Research Interests of the Lagarias Laboratory

Plants and other oxygenic photosynthetic organisms harvest light energy from the sun to fix carbon dioxide into the food and fiber required to sustain the biosphere. Since plants cannot move, they must cope with regular day-night cycles, seasonal cycles and neighboring vegetation, all of which influence the intensity, direction and spectral quality of light impinging on their leaves. To optimize light harvesting under low light conditions and to minimize photodamage when light is too bright, plants must continuously adjust the sensitivity of light harvesting by regulating the components of the photosynthetic apparatus or by altering the architecture of their leaves and stems. The ability to sense the ambient light level is conferred by protein light sensors that perceive different colors of visible light that are most effective in photosynthesis. For plants, red light is the most effective wavelength to drive photosynthesis therefore the most important of these photosensors, the phytochromes, are most sensitive to this region of the light spectrum.

Our laboratory studies phytochromes, which are protein-based sensors that strongly absorb red light due to a blue-colored (bilin) pigment that is physically attached. Red light absorption by the Pr form of phytochromes drives conversion to the turquoise-colored Pfr form that absorbs strongly in the near infrared (far-red) region. Unlike rhodopsins that primarily sense visible light, this red light-activated species of phytochrome can be switched off by far-red light that lies beyond the range of human vision. This red/far-red reversibility is the basis for phytochrome’s major role in plants, that of a shade detector. Through the action of phytochromes, plants seek to avoid shade that is depleted in the energy-rich red region of the spectrum. This growth response reflects the most obvious of the ‘shade avoidance’ responses that include altered leaf architecture and early flowering (see associated figure). Since these responses contribute to significant crop yield reduction in high-density field plantings, an understanding of the molecular basis of phytochrome signaling is expected to lead to new approaches to sustain crop yield at increased plant density.

Project 1 focuses on the molecular mechanism of light sensing and signal transduction by phytochrome sensors. These National Institutes of Health funded studies seek to define how bilin and light signals are perceived by, and propagated within, the phytochrome molecule that effect transduction to downstream targets. Our investigations address the hypothesis that the fundamental mechanism of light sensing has remained conserved throughout billions of years of evolution since endosymbiotic capture of a cyanobacterium by a eukaryotic host. By examining phytochromes from evolutionarily distant species ranging from cyanobacteria to plants, we seek to elucidate the molecular basis of light sensing and the intramolecular structural changes that are leveraged to control gene expression. Phytochromes from the glaucophyte Cyanophora paradoxa, (photo courtesy of NCMA) the chlorophyte Micromonas pusilla, and representative land plants are the focus of investigations that address the hypothesis that light-regulated conformational change triggers translocation to the nucleus in all extant eukaryotic phytochromes. In addition to leading to new approaches to regulate light responsiveness and productivity of plants, the primary food and energy source for life on earth, another long term objective of these studies is development of phytochrome-based optogenetic approaches for new light-based optogenetic therapies in eukaryotes. Key collaborators on this project include the laboratories of Alexandria Worden and Debashish Bhattacharya.

Project 2 exploits photophysical, structural and reverse genetic approaches to understand, and ultimately, to manipulate the regulatory functions of the cyanobacteriochromes, members of the extended phytochrome family in the nitrogen-fixing cyanobacterium Nostoc punctiforme. Cyanobacteriochromes extend the color sensitivity of phytochromes throughout the visible and near ultraviolet region of the light spectrum permitting optimum photosynthetic light harvesting, growth and development of cyanobacteria in many light environments. Initiated in 2009, this research seeks to understand the many regulatory roles of these phytobilin-based sensors in the biology of an organism that is capable of assimilating diatomic nitrogen, carbon dioxide and inorganic sulfate into the molecules of life. This project combines approaches ranging from ultrafast characterization of photochemical processes through biochemical analysis of signal transduction and genetic examination of this cyanobacterium. A long-term goal of these studies is to engineer these light-sensing proteins for synthetic biology applications, e.g. regulation of metabolic pathways in response to the color and intensity of light. Such tools will be used to tailor cyanobacteria for efficient, sustainable, and carbon-neutral biological capture of sunlight and conversion and storage of that light as chemical energy. These studies hope to exploit the metabolic diversity of cyanobacteria for light-driven biomass accumulation. Co-principal investigators include James B. Ames, R. David Britt, Delmar S. Larson and Jack Meeks.

Project 3 focuses on translational applications of dominant, gain-of-function phytochromes for crop improvement. Modern agriculture relies on crops that have been carefully tailored for environments by selective breeding. Phytochromes are an attractive target for breeding projects, because they function as key regulators of plant growth and development in response to light and shade. The specific aims are (1) to characterize and exploit spatial and temporal regulation of these alleles to selectively regulate light responses in plants; and, (2) to develop and exploit these alleles as plant-derived, chemical-free selection markers for in planta and tissue culture-based genetic selection. If successful, this project will provide new insight into phytochrome function that may have potential broad impact for the improvement of crop plants. Our key collaborator on this project is David Tricoli, Director of the UCD Plant Transformation Facility.

Project 4 addresses the biosynthesis and biological functions of phytobilins. Phytobilins are heme-derived linear tetrapyrrole pigments, produced exclusively by oxygenic photosynthetic organisms, whose optical and photochemical properties are exquisitely tuned by the proteins with which they are associated. When bound to (apo)phycobiliproteins, phytobilins harvest light throughout the visible spectrum and efficiently transfer this energy to photosynthetic reaction centers, enabling cyanobacteria, red algae and cryptophytes to colonize light-limiting environments unsuitable for other photosynthetic organisms. Phytobilins also play a key role as light harvesting pigments of plant and cyanobacterial phytochromes. This project addresses the structure, enzymatic mechanism and function of representative cyanobacterial and green algal phycocyanobilin:ferredoxin oxidoreductases and heme oxygenases using enzymology, x-ray crystallography and genetics. Notably, our studies seek to understand the reasons for presence of the phytobilin biosynthetic pathway in chlorophytes (green algae) most of which lack both phytochromes and phycobiliproteins. These investigations leverage the well developed molecular tools, forward/reverse genetic methodologies and genomic resources of the model chlorophyte Chlamydomonas reinhardtii. Key collaborators on this project include the laboratories of Arthur Grossman, Sabeeha Merchant and Krishna Niyogi.