A new regulatory role for the chloroplast ATP synthase

One of the challenges of modern biology is the synthesis of vast amounts of data into a deep understanding of organism structure and function. At present, the most visible effort toward meeting this challenge is the use of computing technology to effectively reassemble organisms that have been fragmented and processed into DNA sequences, relative abundances of RNA transcripts, peptide patterns, or profiles of metabolites (1–8). An important complement to this approach is the use of nondestructive methods to observe function in intact organisms as they live. Quantitative analysis of specific functions at the molecular level is often difficult in intact organisms, owing to their complexity, but such analyses must be attempted, if only to validate models derived from the fragmentation and computation approach. In cases where the function of interest is perturbed by the extraction of chemical information or occurs too rapidly to be resolved by such extraction, in vivo study is essential. The intimacy of plants with their physical environment, including the fact that they cannot move, has rendered them highly sensitive and responsive to physical factors. The article in this issue of PNAS by Kanazawa and Kramer (9) is an elegant example of how sophisticated hypotheses of function can be tested in intact organisms. This study applies a combination of nonfocusing optics (10) and absorbance difference spectroscopy to study H+ flux through the chloroplast ATPases of plant leaves as they adjust their photosynthetic systems to different irradiances and external levels of CO2. Plants and other photosynthetic organisms exhibit rich absorption and fluorescence differences between their dark and illuminated states (11–14). In the green region of the spectrum, the charge difference generated across the thylakoid membranes of chloroplasts by illumination …