Measuring Chemical Changes Inside Living Cells

The instability of many of the intermediates greatly complicates measurements of cell extracts and their analyses.

The Science

Understanding how microbes adapt to changing chemical environments is a critical aspect of using them to solve DOE challenges. With synchrotron radiation-based Fourier transform infrared microscopy at the Advanced Light Source, researchers tracked the chemistry of living Desulfovibrio vulgaris cells in real time. Researchers investigated the dynamics of cellular chemical environment in a model oxygen-stress adaptive response system, namely that of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough during transient exposure to air. The ability to make these dynamic measurements continuously inside selected living cells dramatically increases the usefulness and reliability of information traditionally derived from cells that have been killed and broken apart.

The Impact

The cellular chemical environment fundamentally comprises the nexus between external stimuli and internal biochemical regulatory mechanisms—and affects many properties of cellular adaptive response as well. Determining this transient chemical environment in vivo is critical for achieving a more coherent understanding of how some obligate anaerobes adapt to the extreme fluctuations in oxygenation. Such knowledge is seldom complete because it is difficult to make in vivo molecular measurements without disturbing cells.

Researchers have demonstrated both the efficacy of using the hydrogen bonding in water of living cells to profile intracellular chemical environment and their significant consequences for understanding functional metabolic controls in “obligate” anaerobic bacteria that can survive oxygen-stress transiently at the chemical level, by providing direct observations of molecular events measured in the same cells over time. Together, these high-resolution synchrotron radiation-based FTIR experiments have revealed a remarkable sequence of well-orchestrated mechanisms that some D. vulgaris use to temporarily survive oxygen exposure. When extending this approach to other adaptive-response cellular systems, the experimental design and interpretation of the data should be straightforward in cases where transient chemistry is dominated by ions or other small chemical species.


This work was supported by the U.S. Department of Energy Office of Biological and Environmental Research’s Structural Biology Program, and Genomics:GTL Program through contract DE-AC02–05CH11231 with Lawrence Berkeley National Laboratory.


Holman, H.-Y., Wozei, E., Lin, Z., Comolli, L., Ball, D., Borglin, S., Fields, M., Hazen, T. C., and K. Downing. 2009. “Real-Time Molecular Monitoring of Chemical Environment in Obligate Anaerobes During Oxygen Adaptive Response,” Proceedings of the National Academy of Sciences (USA) 106, 12599–604.