vanderbilt.edu.
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Affiliation(s)
- David L Tabb
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8575, USA.
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45
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Selao TT, Nordlund S, Norén A. Comparative Proteomic Studies in Rhodospirillum rubrum Grown under Different Nitrogen Conditions. J Proteome Res 2008; 7:3267-75. [DOI: 10.1021/pr700771u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tiago T. Selao
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
| | - Stefan Nordlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
| | - Agneta Norén
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
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46
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Pan C, Oda Y, Lankford PK, Zhang B, Samatova NF, Pelletier DA, Harwood CS, Hettich RL. Characterization of Anaerobic Catabolism of p-Coumarate in Rhodopseudomonas palustris by Integrating Transcriptomics and Quantitative Proteomics. Mol Cell Proteomics 2008; 7:938-48. [DOI: 10.1074/mcp.m700147-mcp200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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47
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Rohmer L, Guina T, Chen J, Gallis B, Taylor GK, Shaffer SA, Miller SI, Brittnacher MJ, Goodlett DR. Determination and Comparison of the Francisella tularensis subsp.novicida U112 Proteome to Other Bacterial Proteomes. J Proteome Res 2008; 7:2016-24. [DOI: 10.1021/pr700760z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laurence Rohmer
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Tina Guina
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Jinzhi Chen
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Byron Gallis
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Greg K. Taylor
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Scott A. Shaffer
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Samuel I. Miller
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Mitchell J. Brittnacher
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - David R. Goodlett
- Department of Genome Sciences, Microbiology, Medicine, Medicinal Chemistry, and Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, Washington 98195
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48
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Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD. Proteomics analysis of the causative agent of typhoid fever. J Proteome Res 2008; 7:546-57. [PMID: 18166006 DOI: 10.1021/pr070434u] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Typhoid fever is a potentially fatal disease caused by the bacterial pathogen Salmonella enterica serotype Typhi ( S. typhi). S. typhi infection is a complex process that involves numerous bacterially encoded virulence determinants, and these are thought to confer both stringent human host specificity and a high mortality rate. In the present study, we used a liquid chromatography-mass spectrometry (LC-MS)-based proteomics strategy to investigate the proteome of logarithmic, stationary phase, and low pH/low magnesium (MgM) S. typhi cultures. This represents the first large-scale comprehensive characterization of the S. typhi proteome. Our analysis identified a total of 2066 S. typhi proteins. In an effort to identify putative S. typhi-specific virulence factors, we then compared our S. typhi results to those obtained in a previously published study of the S. typhimurium proteome under similar conditions ( Adkins, J. N. et al. Mol. Cell. Proteomics 2006, 5, 1450-1461 ). Comparative proteomics analysis of S. typhi strain Ty2 and S. typhimurium strain LT2 revealed a subset of highly expressed proteins unique to S. typhi that were exclusively detected under conditions that are thought to mimic the infective state in macrophage cells. These proteins included CdtB, HlyE, and gene products of t0142, t1108, t1109, t1476, and t1602. The differential expression of T1108, T1476, and HlyE was confirmed by Western blot analysis. When our observations are taken together with the current literature, they suggest that this subset of proteins may play a role in S. typhi pathogenesis and human host specificity.
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Affiliation(s)
- Charles Ansong
- Biological Sciences Division, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Kim SI, Choi JS, Kahng HY. A proteomics strategy for the analysis of bacterial biodegradation pathways. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:280-94. [PMID: 17883339 DOI: 10.1089/omi.2007.0019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Bacterial biodegradation (bioremediation) is the use of microorganisms to break down organic materials into simpler compounds; it plays a pivotal role in the clean-up of hazardous wastes in the environment. Following the completion of genome sequencing in bacteria capable of biodegradation, functional genomic studies have played a major role in obtaining information on bacterial biodegradation pathways. Novel proteomics technologies have recently been developed to make it possible to analyze global protein expression. Proteomics can also provide important information on the life cycle, regulation, and post-translational modification of proteins induced under specific conditions. Proteomics technologies have been applied to the comprehensive study of bacterial biodegradation. In this paper, we introduce the proteomics technologies applicable to bacterial biodegradation studies, review the results of the proteomics analysis of representative biodegrading bacteria, and discuss the potential use of proteomics technologies in future biodegradation studies.
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Affiliation(s)
- Seung Il Kim
- Proteomics Team, Korea Basic Science Institute, Daejeon, Republic of Korea.
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50
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Hervey WJ, Strader MB, Hurst GB. Comparison of Digestion Protocols for Microgram Quantities of Enriched Protein Samples. J Proteome Res 2007; 6:3054-61. [PMID: 17616116 DOI: 10.1021/pr070159b] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Standard biochemical techniques that are used for protein enrichments, such as affinity isolation and density gradient centrifugation, frequently yield high-nanogram to low-microgram quantities at a significant expenditure of resources and time. The characterization of selected protein enrichments by the "shotgun" mass spectrometry approach is often compromised by the lack of effective and efficient in-solution proteolysis protocols specifically tailored for these small quantities of proteins. This study compares the results of five different digestion protocols that were applied to 2.5 mug portions of protein isolates from two disparate sources: Rhodopseudomonas palustris 70S ribosomal proteins, and Bos taurus microtubule-associated proteins (MAPs). Proteolytic peptides produced according to each protocol in each type of protein isolate were analyzed by one-dimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). The effectiveness of each digestion protocol was assessed on the basis of three parameters: number of peptide identifications, number of protein identifications, and sequence coverage. The two protocols using a solvent containing 80% acetonitrile (CH3CN) for trypsin digestions performed as well as, and in some instances better than, protocols employing other solvents and chaotropes in both types of protein isolates. A primary advantage of the 80% CH3CN protocol is that it requires fewer sample manipulation steps.
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Affiliation(s)
- W Judson Hervey
- Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P. O. Box 2008, Oak Ridge, Tennessee 37831-6131, USA
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