The proteome of a day in the life of Chlamydomonas
EMSL Project ID
49262
Abstract
Nearly all organisms exhibit diurnal metabolic cycles. In photosynthetic organisms, light is a key input into metabolic cycles. Transcriptomics experiments in cyanobacteria, algae and plants have indicated that good fractions of the genome are regulated periodically in a diurnal pattern. In a unicellular organism, such as Chlamydomonas, this fraction approaches 90%, and reflects the temporal segregation of various metabolic pathways as a cell progresses through the cell cycle, which in synchronized Chlamydomonas cells corresponds to one 24h period or one day. For instance, genes encoding components of the photosynthetic apparatus are coordinately expressed early in the light phase: dense sampling during the light phase can distinguish early (by 2h in a 24h cycle) expression of the proton pumping components (ATP synthase and the b6f complex) from the photosystem components. Measurements of photosynthetic capacity are consistent with the pattern of gene expression and accumulation of the corresponding proteins, but the relationship between the proteome and the transcriptome has not been experimentally documented. The expression of respiratory components on the other hand occurs in the dark part of the diurnal cycle, but respiratory capacity increases in the light in parallel with the increase in biomass rather than in the dark, suggesting that translational or post-translational mechanisms govern the function of the respiratory complexes, presumably because photosynthesis is a driver for respiratory carbon metabolism. The dark to light transition is accompanied by a period of stress response, reflected by photoinhibition (reduced Fv/Fm), increased expression of heat shock proteins and genes encoding chlorophyll proteins, LHCSR and PSBS, involved in photoprotection. This response is transient and strongly dependent on the magnitude of the transition. A second more sustained stress response follows in continuous light and involves the expression of only the LHCSR genes: it may depend on accumulation of reducing power in the plastid and the inability of the Calvin-Benson cycle to keep up with the light reactions. We have 2 objectives: 1) to monitor the proteome of the Chlamydomonas cell during synchronized cell division with dense sampling to parallel measurements of the transcriptome and bioenergetics physiology in order to understand the relationship between gene expression and metabolic capacity, and 2) to monitor modifications of the proteome during metabolic cycles, especially change in thiol status of chloroplast proteins, which would reflect the operation of regulatory redox sensors and protein carbonylation, reflecting oxidative damage. The project will yield an unprecedented (in terms of associated metadata and other measurements) wealth of data, which will inform the development of models of macromolecular and small molecule metabolism in a flagship organism for the DOE. This work advances the use of systems biology approaches for developing a predictive understanding of biological, environmental and energy systems, which is a pre-requisite for finding solutions to energy and environmental challenges.
The EMSL user program is ideally suited for the project because of the strong tradition of quantitative proteomics at PNNL, the large number of samples, which will leverage other high throughput and quantitative 'omics data types, and the existing infrastructure of methodological developments at PNNL for monitoring protein redox states.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2016-10-01
End Date
2018-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Related Publications
Gallaher, S.D., Fitz-Gibbon, S.T., Strenkert, D., Purvine, S.O., Pellegrini, M., Merchant, S.S. (2018) High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates, The Plant J. 93:545-565. doi: 10.1111/tpj.13788
Gallaher SD, ST Fitz-Gibbon, D Strenkert, SO Purvine, M Pellegrini, and SS Merchant. 2018. "High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates." The Plant Journal 93(3):545-565. doi:10.1111/tpj.13788
Strenkert D., S. Schmollinger, S.D. Gallaher, P.A. Salome, S.O. Purvine, C.D. Nicora, and T. Mettler-Altmann, et al. 2019. "Multiomics resolution of molecular events during a day in the life of Chlamydomonas." Proceedings of the National Academy of Sciences of the United States of America 116, no. 6:2374-2383. PNNL-SA-140230. doi:10.1073/pnas.1815238116
Strenkert D., S. Schmollinger, S.D. Gallaher, P.A. Salome, S.O. Purvine, C.D. Nicora, and T. Mettler-Altmann, et al. 2019. "Multiomics resolution of molecular events during a day in the life of Chlamydomonas." Proceedings of the National Academy of Sciences (PNAS). 116, no. 6:2374-2383. PNNL-SA-140230. doi:10.1073/pnas.1815238116