1
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Xiong Y, Mueller RS, Feng S, Guo X, Pan C. Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins. MICROBIOME 2024; 12:148. [PMID: 39118147 PMCID: PMC11313024 DOI: 10.1186/s40168-024-01866-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Proteomic stable isotope probing (SIP) is used in microbial ecology to trace a non-radioactive isotope from a labeled substrate into de novo synthesized proteins in specific populations that are actively assimilating and metabolizing the substrate in a complex microbial community. The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching. RESULTS In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard E. coli cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% 13C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with ≥ 5 atom% 13C labeling. The computational speed on Sipros 4 was > 20 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two 13C-SIP experiments on a real-world soil community. The labeled proteins were used to trace 13C from 13C-methanol and 13C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins. CONCLUSION Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community. Video Abstract.
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Affiliation(s)
- Yi Xiong
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Shichao Feng
- Department of Computer Science and Engineering, University of North Texas, Denton, TX, USA
| | - Xuan Guo
- Department of Computer Science and Engineering, University of North Texas, Denton, TX, USA
| | - Chongle Pan
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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2
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Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. MICROBIOME 2023; 11:24. [PMID: 36755313 PMCID: PMC9909930 DOI: 10.1186/s40168-022-01454-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. RESULTS Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50-99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC-MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. CONCLUSIONS We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
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Affiliation(s)
- Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Marlene Violette
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Grace D'Angelo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yihua Liu
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- Max Planck Institute for Biology, Tübingen, Germany
| | - Abigail Korenek
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Nikola Tolić
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Janine McCalder
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Mary S Lipton
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.
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3
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Jameson E, Taubert M, Angel R, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol 2023; 2555:261-282. [PMID: 36306091 DOI: 10.1007/978-1-0716-2795-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.
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Affiliation(s)
- Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Martin Taubert
- Aquatic Geochemistry, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Roey Angel
- Soil & Water Research Infrastructure and Institute of Soil Biology, Biology Centre CAS, České Budějovice, Czechia
| | - Sara Coyotzi
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Özge Eyice
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton, UK.
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4
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Kieft B, Li Z, Bryson S, Hettich RL, Pan C, Mayali X, Mueller RS. Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits. Proc Natl Acad Sci U S A 2021; 118:e2101178118. [PMID: 34620710 PMCID: PMC8521717 DOI: 10.1073/pnas.2101178118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology, Oregon State University, Corvallis, OR 97331;
| | - Zhou Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Samuel Bryson
- Department of Microbiology, Oregon State University, Corvallis, OR 97331
- Department of Civil & Environmental Engineering, The University of Washington, Seattle, WA 98195
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Chongle Pan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
- Department of Microbiology and Plant Microbiology, University of Oklahoma, Norman, OK 73019
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR 97331;
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5
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Abdul Aziz FA, Suzuki K, Honjo M, Amano K, Mohd Din ARJB, Tashiro Y, Futamata H. Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture. J Biosci Bioeng 2020; 131:77-83. [PMID: 33268319 DOI: 10.1016/j.jbiosc.2020.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/24/2022]
Abstract
The coexisting mechanism of a synthetic bacterial community (SBC) was investigated to better understand how to manage microbial communities. The SBC was constructed with three kinds of phenol-utilizing bacteria, Pseudomonas sp. LAB-08, Comamonas testosteroni R2, and Cupriavidus sp. P-10, under chemostat conditions supplied with phenol as a sole carbon and energy source. Population densities of all strains were monitored by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase. Although the supply of phenol was stopped to allow perturbation in the SBC, all of the strains coexisted and the degradation of phenol was maintained for more than 800 days. The qPCR analyses showed that strains LAB-08 and R2 became dominant simultaneously, whereas strain P-10 was a minor population. This phenomenon was observed before and after the phenol-supply stoppage. The kinetic parameters for phenol of the SBC changed before and after the phenol-supply stoppage, which suggests a change in functional roles of strains in the SBC. Transcriptional levels of phenol hydroxylase and catechol dioxygenases of three strains were monitored by reverse-transcription qPCR (RT-qPCR). The RT-qPCR analyses revealed that all strains shared phenol and survived independently before the phenol-supply stoppage. After the stoppage, strain P-10 would incur the cost for degradation of phenol and catechol, whereas strains LAB-08 and R2 seemed to be cheaters using metabolites, indicating the development of the metabolic network. These results indicated that it is important for the management and redesign of microbial communities to understand the metabolism of bacterial communities.
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Affiliation(s)
- Fatma Azwani Abdul Aziz
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Kenshi Suzuki
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Masahiro Honjo
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Koki Amano
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | | | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan; Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan; Research Institution of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan.
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6
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Steinke L, Slysz GW, Lipton MS, Klatt C, Moran JJ, Romine MF, Wood JM, Anderson G, Bryant DA, Ward DM. Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat. Appl Environ Microbiol 2020; 86:e01829-19. [PMID: 31953342 PMCID: PMC7082580 DOI: 10.1128/aem.01829-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/12/2020] [Indexed: 11/20/2022] Open
Abstract
The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation.IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.
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Affiliation(s)
- Laurey Steinke
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Gordon W Slysz
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christian Klatt
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - James J Moran
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Margie F Romine
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Gordon Anderson
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, Pennsylvania, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
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7
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Li Z, Yao Q, Guo X, Crits-Christoph A, Mayes MA, Hervey WJ, Lebeis SL, Banfield JF, Hurst GB, Hettich RL, Pan C. Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO 2 and 13C-Methanol. Front Microbiol 2019; 10:2706. [PMID: 31866955 PMCID: PMC6908837 DOI: 10.3389/fmicb.2019.02706] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/08/2019] [Indexed: 11/15/2022] Open
Abstract
Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.
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Affiliation(s)
- Zhou Li
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Qiuming Yao
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xuan Guo
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Melanie A Mayes
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - William Judson Hervey
- Naval Research Laboratory, Center for Biomolecular Science and Engineering, Washington, DC, United States
| | - Sarah L Lebeis
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Gregory B Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Chongle Pan
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,School of Computer Science and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
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8
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Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics. J Proteomics 2019; 198:50-58. [DOI: 10.1016/j.jprot.2018.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
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9
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Abstract
Stable isotope probing combined with metaproteomics enables the detection and characterization of active key species in microbial populations under near-natural conditions, which greatly helps to understand the metabolic functions of complex microbial communities. This is achieved by providing growth substrates labeled with heavy isotopes such as 13C, which will be assimilated into microbial biomass. After subsequent extraction of proteins and proteolytic cleavage into peptides, the heavy isotope enrichment can be detected by high-resolution mass spectrometric analysis, and linked to the functional and taxonomic characterization of these biomarkers. Here we provide protocols for obtaining isotopically labeled proteins and for downstream SIP-metaproteomics analysis.
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Affiliation(s)
- Martin Taubert
- Faculty of Biological Sciences, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
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10
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Guo X, Li Z, Yao Q, Mueller RS, Eng JK, Tabb DL, Hervey WJ, Pan C. Sipros Ensemble improves database searching and filtering for complex metaproteomics. Bioinformatics 2018; 34:795-802. [PMID: 29028897 PMCID: PMC6192206 DOI: 10.1093/bioinformatics/btx601] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/19/2017] [Indexed: 01/14/2023] Open
Abstract
Motivation Complex microbial communities can be characterized by metagenomics and metaproteomics.
However, metagenome assemblies often generate enormous, and yet incomplete, protein
databases, which undermines the identification of peptides and proteins in
metaproteomics. This challenge calls for increased discrimination of true
identifications from false identifications by database searching and filtering
algorithms in metaproteomics. Results Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three
diverse scoring functions from MyriMatch, Comet and the original Sipros were
incorporated within a single database searching engine. Supervised classification with
logistic regression was used to filter database searching results. Benchmarking with
soil and marine microbial communities demonstrated a higher number of peptide and
protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator,
MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch &
MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on
supercomputers. Availability and implementation Freely available under the GNU GPL license at http://sipros.omicsbio.org. Supplementary information Supplementary data are
available at Bioinformatics online.
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Affiliation(s)
- Xuan Guo
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.,Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Computer Science and Engineering, University of North Texas, Denton, TX 76203, USA
| | - Zhou Li
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.,Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Qiuming Yao
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Jimmy K Eng
- Proteomics Resource, University of Washington, Seattle, WA 98195, USA
| | - David L Tabb
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - William Judson Hervey
- Naval Research Laboratory, Center for Bio/Molecular Science & Engineering (Code 6910), Washington, DC, 20375, USA
| | - Chongle Pan
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.,Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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11
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Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, Strous M. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A 2018; 115:E5576-E5584. [PMID: 29844191 PMCID: PMC6004456 DOI: 10.1073/pnas.1722325115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present "direct protein-SIF" and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts' metabolism. This confirms the usefulness of this approach to accurately determine δ13C values for different species in microbial community samples.
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Affiliation(s)
- Manuel Kleiner
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Tjorven Hinzke
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Juliane Wippler
- Symbiosis Department, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Erin Thorson
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
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12
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Hauser M, Qian C, King ST, Kauffman S, Naider F, Hettich RL, Becker JM. Identification of peptide-binding sites within BSA using rapid, laser-induced covalent cross-linking combined with high-performance mass spectrometry. J Mol Recognit 2017; 31. [PMID: 28994207 DOI: 10.1002/jmr.2680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/31/2017] [Accepted: 09/17/2017] [Indexed: 11/07/2022]
Abstract
We are developing a rapid, time-resolved method using laser-activated cross-linking to capture protein-peptide interactions as a means to interrogate the interaction of serum proteins as delivery systems for peptides and other molecules. A model system was established to investigate the interactions between bovine serum albumin (BSA) and 2 peptides, the tridecapeptide budding-yeast mating pheromone (α-factor) and the decapeptide human gonadotropin-releasing hormone (GnRH). Cross-linking of α-factor, using a biotinylated, photoactivatable p-benzoyl-L-phenylalanine (Bpa)-modified analog, was energy-dependent and achieved within seconds of laser irradiation. Protein blotting with an avidin probe was used to detect biotinylated species in the BSA-peptide complex. The cross-linked complex was trypsinized and then interrogated with nano-LC-MS/MS to identify the peptide cross-links. Cross-linking was greatly facilitated by Bpa in the peptide, but some cross-linking occurred at higher laser powers and high concentrations of a non-Bpa-modified α-factor. This was supported by experiments using GnRH, a peptide with sequence homology to α-factor, which was likewise found to be cross-linked to BSA by laser irradiation. Analysis of peptides in the mass spectra showed that the binding site for both α-factor and GnRH was in the BSA pocket defined previously as the site for fatty acid binding. This model system validates the use of laser-activation to facilitate cross-linking of Bpa-containing molecules to proteins. The rapid cross-linking procedure and high performance of MS/MS to identify cross-links provides a method to interrogate protein-peptide interactions in a living cell in a time-resolved manner.
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Affiliation(s)
- Melinda Hauser
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Chen Qian
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Steven T King
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Sarah Kauffman
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Fred Naider
- Department of Chemistry and Macromolecular Assemblies Institute, College of Staten Island, CUNY, New York, NY, USA
- Programs in Biochemistry and Chemistry, Graduate Center, The City University of New York, New York, NY, USA
| | - Robert L Hettich
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Jeffrey M Becker
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
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13
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Bryson S, Li Z, Chavez F, Weber PK, Pett-Ridge J, Hettich RL, Pan C, Mayali X, Mueller RS. Phylogenetically conserved resource partitioning in the coastal microbial loop. ISME JOURNAL 2017; 11:2781-2792. [PMID: 28800138 PMCID: PMC5702734 DOI: 10.1038/ismej.2017.128] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 11/09/2022]
Abstract
Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.
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Affiliation(s)
- Samuel Bryson
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Zhou Li
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Robert L Hettich
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Chongle Pan
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
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14
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Qian C, Hettich RL. Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements. J Proteome Res 2017; 16:2537-2546. [DOI: 10.1021/acs.jproteome.7b00103] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chen Qian
- Graduate
School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert L. Hettich
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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15
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Li Z, Yao Q, Dearth SP, Entler MR, Castro Gonzalez HF, Uehling JK, Vilgalys RJ, Hurst GB, Campagna SR, Labbé JL, Pan C. Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system. Environ Microbiol 2017; 19:1041-1053. [DOI: 10.1111/1462-2920.13605] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/08/2016] [Accepted: 11/16/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Zhou Li
- Computer Science and Mathematics Division, Oak Ridge National Laboratory; Oak Ridge TN USA
- Chemical Sciences Division, Oak Ridge National Laboratory; Oak Ridge TN USA
| | - Qiuming Yao
- Computer Science and Mathematics Division, Oak Ridge National Laboratory; Oak Ridge TN USA
| | | | - Matthew R. Entler
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory; Knoxville TN USA
- Biosciences Division, Oak Ridge National Laboratory; Oak Ridge USA
| | | | | | | | - Gregory B. Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory; Oak Ridge TN USA
| | | | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory; Oak Ridge USA
| | - Chongle Pan
- Computer Science and Mathematics Division, Oak Ridge National Laboratory; Oak Ridge TN USA
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory; Knoxville TN USA
- Biosciences Division, Oak Ridge National Laboratory; Oak Ridge USA
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16
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Abstract
In vivo isotopic labeling coupled with high-resolution proteomics is used to investigate primary metabolism in techniques such as stable isotope probing (protein-SIP) and peptide-based metabolic flux analysis (PMFA). Isotopic enrichment of carbon substrates and intracellular metabolism determine the distribution of isotopes within amino acids. The resulting amino acid mass distributions (AMDs) are convoluted into peptide mass distributions (PMDs) during protein synthesis. With no a priori knowledge on metabolic fluxes, the PMDs are therefore unknown. This complicates labeled peptide identification because prior knowledge on PMDs is used in all available peptide identification software. An automated framework for the identification and quantification of PMDs for nonuniformly labeled samples is therefore lacking. To unlock the potential of peptide labeling experiments for high-throughput flux analysis and other complex labeling experiments, an unsupervised peptide identification and quantification method was developed that uses discrete deconvolution of mass distributions of identified peptides to inform on the mass distributions of otherwise unidentifiable peptides. Uniformly (13)C-labeled Escherichia coli protein was used to test the developed feature reconstruction and deconvolution algorithms. The peptide identification was validated by comparing MS(2)-identified peptides to peptides identified from PMDs using unlabeled E. coli protein. Nonuniformly labeled Glycine max protein was used to demonstrate the technology on a representative sample suitable for flux analysis. Overall, automatic peptide identification and quantification were comparable or superior to manual extraction, enabling proteomics-based technology for high-throughput flux analysis studies.
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Affiliation(s)
- Joshua E Goldford
- Biotechnology Institute, University of Minnesota , Saint Paul, Minnesota 55108, United States
| | - Igor G L Libourel
- Biotechnology Institute, University of Minnesota , Saint Paul, Minnesota 55108, United States
- Department of Plant Biology, 1500 Gortner Avenue, University of Minnesota , Saint Paul, Minnesota 55108, United States
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17
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Marlow JJ, Skennerton CT, Li Z, Chourey K, Hettich RL, Pan C, Orphan VJ. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. Front Microbiol 2016; 7:563. [PMID: 27199908 PMCID: PMC4850331 DOI: 10.3389/fmicb.2016.00563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were 15N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis—including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)—were all observed to be actively synthesized (15N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of 15N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here demonstrates the active synthesis of a metabolically specific minority of enzymes, revealing the surprising longevity of most proteins over the course of an extended incubation experiment in an established, slow-growing, methane-impacted environmental system.
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Affiliation(s)
- Jeffrey J Marlow
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Connor T Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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18
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Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton. mSystems 2016; 1:mSystems00027-15. [PMID: 27822523 PMCID: PMC5069745 DOI: 10.1128/msystems.00027-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/17/2016] [Indexed: 01/21/2023] Open
Abstract
An estimated 50 gigatons of carbon is annually fixed within marine systems, of which heterotrophic microbial populations process nearly half. These communities vary in composition and activity across spatial and temporal scales, so understanding how these changes affect global processes requires the delineation of functional roles for individual members. In a step toward ascertaining these roles, we applied proteomic stable isotope probing to quantify the assimilation of organic carbon from DFAAs into microbial protein biomass, since the turnover of DFAAs accounts for a substantial fraction of marine microbial carbon metabolism that is directed into biomass production. We conducted experiments at two coastal North Pacific locations and found taxonomically distinct responses. This approach allowed us to compare amino acid assimilation by specific bacterioplankton populations and characterize their allocation of this substrate among cellular functions. Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual primary production, yet defining how substrate utilization preferences and resource partitioning structure microbial communities remains a challenge. In this study, proteomic stable isotope probing (proteomic SIP) was used to characterize population-specific assimilation of dissolved free amino acids (DFAAs), a major source of dissolved organic carbon for bacterial secondary production in aquatic environments. Microcosms of seawater collected from Newport, Oregon, and Monterey Bay, California, were incubated with 1 µM 13C-labeled amino acids for 15 and 32 h. The taxonomic compositions of microcosm metaproteomes were highly similar to those of the sampled natural communities, with Rhodobacteriales, SAR11, and Flavobacteriales representing the dominant taxa. Analysis of 13C incorporation into protein biomass allowed for quantification of the isotopic enrichment of identified proteins and subsequent determination of differential amino acid assimilation patterns between specific bacterioplankton populations. Proteins associated with Rhodobacterales tended to have a significantly high frequency of 13C-enriched peptides, opposite the trend for Flavobacteriales and SAR11 proteins. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13C-enriched spectra at time point 2. Alteromonadales proteins also had a significantly high frequency of 13C-enriched peptides, particularly within ribosomal proteins, demonstrating their rapid growth during incubations. Overall, proteomic SIP facilitated quantitative comparisons of DFAA assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population level metabolic responses to resource acquisition in complex microbial communities. IMPORTANCE An estimated 50 gigatons of carbon is annually fixed within marine systems, of which heterotrophic microbial populations process nearly half. These communities vary in composition and activity across spatial and temporal scales, so understanding how these changes affect global processes requires the delineation of functional roles for individual members. In a step toward ascertaining these roles, we applied proteomic stable isotope probing to quantify the assimilation of organic carbon from DFAAs into microbial protein biomass, since the turnover of DFAAs accounts for a substantial fraction of marine microbial carbon metabolism that is directed into biomass production. We conducted experiments at two coastal North Pacific locations and found taxonomically distinct responses. This approach allowed us to compare amino acid assimilation by specific bacterioplankton populations and characterize their allocation of this substrate among cellular functions.
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19
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Jehmlich N, Vogt C, Lünsmann V, Richnow HH, von Bergen M. Protein-SIP in environmental studies. Curr Opin Biotechnol 2016; 41:26-33. [PMID: 27116035 DOI: 10.1016/j.copbio.2016.04.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022]
Abstract
Metaproteomics coupled to stable isotope probing (SIP) was established to detect metabolically active key players in microbial communities. Here, we discuss the current state of protein-based stable isotope probing (protein-SIP) and the perspectives of using different stable isotope atoms (i.e. 13C, 15N, 18O, 34/36S), multiple isotope labelling, the utilisation of substrates of major abundance and micro-pollutants [pesticides, herbicides and pharmaceuticals present in the environment at very low concentrations (ngμg/L)], and applications in complex model systems and in situ studies in the environment.
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Affiliation(s)
- Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Helmholtz-Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Permoserstr. 15, 04318 Leipzig, Germany
| | - Vanessa Lünsmann
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstr. 15, 04318 Leipzig, Germany; Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Hans Hermann Richnow
- Helmholtz-Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Permoserstr. 15, 04318 Leipzig, Germany
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstr. 15, 04318 Leipzig, Germany; University of Leipzig, Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany; Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark.
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20
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Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF. Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Front Microbiol 2016; 7:238. [PMID: 26973616 PMCID: PMC4776211 DOI: 10.3389/fmicb.2016.00238] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 11/22/2022] Open
Abstract
The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.
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Affiliation(s)
- Annika C. Mosier
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Christopher S. Miller
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Kyle R. Frischkorn
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
| | - Robin A. Ohm
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Zhou Li
- Oak Ridge National LaboratoryOak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National LaboratoryKnoxville, TN, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Alla Lapidus
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Cindy Chen
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Jenifer Johnson
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | | | - Chongle Pan
- Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | | | - Steven W. Singer
- Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA
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21
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Maaß S, Becher D. Methods and applications of absolute protein quantification in microbial systems. J Proteomics 2016; 136:222-33. [PMID: 26825536 DOI: 10.1016/j.jprot.2016.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/05/2016] [Accepted: 01/21/2016] [Indexed: 02/05/2023]
Abstract
In the last years the scientific community faced an increased need to provide high-quality data on the concentration of single proteins within a cell. Especially against the background of the fast evolving field of systems biology this does not only apply for a few proteins but preferably for the whole proteome of the organism. Therefore there has been a rapid development from pure identification of proteins via characterization of changes between different conditions by relative protein quantification towards determination of absolute protein amounts for hundreds of protein species in a cell. This review aims for discussion of different small-scale and large-scale approaches for absolute protein quantification in bacterial cells to picture biological processes and explore life in deeper detail. The presented advantages and limitations of various methods may provide interested researchers help to appraise available methods, select the most appropriate technique and avoid common pitfalls during determination of protein concentration in a complex sample.
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Affiliation(s)
- Sandra Maaß
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany
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22
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Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH. Enhancing metaproteomics--The value of models and defined environmental microbial systems. Proteomics 2016; 16:783-98. [PMID: 26621789 DOI: 10.1002/pmic.201500305] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 12/24/2022]
Abstract
Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.
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Affiliation(s)
- Florian-Alexander Herbst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Vanessa Lünsmann
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Henrik Kjeldal
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin von Bergen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.,Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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23
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The activity of protein phosphatase 5 towards native clients is modulated by the middle- and C-terminal domains of Hsp90. Sci Rep 2015; 5:17058. [PMID: 26593036 PMCID: PMC4655416 DOI: 10.1038/srep17058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023] Open
Abstract
Protein phosphatase 5 is involved in the regulation of kinases and transcription factors. The dephosphorylation activity is modulated by the molecular chaperone Hsp90, which binds to the TPR-domain of protein phosphatase 5. This interaction is dependent on the C-terminal MEEVD motif of Hsp90. We show that C-terminal Hsp90 fragments differ in their regulation of the phosphatase activity hinting to a more complex interaction. Also hydrodynamic parameters from analytical ultracentrifugation and small-angle X-ray scattering data suggest a compact structure for the Hsp90-protein phosphatase 5 complexes. Using crosslinking experiments coupled with mass spectrometric analysis and structural modelling we identify sites, which link the middle/C-terminal domain interface of C. elegans Hsp90 to the phosphatase domain of the corresponding kinase. Studying the relevance of the domains of Hsp90 for turnover of native substrates we find that ternary complexes with the glucocorticoid receptor (GR) are cooperatively formed by full-length Hsp90 and PPH-5. Our data suggest that the direct stimulation of the phosphatase activity by C-terminal Hsp90 fragments leads to increased dephosphorylation rates. These are further modulated by the binding of clients to the N-terminal and middle domain of Hsp90 and their presentation to the phosphatase within the phosphatase-Hsp90 complex.
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Petzold CJ, Chan LJG, Nhan M, Adams PD. Analytics for Metabolic Engineering. Front Bioeng Biotechnol 2015; 3:135. [PMID: 26442249 PMCID: PMC4561385 DOI: 10.3389/fbioe.2015.00135] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/24/2015] [Indexed: 12/20/2022] Open
Abstract
Realizing the promise of metabolic engineering has been slowed by challenges related to moving beyond proof-of-concept examples to robust and economically viable systems. Key to advancing metabolic engineering beyond trial-and-error research is access to parts with well-defined performance metrics that can be readily applied in vastly different contexts with predictable effects. As the field now stands, research depends greatly on analytical tools that assay target molecules, transcripts, proteins, and metabolites across different hosts and pathways. Screening technologies yield specific information for many thousands of strain variants, while deep omics analysis provides a systems-level view of the cell factory. Efforts focused on a combination of these analyses yield quantitative information of dynamic processes between parts and the host chassis that drive the next engineering steps. Overall, the data generated from these types of assays aid better decision-making at the design and strain construction stages to speed progress in metabolic engineering research.
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Affiliation(s)
- Christopher J Petzold
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Melissa Nhan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Paul D Adams
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
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Arsène-Ploetze F, Bertin PN, Carapito C. Proteomic tools to decipher microbial community structure and functioning. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13599-13612. [PMID: 25475614 PMCID: PMC4560766 DOI: 10.1007/s11356-014-3898-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.
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Affiliation(s)
- Florence Arsène-Ploetze
- Génétique moléculaire, Génomique et Microbiologie, Université de Strasbourg, UMR7156 CNRS, Strasbourg, France,
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26
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Xiong W, Abraham PE, Li Z, Pan C, Hettich RL. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Proteomics 2015; 15:3424-38. [PMID: 25914197 DOI: 10.1002/pmic.201400571] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/08/2015] [Accepted: 04/21/2015] [Indexed: 01/12/2023]
Abstract
The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults.
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Affiliation(s)
- Weili Xiong
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Paul E Abraham
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zhou Li
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Chongle Pan
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L Hettich
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
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Trouillard R, Hubert-Roux M, Tognetti V, Guilhaudis L, Plasson C, Menu-Bouaouiche L, Coquet L, Guerineau F, Hardouin J, Ele Ekouna JP, Cosette P, Lerouge P, Boitel-Conti M, Afonso C, Ségalas-Milazzo I. Determination of Multimodal Isotopic Distributions: The Case of a (15)N Labeled Protein Produced into Hairy Roots. Anal Chem 2015; 87:5938-46. [PMID: 25973921 DOI: 10.1021/acs.analchem.5b01558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Isotopic labeling is widely used in various fields like proteomics, metabolomics, fluxomics, as well as in NMR structural studies, but it requires an efficient determination of the isotopic enrichment. Mass spectrometry is the method of choice for such analysis. However, when complex expression systems like hairy roots are used for production, multiple populations of labeled proteins may be obtained. If the isotopic incorporation determination is actually well-known for unimodal distributions, the multimodal distributions have scarcely been investigated. Actually, only a few approaches allow the determination of the different labeled population proportions from multimodal distributions. Furthermore, they cannot be used when the number of the populations and their respective isotope ratios are unknown. The present study implements a new strategy to measure the (15)N labeled populations inside a multimodal distribution knowing only the peptide sequence and peak intensities from mass spectrometry analyses. Noteworthy, it could be applied to other elements, like carbon and hydrogen, and extended to a larger range of biomolecules.
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Affiliation(s)
- Romain Trouillard
- †Normandie Université, COBRA, UMR6014 and IRIB; Université de Rouen; INSA de Rouen; CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Marie Hubert-Roux
- ‡Normandie Université, COBRA, UMR6014 and FR3038; Université de Rouen; INSA de Rouen; CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Vincent Tognetti
- ‡Normandie Université, COBRA, UMR6014 and FR3038; Université de Rouen; INSA de Rouen; CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Laure Guilhaudis
- †Normandie Université, COBRA, UMR6014 and IRIB; Université de Rouen; INSA de Rouen; CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Carole Plasson
- §Normandie Université, Glyco-MEV, EA 4358 and IRIB, Université de Rouen, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Laurence Menu-Bouaouiche
- §Normandie Université, Glyco-MEV, EA 4358 and IRIB, Université de Rouen, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Laurent Coquet
- ∥CNRS UMR 6270, PBS, Plateforme Protéomique PISSARO, IRIB, FR3038 INC3M, Normandie Université, Université de Rouen, Boulevard Maurice de Broglie, 76821 Mont-Saint-Aignan Cedex, France
| | - François Guerineau
- ⊥Biologie des plantes et innovation (BioPI), Université de Picardie Jules Verne, 33 rue St Leu, 80039 Amiens, France
| | - Julie Hardouin
- ∥CNRS UMR 6270, PBS, Plateforme Protéomique PISSARO, IRIB, FR3038 INC3M, Normandie Université, Université de Rouen, Boulevard Maurice de Broglie, 76821 Mont-Saint-Aignan Cedex, France
| | - Jean-Pierre Ele Ekouna
- ⊥Biologie des plantes et innovation (BioPI), Université de Picardie Jules Verne, 33 rue St Leu, 80039 Amiens, France
| | - Pascal Cosette
- ∥CNRS UMR 6270, PBS, Plateforme Protéomique PISSARO, IRIB, FR3038 INC3M, Normandie Université, Université de Rouen, Boulevard Maurice de Broglie, 76821 Mont-Saint-Aignan Cedex, France
| | - Patrice Lerouge
- §Normandie Université, Glyco-MEV, EA 4358 and IRIB, Université de Rouen, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Michèle Boitel-Conti
- ⊥Biologie des plantes et innovation (BioPI), Université de Picardie Jules Verne, 33 rue St Leu, 80039 Amiens, France
| | - Carlos Afonso
- ‡Normandie Université, COBRA, UMR6014 and FR3038; Université de Rouen; INSA de Rouen; CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
| | - Isabelle Ségalas-Milazzo
- †Normandie Université, COBRA, UMR6014 and IRIB; Université de Rouen; INSA de Rouen; CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan Cedex, France
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Hedlund BP, Dodsworth JA, Staley JT. The changing landscape of microbial biodiversity exploration and its implications for systematics. Syst Appl Microbiol 2015; 38:231-6. [PMID: 25921438 DOI: 10.1016/j.syapm.2015.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 12/31/2022]
Abstract
A vast diversity of Bacteria and Archaea exists in nature that has evaded axenic culture. Advancements in single-cell genomics, metagenomics, and molecular microbial ecology approaches provide ever-improving insight into the biology of this so-called "microbial dark matter"; however, due to the International Code of Nomenclature of Prokaryotes, yet-uncultivated microorganisms are not accommodated in formal taxonomy regardless of the quantity or quality of data. Meanwhile, efforts to calibrate the existing taxonomy with phylogenetic anchors and genomic data are increasingly robust. The current climate provides an exciting opportunity to leverage rapidly expanding single-cell genomics and metagenomics datasets to improve the taxonomy of Bacteria and Archaea. However, this opportunity must be weighted carefully in light of the strengths and limitations of these approaches. We propose to expand the definition of the Candidatus taxonomy to include taxa, from the phylum level to the species level, that are described genomically, particularly when genomic work is coupled with advanced molecular ecology approaches to probe metabolic functions in situ. This system would preserve the rigor and value of traditional microbial systematics while enabling growth of a provisional taxonomic structure to facilitate communication about "dark" lineages on the tree of life.
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Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA.
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - James T Staley
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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29
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Wörmer L, Lipp JS, Hinrichs KU. Comprehensive Analysis of Microbial Lipids in Environmental Samples Through HPLC-MS Protocols. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci U S A 2014; 112:E194-203. [PMID: 25550518 DOI: 10.1073/pnas.1420406112] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.
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31
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Mao L, Franke J. Symbiosis, dysbiosis, and rebiosis-The value of metaproteomics in human microbiome monitoring. Proteomics 2014; 15:1142-51. [DOI: 10.1002/pmic.201400329] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Lei Mao
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
| | - Jacqueline Franke
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
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32
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You L, Liu H, Blankenship RE, Tang YJ. Using photosystem I as a reporter protein for ¹³C analysis in a coculture containing cyanobacterium and a heterotrophic bacterium. Anal Biochem 2014; 477:86-8. [PMID: 25527068 DOI: 10.1016/j.ab.2014.12.005] [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] [Received: 09/10/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
(13)C metabolism analysis of a microbial community is often hindered by the time-consuming and complicated separation procedure for a single species. However, a "reporter protein," produced uniquely by one cell type, retains (13)C fingerprint information in microbial consortia. This study describes the use of photosystem I (PSI), a multi-subunit protein complex universally found in oxygenic phototrophs, as a reliable reporter protein to probe microalgal metabolism (i.e., cyanobacterium Synechocystis sp. PCC 6803) in a mixed culture with heterotrophic bacteria (i.e., Escherichia coli). We demonstrate that efficient purification of PSI and subsequent (13)C-based amino acid analyses may decipher photomixotrophic metabolism of Synechocystis 6803 in the coculture. This study also indicates that a supplement of NaHCO3 at high concentration could significantly improve the robustness of cyanobacterial growth against bacterial contamination.
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Affiliation(s)
- Le You
- Department of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Haijun Liu
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Robert E Blankenship
- Department of Biology, Washington University, St. Louis, MO 63130, USA; Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Yinjie J Tang
- Department of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, MO 63130, USA.
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33
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Abram F. Systems-based approaches to unravel multi-species microbial community functioning. Comput Struct Biotechnol J 2014; 13:24-32. [PMID: 25750697 PMCID: PMC4348430 DOI: 10.1016/j.csbj.2014.11.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 01/24/2023] Open
Abstract
Some of the most transformative discoveries promising to enable the resolution of this century's grand societal challenges will most likely arise from environmental science and particularly environmental microbiology and biotechnology. Understanding how microbes interact in situ, and how microbial communities respond to environmental changes remains an enormous challenge for science. Systems biology offers a powerful experimental strategy to tackle the exciting task of deciphering microbial interactions. In this framework, entire microbial communities are considered as metaorganisms and each level of biological information (DNA, RNA, proteins and metabolites) is investigated along with in situ environmental characteristics. In this way, systems biology can help unravel the interactions between the different parts of an ecosystem ultimately responsible for its emergent properties. Indeed each level of biological information provides a different level of characterisation of the microbial communities. Metagenomics, metatranscriptomics, metaproteomics, metabolomics and SIP-omics can be employed to investigate collectively microbial community structure, potential, function, activity and interactions. Omics approaches are enabled by high-throughput 21st century technologies and this review will discuss how their implementation has revolutionised our understanding of microbial communities.
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Affiliation(s)
- Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland
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Sachsenberg T, Herbst FA, Taubert M, Kermer R, Jehmlich N, von Bergen M, Seifert J, Kohlbacher O. MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. J Proteome Res 2014; 14:619-27. [PMID: 25412983 DOI: 10.1021/pr500245w] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a joint experimental and theoretical approach to the automated reconstruction of elemental fluxes in microbial communities. While stable isotope probing of proteins (protein-SIP) has been successfully applied to study interactions and elemental carbon and nitrogen fluxes, the volume and complexity of mass spectrometric data in protein-SIP experiments pose new challenges for data analysis. Together with a flexible experimental setup, the novel bioinformatics tool MetaProSIP offers an automated high-throughput solution for a wide range of (13)C or (15)N protein-SIP experiments with special emphasis on the analysis of metaproteomic experiments where differential labeling of organisms can occur. The information calculated in MetaProSIP includes the determination of multiple relative isotopic abundances, the labeling ratio between old and new synthesized proteins, and the shape of the isotopic distribution. These parameters define the metabolic capacities and dynamics within the investigated microbial culture. MetaProSIP features a high degree of reproducibility, reliability, and quality control reporting. The ability to embed into the OpenMS framework allows for flexible construction of custom-tailored workflows. Software and documentation are available under an open-source license at www.openms.de/MetaProSIP.
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Affiliation(s)
- Timo Sachsenberg
- Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen , 72074 Tübingen, Germany
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35
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Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014; 14:547-65. [PMID: 24376008 DOI: 10.1002/pmic.201300403] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/15/2013] [Accepted: 12/06/2013] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.
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Affiliation(s)
- Andreas Otto
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Germany
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36
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Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities. PLoS Comput Biol 2014; 10:e1003827. [PMID: 25188426 PMCID: PMC4154649 DOI: 10.1371/journal.pcbi.1003827] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/23/2014] [Indexed: 01/08/2023] Open
Abstract
The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species. Microbial communities underlie a variety of important biochemical processes ranging from underground cave formation to gold mining or the onset of obesity. Metabolic fluxes describe how carbon and energy flow through the microbial community and therefore provide insights that are rarely captured by other techniques, such as metatranscriptomics or metaproteomics. The most authoritative method to measure fluxes for pure cultures consists of feeding the cells a labeled carbon source and deriving the fluxes from the ensuing metabolite labeling pattern (typically amino acids). Since we cannot easily separate cells of metabolite for each species in a community, this approach is not generally applicable to microbial communities. Here we present a method to derive fluxes from the labeling of peptides, instead of amino acids. This approach has the advantage that peptides can be assigned to each species in a community in a high-throughput fashion through modern proteomic methods. We show that, by using this method, it is theoretically possible to recover the same amount of information as through the standard approach, if enough peptides are used. We computationally tested this method with a well-characterized simple microbial community consisting of two species.
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Affiliation(s)
- Amit Ghosh
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Jerome Nilmeier
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Daniel Weaver
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Jay D. Keasling
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, United States of America
| | - Aindrila Mukhopadhyay
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Christopher J. Petzold
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Héctor García Martín
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
- * E-mail:
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37
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Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat Commun 2014; 5:4405. [PMID: 25059763 PMCID: PMC4279252 DOI: 10.1038/ncomms5405] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 06/16/2014] [Indexed: 12/27/2022] Open
Abstract
Detailed characterization of post-translational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.
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Song H, Ding MZ, Jia XQ, Ma Q, Yuan YJ. Synthetic microbial consortia: from systematic analysis to construction and applications. Chem Soc Rev 2014; 43:6954-81. [PMID: 25017039 DOI: 10.1039/c4cs00114a] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.
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Affiliation(s)
- Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, and Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China.
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Justice NB, Li Z, Wang Y, Spaudling SE, Mosier AC, Hettich RL, Pan C, Banfield JF. (15)N- and (2)H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity. Environ Microbiol 2014; 16:3224-37. [PMID: 24750948 DOI: 10.1111/1462-2920.12488] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/14/2014] [Indexed: 11/29/2022]
Abstract
Understanding how individual species contribute to nutrient transformations in a microbial community is critical to prediction of overall ecosystem function. We conducted microcosm experiments in which floating acid mine drainage (AMD) microbial biofilms were submerged - recapitulating the final stage in a natural biofilm life cycle. Biofilms were amended with either (15)NH4(+) or deuterium oxide ((2)H2O) and proteomic stable isotope probing (SIP) was used to track the extent to which different members of the community used these molecules in protein synthesis across anaerobic iron-reducing, aerobic iron-reducing and aerobic iron-oxidizing environments. Sulfobacillus spp. synthesized (15)N-enriched protein almost exclusively under iron-reducing conditions whereas the Leptospirillum spp. synthesized (15)N-enriched protein in all conditions. There were relatively few (15)N-enriched archaeal proteins, and all showed low atom% enrichment, consistent with Archaea synthesizing protein using the predominantly (14)N biomass derived from recycled biomolecules. In parallel experiments using (2)H2O, extensive archaeal protein synthesis was detected in all conditions. In contrast, the bacterial species showed little protein synthesis using (2)H2O. The nearly exclusive ability of Archaea to synthesize proteins using (2)H2O may be due to archaeal heterotrophy, whereby Archaea offset deleterious effects of (2)H by accessing (1)H generated by respiration of organic compounds.
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Affiliation(s)
- Nicholas B Justice
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
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40
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Li Z, Czarnecki O, Chourey K, Yang J, Tuskan GA, Hurst GB, Pan C, Chen JG. Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in Arabidopsis. J Proteome Res 2014; 13:1359-72. [DOI: 10.1021/pr400925t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zhou Li
- Graduate
School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, F337 Walters Life Science, Knoxville, Tennessee 37996, United States
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41
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Slysz GW, Steinke L, Ward DM, Klatt CG, Clauss TRW, Purvine SO, Payne SH, Anderson GA, Smith RD, Lipton MS. Automated data extraction from in situ protein-stable isotope probing studies. J Proteome Res 2014; 13:1200-10. [PMID: 24467184 DOI: 10.1021/pr400633j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein-stable isotope probing (protein-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. While most protein-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism(s), a key application will be in situ studies of microbial communities for short periods of time under natural conditions that result in small degrees of partial labeling. One hurdle restricting large-scale in situ protein-SIP studies is the lack of algorithms and software for automated data processing of the massive data sets resulting from such studies. In response, we developed Stable Isotope Probing Protein Extraction Resources software (SIPPER) and applied it for large-scale extraction and visualization of data from short-term (3 h) protein-SIP experiments performed in situ on phototrophic bacterial mats isolated from Yellowstone National Park. Several metrics incorporated into the software allow it to support exhaustive analysis of the complex composite isotopic envelope observed as a result of low amounts of partial label incorporation. SIPPER also enables the detection of labeled molecular species without the need for any prior identification.
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Affiliation(s)
- Gordon W Slysz
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
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42
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Mandy DE, Goldford JE, Yang H, Allen DK, Libourel IGL. Metabolic flux analysis using ¹³C peptide label measurements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:476-86. [PMID: 24279886 DOI: 10.1111/tpj.12390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/08/2013] [Accepted: 11/15/2013] [Indexed: 05/09/2023]
Abstract
¹³C metabolic flux analysis (MFA) has become the experimental method of choice to investigate the cellular metabolism of microbes, cell cultures and plant seeds. Conventional steady-state MFA utilizes isotopic labeling measurements of amino acids obtained from protein hydrolysates. To retain spatial information in conventional steady-state MFA, tissues or subcellular fractions must be dissected or biochemically purified. In contrast, peptides retain their identity in complex protein extracts, and may therefore be associated with a specific time of expression, tissue type and subcellular compartment. To enable 'single-sample' spatially and temporally resolved steady-state flux analysis, we investigated the suitability of peptide mass distributions (PMDs) as an alternative to amino acid label measurements. PMDs are the discrete convolution of the mass distributions of the constituent amino acids of a peptide. We investigated the requirements for the unique deconvolution of PMDs into amino acid mass distributions (AAMDs), the influence of peptide sequence length on parameter sensitivity, and how AAMD and flux estimates that are determined through deconvolution compare to estimates from a conventional GC-MS measurement-based approach. Deconvolution of PMDs of the storage protein β-conglycinin of soybean (Glycine max) resulted in good AAMD and flux estimates if fluxes were directly fitted to PMDs. Unconstrained deconvolution resulted in inferior AAMD and flux estimates. PMD measurements do not include amino acid backbone fragments, which increase the information content in GC-MS-derived analyses. Nonetheless, the resulting flux maps were of comparable quality due to the precision of Orbitrap quantification and the larger number of peptide measurements.
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Affiliation(s)
- Dominic E Mandy
- Department of Plant Biology, University of Minnesota, 1500 Gortner Avenue, St Paul, MN, 55108, USA
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43
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Pan C, Banfield JF. Quantitative metaproteomics: functional insights into microbial communities. Methods Mol Biol 2014; 1096:231-240. [PMID: 24515373 DOI: 10.1007/978-1-62703-712-9_18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Quantitative metaproteomics aims to accurately determine the relative abundances of thousands of proteins in a microbial community. This approach can be used to provide a comprehensive view of metabolic activities of organisms in microbial communities and uncover significant changes in protein expression between communities at different developmental stages, environment types or in response to different perturbations. Here, we describe three strategies for quantitative metaproteomics, including label-free, (15)N metabolic labeling, and isobaric chemical labeling. The measurements are all based on a shotgun proteomics workflow involving proteolysis, two-dimensional liquid chromatogram-tandem mass spectrometry, and database searching against a metagenomic protein database. Quantitative metaproteomics was established and demonstrated using a model microbial community from acid mine drainage.
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Affiliation(s)
- Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Wöhlbrand L, Trautwein K, Rabus R. Proteomic tools for environmental microbiology-A roadmap from sample preparation to protein identification and quantification. Proteomics 2013; 13:2700-30. [DOI: 10.1002/pmic.201300175] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/07/2013] [Accepted: 06/28/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Kathleen Trautwein
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
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Fischer CR, Bowen BP, Pan C, Northen TR, Banfield JF. Stable-isotope probing reveals that hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific. ACS Chem Biol 2013; 8:1755-63. [PMID: 23713674 DOI: 10.1021/cb400210q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fractionation of hydrogen stable isotopes during lipid biosynthesis is larger in autotrophic than in heterotrophic microorganisms, possibly due to selective incorporation of hydrogen from water into NAD(P)H, resulting in D-depleted lipids. An analogous fractionation should occur during amino acid biosynthesis. Whereas these effects are traditionally measured using gas-phase isotope ratio on 1H-1H and 1H-2H, using an electrospray mass spectrometry-based technique on the original biomolecular structure and fitting of isotopic patterns we measured the hydrogen isotope compositions of proteins from an acidophilic microbial community with organism specificity and compared values with those for lipids. We showed that lipids were isotopically light by -260 ‰ relative to water in the growth solution; alternatively protein isotopic composition averaged -370 ‰. This difference suggests that steps in addition to NAD(P)H formation contribute to D/H fractionation. Further, autotrophic bacteria sharing 94% 16S rRNA gene sequence identity displayed statistically significant differences in protein hydrogen isotope fractionation, suggesting different metabolic traits consistent with distinct ecological niches or incorrectly annotated gene function. In addition, it was found that heterotrophic, archaeal members of the community had isotopically light protein (-323 ‰) relative to growth water and were significantly different from coexisting bacteria. This could be attributed to metabolite transfer from autotrophs and unknown aspects of fractionation associated with iron reduction. Differential fractionation of hydrogen stable isotopes into metabolites and proteins may reveal trophic levels of members of microbial communities. The approach developed here provided insights into the metabolic characteristics of organisms in natural communities and may be applied to analyze other systems.
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Affiliation(s)
| | - Benjamin P. Bowen
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United
States
| | - Chongle Pan
- BioSciences Division
and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Trent R. Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United
States
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Seifert J, Herbst FA, Halkjaer Nielsen P, Planes FJ, Jehmlich N, Ferrer M, von Bergen M. Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities. Proteomics 2013; 13:2786-804. [PMID: 23625762 DOI: 10.1002/pmic.201200566] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/07/2013] [Accepted: 03/28/2013] [Indexed: 11/06/2022]
Abstract
Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used MS pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.
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Affiliation(s)
- Jana Seifert
- Department of Proteomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany; Institute of Animal Nutrition, University of Hohenheim, Stuttgart, Germany
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Wang Y, Ahn TH, Li Z, Pan C. Sipros/ProRata: a versatile informatics system for quantitative community proteomics. ACTA ACUST UNITED AC 2013; 29:2064-5. [PMID: 23793753 DOI: 10.1093/bioinformatics/btt329] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
SUMMARY Sipros/ProRata is an open-source software package for end-to-end data analysis in a wide variety of community proteomics measurements. A database-searching program, Sipros 3.0, was developed for accurate general-purpose protein identification and broad-range post-translational modification searches. Hybrid Message Passing Interface/OpenMP parallelism of the new Sipros architecture allowed its computation to be scalable from desktops to supercomputers. The upgraded ProRata 3.0 performs label-free quantification and isobaric chemical labeling quantification in addition to metabolic labeling quantification. Sipros/ProRata is a versatile informatics system that enables identification and quantification of proteins and their variants in many types of community proteomics studies. AVAILABILITY Both programs are freely available under the GNU GPL license at Sipros.omicsbio.org and ProRata.omicsbio.org.
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Affiliation(s)
- Yingfeng Wang
- Computer Science and Mathematics Division, Oak Ridge National Laboratory and Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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48
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Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME JOURNAL 2013; 7:1877-85. [PMID: 23677009 DOI: 10.1038/ismej.2013.78] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 04/08/2013] [Accepted: 04/13/2013] [Indexed: 01/09/2023]
Abstract
The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.
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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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50
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Microbial competition in polar soils: a review of an understudied but potentially important control on productivity. BIOLOGY 2013; 2:533-54. [PMID: 24832797 PMCID: PMC3960893 DOI: 10.3390/biology2020533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 01/29/2023]
Abstract
Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants.
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