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Hagen LH, Brooke CG, Shaw CA, Norbeck AD, Piao H, Arntzen MØ, Olson HM, Copeland A, Isern N, Shukla A, Roux S, Lombard V, Henrissat B, O'Malley MA, Grigoriev IV, Tringe SG, Mackie RI, Pasa-Tolic L, Pope PB, Hess M. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISME J 2020; 15:421-434. [PMID: 32929206 PMCID: PMC8026616 DOI: 10.1038/s41396-020-00769-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
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Affiliation(s)
- Live H Hagen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.
| | | | | | | | - Hailan Piao
- Washington State University, Richland, WA, USA
| | - Magnus Ø Arntzen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Heather M Olson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nancy Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Anil Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Phillip B Pope
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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2
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Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB. "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system. Microbiome 2018; 6:44. [PMID: 29490697 PMCID: PMC5831590 DOI: 10.1186/s40168-018-0421-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/07/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. RESULTS The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from Ca. P. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected Ca. P. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage β-glucans. CONCLUSION We propose that Ca. P. polyenzymogene genotypes and other Ca. MH11 members actively degrade plant biomass in the rumen of cows, sheep and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.
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Affiliation(s)
- A E Naas
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - L M Solden
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - A D Norbeck
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Brewer
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - L H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - I M Heggenes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - A C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraβe 7, 38124, Braunschweig, Germany
| | - R I Mackie
- Institute for Genomic Biology and Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - L Paša-Tolić
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - M Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - V G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - N M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - M Hess
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - K C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - P B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway.
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3
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Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, del Rio TG, Suttle CA, Tringe S, Hallam SJ. A compendium of multi-omic sequence information from the Saanich Inlet water column. Sci Data 2017; 4:170160. [PMID: 29087368 PMCID: PMC5663217 DOI: 10.1038/sdata.2017.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/02/2017] [Indexed: 01/08/2023] Open
Abstract
Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.
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Affiliation(s)
- Alyse K. Hawley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Elena Zaikova
- Department of Biology, Georgetown University,
Washington, District Of Columbia 20057,
USA
| | - David A. Walsh
- Department of Biology, Concordia University,
Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Esther A. Gies
- Department of Civil Engineering, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | | | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Heather M. Brewer
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Ljiljana Pasa-Tolic
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | | | - Curtis A. Suttle
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
- Department of Botany, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Susannah Tringe
- Department of Energy Joint Genome Institute,
Walnut Creek, California 94598, USA
| | - Steven J. Hallam
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Peter Wall Institute for Advanced Studies, University of
British Columbia, Canada V6T 1Z2
- Genome Science and Technology Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- Graduate Program in Bioinformatics, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- ECOSCOPE Training Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
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4
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Staley C, Ferrieri AP, Tfaily MM, Cui Y, Chu RK, Wang P, Shaw JB, Ansong CK, Brewer H, Norbeck AD, Markillie M, do Amaral F, Tuleski T, Pellizzaro T, Agtuca B, Ferrieri R, Tringe SG, Paša-Tolić L, Stacey G, Sadowsky MJ. Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism. Microbiome 2017; 5:65. [PMID: 28646918 PMCID: PMC5483260 DOI: 10.1186/s40168-017-0287-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/07/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated. RESULTS Significantly different bacterial community structures (P = 0.031) were observed in the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles. CONCLUSIONS The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN, 55108, USA
| | - Abigail P Ferrieri
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yaya Cui
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ping Wang
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN, 55108, USA
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Charles K Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Heather Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Angela D Norbeck
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Fernanda do Amaral
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Thalita Tuleski
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Tomás Pellizzaro
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Beverly Agtuca
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Richard Ferrieri
- Department of Chemistry, University of Missouri Research Reactor, Columbia, MO, 65211, USA
| | - Susannah G Tringe
- Microbial Systems Group, Metagenome Program, DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Gary Stacey
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN, 55108, USA.
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5
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Ream TS, Haag JR, Pontvianne F, Nicora CD, Norbeck AD, Paša-Tolić L, Pikaard CS. Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit. Nucleic Acids Res 2015; 43:4163-78. [PMID: 25813043 PMCID: PMC4417161 DOI: 10.1093/nar/gkv247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 03/10/2015] [Indexed: 12/17/2022] Open
Abstract
Using affinity purification and mass spectrometry, we identified the subunits of Arabidopsis thaliana multisubunit RNA polymerases I and III (abbreviated as Pol I and Pol III), the first analysis of their physical compositions in plants. In all eukaryotes examined to date, AC40 and AC19 subunits are common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes. Surprisingly, A. thaliana and related species express two distinct AC40 paralogs, one of which assembles into Pol I and the other of which assembles into Pol III. Changes at eight amino acid positions correlate with the functional divergence of Pol I- and Pol III-specific AC40 paralogs. Two genes encode homologs of the yeast C53 subunit and either protein can assemble into Pol III. By contrast, only one of two potential C17 variants, and one of two potential C31 variants were detected in Pol III. We introduce a new nomenclature system for plant Pol I and Pol III subunits in which the 12 subunits that are structurally and functionally homologous among Pols I through V are assigned equivalent numbers.
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Affiliation(s)
- Thomas S Ream
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA
| | - Jeremy R Haag
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Frederic Pontvianne
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carrie D Nicora
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Angela D Norbeck
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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6
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Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol 2013; 4:280. [PMID: 24065962 PMCID: PMC3777014 DOI: 10.3389/fmicb.2013.00280] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/29/2013] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
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Affiliation(s)
- Kristen M Deangelis
- Department of Microbiology, University of Massachusetts Amherst Amherst, MA, USA
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7
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Nicora CD, Anderson BJ, Callister SJ, Norbeck AD, Purvine SO, Jansson JK, Mason OU, David MM, Jurelevicius D, Smith RD, Lipton MS. Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics 2013; 13:2776-85. [PMID: 23776032 DOI: 10.1002/pmic.201300003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 04/23/2013] [Accepted: 05/10/2013] [Indexed: 11/07/2022]
Abstract
Characterization of microbial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities that contribute to atmospheric CO2 levels and the earth's changing climate. A significant challenge in studying the soil microbial community proteome is the initial dissociation of bacterial proteins from the complex mixture of particles found in natural soil. The differential extraction of intact bacterial cells limits the characterization of the complete representation of a microbial community. However, in situ lysis of bacterial cells in soil can lead to potentially high levels of protein adsorption to soil particles. Here, we investigated various amino acids for their ability to block soil protein adsorption sites prior to in situ lysis of bacterial cells, as well as their compatibility with both tryptic digestion and mass spectrometric analysis. The treatments were tested by adding proteins from lysed Escherichia coli cells to representative treated and untreated soil samples. The results show that it is possible to significantly increase protein identifications through blockage of binding sites on a variety of soil and sediment textures; use of an optimized desorption buffer further increases the number of identifications.
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8
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Hawley AK, Kheirandish S, Mueller A, Leung HTC, Norbeck AD, Brewer HM, Pasa-Tolic L, Hallam SJ. Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters. Methods Enzymol 2013; 531:305-29. [PMID: 24060128 DOI: 10.1016/b978-0-12-407863-5.00016-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics.
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Affiliation(s)
- Alyse K Hawley
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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9
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Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L, Pikaard CS. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell 2012; 48:811-8. [PMID: 23142082 DOI: 10.1016/j.molcel.2012.09.027] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 08/13/2012] [Accepted: 09/19/2012] [Indexed: 01/05/2023]
Abstract
In Arabidopsis, RNA-dependent DNA methylation and transcriptional silencing involves three nuclear RNA polymerases that are biochemically undefined: the presumptive DNA-dependent RNA polymerases Pol IV and Pol V and the putative RNA-dependent RNA polymerase RDR2. Here we demonstrate their RNA polymerase activities in vitro. Unlike Pol II, Pols IV and V require an RNA primer, are insensitive to α-amanitin, and differ in their ability to displace the nontemplate DNA strand during transcription. Biogenesis of 24 nt small interfering RNAs (siRNAs), which guide cytosine methylation to corresponding sequences, requires both Pol IV and RDR2, which physically associate in vivo. Whereas Pol IV does not require RDR2 for activity, RDR2 is nonfunctional in the absence of associated Pol IV. These results suggest that the physical and mechanistic coupling of Pol IV and RDR2 results in the channeled synthesis of double-stranded precursors for 24 nt siRNA biogenesis.
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Affiliation(s)
- Jeremy R Haag
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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10
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Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. J Proteome Res 2012; 11:3520-32. [PMID: 22578083 DOI: 10.1021/pr3002996] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prevalence of diabetes mellitus is increasing dramatically throughout the world, and the disease has become a major public health issue. The most common form of the disease, type 2 diabetes, is characterized by insulin resistance and insufficient insulin production from the pancreatic beta-cell. Since glucose is the most potent regulator of beta-cell function under physiological conditions, identification of the insulin secretory defect underlying type 2 diabetes requires a better understanding of glucose regulation of human beta-cell function. To this aim, a bottom-up LC-MS/MS-based proteomics approach was used to profile pooled islets from multiple donors under basal (5 mM) or high (15 mM) glucose conditions. Our analysis discovered 256 differentially abundant proteins (∼p < 0.05) after 24 h of high glucose exposure from more than 4500 identified in total. Several novel glucose-regulated proteins were elevated under high glucose conditions, including regulators of mRNA splicing (pleiotropic regulator 1), processing (retinoblastoma binding protein 6), and function (nuclear RNA export factor 1), in addition to neuron navigator 1 and plasminogen activator inhibitor 1. Proteins whose abundances markedly decreased during incubation at 15 mM glucose included Bax inhibitor 1 and synaptotagmin-17. Up-regulation of dicer 1 and SLC27A2 and down-regulation of phospholipase Cβ4 were confirmed by Western blots. Many proteins found to be differentially abundant after high glucose stimulation are annotated as uncharacterized or hypothetical. These findings expand our knowledge of glucose regulation of the human islet proteome and suggest many hitherto unknown responses to glucose that require additional studies to explore novel functional roles.
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11
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Sigdel TK, Kaushal A, Gritsenko M, Norbeck AD, Qian WJ, Xiao W, Camp DG, Smith RD, Sarwal MM. Shotgun proteomics identifies proteins specific for acute renal transplant rejection. Proteomics Clin Appl 2011; 4:32-47. [PMID: 20543976 DOI: 10.1002/prca.200900124] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE Acute rejection (AR) remains the primary risk factor for renal transplant outcome; development of non-invasive diagnostic biomarkers for AR is an unmet need. EXPERIMENTAL DESIGN We used shotgun proteomics applying LC-MS/MS and ELISA to analyze a set of 92 urine samples, from patients with AR, stable grafts (STA), proteinuria (NS), and healthy controls. RESULTS A total of 1446 urinary proteins (UP) were identified along with a number of nonspecific proteinuria-specific, renal transplantation specific and AR-specific proteins. Relative abundance of identified UP was measured by protein-level spectral counts adopting a weighted fold-change statistic, assigning increased weight for more frequently observed proteins. We have identified alterations in a number of specific UP in AR, primarily relating to MHC antigens, the complement cascade and extra-cellular matrix proteins. A subset of proteins (uromodulin, SERPINF1 and CD44), have been further cross-validated by ELISA in an independent set of urine samples, for significant differences in the abundance of these UP in AR. CONCLUSIONS AND CLINICAL RELEVANCE This label-free, semi-quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of UP for serial, non-invasive clinical monitoring for graft rejection after kidney transplantation.
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Affiliation(s)
- Tara K Sigdel
- Department of Pediatrics, Stanford University School of Medicine, CA 94304, USA
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12
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Lin M, Kikuchi T, Brewer HM, Norbeck AD, Rikihisa Y. Global proteomic analysis of two tick-borne emerging zoonotic agents: anaplasma phagocytophilum and ehrlichia chaffeensis. Front Microbiol 2011; 2:24. [PMID: 21687416 PMCID: PMC3109344 DOI: 10.3389/fmicb.2011.00024] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Accepted: 01/31/2011] [Indexed: 11/29/2022] Open
Abstract
Anaplasma phagocytophilum and Ehrlichia chaffeensis are obligatory intracellular α-proteobacteria that infect human leukocytes and cause potentially fatal emerging zoonoses. In the present study, we determined global protein expression profiles of these bacteria cultured in the human promyelocytic leukemia cell line, HL-60. Mass spectrometric (MS) analyses identified a total of 1,212 A. phagocytophilum and 1,021 E. chaffeensis proteins, representing 89.3 and 92.3% of the predicted bacterial proteomes, respectively. Nearly all bacterial proteins (≥99%) with known functions were expressed, whereas only approximately 80% of “hypothetical” proteins were detected in infected human cells. Quantitative MS/MS analyses indicated that highly expressed proteins in both bacteria included chaperones, enzymes involved in biosynthesis and metabolism, and outer membrane proteins, such as A. phagocytophilum P44 and E. chaffeensis P28/OMP-1. Among 113 A. phagocytophilum p44 paralogous genes, 110 of them were expressed and 88 of them were encoded by pseudogenes. In addition, bacterial infection of HL-60 cells up-regulated the expression of human proteins involved mostly in cytoskeleton components, vesicular trafficking, cell signaling, and energy metabolism, but down-regulated some pattern recognition receptors involved in innate immunity. Our proteomics data represent a comprehensive analysis of A. phagocytophilum and E. chaffeensis proteomes, and provide a quantitative view of human host protein expression profiles regulated by bacterial infection. The availability of these proteomic data will provide new insights into biology and pathogenesis of these obligatory intracellular pathogens.
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Affiliation(s)
- Mingqun Lin
- Department of Veterinary Biosciences, The Ohio State University Columbus, OH, USA
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13
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Smith DP, Kitner JB, Norbeck AD, Clauss TR, Lipton MS, Schwalbach MS, Steindler L, Nicora CD, Smith RD, Giovannoni SJ. Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique. PLoS One 2010; 5:e10487. [PMID: 20463970 PMCID: PMC2864753 DOI: 10.1371/journal.pone.0010487] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/11/2010] [Indexed: 11/19/2022] Open
Abstract
Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Thus, we propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. We propose a model in which the RNA-binding activity of CspE and CspL selectively enables protein synthesis of the iron acquisition protein SfuC during transient growth-limiting episodes of iron scarcity.
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Affiliation(s)
- Daniel P. Smith
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Joshua B. Kitner
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Therese R. Clauss
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mary S. Lipton
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Michael S. Schwalbach
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Laura Steindler
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Carrie D. Nicora
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Richard D. Smith
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Stephen J. Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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14
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Zhou JY, Petritis BO, Petritis K, Norbeck AD, Weitz KK, Moore RJ, Camp DG, Kulkarni RN, Smith RD, Qian WJ. Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome. J Proteome Res 2010; 8:5387-95. [PMID: 19722698 DOI: 10.1021/pr900564f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report on a mouse specific SuperMix immunoaffinity separation system for separating low-abundance proteins from high and moderate abundance proteins in mouse plasma. When applied in tandem with a mouse IgY7 column that removes the seven most abundant proteins in plasma, the SuperMix column captures more than 100 additional moderate abundance proteins, thus allowing significant enrichment of low-abundance proteins in the flow-through fraction. A side-by-side comparison of results obtained from 2D-LC-MS/MS analyses of flow-through samples from IgY7 and SuperMix columns revealed a nearly 2-fold improvement in the overall proteome coverage. Detection of low-abundance proteins was also enhanced, as evidenced by a more than 2-fold increase in the coverage of cytokines, growth factors, and other low-abundance proteins. Moreover, the tandem separations are automated, reproducible, and allow effective identification of protein abundance differences from LC-MS/MS analyses. Considering the overall reproducibility and increased sensitivity using the IgY7-SuperMix separation system, we anticipate broad applications of this strategy for biomarker discovery using mouse models.
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Affiliation(s)
- Jian-Ying Zhou
- Biological Science Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Chowdhury SM, Shi L, Yoon H, Ansong C, Rommereim LM, Norbeck AD, Auberry KJ, Moore RJ, Adkins JN, Heffron F, Smith RD. A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis. J Proteome Res 2009; 8:1504-14. [PMID: 19206470 DOI: 10.1021/pr800865d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella enterica serovar Typhimurium (Salmonella Typhimurium). This method includes (i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques, (ii) in vivo cross-linking with formaldehyde, (iii) tandem affinity purification of bait proteins under fully denaturing conditions, and (iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions and permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of noncross-linked proteins to bait proteins. Two different negative controls were employed to eliminate the possibility of identifying background and nonspecific proteins as interacting partners, especially those caused by nonspecific binding to the stationary phase used for protein purification. In an initial demonstration of this approach, we tagged three Salmonella proteinsHimD, PduB and PhoPwith known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified for each bait protein, including the known binding partners such as HimA for HimD, as well as unexpected binding partners. Our results suggest that novel protein-protein interactions identified may be critical to pathogenesis by Salmonella.
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Affiliation(s)
- Saiful M Chowdhury
- Pacific Northwest National Laboratory, Richland, Washington 99352, Oregon Health and Science University, Portland, Oregon 97239, USA
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17
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Yang F, Wu S, Stenoien DL, Zhao R, Monroe ME, Gristenko MA, Purvine SO, Polpitiya AD, Tolić N, Zhang Q, Norbeck AD, Orton DJ, Moore RJ, Tang K, Anderson GA, Paša-Tolić L, Camp DG, Smith RD. Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides. Anal Chem 2009; 81:4137-43. [PMID: 19371082 PMCID: PMC2749721 DOI: 10.1021/ac802605m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Here, we report a new approach that integrates pulsed Q dissociation (PQD) and electron transfer dissociation (ETD) techniques for confident and quantitative identification of iTRAQ-labeled phosphopeptides. The use of isobaric tags for relative and absolute quantification enables a high-throughput quantification of peptides via reporter ion signals in the low m/z range of tandem mass spectra. PQD, a form of ion trap collision activated dissociation, allows for detection of low mass-to-charge fragment ions, and electron transfer dissociation is especially useful for sequencing peptides that contain post-translational modifications. Analysis of the phosphoproteome of human fibroblast cells using a sensitive linear ion trap mass spectrometer demonstrated that this hybrid approach improves both identification and quantification of phosphopeptides. ETD improved phosphopeptide identification, while PQD provides improved quantification of iTRAQ-labeled phosphopeptides.
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Affiliation(s)
| | | | - David L. Stenoien
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Marina A. Gristenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Samuel O. Purvine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Ashoka D. Polpitiya
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Nikola Tolić
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Qibin Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Angela D. Norbeck
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Daniel J. Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Gordon A. Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Ljiljana Paša-Tolić
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
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18
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Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, Zhu JK, Hagen G, Guilfoyle TJ, Pasa-Tolić L, Pikaard CS. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol Cell 2008; 33:192-203. [PMID: 19110459 DOI: 10.1016/j.molcel.2008.12.015] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 12/08/2008] [Accepted: 12/10/2008] [Indexed: 01/09/2023]
Abstract
In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, abbreviated as Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. We show that Arabidopsis Pol IV and Pol V are composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Four subunits of Pol IV are distinct from their Pol II paralogs, six subunits of Pol V are distinct from their Pol II paralogs, and four subunits differ between Pol IV and Pol V. Importantly, the subunit differences occur in key positions relative to the template entry and RNA exit paths. Our findings support the hypothesis that Pol IV and Pol V are Pol II-like enzymes that evolved specialized roles in the production of noncoding transcripts for RNA silencing and genome defense.
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Affiliation(s)
- Thomas S Ream
- Biology Department, Washington University, St. Louis, MO 63130, USA
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19
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Mottaz-Brewer HM, Norbeck AD, Adkins JN, Manes NP, Ansong C, Shi L, Rikihisa Y, Kikuchi T, Wong SW, Estep RD, Heffron F, Pasa-Tolic L, Smith RD. Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems. J Biomol Tech 2008; 19:285-295. [PMID: 19183792 PMCID: PMC2628077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mass spectrometry-based proteomics is a powerful analytical tool for investigating pathogens and their interactions within a host. The sensitivity of such analyses provides broad proteome characterization, but the sample-handling procedures must first be optimized to ensure compatibility with the technique and to maximize the dynamic range of detection. The decision-making process for determining optimal growth conditions, preparation methods, sample analysis methods, and data analysis techniques in our laboratory is discussed herein with consideration of the balance in sensitivity, specificity, and biomass losses during analysis of host-pathogen systems.
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Affiliation(s)
- Heather M. Mottaz-Brewer
- Pacific Northwest National Laboratory, Environmental and Molecular Sciences Laboratory, Richland
| | - Angela D. Norbeck
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA
| | - Joshua N. Adkins
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA
| | - Nathan P. Manes
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA
| | - Charles Ansong
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA
| | - Liang Shi
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA
| | - Yasuko Rikihisa
- Ohio State University, Department of Veterinary Biosciences, Columbus, OH
| | - Takane Kikuchi
- Ohio State University, Department of Veterinary Biosciences, Columbus, OH
| | - Scott W. Wong
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR
| | - Ryan D. Estep
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR
| | - Fred Heffron
- Department of Molecular Microbiolog y and Immunolog y, Oregon Health & Science University, Portland, OR
| | - Ljiljana Pasa-Tolic
- Pacific Northwest National Laboratory, Environmental and Molecular Sciences Laboratory, Richland
| | - Richard D. Smith
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA
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20
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Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, Carlson CA, Smith RD, Giovanonni SJ. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 2008; 3:93-105. [PMID: 18769456 DOI: 10.1038/ismej.2008.83] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The northwestern Sargasso Sea undergoes annual cycles of productivity with increased production in spring corresponding to periods of upwelling, and oligotrophy in summer and autumn, when the water column becomes highly stratified. The biological productivity of this region is reduced during stratified periods as a result of low concentrations of phosphorus and nitrogen in the euphotic zone. To better understand the mechanisms of microbial survival in this oligotrophic environment, we used capillary liquid chromatography (LC)-tandem mass spectrometry to detect microbial proteins in surface samples collected in September 2005. A total of 2215 peptides that mapped to 236 SAR11 proteins, 1911 peptides that mapped to 402 Prochlorococcus proteins and 2407 peptides that mapped to 404 Synechococcus proteins were detected. Mass spectra from SAR11 periplasmic substrate-binding proteins accounted for a disproportionately large fraction of the peptides detected, consistent with observations that these extremely small cells devote a large proportion of their volume to periplasm. Abundances were highest for periplasmic substrate-binding proteins for phosphate, amino acids, phosphonate, sugars and spermidine. Proteins implicated in the prevention of oxidative damage and protein refolding were also abundant. Our findings support the view that competition for multiple nutrients in oligotrophic systems is extreme, but nutrient flux is sufficient to sustain microbial community activity.
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Affiliation(s)
- Sarah M Sowell
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JSD, Metz TO, Adkins JN, Smith RD, Heffron F. Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics. Mol Cell Proteomics 2007; 6:717-27. [PMID: 17228056 DOI: 10.1074/mcp.m600282-mcp200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The pathogen Salmonella enterica is known to cause both food poisoning and typhoid fever. Because of the emergence of antibiotic-resistant isolates and the threat of bioterrorism (e.g. contamination of the food supply), there is a growing need to study this bacterium. In this investigation, comparative peptidomics was used to study S. enterica serovar Typhimurium cultured in either a rich medium or in an acidic, low magnesium, and minimal nutrient medium designed to roughly mimic the macrophage phagosomal environment (within which Salmonella are known to survive). Native peptides from cleared cell lysates were enriched by using isopropanol extraction and analyzed by using both LC-MS/MS and LC-FTICR-MS. We identified and quantified 5,163 peptides originating from 682 proteins, and the data clearly indicated that compared with Salmonella cultured in the rich medium, cells cultured in the phagosome-mimicking medium had dramatically higher abundances of a wide variety of protein degradation products, especially from ribosomal proteins. Salmonella from the same cultures were also analyzed using traditional, bottom-up proteomic methods, and when the peptidomics and proteomics data were analyzed together, two clusters of proteins targeted for proteolysis were tentatively identified. Possible roles of targeted proteolysis by phagocytosed Salmonella are discussed.
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Affiliation(s)
- Nathan P Manes
- Fundamental Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Norbeck AD, Callister SJ, Monroe ME, Jaitly N, Elias DA, Lipton MS, Smith RD. Proteomic approaches to bacterial differentiation. J Microbiol Methods 2006; 67:473-86. [PMID: 16919344 DOI: 10.1016/j.mimet.2006.04.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 04/19/2006] [Accepted: 04/28/2006] [Indexed: 01/30/2023]
Abstract
Mass spectrometry-based proteomics has been used extensively to explore the proteomes of various organisms, and this technology is now being applied to the characterization of bacterial species. Predominantly, two methods emerge as leaders in this application. Intact protein profiling creates fingerprints of bacterial species which can be used for differentiation and tracking over time. Peptide-centric approaches, analyzed after enzymatic digestion, enable high-throughput proteome characterization in addition to species determination from the identification of peptides distinctive to a species. Highlighted herein is an application of a peptide-centric approach to the identification and quantitation of species-specific peptide identifiers using an in silico exploration and an experimental mass spectrometry-based method. The application to microbial communities is addressed with an in silico analysis of an artificial complex community of 25 microorganisms.
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Affiliation(s)
- Angela D Norbeck
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN, K8-98, Richland, WA 99352, USA
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24
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Shi L, Adkins JN, Coleman JR, Schepmoes AA, Dohnkova A, Mottaz HM, Norbeck AD, Purvine SO, Manes NP, Smallwood HS, Wang H, Forbes J, Gros P, Uzzau S, Rodland KD, Heffron F, Smith RD, Squier TC. Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. J Biol Chem 2006; 281:29131-40. [PMID: 16893888 DOI: 10.1074/jbc.m604640200] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To evade host resistance mechanisms, Salmonella enterica serovar Typhimurium (STM), a facultative intracellular pathogen, must alter its proteome following macrophage infection. To identify new colonization and virulence factors that mediate STM pathogenesis, we have isolated STM cells from RAW 264.7 macrophages at various time points following infection and used a liquid chromatography-mass spectrometry-based proteomic approach to detect the changes in STM protein abundance. Because host resistance to STM infection is strongly modulated by the expression of a functional host-resistant regulator, i.e. natural resistance-associated macrophage protein 1 (Nramp1, also called Slc11a1), we have also examined the effects of Nramp1 activity on the changes of STM protein abundances. A total of 315 STM proteins have been identified from isolated STM cells, which are largely housekeeping proteins whose abundances remain relatively constant during the time course of infection. However, 39 STM proteins are strongly induced after infection, suggesting their involvement in modulating colonization and infection. Of the 39 induced proteins, 6 proteins are specifically modulated by Nramp1 activity, including STM3117, as well as STM3118-3119 whose time-dependent abundance changes were confirmed using Western blot analysis. Deletion of the gene encoding STM3117 resulted in a dramatic reduction in the ability of STM to colonize wild-type RAW 264.7 macrophages, demonstrating a critical involvement of STM3117 in promoting the replication of STM inside macrophages. The predicted function common for STM3117-3119 is biosynthesis and modification of the peptidoglycan layer of the STM cell wall.
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Affiliation(s)
- Liang Shi
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA.
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25
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Liu T, Qian WJ, Mottaz HM, Gritsenko MA, Norbeck AD, Moore RJ, Purvine SO, Camp DG, Smith RD. Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol Cell Proteomics 2006; 5:2167-74. [PMID: 16854842 PMCID: PMC1850944 DOI: 10.1074/mcp.t600039-mcp200] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Strategies for removal of high abundance proteins have been increasingly utilized in proteomic studies of serum/plasma and other body fluids to enhance the detection of low abundance proteins and achieve broader proteome coverage; however, both the reproducibility and specificity of the high abundance protein depletion process still represent common concerns. Here we report a detailed evaluation of immunoaffinity subtraction performed applying the ProteomeLab IgY-12 system that is commonly used in human serum/plasma proteome characterization in combination with high resolution LC-MS/MS. Plasma samples were repeatedly processed using this approach, and the resulting flow-through fractions and bound fractions were individually analyzed for comparison. The removal of target proteins by the immunoaffinity subtraction system and the overall process was highly reproducible. Non-target proteins, including one spiked protein standard (rabbit glyceraldehyde-3-phosphate dehydrogenase), were also observed to bind to the column at different levels but also in a reproducible manner. The results suggest that multiprotein immunoaffinity subtraction systems can be readily integrated into quantitative strategies to enhance detection of low abundance proteins in biomarker discovery studies.
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Affiliation(s)
- Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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26
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Adkins JN, Mottaz HM, Norbeck AD, Gustin JK, Rue J, Clauss TRW, Purvine SO, Rodland KD, Heffron F, Smith RD. Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Mol Cell Proteomics 2006; 5:1450-61. [PMID: 16684765 DOI: 10.1074/mcp.m600139-mcp200] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (also known as Salmonella typhimurium) is a facultative intracellular pathogen that causes approximately 8,000 reported cases of acute gastroenteritis and diarrhea each year in the United States. Although many successful physiological, biochemical, and genetic approaches have been taken to determine the key virulence determinants encoded by this organism, the sheer number of uncharacterized reading frames observed within the S. enterica genome suggests that many more virulence factors remain to be discovered. We used a liquid chromatography-mass spectrometry-based "bottom-up" proteomic approach to generate a more complete picture of the gene products that S. typhimurium synthesizes under typical laboratory conditions as well as in culture media that are known to induce expression of virulence genes. When grown to logarithmic phase in rich medium, S. typhimurium is known to express many genes that are required for invasion of epithelial cells. Conversely stationary phase cultures of S. typhimurium express genes that are needed for both systemic infection and growth within infected macrophages. Lastly bacteria grown in an acidic, magnesium-depleted minimal medium (MgM) designed to mimic the phagocytic vacuole have been shown to up-regulate virulence gene expression. Initial comparisons of protein abundances from bacteria grown under each of these conditions indicated that the majority of proteins do not change significantly. However, we observed subsets of proteins whose expression was largely restricted to one of the three culture conditions. For example, cells grown in MgM had a higher abundance of Mg(2+) transport proteins than found in other growth conditions. A second more virulent S. typhimurium strain (14028) was also cultured under these same growth conditions, and the results were directly compared with those obtained for strain LT2. This comparison offered a unique opportunity to contrast protein populations in these closely related bacteria. Among a number of proteins displaying a higher abundance in strain 14028 were the products of the pdu operon, which encodes enzymes required for propanediol utilization. These pdu operon proteins were validated in culture and during macrophage infection. Our work provides further support for earlier observations that suggest pdu gene expression contributes to S. typhimurium pathogenesis.
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Affiliation(s)
- Joshua N Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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27
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Norbeck AD, Monroe ME, Adkins JN, Smith RD. The utility of accurate mass and LC elution time information in the analysis of complex proteomes. J Am Soc Mass Spectrom 2005; 16:1239-49. [PMID: 15979333 PMCID: PMC1769320 DOI: 10.1016/j.jasms.2005.05.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Revised: 05/20/2005] [Accepted: 05/23/2005] [Indexed: 05/03/2023]
Abstract
The combination of mass and normalized elution time (NET) of a peptide identified by liquid chromatography-mass spectrometry (LC-MS) measurements can serve as a unique signature for that peptide. However, the specificity of an LC-MS measurement depends upon the complexity of the proteome (i.e., the number of possible peptides) and the accuracy of the LC-MS measurements. In this work, theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity. Accuracy of the LC-MS measurement of mass-NET pairs (on a 0 to 1.0 NET scale) was described by bivariate normal sampling distributions centered on the peptide signatures. Measurement accuracy (i.e., mass and NET standard deviations of +/-0.1, 1, 5, and 10 ppm, and +/-0.01 and 0.05, respectively) was varied to evaluate improvements in process quality. The spatially localized confidence score, a conditional probability of peptide uniqueness, formed the basis for the peptide identification. Application of this approach to organisms with comparatively small proteomes, such as Deinococcus radiodurans, shows that modest mass and elution time accuracies are generally adequate for confidently identifying most peptides. For more complex proteomes, more accurate measurements are required. However, the study suggests that the majority of proteins for even the human proteome should be identifiable with reasonable confidence by using LC-MS measurements with mass accuracies within +/-1 ppm and high efficiency separations having elution time measurements within +/-0.01 NET.
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Affiliation(s)
| | | | | | - Richard D. Smith
- Address reprint requests to: Richard D. Smith, Pacific Northwest National Laboratories, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, Phone: 509-376-0723, Fax: 509-376-7722,
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28
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Farr CD, Gafken PR, Norbeck AD, Doneanu CE, Stapels MD, Barofsky DF, Minami M, Saugstad JA. Proteomic analysis of native metabotropic glutamate receptor 5 protein complexes reveals novel molecular constituents. J Neurochem 2004; 91:438-50. [PMID: 15447677 PMCID: PMC2747775 DOI: 10.1111/j.1471-4159.2004.02735.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We used a proteomic approach to identify novel proteins that may regulate metabotropic glutamate receptor 5 (mGluR5) responses by direct or indirect protein interactions. This approach does not rely on the heterologous expression of proteins and offers the advantage of identifying protein interactions in a native environment. The mGluR5 protein was immunoprecipitated from rat brain lysates; co-immunoprecipitating proteins were analyzed by mass spectrometry and identified peptides were matched to protein databases to determine the correlating parent proteins. This proteomic approach revealed the interaction of mGluR5 with known regulatory proteins, as well as novel proteins that reflect previously unidentified molecular constituents of the mGluR5-signaling complex. Immunoblot analysis confirmed the interaction of high confidence proteins, such as phosphofurin acidic cluster sorting protein 1, microtubule-associated protein 2a and dynamin 1, as mGluR5-interacting proteins. These studies show that a proteomic approach can be used to identify candidate interacting proteins. This approach may be particularly useful for neurobiology applications where distinct protein interactions within a signaling complex can dramatically alter the outcome of the response to neurotransmitter release, or the disruption of normal protein interactions can lead to severe neurological and psychiatric disorders.
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Affiliation(s)
- Carol D. Farr
- Robert S. Dow Neurobiology Laboratories, Legacy Research, Portland, Oregon, USA
| | - Philip R. Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Angela D. Norbeck
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Catalin E. Doneanu
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Martha D. Stapels
- Department of Chemistry, Oregon State University, Corvallis, Oregon, USA
| | - Douglas F. Barofsky
- Department of Chemistry, Oregon State University, Corvallis, Oregon, USA
- Mass Spectrometry Core Facility of the Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Manabu Minami
- Robert S. Dow Neurobiology Laboratories, Legacy Research, Portland, Oregon, USA
| | - Julie A. Saugstad
- Robert S. Dow Neurobiology Laboratories, Legacy Research, Portland, Oregon, USA
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