Learning the pattern of epistasis linking genotype and phenotype in a protein

Abstract Understanding the pattern of epistasis—the non-independence of mutations—is critical for relating genotype and phenotype. However, the combinatorial complexity of potential epistatic interactions has severely limited the analysis of this problem. Using new mutational approaches, we report a comprehensive experimental study of all 213 mutants that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein—an opportunity to examine epistasis up to the 13th order. The data show the existence of many high-order epistatic interactions between mutations, but also reveal extraordinary sparsity, enabling novel experimental and computational strategies for learning the relevant epistasis. We demonstrate that such information, in turn, can be used to accurately predict phenotypes in practical situations where the number of measurements is limited. Finally, we show how the observed epistasis shapes the solution space of single-mutation trajectories between the parental fluorescent proteins, informative about the protein’s evolutionary potential. This work provides conceptual and experimental strategies to profoundly characterize epistasis in a protein, relevant to both natural and laboratory evolution.

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Learning the pattern of epistasis linking genotype and phenotype in a protein

10.1101/213835 ◽

2017 ◽

Cited By ~ 7

Author(s):

Frank J. Poelwijk ◽

Michael Socolich ◽

Rama Ranganathan

Keyword(s):

Experimental Study ◽

Sequence Space ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

High Order ◽

Epistatic Interactions ◽

Stepwise Variation ◽

Experimental Strategies ◽

Variation And Selection ◽

Entacmaea Quadricolor

Understanding the pattern of epistasis – the non-independence of mutations – is critical for relating genotype and phenotype in biological systems. However, the complexity of potential epistatic interactions has limited approaches to this problem at any level. To develop practical strategies, we carried out a comprehensive experimental study of epistasis between all mutations that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein. The data demonstrate significant high-order epistatic interactions between mutations, but also reveals extraordinary sparsity, enabling novel experimental strategies and sequence-based statistical methods for learning the relevant epistasis. The sequence space linking the parental fluorescent proteins is functionally connected through paths of single mutations; thus, high-order epistasis in proteins is consistent with evolution through stepwise variation and selection. This work initiates a path towards characterizing epistasis in proteins in general.

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Fluorescent proteins for in vivo imaging, where's the biliverdin?

Biochemical Society Transactions ◽

10.1042/bst20200444 ◽

2020 ◽

Vol 48 (6) ◽

pp. 2657-2667

Author(s):

Felipe Montecinos-Franjola ◽

John Y. Lin ◽

Erik A. Rodriguez

Keyword(s):

Hydrogen Peroxide ◽

In Vivo Imaging ◽

Near Infrared ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

Fluorescent Imaging ◽

Infrared Light ◽

Red Fluorescent Protein ◽

Color Palette

Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10−18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.

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Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins

10.26434/chemrxiv.9209450.v1 ◽

2019 ◽

Author(s):

Jeffrey Chang ◽

Matthew Romei ◽

Steven Boxer

Keyword(s):

Rational Design ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

Super Resolution ◽

Unit Cell Size ◽

Chlorine Substituent ◽

Gfp Chromophore ◽

The One ◽

Green Fluorescent ◽

Super Resolution Microscopy

Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of cis and trans rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the trans state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas in a tighter packing (7% smaller unit cell size), the hula-twist occurs.

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Split-wrmScarlet and split-sfGFP: Tools for faster, easier fluorescent l abeling of endogenous proteins in Caenorhabditis elegans

Genetics ◽

10.1093/genetics/iyab014 ◽

2021 ◽

Author(s):

Jérôme Goudeau ◽

Catherine S Sharp ◽

Jonathan Paw ◽

Laura Savy ◽

Manuel D Leonetti ◽

...

Keyword(s):

Fluorescent Protein ◽

Fluorescent Proteins ◽

Fluorescent Labeling ◽

Large Fragment ◽

C Elegans ◽

High Affinity ◽

Red Fluorescent Proteins ◽

Invaluable Tool ◽

Endogenous Proteins ◽

Fluorescent Tags

Abstract We create and share a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenous C. elegans proteins with fluorescent tags. CRISPR-mediated fluorescent labeling of C. elegans proteins is an invaluable tool, but it is much more difficult to insert fluorophore-size DNA segments than it is to make small gene edits. In principle, high-affinity asymmetrically split fluorescent proteins solve this problem in C. elegans: the small fragment can quickly and easily be fused to almost any protein of interest, and can be detected wherever the large fragment is expressed and complemented. However, there is currently only one available strain stably expressing the large fragment of a split fluorescent protein, restricting this solution to a single tissue (the germline) in the highly autofluorescent green channel. No available C. elegans lines express unbound large fragments of split red fluorescent proteins, and even state-of-the-art split red fluorescent proteins are dim compared to the canonical split-sfGFP protein. In this study, we engineer a bright, high-affinity new split red fluorophore, split-wrmScarlet. We generate transgenic C. elegans lines to allow easy single-color labeling in muscle or germline cells and dual-color labeling in somatic cells. We also describe a novel expression strategy for the germline, where traditional expression strategies struggle. We validate these strains by targeting split-wrmScarlet to several genes whose products label distinct organelles, and we provide a protocol for easy, cloning-free CRISPR/Cas9 editing. As the collection of split-FP strains for labeling in different tissues or organelles expands, we will post updates at doi.org/10.5281/zenodo.3993663

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Fluorescent protein expression in temperature tolerant and susceptible reef-building corals

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315421000059 ◽

2021 ◽

pp. 1-10

Author(s):

Exequiel Gabriel S. Dizon ◽

Jeric P. Da-Anoy ◽

Melissa S. Roth ◽

Cecilia Conaco

Keyword(s):

Spectral Properties ◽

Coral Species ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

Expression Profiles ◽

Expression Patterns ◽

Antioxidant Properties ◽

Variable Expression ◽

Acropora Digitifera ◽

Insight Into

Abstract Fluorescent proteins (FPs) are reported to play an important role as photoprotectants and antioxidants in corals subjected to stressful conditions. Identifying the various FP genes expressed and FP gene expression patterns under stress in diverse coral species can provide insight into FP function. In this study, we identified 16 putative FP homologues from the transcriptomes of corals with varying susceptibility to elevated temperature, including Acropora digitifera, Favites colemani, Montipora digitata and Seriatopora caliendrum. Each coral expressed a different complement of FP transcripts, which were predicted to have distinct spectral properties. The most diverse and abundant repertoire of FP transcripts, including at least 6 green FPs, were expressed in the temperature-tolerant coral, F. colemani. In comparison, the other corals expressed fewer FP types. Specific FP transcripts exhibited variable expression profiles in coral fragments subjected to 32 ± 1 °C (treatment) or 28 ± 1 °C (control) for up to 72 h, suggesting that distinct FPs may have different roles. Further studies on the expression of the proteins encoded by these FP transcripts, their fluorescence activity, tissue localization, and possible antioxidant properties, are needed to reveal their contribution to thermal stress tolerance in certain species of corals.

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CRISPR/Cas9-mediated targeted mutagenesis in Japanese cedar (Cryptomeria japonica D. Don)

Scientific Reports ◽

10.1038/s41598-021-95547-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yoshihiko Nanasato ◽

Masafumi Mikami ◽

Norihiro Futamura ◽

Masaki Endo ◽

Mitsuru Nishiguchi ◽

...

Keyword(s):

Genome Editing ◽

Cryptomeria Japonica ◽

Fluorescent Protein ◽

Japanese Cedar ◽

Targeted Mutagenesis ◽

Embryogenic Tissue ◽

Breeding Period ◽

Single Mutation ◽

Knock Out ◽

Guide Rna

AbstractCryptomeria japonica (Japanese cedar or sugi) is one of the most important coniferous tree species in Japan and breeding programs for this species have been launched since 1950s. Genome editing technology can be used to shorten the breeding period. In this study, we performed targeted mutagenesis using the CRISPR/Cas9 system in C. japonica. First, the CRISPR/Cas9 system was tested using green fluorescent protein (GFP)-expressing transgenic embryogenic tissue lines. Knock-out efficiency of GFP ranged from 3.1 to 41.4% depending on U6 promoters and target sequences. The GFP knock-out region was mottled in many lines, indicating genome editing in individual cells. However, in 101 of 102 mutated individuals (> 99%) from 6 GFP knock-out lines, embryos had a single mutation pattern. Next, we knocked out the endogenous C. japonica magnesium chelatase subunit I (CjChlI) gene using two guide RNA targets. Green, pale green, and albino phenotypes were obtained in the gene-edited cell lines. Sequence analysis revealed random deletions, insertions, and replacements in the target region. Thus, targeted mutagenesis using the CRISPR/Cas9 system can be used to modify the C. japonica genome.

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Biogenic fluorescent protein–silk fibroin phosphors for high performing light-emitting diodes

Materials Horizons ◽

10.1039/d0mh00503g ◽

2020 ◽

Vol 7 (7) ◽

pp. 1790-1800

Author(s):

Verónica Fernández-Luna ◽

Juan P. Fernández-Blázquez ◽

Miguel A. Monclús ◽

Francisco Javier Rojo ◽

Rafael Daza ◽

...

Keyword(s):

Silk Fibroin ◽

Light Emitting Diodes ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

Light Emitting ◽

High Performing ◽

New Family

This work presents a new family of bio-hybrid light-emitting diodes (Bio-HLEDs) using all-bio color down-converting coatings that combine silk fibroin (SF) as a packaging matrix and fluorescent proteins (FPs) as emitters.

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Insulin Stimulates Membrane Fusion and GLUT4 Accumulation in Clathrin Coats on Adipocyte Plasma Membranes

Molecular and Cellular Biology ◽

10.1128/mcb.01719-06 ◽

2007 ◽

Vol 27 (9) ◽

pp. 3456-3469 ◽

Cited By ~ 85

Author(s):

Shaohui Huang ◽

Larry M. Lifshitz ◽

Christine Jones ◽

Karl D. Bellve ◽

Clive Standley ◽

...

Keyword(s):

Plasma Membrane ◽

Membrane Fusion ◽

Insulin Signaling ◽

Plasma Membranes ◽

Glucose Transporter ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

Tirf Microscopy ◽

Adipocyte Plasma Membranes ◽

Kinetics Of

ABSTRACT Total internal reflection fluorescence (TIRF) microscopy reveals highly mobile structures containing enhanced green fluorescent protein-tagged glucose transporter 4 (GLUT4) within a zone about 100 nm beneath the plasma membrane of 3T3-L1 adipocytes. We developed a computer program (Fusion Assistant) that enables direct analysis of the docking/fusion kinetics of hundreds of exocytic fusion events. Insulin stimulation increases the fusion frequency of exocytic GLUT4 vesicles by ∼4-fold, increasing GLUT4 content in the plasma membrane. Remarkably, insulin signaling modulates the kinetics of the fusion process, decreasing the vesicle tethering/docking duration prior to membrane fusion. In contrast, the kinetics of GLUT4 molecules spreading out in the plasma membrane from exocytic fusion sites is unchanged by insulin. As GLUT4 accumulates in the plasma membrane, it is also immobilized in punctate structures on the cell surface. A previous report suggested these structures are exocytic fusion sites (Lizunov et al., J. Cell Biol. 169:481-489, 2005). However, two-color TIRF microscopy using fluorescent proteins fused to clathrin light chain or GLUT4 reveals these structures are clathrin-coated patches. Taken together, these data show that insulin signaling accelerates the transition from docking of GLUT4-containing vesicles to their fusion with the plasma membrane and promotes GLUT4 accumulation in clathrin-based endocytic structures on the plasma membrane.

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Illuminating subcellular structures and dynamics in plants: a fluorescent protein toolboxThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology.

Canadian Journal of Botany ◽

10.1139/b06-060 ◽

2006 ◽

Vol 84 (4) ◽

pp. 515-522 ◽

Cited By ~ 8

Author(s):

Preetinder K. Dhanoa ◽

Alison M. Sinclair ◽

Robert T. Mullen ◽

Jaideep Mathur

Keyword(s):

Plant Cell ◽

Cell Biology ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

Live Imaging ◽

Living Cells ◽

Special Issue ◽

Exciting Possibility ◽

Selection Of

The discovery and development of multicoloured fluorescent proteins has led to the exciting possibility of observing a remarkable array of subcellular structures and dynamics in living cells. This minireview highlights a number of the more common fluorescent protein probes in plants and is a testimonial to the fact that the plant cell has not lagged behind during the live-imaging revolution and is ready for even more in-depth exploration.

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Single-Molecule Studies on a FRET Biosensor: Lessons from a Comparison of Fluorescent Protein Equipped versus Dye-Labeled Species

Molecules ◽

10.3390/molecules23123105 ◽

2018 ◽

Vol 23 (12) ◽

pp. 3105 ◽

Cited By ~ 1

Author(s):

Henning Höfig ◽

Michele Cerminara ◽

Ilona Ritter ◽

Antonie Schöne ◽

Martina Pohl ◽

...

Keyword(s):

Conformational Change ◽

Single Molecule ◽

Fluorescent Dyes ◽

Fluorescent Protein ◽

Fluorescent Proteins ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Strong Increase ◽

Single Molecule Level ◽

Labeling Scheme

Bacterial periplasmic binding proteins (PBPs) undergo a pronounced ligand-induced conformational change which can be employed to monitor ligand concentrations. The most common strategy to take advantage of this conformational change for a biosensor design is to use a Förster resonance energy transfer (FRET) signal. This can be achieved by attaching either two fluorescent proteins (FPs) or two organic fluorescent dyes of different colors to the PBPs in order to obtain an optical readout signal which is closely related to the ligand concentration. In this study we compare a FP-equipped and a dye-labeled version of the glucose/galactose binding protein MglB at the single-molecule level. The comparison demonstrates that changes in the FRET signal upon glucose binding are more pronounced for the FP-equipped sensor construct as compared to the dye-labeled analog. Moreover, the FP-equipped sensor showed a strong increase of the FRET signal under crowding conditions whereas the dye-labeled sensor was not influenced by crowding. The choice of a labeling scheme should therefore be made depending on the application of a FRET-based sensor.

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