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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Jake McKinlay

Photo of Jake McKinlay
Research Images
Research photo by Jake McKinlay

R. palustris is the Swiss army knife of the bacterial kingdom. The versatility of its metabolism allows it to use the right metabolic tools for the right environment and presents a variety of options for applications using a single organism. 

Research photo by Jake McKinlay

Metabolic flux maps obtained from performing 13C-labeling experiments on R. palustris. Arrow thickness indicates the amount of metabolic flow through a pathway. In the absence of H2 production (left) excess reducing power is diverted to the Calvin cycle resulting in a high level of CO2 fixation (green arrows). When H2 is produced (right) reducing power is naturally diverted away from the Calvin cycle towards H2 production (yellow). This effect can be enhanced by genetically eliminating CO2 fixation.

Assistant Professor of Biology
Contact Information
By telephone: 812-855-0359/5-9332(lab)
JH A309 / A308 (lab)

McKinlay Lab website

Research Areas
  • Genomics and Bioinformatics
  • Microbial Cell Biology and Environmental Responses
  • Microbial Interactions and Pathogenesis

Ph.D., Michigan State University, 2006
Postdoctoral Fellow, University of Washington, 2007-2011


ORAU Ralph E. Powe Junior Faculty Enhancement Award, 2012

US Department of Energy Early Career Award, 2012-2017

Research Description

Nearly all of our society's energy and chemical needs are met by fossil fuels. Microbes have evolved a profound diversity of metabolic attributes which can be harnessed as sustainable alternatives for the production of fuels and chemicals. Our lab seeks to understand the metabolism underlying the production of useful compounds and to engineer strains for enhanced production rates and yields. In doing so, we invariably learn about how a microbe's metabolism contributes to its physiology and how it interacts with the external environment. Our lab uses biochemical assays, genetic manipulation, functional genomics, and stable isotope tracer studies (13C-metabolic flux analysis) to study microbial metabolism.

A bacterium of central interest is Rhodopseudomonas palustris - one of the most metabolically versatile bacteria ever described. It can grow photosynthetically in light or by using aerobic or anaerobic respiration in the dark. We primarily study the ability of R. palustris to use energy from light and electrons from various waste compounds into the transportable fuel, H2. Previous work showed that R. palustris can only use half of its reducing power for growth and that the rest must be disposed of. Under certain conditions, some of this excess reducing power is channeled towards H2 production, but the rest is used to fix CO2 into more biomass. By genetically deleting enzymes involved in CO2 fixation, all of the excess reducing power was diverted to H2 production resulting in increased yields on all substrates tested.

Current work is focused on: (i) understanding the metabolism and physiology of R. palustris under non-growing conditions where the highest H2 yields are observed, (ii) determining the role of microbial metabolism in interspecies interactions, and (iii) exploring how the performance of engineered microbes can be maintained over the long term.

Select Publications
McKinlay, JB, Y Oda, M Rühl, AL Posto, U Sauer, CS Harwood. 2014. Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle. J. Biol. Chem. 289: 1960-1970.  [article]
Gordon, GC and JB McKinlay. 2014. Calvin cycle mutants of photoheterotrophic purple non-sulfur bacteria fail to grow due to an electron imbalance rather than toxic metabolite accumulation. J. Bacteriol. doi:10.1128/JB.01299-13  [article]
McKinlay, JB and CS Harwood. 2011. Calvin cycle flux, pathway constraints and substrate redox state together determine the H2 biofuel yield in photoheterotrophic bacteria. mBio. 2: e00323-10. doi:10.1128/mBio.00323-10.
McKinlay, JB and CS Harwood. 2010. Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria. Proceedings of the National Academy of Sciences USA. 107: 11669-11675.
McKinlay, JB and CS Harwood. 2010. Mini-review. Photobiological production of hydrogen gas as a biofuel. Current Opinion in Biotechnology. 21: 244-251.
McKinlay, JB, M Laivenieks, BD Schindler, AA McKinlay, S Siddaramappa, JF Challacombe, SR Lowry, A Clum, AL Lapidus, KB Burkhart, V Harkins and C Vieille. 2010. A genomic perspective on the potential of Actinobacillus succinogenes for industrial chemical production. BMC Genomics. 11: 680.
Huang, JJ, EK Heiniger, JB McKinlay, and CS Harwood. 2010. Production of hydrogen gas from light and the inorganic electron donor thiosulfate by Rhodopseudomonas palustris. Applied and Environmental Microbiology. 76: 7717-7722.
McKinlay, JB, C Vieille, and JG Zeikus. 2007. Mini-review. Prospects for a bio-based succinate industry. Applied Microbiology and Biotechnology. 76: 727-740.
McKinlay, JB, Y Shachar-Hill, JG Zeikus, and C Vieille. 2007. Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analysis of 13C-labeled metabolic product isotopomers. Metabolic Engineering. 9: 177-192.

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