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Title: Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H

Abstract

Colwellia psychrerythraea 34H is a model psychrophilic bacterium found in the cold ocean—polar sediments, sea ice, and the deep sea. Although the genomes of such psychrophiles have been sequenced, their metabolic strategies at low temperature have not been quantified. We measured the metabolic fluxes and gene expression of 34H at 4 °C (the mean global-ocean temperature and a normal-growth temperature for 34H), making comparative analyses at room temperature (above its upper-growth temperature of 18 °C) and with mesophilic Escherichia coli . When grown at 4 °C, 34H utilized multiple carbon substrates without catabolite repression or overflow byproducts; its anaplerotic pathways increased flux network flexibility and enabled CO 2 fixation. In glucose-only medium, the Entner–Doudoroff (ED) pathway was the primary glycolytic route; in lactate-only medium, gluconeogenesis and the glyoxylate shunt became active. In comparison, E. coli , cold stressed at 4 °C, had rapid glycolytic fluxes but no biomass synthesis. At their respective normal-growth temperatures, intracellular concentrations of TCA cycle metabolites (α-ketoglutarate, succinate, malate) were 4–17 times higher in 34H than in E. coli , while levels of energy molecules (ATP, NADH, NADPH) were 10- to 100-fold lower. Experiments with E. coli mutants supported the thermodynamic advantage of the ED pathwaymore » at cold temperature. Heat-stressed 34H at room temperature (2 hours) revealed significant down-regulation of genes associated with glycolytic enzymes and flagella, while 24 hours at room temperature caused irreversible cellular damage. We suggest that marine heterotrophic bacteria in general may rely upon simplified metabolic strategies to overcome thermodynamic constraints and thrive in the cold ocean.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1482429
Alternate Identifier(s):
OSTI ID: 1559169
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 115 Journal Issue: 49; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 54 ENVIRONMENTAL SCIENCES; marine psychrophile; metabolic flux; ED pathway; short-chain fatty acids; gluconeogensis

Citation Formats

Czajka, Jeffrey J., Abernathy, Mary H., Benites, Veronica T., Baidoo, Edward E. K., Deming, Jody W., and Tang, Yinjie J. Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H. United States: N. p., 2018. Web. doi:10.1073/pnas.1807804115.
Czajka, Jeffrey J., Abernathy, Mary H., Benites, Veronica T., Baidoo, Edward E. K., Deming, Jody W., & Tang, Yinjie J. Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H. United States. doi:10.1073/pnas.1807804115.
Czajka, Jeffrey J., Abernathy, Mary H., Benites, Veronica T., Baidoo, Edward E. K., Deming, Jody W., and Tang, Yinjie J. Fri . "Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H". United States. doi:10.1073/pnas.1807804115.
@article{osti_1482429,
title = {Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H},
author = {Czajka, Jeffrey J. and Abernathy, Mary H. and Benites, Veronica T. and Baidoo, Edward E. K. and Deming, Jody W. and Tang, Yinjie J.},
abstractNote = {Colwellia psychrerythraea 34H is a model psychrophilic bacterium found in the cold ocean—polar sediments, sea ice, and the deep sea. Although the genomes of such psychrophiles have been sequenced, their metabolic strategies at low temperature have not been quantified. We measured the metabolic fluxes and gene expression of 34H at 4 °C (the mean global-ocean temperature and a normal-growth temperature for 34H), making comparative analyses at room temperature (above its upper-growth temperature of 18 °C) and with mesophilic Escherichia coli . When grown at 4 °C, 34H utilized multiple carbon substrates without catabolite repression or overflow byproducts; its anaplerotic pathways increased flux network flexibility and enabled CO 2 fixation. In glucose-only medium, the Entner–Doudoroff (ED) pathway was the primary glycolytic route; in lactate-only medium, gluconeogenesis and the glyoxylate shunt became active. In comparison, E. coli , cold stressed at 4 °C, had rapid glycolytic fluxes but no biomass synthesis. At their respective normal-growth temperatures, intracellular concentrations of TCA cycle metabolites (α-ketoglutarate, succinate, malate) were 4–17 times higher in 34H than in E. coli , while levels of energy molecules (ATP, NADH, NADPH) were 10- to 100-fold lower. Experiments with E. coli mutants supported the thermodynamic advantage of the ED pathway at cold temperature. Heat-stressed 34H at room temperature (2 hours) revealed significant down-regulation of genes associated with glycolytic enzymes and flagella, while 24 hours at room temperature caused irreversible cellular damage. We suggest that marine heterotrophic bacteria in general may rely upon simplified metabolic strategies to overcome thermodynamic constraints and thrive in the cold ocean.},
doi = {10.1073/pnas.1807804115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 49,
volume = 115,
place = {United States},
year = {2018},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1073/pnas.1807804115

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Cited by: 2 works
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Figures / Tables:

Fig. 1 Fig. 1: 12C- and 13C-fingerprinting experiments with 34H revealing its ability to incorporate CO2 into TCA cycle metabolites, bypass the lower half of the TCA cycle (glyoxylate shunt), and utilize multiple substrates simultaneously (no glucose catabolic repression). (A) Labeling profiles of amino acids derived from OAA in cultures grown withmore » U-13C glucose. (B) Entry points for the incorporation of glucose and glyoxylate into the TCA cycle (indicated by red arrow). See SI Appendix for abbreviations for metabolites. (C) Labeling profiles of proteinogenic amino acids from the TCA cycle in cultures grown with only U-13C glucose and with U-13C glucose and 12C glyoxylate. (D) Labeling profiles of amino acids derived from the TCA cycle in cultures grown on unlabeled glucose supplemented with 1,2-13C acetate or 3-13C lactate. Error bars indicate SD of the mean (n = 2).« less

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Works referenced in this record:

Glycolysis without pyruvate kinase in Clostridium thermocellum
journal, January 2017


Motility of Colwellia psychrerythraea Strain 34H at Subzero Temperatures
journal, July 2003


A Unique Capsular Polysaccharide Structure from the Psychrophilic Marine Bacterium Colwellia psychrerythraea 34H That Mimics Antifreeze (Glyco)proteins
journal, January 2015

  • Carillo, Sara; Casillo, Angela; Pieretti, Giuseppina
  • Journal of the American Chemical Society, Vol. 137, Issue 1
  • DOI: 10.1021/ja5075954

Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production
journal, July 2017


Microbial ecology of the cryosphere: sea ice and glacial habitats
journal, September 2015

  • Boetius, Antje; Anesio, Alexandre M.; Deming, Jody W.
  • Nature Reviews Microbiology, Vol. 13, Issue 11
  • DOI: 10.1038/nrmicro3522

Characterization of a cold-active bacteriophage on two psychrophilic marine hosts
journal, October 2006


Distinct features of protein folding by the GroEL system from a psychrophilic bacterium, Colwellia psychrerythraea 34H
journal, September 2012


Large‐scale 13 C‐flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
journal, January 2011

  • Haverkorn van Rijsewijk, Bart R. B.; Nanchen, Annik; Nallet, Sophie
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.9

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
journal, February 2014


An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
journal, May 2012


The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation
journal, April 2009

  • Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.
  • The ISME Journal, Vol. 3, Issue 9
  • DOI: 10.1038/ismej.2009.45

Non-growing Rhodopseudomonas palustris Increases the Hydrogen Gas Yield from Acetate by Shifting from the Glyoxylate Shunt to the Tricarboxylic Acid Cycle
journal, December 2013

  • McKinlay, James B.; Oda, Yasuhiro; Rühl, Martin
  • Journal of Biological Chemistry, Vol. 289, Issue 4
  • DOI: 10.1074/jbc.M113.527515

Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model
journal, October 1998


Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill
journal, July 2014


Propane Respiration Jump-Starts Microbial Response to a Deep Oil Spill
journal, September 2010

  • Valentine, David L.; Kessler, John D.; Redmond, Molly C.
  • Science, Vol. 330, Issue 6001, p. 208-211
  • DOI: 10.1126/science.1196830

Polar ocean ecosystems in a changing world
journal, September 2005


Diversity and genomics of Antarctic marine micro-organisms
journal, May 2007

  • Murray, Alison E.; Grzymski, Joseph J.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 362, Issue 1488
  • DOI: 10.1098/rstb.2006.1944

Remarkably low temperature optima for extracellular enzyme activity from Arctic bacteria and sea ice
journal, August 2000


Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for 13C metabolic flux analysis
journal, November 2014


Proteorhodopsin phototrophy in the ocean
journal, June 2001

  • Béjà, Oded; Spudich, Elena N.; Spudich, John L.
  • Nature, Vol. 411, Issue 6839
  • DOI: 10.1038/35081051

Genomic analysis of cold-active Colwelliaphage 9A and psychrophilic phage–host interactions
journal, December 2012


Bacterial use of choline to tolerate salinity shifts in sea-ice brines
journal, August 2016


Global Metabolic Responses to Salt Stress in Fifteen Species
journal, February 2016


Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
journal, April 2007


Colwellia psychrerythraea Strains from Distant Deep Sea Basins Show Adaptation to Local Conditions
journal, May 2016

  • Techtmann, Stephen M.; Fitzgerald, Kathleen S.; Stelling, Savannah C.
  • Frontiers in Environmental Science, Vol. 4
  • DOI: 10.3389/fenvs.2016.00033

Large-Scale 13 C Flux Profiling Reveals Conservation of the Entner-Doudoroff Pathway as a Glycolytic Strategy among Marine Bacteria That Use Glucose
journal, January 2015

  • Klingner, Arne; Bartsch, Annekathrin; Dogs, Marco
  • Applied and Environmental Microbiology, Vol. 81, Issue 7
  • DOI: 10.1128/AEM.03157-14

Glycolytic strategy as a tradeoff between energy yield and protein cost
journal, April 2013

  • Flamholz, A.; Noor, E.; Bar-Even, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 24
  • DOI: 10.1073/pnas.1215283110

Cold active lipases – an update
journal, May 2016


The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
journal, July 2005

  • Methe, B. A.; Nelson, K. E.; Deming, J. W.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 31
  • DOI: 10.1073/pnas.0504766102

Isotopically nonstationary 13 C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation
journal, November 2014

  • Ma, Fangfang; Jazmin, Lara J.; Young, Jamey D.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 47
  • DOI: 10.1073/pnas.1319485111

Recent advances in mapping environmental microbial metabolisms through 13 C isotopic fingerprints
journal, June 2012

  • Tang, Joseph Kuo-Hsiang; You, Le; Blankenship, Robert E.
  • Journal of The Royal Society Interface, Vol. 9, Issue 76
  • DOI: 10.1098/rsif.2012.0396

Molecular adaptations to psychrophily: the impact of ‘omic’ technologies
journal, August 2010


Low‐temperature chemotaxis, halotaxis and chemohalotaxis by the psychrophilic marine bacterium Colwellia psychrerythraea 34H
journal, December 2017

  • Showalter, G. M.; Deming, J. W.
  • Environmental Microbiology Reports, Vol. 10, Issue 1
  • DOI: 10.1111/1758-2229.12610

Comparative studies of glycolytic pathways and channeling under in vitro and in vivo modes
journal, September 2018

  • Abernathy, Mary H.; Zhang, Yuchen; Hollinshead, Whitney D.
  • AIChE Journal, Vol. 65, Issue 2
  • DOI: 10.1002/aic.16367

WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism
journal, November 2016


Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members
journal, January 2015

  • Ramond, J. -B.; Makhalanyane, T. P.; Tuffin, M. I.
  • Letters in Applied Microbiology, Vol. 60, Issue 4
  • DOI: 10.1111/lam.12380

Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill
journal, October 2011

  • Redmond, M. C.; Valentine, D. L.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 50
  • DOI: 10.1073/pnas.1108756108

Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis
journal, November 2017


Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence: Cyanobacterial Carbon Metabolism
journal, March 2017

  • Wan, Ni; DeLorenzo, Drew M.; He, Lian
  • Biotechnology and Bioengineering, Vol. 114, Issue 7
  • DOI: 10.1002/bit.26287

New tools for mass isotopomer data evaluation in13C flux analysis: Mass isotope correction, data consistency checking, and precursor relationships
journal, January 2004

  • Wahl, S. Aljoscha; Dauner, Michael; Wiechert, Wolfgang
  • Biotechnology and Bioengineering, Vol. 85, Issue 3
  • DOI: 10.1002/bit.10909

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