A photoactivatable green-fluorescent protein from the phylum Ctenophora

Haddock, Steven H. D.; Mastroianni, Nadia; Christianson, Lynne M.

doi:10.1098/rspb.2009.1774

Cited by 27 publications

(15 citation statements)

References 37 publications

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“…Ctenophore FP clustered with hydrozoan FP, therefore the cnidarian clade was not monophyletic. Others have shown that incongruence with taxonomy is not unusual in fluorescent proteins [43]. For better visualization, a smaller maximum likelihood sub-tree was generated from 46 scleractinian FP sequences (Figure 4).…”

Section: Resultsmentioning

confidence: 99%

Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

et al. 2013

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BackgroundGenomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea.ResultsWe obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e-30). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals’ algal symbiont, Symbiodinium spp.ConclusionsHere we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals.

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Section: Resultsmentioning

confidence: 99%

Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

et al. 2013

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“…Photophores (bioluminescent organs) in fact often convert their naturally blue bioluminescent light to green using what is aptly named 'green fluorescent protein' (GFP). This is common in jellyfish and other cnidarians and may be used to increase visibility range in greener coastal waters where this conversion is common [27]. Orange and red light is also made by fluorophores converting blue bioluminescence and potentially ambient light in deeper-sea bioluminescent species [28,29].…”

Section: (C) Spectral Sensitivity Ranges Of Potential Viewersmentioning

confidence: 99%

“…Haddock and co-workers [27,29,40] have made the case that some hydromedusan gelatinous zooplankton species construct fluorescent lures to bring in prey. This includes the tentacle tip (tentilla) in Erenna, a deep-sea, fish-eating siphonophore with fluorescent tissue emitting yellow to red (583-680 nm) surrounding a bioluminescent photophore.…”

Section: (E) Birdsmentioning

confidence: 99%

Fluorescence as a means of colour signal enhancement

Marshall

Johnsen

2017

Phil. Trans. R. Soc. B

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Fluorescence is a physico-chemical energy exchange where shorter-wavelength photons are absorbed by a molecule and are re-emitted as longer-wavelength photons. It has been suggested a means of communication in several taxa including flowers, pitcher plants, corals, algae, worms, squid, spiders, stomatopods, fish, reptiles, parrots and humans. The surface or object that the pigment molecule is part of appears to glow due to its setting rather than an actual production of light, and this may enhance both signals and, in some cases, camouflage. This review examines some known uses of fluorescence, mainly in the context of visual communication in animals, the challenge being to distinguish when fluorescence is a functional feature of biological coloration or when it is a by-product of a pigment or other molecule. In general, we conclude that most observations of fluorescence lack enough evidence to suggest they are used in visually driven behaviours.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.

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“…To date, GFP-like proteins have been found in several distant groups of marine animals: in two classes [the hydroid jellyfishes Hydrozoa (Prasher et al, 1992) and the coral polyps Anthozoa (Matz et al, 1999)] of the phylum Cnidaria; in one species from the comb jelly phlyum Ctenophora (Haddock et al, 2010); in several species of copepods (phylum Arthropoda; Shagin et al, 2004) and in lancelets (phylum Chordata; Deheyn et al, 2007). The greatest spectral diversity has been demonstrated for Anthozoa GFP-like proteins.…”

Section: Introductionmentioning

confidence: 99%

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

Плетнев

Pletneva

Lukyanov

et al. 2013

Acta Crystallogr D Biol Cryst

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A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the `core' structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λex/λem = 502/511 nm) and red laRFP (λex/λem ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C(β) atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (∼70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis.

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A photoactivatable green-fluorescent protein from the phylum Ctenophora

Cited by 27 publications

References 37 publications

Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

Fluorescence as a means of colour signal enhancement

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

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