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McCain JSP. Mapping combinatorial expression perturbations to growth in Escherichia coli. Cell Syst 2024; 15:106-108. [PMID: 38387440 DOI: 10.1016/j.cels.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
The connection between growth and gene expression has often been considered in a single gene. Repurposing a drug-drug interaction model, the multidimensional effects of several simultaneous gene expression perturbations on growth have been examined in the model bacteria Escherichia coli.
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Affiliation(s)
- J Scott P McCain
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Omar NM, Prášil O, McCain JSP, Campbell DA. Diffusional Interactions among Marine Phytoplankton and Bacterioplankton: Modelling H 2O 2 as a Case Study. Microorganisms 2022; 10:821. [PMID: 35456871 PMCID: PMC9030875 DOI: 10.3390/microorganisms10040821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 02/04/2023] Open
Abstract
Marine phytoplankton vary widely in size across taxa, and in cell suspension densities across habitats and growth states. Cell suspension density and total biovolume determine the bulk influence of a phytoplankton community upon its environment. Cell suspension density also determines the intercellular spacings separating phytoplankton cells from each other, or from co-occurring bacterioplankton. Intercellular spacing then determines the mean diffusion paths for exchanges of solutes among co-occurring cells. Marine phytoplankton and bacterioplankton both produce and scavenge reactive oxygen species (ROS), to maintain intracellular ROS homeostasis to support their cellular processes, while limiting damaging reactions. Among ROS, hydrogen peroxide (H2O2) has relatively low reactivity, long intracellular and extracellular lifetimes, and readily crosses cell membranes. Our objective was to quantify how cells can influence other cells via diffusional interactions, using H2O2 as a case study. To visualize and constrain potentials for cell-to-cell exchanges of H2O2, we simulated the decrease of [H2O2] outwards from representative phytoplankton taxa maintaining internal [H2O2] above representative seawater [H2O2]. [H2O2] gradients outwards from static cell surfaces were dominated by volumetric dilution, with only a negligible influence from decay. The simulated [H2O2] fell to background [H2O2] within ~3.1 µm from a Prochlorococcus cell surface, but extended outwards 90 µm from a diatom cell surface. More rapid decays of other, less stable ROS, would lower these threshold distances. Bacterioplankton lowered simulated local [H2O2] below background only out to 1.2 µm from the surface of a static cell, even though bacterioplankton collectively act to influence seawater ROS. These small diffusional spheres around cells mean that direct cell-to-cell exchange of H2O2 is unlikely in oligotrophic habits with widely spaced, small cells; moderate in eutrophic habits with shorter cell-to-cell spacing; but extensive within phytoplankton colonies.
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Affiliation(s)
- Naaman M. Omar
- Department of Biology, Mount Allison University, Sackville, NB E4L1G7, Canada;
| | - Ondřej Prášil
- Center Algatech, Laboratory of Photosynthesis, Novohradska 237, CZ 37981 Trebon, Czech Republic;
| | - J. Scott P. McCain
- Department of Biology, Massachusetts Institute of Technology, Boston, MA 02142, USA;
| | - Douglas A. Campbell
- Department of Biology, Mount Allison University, Sackville, NB E4L1G7, Canada;
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Affiliation(s)
- Loay Jabre
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
| | - Catherine Bannon
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - J. Scott P. McCain
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yana Eglit
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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McCain JSP, Tagliabue A, Susko E, Achterberg EP, Allen AE, Bertrand EM. Cellular costs underpin micronutrient limitation in phytoplankton. Sci Adv 2021; 7:7/32/eabg6501. [PMID: 34362734 PMCID: PMC8346223 DOI: 10.1126/sciadv.abg6501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/22/2021] [Indexed: 05/08/2023]
Abstract
Micronutrients control phytoplankton growth in the ocean, influencing carbon export and fisheries. It is currently unclear how micronutrient scarcity affects cellular processes and how interdependence across micronutrients arises. We show that proximate causes of micronutrient growth limitation and interdependence are governed by cumulative cellular costs of acquiring and using micronutrients. Using a mechanistic proteomic allocation model of a polar diatom focused on iron and manganese, we demonstrate how cellular processes fundamentally underpin micronutrient limitation, and how they interact and compensate for each other to shape cellular elemental stoichiometry and resource interdependence. We coupled our model with metaproteomic and environmental data, yielding an approach for estimating biogeochemical metrics, including taxon-specific growth rates. Our results show that cumulative cellular costs govern how environmental conditions modify phytoplankton growth.
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Affiliation(s)
- J Scott P McCain
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Edward Susko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Eric P Achterberg
- GEOMAR Helmholtz Center for Ocean Research Kiel, Wischhofstrasse 1-3, 24148 Kiel, Germany
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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Abstract
Metaproteomics can provide critical information about biological systems, but peptides are found within a complex background of other peptides. This complex background can change across samples, in some cases drastically. Cofragmentation, the coelution of peptides with similar mass to charge ratios, is one factor that influences which peptides are identified in an LC-MS/MS experiment: it is dependent on the nature and complexity of this dynamic background. Metaproteomics applications are particularly susceptible to cofragmentation-induced bias; they have vast protein sequence diversity and the abundance of those proteins can span many orders of magnitude. We have developed a mechanistic model that determines the number of potentially cofragmenting peptides in a given sample (called cobia, https://github.com/bertrand-lab/cobia ). We then used previously published data sets to validate our model, showing that the resulting peptide-specific score reflects the cofragmentation "risk" of peptides. Using an Antarctic sea ice edge metatranscriptome case study, we found that more rare taxonomic and functional groups are associated with higher cofragmentation bias. We also demonstrate how cofragmentation scores can be used to guide the selection of protein- or peptide-based biomarkers. We illustrate potential consequences of cofragmentation for multiple metaproteomic approaches, and suggest practical paths forward to cope with cofragmentation-induced bias.
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Affiliation(s)
- J Scott P McCain
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Erin M Bertrand
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
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Wu M, McCain JSP, Rowland E, Middag R, Sandgren M, Allen AE, Bertrand EM. Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators. Nat Commun 2019; 10:3582. [PMID: 31395884 PMCID: PMC6687791 DOI: 10.1038/s41467-019-11426-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 07/15/2019] [Indexed: 11/10/2022] Open
Abstract
Iron and light are recognized as limiting factors controlling Southern Ocean phytoplankton growth. Recent field-based evidence suggests, however, that manganese availability may also play a role. Here we examine the influence of iron and manganese on protein expression and physiology in Phaeocystis antarctica, a key Antarctic primary producer. We provide taxon-specific proteomic evidence to show that in-situ Southern Ocean Phaeocystis populations regularly experience stress due to combined low manganese and iron availability. In culture, combined low iron and manganese induce large-scale changes in the Phaeocystis proteome and result in reorganization of the photosynthetic apparatus. Natural Phaeocystis populations produce protein signatures indicating late-season manganese and iron stress, consistent with concurrently observed stimulation of chlorophyll production upon additions of manganese or iron. These results implicate manganese as an important driver of Southern Ocean productivity and demonstrate the utility of peptide mass spectrometry for identifying drivers of incomplete macronutrient consumption. Low manganese availability could be a major control of phytoplankton growth in the Southern Ocean. Here the authors identify proteomic signatures of low manganese and iron availability in phytoplankton cultures and detect those signatures in Antarctic field samples.
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Affiliation(s)
- Miao Wu
- Department of Biology, Dalhousie University, 1355 Oxford Street PO Box 15000, Halifax, B3H 4R2, NS, Canada.,Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden
| | - J Scott P McCain
- Department of Biology, Dalhousie University, 1355 Oxford Street PO Box 15000, Halifax, B3H 4R2, NS, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, 1355 Oxford Street PO Box 15000, Halifax, B3H 4R2, NS, Canada
| | - Rob Middag
- Department of Ocean Systems, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, Den Burg, Texel, 1790 AB, Netherlands
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.,Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, 1355 Oxford Street PO Box 15000, Halifax, B3H 4R2, NS, Canada.
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