Xiaojing Yang

Assistant Professor

Website:  Yang Research Group

The University of Chicago, Ph.D. 1995Northwestern University, Postdoctoral Fellow 1996-1999.

Areas of Research:

In the Yang Laboratory, our research centers on a fundamental question - how living organisms perceive, convert, and integrate physical and chemical signals into biological signals at the molecular level? To address this question, we focus on three areas of research: 1) signaling mechanisms of bacterial sensor proteins in response to light and oxygen; 2) structures and dynamics of circadian photoreceptors in plants and animals; 3) light harvesting and photosynthesis in cyanobacteria. Our research aims to gain mechanistic understanding of important biological processes via an integrated approach of crystallography, spectroscopy and biochemistry. We are also committed to further development and wide applications of dynamic crystallography that aims at direct observations of transient molecular events and reaction intermediates at the atomic resolution.

1) Bacterial Light and Oxygen Sensor Proteins

Light and oxygen are two fundamental environmental signals for all living organisms. They regulate a wide range of important physiological processes such as photomorphogenesis, circadian rhythm, and photosynthesis. In bacteria, light and oxygen sensor proteins share many common structural characteristics. They often possess modular architecture, in which distinct sensory and effector domains of diverse enzymatic activities are coupled in a “mix-and-match” fashion via domain fusion (Figure 1). Sensory domains are responsible for perceiving environmental signals, usually via non-protein moieties such as chromophores or heme. Structural signals originating in the sensory domains are transmitted to the covalently linked output domains to generate distinct biological signals, e.g., auto-phosphorylation of histidine kinases, or synthesis/degradation of second messengers. Similar modular scaffolds and recurrent structural motifs among bacterial sensor proteins suggest common signaling mechanisms. We are interested in two families of bacterial sensor proteins - bilin-based photoreceptors and heme-based direct oxygen sensors. We aim to answer the following questions. What conformational changes occur upon light absorption by chromophore or oxygen binding to heme? How do conformational changes generated in the sensory domains regulate enzymatic activities of the remote effector domains? Given their remarkable similarities in modular structures and domain architecture, we are particularly interested to learn general principles of long-range signal transduction via “compare-and-contrast” of different bacterial sensor proteins.

2) Circadian Photoreceptors

Circadian rhythm provides a biological timing mechanism that ensures proper temporal organization of metabolism, physiology and behavior in organisms ranging from cyanobacteria to humans. Light signals provide major inputs to entrain the circadian clock. This is achieved via light-dependent interactions between circadian photoreceptors and downstream signaling proteins. We currently focus on two plant circadian photoreceptors - UV-B photoreceptor UVR8 and red-light photoreceptor phytochromes (PHYs). UVR8 and PHYs adopt very different architectures and use chemically distinct chromophores to perceive light signals from different wavelength ranges of the solar spectrum (Figure 2). However, they both interact with COP1, a master regulator of light signaling in plants, in a light-dependent manner. We are also actively pursuing structural studies of melanopsin(OPN4), a non-image-forming (NIR) photoreceptor in retina that plays important roles in circadian rhythm and pupillary light reflex in animals. OPN4 is a membrane protein that belongs to the GPCR superfamily. We apply both static and dynamic crystallography to understand the structural basis for photoreception of circadian photoreceptors and how protein-protein interactions are regulated by light at the molecular level.

3) Light Harvesting and Photosynthesis in Cyanobacteria

In oxygenic photosynthetic organisms such as cyanobacteria, light energy is converted to chemical energy via light-driven reactions in photosystems located in thylakoid membranes. Phycobilisomes (PBS) are light-harvesting antenna complexes in cyanobacteria. PBS has a distinctive architecture consisting of rods and a core. Light energy harvested by hundreds of antenna pigments in the rods is funneled to the core via highly efficient radiationless energy transfer, and eventually to a special pair of chlorophylls in photosystem II (PSII) that drives photosynthesis (Figure 3a). This area of research is carried out with an established collaboration with the Zhao Group of HuazhongAgricultural University in China. We pursue crystallographic investigations of key components involved in light harvesting, photosynthesis and photo-protection. By solving crystal structures of the PBS core, piece-by-piece and in its entirety, we aim to understand the structural basis of directional energy transfer. We have recently determined the crystal structure of a terminal emitter AP-B in phycobilisomes from Synechocystis sp. PCC 6803 at 1.8 Å resolution (Acta Cryst. D, in press, Figure 3b). Findings from structural studies of light-harvesting antenna and PSII are expected to have broad impacts on agricultural and bioenergy research.

4) Dynamic Crystallography

Watching a biochemical reaction and/or a biological process by dynamic crystallography would provide unparalleled insights into how proteins work at the atomic level. Transient intermediate structures are difficult to capture by static crystallography, but they hold the key to mechanistic understanding of protein functions. One of the major hurdles for wider applications of dynamic crystallography is that almost all reactions initiated in crystals are in effect irreversible at room temperature, due to X-ray radiation damage, slow reversion rate and/or lattice disorders induced by large-amplitude structural changes. As a result, many important biological processes - even when a reaction is active in the crystal - are not easily accessible. To study irreversible reactions, we continue to develop experimental and analytical methods in dynamic crystallography.

Temperature-scan cryo-crystallography
 - The rationale behind this T-scan strategy is “temperature mimics time”. In other words, the higher the cryo-temperature at which a reaction is initiated, the further it proceeds along its pathway while relative populations of distinct structural species vary with temperatures. This enables subsequent resolution of structural heterogeneity by posterior analytical deconvolution. Reaction initiation at cryogenic temperatures is particularly suitable for capturing intermediates with small-amplitude and/or local structural changes that can be tolerated by crystal lattices (Figure 4). We are also interested in developing methods that would extend T-scan to systems that are naturally inert to light, such as oxygen-dependent enzymes and direct oxygen sensor proteins.

Serial crystallography at room temperature - Reaction progression towards the end product(s) often requires higher temperatures that are not accessible by T-scan. Room-temperature (RT) diffraction experiments are needed in order to capture structural changes associated with formation of late reaction intermediates. However, due to severe X-ray radiation damage, only very few images of good diffraction quality can be acquired from one crystal volume at RT. As a result, the “diffract-before-destroy” experiments at RT demands implementation of serial crystallography that entails high-throughput introduction of a large number of crystals into the X-ray beam as well as algorithms/software to effectively handle joint data analysis from hundreds of crystals.

Selected Publications

(*Corresponding authors)

1. Yang, X., Gerczei, T., Glover, L. and Correll, C.* Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nature Struct Biol. 8:968-73 (2001).

2.    Krasilnikov, A., Yang, X., Pan, T. and Mondragon, A.* Crystal structure of the specificity domain of ribonuclease P. Nature, 421:760-4 (2003).

3.    Yang, X., Stojkovic, E. A, Kuk, J. and Moffat, K.* Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion. PNAS, 104:12571-6 (2007).

4.    Yang, X.*, Kuk, J. and Moffat, K.*  Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction. PNAS, 105:14715-20 (2008).

5.    Yang, X.*, Kuk, J. and Moffat, K.* Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome. PNAS, 106:15639-44 (2009).

6.    Möglich A., Yang, X., Ayers RA and Moffat, K. Structure and Function of Plant Photoreceptors. Annu Rev Plant Biol.  61:21-47 (2010).

7.    Yang, X*., Ren, Z., Kuk, J. and Moffat, K*. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome. Nature, 479:428-32 (2011).

8.    Yang, X.  Structures of Phytochromes.  G.C.K. Roberts (ed.) Encyclopedia of Biophysics. Springer-Verlag Berlin Heilelberg (2012).

9.    Ren, Z.*, Chan, P., Moffat, K., Pai, E.F., Royer, W.E., Srajer, V and Yang, X.  Resolution of Structural Heterogeneity in Dynamic Crystallography. Acta Cryst. D.  69:946-59 (2013).

10.  Peng, P.P., Dong, L.L, Sun, Y.F., Zeng, X.L., Ding, W.L., Scheer, H., Yang, X*.  and Zhao, K.H.*  Crystal structure of allophycocyanin B from Synechocystis PCC 6803 reveals structural basis for extreme red-shift of terminal emitter in phycobilisomes.Acta Cryst. D. in press (2014).

11.  Zhou, W., Ding, W.L., Zeng, X.L., Dong, L.L., Zhao, B., Zhou, M., Scheer, H., Zhao, K.H.* and Yang, X.*  Structure and mechanism of the phycobiliprotein lyase CpcT. J. Biol. Chem. in press (2014).

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Contact Information

Office: 3166 SES, MC 111
Phone: 312-413-9406
Fax: 312-996-0431
Email: xiaojing@uic.edu