Biliproteins and their Applications in Bioimaging

Scheer, Hugo; Yang, Xiaojing; Zhao, Kai‐Hong

doi:10.1016/j.proche.2015.03.026

Cited by 14 publications

(17 citation statements)

References 44 publications

(50 reference statements)

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“…FR-CBCRs have evolved from green/red CBCRs as part of a Greater Green/Red (GGR) lineage, diversification comparable to that seen in the XRG (extended red/green) lineage (35,40,41). Owing to their small size and spectral overlap with the therapeutic window of optimum tissue penetrance (700-800 nm) (42)(43)(44)(45)(46), FR-CBCRs provide a tantalizing scaffold for development of FR-responsive optogenetic reagents for biomedical research and clinical applications (45,(47)(48)(49)(50).…”

Section: /Bodymentioning

confidence: 99%

Molecular Basis of Far-red Sensing in Cyanobacteriochrome

Bandara

Rockwell

Zeng

et al. 2020

Preprint

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Author contributionsXY designed the project; SB, SSM and XZ carried out cloning, purification, and crystallization; SB, XZ, SSM and NR conducted mutagenesis and spectroscopic experiments; SB, XZ, ZR, HS and XY collected monochromatic diffraction data; HS, CW and ZR collected Laue diffraction data; ZR processed the Laue data and carried out singlecrystal spectroscopic experiments; SB and XY determined, refined and analyzed crystal structures; NR carried out phylogenetic analysis; SB, XY, NR, MVM, and JCL interpreted the data; XY, NR, and JCL wrote the paper with inputs from all authors. Abstract (156 words)Cyanobacteriochromes are small, panchromatic photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. The molecular basis of far-red (FR) light perception by cyanobacteriochromes is currently unknown. Here we report the crystal structure of a far-red-sensing cyanobacteriochrome from Anabaena cylindrica PCC 7122, which exhibits a reversible far-red/orange photocycle.The 2.7 Å structure of its FR-absorbing dark state, determined by room temperature serial crystallography and cryo-crystallography, reveals an all-Z,syn configuration of its bound linear tetrapyrrole (bilin) chromophore that is less extended than the bilin chromophores of all known phytochromes. Based on structural comparisons with other bilin-binding proteins and extensive spectral analyses on mutants, we identify key proteinchromophore interactions that enable far-red sensing in bilin-binding proteins. We propose that FR-CBCRs employ two distinct tuning mechanisms, which work together to produce a large batho-chromatic shift. Findings of this work have important implications for development and improvement of photoproteins with far-red absorption and fluorescence. Significance Statement (99 words)Phytochromes are well known far-red-light sensors found in plants that trigger adaptive responses to facilitate competition for light capture with neighboring plants. Red-and farred-sensing are critical to cyanobacteria living in the far-red-enriched shade of plants.Here we report the crystal structure of a far-red-sensing cyanobacteriochrome, a distant cyanobacterial relative of phytochrome. These studies shed insight into the poorly understood molecular basis of far-red-sensing by phytobilin-based photoreceptors.Owing to the deep tissue penetration of far-red light, far-red-sensing photoreceptors offer promising protein scaffolds for developing gene-based photoswitches, optoacoustic contrast agents and fluorescent probes for in situ imaging and optogenetic applications.

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Section: /Bodymentioning

confidence: 99%

Molecular Basis of Far-red Sensing in Cyanobacteriochrome

Bandara

Rockwell

Zeng

et al. 2020

Preprint

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“…The wide range of available mutant structures and those reconstituted with different chromophores offers significant potential to develop new cell biological reporter molecules and in optogenetics. 17,193 An example for the former is the use of small phytochrome fragments with mutations which result in highly fluorescent molecules. 274 Together with the ability to tune the specific absorption and emission wavelength, this leads to new fluorescent tag molecules with more scope for use than the commonly used green fluorescent proteins.…”

mentioning

confidence: 99%

“…274 Together with the ability to tune the specific absorption and emission wavelength, this leads to new fluorescent tag molecules with more scope for use than the commonly used green fluorescent proteins. 193 Recent reviews by Scheer et al 17 and Burgie and Vierstra 193 further illuminate this use of biliproteins as bioimaging agents and the path to designer photoresponsive proteins.…”

mentioning

confidence: 99%

Conformational control of cofactors in nature – the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

2015

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Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigmentprotein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P 450 ). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H 2 O 2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.

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“…PCC 6803, and binds its weakly absorbing and fluorescing linear tetrapyrrole (bilin) ligands within a sterically defined site, which transforms these pigments into highly coloured and strongly fluorescent chromophores 3 . Free bilin chromophores, as well as those of denatured proteins, adopt a cyclo-helical conformation that is only very weakly fluorescent 17 , 18 . Thus, there is almost no background signal from the apoprotein or unattached bilins (Supplementary Figure S6 ), and the only localization signals observed are from the CpcA-bound form of the pigment.…”

Section: Discussionmentioning

confidence: 99%

Repurposing a photosynthetic antenna protein as a super-resolution microscopy label

Barnett¹,

Hitchcock²,

Mandal

et al. 2017

Sci Rep

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Techniques such as Stochastic Optical Reconstruction Microscopy (STORM) and Structured Illumination Microscopy (SIM) have increased the achievable resolution of optical imaging, but few fluorescent proteins are suitable for super-resolution microscopy, particularly in the far-red and near-infrared emission range. Here we demonstrate the applicability of CpcA, a subunit of the photosynthetic antenna complex in cyanobacteria, for STORM and SIM imaging. The periodicity and width of fabricated nanoarrays of CpcA, with a covalently attached phycoerythrobilin (PEB) or phycocyanobilin (PCB) chromophore, matched the lines in reconstructed STORM images. SIM and STORM reconstructions of Escherichia coli cells harbouring CpcA-labelled cytochrome bd 1 ubiquinol oxidase in the cytoplasmic membrane show that CpcA-PEB and CpcA-PCB are suitable for super-resolution imaging in vivo. The stability, ease of production, small size and brightness of CpcA-PEB and CpcA-PCB demonstrate the potential of this largely unexplored protein family as novel probes for super-resolution microscopy.

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Biliproteins and their Applications in Bioimaging

Cited by 14 publications

References 44 publications

Molecular Basis of Far-red Sensing in Cyanobacteriochrome

Molecular Basis of Far-red Sensing in Cyanobacteriochrome

Conformational control of cofactors in nature – the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Repurposing a photosynthetic antenna protein as a super-resolution microscopy label

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