Electron-transfer reactions are fundamental to metabolism. Whether an organism is autotrophic or heterotrophic, free living or an obligate parasite, every cell must solve the energy-conservation problem to survive. At the cellular level, most of our knowledge of electron transfer comes from mechanistic studies of oxygenic photosynthesis and aerobic respiration in bacterial and eukaryotic systems. While we know in exquisite detail the structure and function of various membrane-bound proteins involved in electron-transfer processes (e.g., cytochrome c oxidase in mitochondria), we know far less about the electron-transfer agents of more ancient forms of metabolism that do not traffic in oxygen. As microbiologists interested in the origin and evolution of the biochemical functions that sustain modern life, our work has focused on probing the co-evolution of metabolism with Earth's near-surface environments. Understanding how modern microorganisms with archaic metabolisms function is a step towards this end. Moreover, because many biological microenvironments are anoxic, including those in most chronic infections, this path of inquiry leads inexorably to insights about cellular electron-transfer mechanisms that potentially have profound biomedical implications.
Because rocks provide the primary record of ancient events and processes, our laboratory initially explored microbe-mineral interactions. In particular, we investigated how bacteria catalyze mineral formation, transformation, and dissolution, focusing on how these processes relate to cellular energy conservation or membrane organization, and how they affect the geochemistry of their environment. For every pathway that we studied, we chose model organisms that we could genetically manipulate. Through a combination of classical genetic, biochemical, and molecular biological approaches, we identified the genes and gene products that controlled the processes of interest. As our work progressed, it became increasingly clear that our findings transcended microbe-mineral interactions. Accordingly, our focus has shifted to exploring basic physiological questions that are relevant to diverse biological systems. A geobiological perspective still imbues our approach, compelling us to perform our mechanistic studies under environmental conditions that bear fidelity to the complex contexts that motivate our work—be they the microenvironments of infected tissues or crop rhizospheres.
For more information about our current work and/or microbiology or sustainability research at Caltech, please check out our GROUP WEBSITE.
Publications
- Squyres, Georgia R;Newman, Dianne (2024) Biofilms as more than the sum of their parts: lessons from developmental biologyCurrent Opinion in Microbiology
- Ciemniecki, John A.;Ho, Chia-Lun et al. (2024) Mechanistic study of a low-power bacterial maintenance state using high-throughput electrochemistryCell
- Horak, Richard D.;Ciemniecki, John A. et al. (2024) Bioenergetic suppression by redox-active metabolites promotes antibiotic tolerance in Pseudomonas aeruginosaProceedings of the National Academy of Sciences
- Flamholz, Avi I.;Goldford, Joshua E. et al. (2024) Annotation-free prediction of microbial dioxygen utilizationmSystems
- Zhang, Oumeng;Alcalde, Reinaldo E. et al. (2024) Investigating 3D microbial community dynamics of the rhizosphere using quantitative phase and fluorescence microscopyProceedings of the National Academy of Sciences
- Wang, Renée Z.;Lonergan, Zachery R. et al. (2024) Widespread detoxifying NO reductases impart a distinct isotopic fingerprint on N₂O under anoxiaProceedings of the National Academy of Sciences
- Kim, Jane H.;Dong, Julianna et al. (2024) Pseudomonas aeruginosa Activates Quorum Sensing, Antioxidant Enzymes and Type VI Secretion in Response to Oxidative Stress to Initiate Biofilm Formation and Wound ChronicityAntioxidants
- Tsypin, Lev M. Z.;Saunders, Scott H. et al. (2024) Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidationPLOS Genetics
- Magkiriadou, Sofia;Stepp, Willi L. et al. (2024) Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosaProceedings of the National Academy of Sciences
- Zhang, Irene H.;Borer, Benedict et al. (2024) Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potentialmBio