Cloning and characterization of the homologous genes of firefly luciferase in the mealworm beetle, Tenebrio molitor

Firefly genomes illuminate parallel origins of bioluminescence in beetles

Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of bioluminescence within beetles remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. To compare bioluminescent origins, we also sequenced the genome of a related click beetle, the Caribbean Ignelater luminosus, with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing hypothesis of parallel gains of bioluminescence. Our analyses support independent gains of bioluminescence in fireflies and click beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle.

Lessons Learned from Luminous Luciferins and Latent Luciferases

Compared to the broad palette of fluorescent molecules, there are relatively few structures that are competent to support bioluminescence. Here, we focus on recent advances in the development of luminogenic substrates for firefly luciferase. The scope of this light-emitting chemistry has been found to extend well beyond the natural substrate and to include enzymes incapable of luciferase activity with d-luciferin. The broadening range of luciferin analogues and evolving insight into the bioluminescent reaction offer new opportunities for the construction of powerful optical reporters of use in live cells and animals.

Mass spectrometry analysis and transcriptome sequencing reveal glowing squid crystal proteins are in the same superfamily as firefly luciferase

The Japanese firefly squid Hotaru-ika (Watasenia scintillans) produces intense blue light from photophores at the tips of two arms. These photophores are densely packed with protein microcrystals that catalyse the bioluminescent reaction using ATP and the substrate coelenterazine disulfate. The squid is the only organism known to produce light using protein crystals. We extracted microcrystals from arm tip photophores and identified the constituent proteins using mass spectrometry and transcriptome libraries prepared from arm tip tissue. The crystals contain three proteins, wsluc1–3, all members of the ANL superfamily of adenylating enzymes. They share 19 to 21% sequence identity with firefly luciferases, which produce light using ATP and the unrelated firefly luciferin substrate. We propose that wsluc1–3 form a complex that crystallises inside the squid photophores, and that in the crystal one or more of the proteins catalyses the production of light using coelenterazine disulfate and ATP. These results suggest that ANL superfamily enzymes have independently evolved in distant species to produce light using unrelated substrates.

Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes

Background

The New Zealand glowworm is the larva of a carnivorous fungus gnat that produces bioluminescence to attract prey. The bioluminescent system of the glowworm is evolutionarily distinct from other well-characterised systems, especially that of the fireflies, and the molecules involved have not yet been identified. We have used high throughput sequencing technology to produce a transcriptome for the glowworm and identify transcripts encoding proteins that are likely to be involved in glowworm bioluminescence.

Results

Here we report the sequencing and annotation of the first transcriptome of the glowworm, and a differential analysis of expression from the glowworm light organ compared with non-light organ tissue. The analysis identified six transcripts encoding proteins that are potentially involved in glowworm bioluminescence. Three of these proteins are members of the ANL superfamily of adenylating enzymes, with similar amino acid sequences to that of the luciferase enzyme found in fireflies (31 to 37 % identical), and are candidate luciferases for the glowworm bioluminescent system. The remaining three transcripts encode putative aminoacylase, phosphatidylethanolamine-binding and glutathione S-transferase proteins.

Conclusions

This research provides a basis for further biochemical studies into how the glowworm produces light, and a source of genetic information to aid future ecological and evolutionary studies of the glowworm.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2006-2) contains supplementary material, which is available to authorized users.

A route from darkness to light: emergence and evolution of luciferase activity in AMP-CoA-ligases inferred from a mealworm luciferase-like enzyme

The origin of luciferases and of bioluminescence is enigmatic. In beetles, luciferases seem to have evolved from AMP-CoA-ligases. How the new oxygenase luminogenic function originated from AMP-ligases leading to luciferases is one of the most challenging mysteries of bioluminescence. Comparison of the cloned luciferase-like enzyme from the nonluminescent Zophobas morio mealworm and beetle luciferases showed that the oxygenase activity may have emerged as a stereoselective oxidative drift with d-luciferin, a substrate that cannot be easily thioesterified to CoA as in the case of the l-isomer. While the overall kcat displayed by beetle luciferases is orders of magnitude greater than that of the luciferase-like enzyme, the respective oxidation rates and quantum yields of bioluminescence are roughly similar, suggesting that the rate constant of the AMP-ligase activity exerted on the new d-luciferin substrate in beetle protoluciferases was the main enzymatic property that suffered optimization during the evolution of luciferases. The luciferase-like enzyme and luciferases boost the rate of luciferyl-adenylate chemiluminescent oxidation by factors of 10(6) and 10(7), respectively, as compared to the substrate spontaneous oxidation in buffer. A similar enhancement of luciferyl-adenylate chemiluminescence is provided by nucleophilic aprotic solvents, implying that the peptide bonds in the luciferin binding site of beetle luciferase could provide a similar catalytically favorable environment. These data suggest that the luciferase-like enzyme and other similar AMP-ligases are potential alternative oxygenases. Site-directed mutagenesis studies of the luciferase-like enzyme and the red light-producing luciferase of Phrixotrix hirtus railroadworm confirm here a critical role for T/S345 in luciferase function. Mutations such as I327T/S in the luciferase-like enzyme, which simultaneously increases luciferase activity and promotes blue shifts in the emission spectrum, could have been critical for evolving functional bioluminescence from red-emitting protoluciferases. Through the combination of I327T/S mutations and N-terminal fusion, the luminescence activity of this enzyme was increased to visible levels, with the development of a totally new orange-emitting luciferase. These results open the possibility of engineering luciferase activity in a set of AMP-CoA-ligases.

Firefly luciferase genes from the subfamilies Psilocladinae and Ototretinae (Lampyridae, Coleoptera)

Firefly luciferase genes have been isolated from approximately 20 species of Lampyrinae, Luciolinae, and Photurinae. These are mostly nocturnal luminescent species that use light signals for sexual communication. In this study, we isolated three cDNAs for firefly luciferase from Psilocladinae (Cyphonocerus ruficollis) and Ototretinae (Drilaster axillaris and Stenocladius azumai), which are diurnal non-luminescent or weakly luminescent species that may use pheromones for communication. The amino acid sequences deduced from the three cDNAs showed 81-89% identities to each other and 60-81% identities with known firefly luciferases. The three purified recombinant proteins showed luminescence and fatty acyl-CoA synthetic activities, as observed in other firefly luciferases. The emission maxima by the three firefly luciferases (λmax, 545-546nm) were shorter than those by known luciferases from the nocturnal fireflies (λmax, 550-568nm). These results suggest that the primary structures and enzymatic properties of luciferases are conserved in Lampyridae, but the luminescence colors were red-shifted in nocturnal species compared to diurnal species.

Identification and characterization of a luciferase isotype in the Japanese firefly, Luciola cruciata, involving in the dim glow of firefly eggs

We isolated the cDNA of a luciferase isotype (LcLuc2) from the Japanese firefly, Luciola cruciata (Lampyridae, Coleoptera). The gene product of LcLuc2 (LcLuc2) showed 59% amino acid identity with firefly luciferase LcLuc1, which was previously identified in L. cruciata. The recombinant LcLuc2 showed both luminescence activity and fatty acyl-CoA synthetic activity comparable to those of LcLuc1. The spectral maxima of the luminescence by LcLuc1 and LcLuc2 were 554 and 543 nm, respectively. Reverse transcription-PCR analysis showed that the transcripts of LcLuc1 were abundant in the lanterns of larva, adult male, and adult female, whereas both LcLuc1 and LcLuc2 were expressed in eggs. The luminescence spectra of the lantern extracts from larva, adult male, and adult female were in good agreement with that of recombinant LcLuc1. On the other hand, the emission maximum of the extract from eggs was between those of LcLuc1 and LcLuc2. These results suggest that L. cruciata possesses two luciferases: LcLuc1 is responsible for the major luminescence in larva and adult, whereas LcLuc1 and LcLuc2 are responsible for the dim glow in firefly eggs.

Identification of a functional luciferase gene in the non-luminous diurnal firefly, Lucidina biplagiata

We isolated a luciferase gene (LbLuc) from the non-luminous diurnal firefly, Lucidina biplagiata, with high similarity to that from the nocturnal firefly, Photinus pyralis. The recombinant LbLuc showed luminescence activity comparable to that of the luciferases from P. pyralis and Luciola cruciata. To understand the non-luminosity of L. biplagiata, we determined the amount of luciferase in the adult specimen using the luciferin-luciferase reaction and found that the content of luciferase in L. biplagiata was estimated to be only 0.1% of that in L. cruciata. As previously reported, the content of luciferin in L. biplagiata was less than 0.1% of that in L. cruciata. Thus, the non-luminosity of L. biplagiata might be explained by low levels of both luciferase and luciferin.

The origin of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase): luciferin stereoselectivity as a switch for the oxygenase activity

Beetle luciferases evolved from AMP/CoA-ligases. However, it is unclear how the new luciferase activity evolved. In order to clarify this question, we compared the luminescence and catalytic properties of a recently cloned luciferase-like enzyme from Zophobas mealworm, an AMP/CoA-ligase displaying weak luminescence activity, with those of cloned luciferases from the three main families of luminescent beetles: Phrixthrix hirtus railroad worm; Pyrearinus termitilluminans click beetle and Photinus pyralis firefly. The catalytic constant of the mealworm enzyme was 2-4 orders of magnitude lower than that of beetle luciferases, but 3 orders of magnitude above the non-catalyzed chemiluminescence of luciferyl-adenylate in buffer. Studies with D- and L-luciferin and their adenylates show that the luminescence reaction of the luciferase-like enzyme and beetle luciferases are stereoselective for D-luciferin and its adenylate, and that the selectivity is determined mainly at the adenylation step. Modelling studies showed that the luciferin binding site cavity of this enzyme is smaller and more hydrophobic than that of beetle luciferases. Therefore Zophobas mealworm enzyme displays true luciferase activity, keeping the attributes of an ancient protoluciferase. These results suggest that stereoselectivity for D-luciferin may have been a key event for the origin of oxygenase/luciferase activity in AMP/CoA-ligases, and that efficient luciferase activity may have further evolved mainly by increasing the catalytic constant of the oxidative reaction and the quantum yield of bioluminescence.

Firefly luciferase: an adenylate-forming enzyme for multicatalytic functions

Firefly luciferase is a member of the acyl-adenylate/thioester-forming superfamily of enzymes and catalyzes the oxidation of firefly luciferin with molecular oxygen to emit light. Knowledge of the luminescence mechanism catalyzed by firefly luciferase has been gathered, leading to the discovery of a novel catalytic function of luciferase. Recently, we demonstrated that firefly luciferase has a catalytic function of fatty acyl-CoA synthesis from fatty acids in the presence of ATP, Mg(2+) and coenzyme A. Based on identification of fatty acyl-CoA genes in firefly, Drosophila, and non-luminous click beetles, we then proposed that the evolutionary origin of firefly luciferase is a fatty acyl-CoA synthetase in insects. Further, we succeeded in converting the fatty acyl-CoA synthetase of non-luminous insects into functional luciferase showing luminescence activity by site-directed mutagenesis.

Characterization of luciferases and its paralogue in the Panamanian luminous click beetle Pyrophorus angustus: a click beetle luciferase lacks the fatty acyl-CoA synthetic activity

Two luciferase genes (dPaLuc and vPaLuc) and one paralogue of luciferase (PaLL) were isolated from the Panamanian luminous click beetle, Pyrophorus angustus (Elateridae, Pyrophorinae). The transcripts of dPaLuc and vPaLuc were predominantly detected in the body parts with dorsal photophore and ventral photophore, respectively, and the transcript of PaLL was detected in both parts. The gene products of dPaLuc and vPaLuc possessed luminescence activity with firefly luciferin (lambda(max)=536 and 566 nm, respectively) but did not show significant activity of fatty acyl-CoA synthesis. On the other hand, the gene product of PaLL had fatty acyl-CoA synthetic activity with very weak luminescence activity. The catalytic properties of click beetle luciferase are different from our previous results that firefly luciferase has both luminescence activity and fatty acyl-CoA synthetic activity. These results suggested that the ancestral fatty acyl-CoA synthetase in the Pyrophorinae lineage has undergone gene duplication event, followed by specialization of one copy in luciferase. Subsequently, the luciferase was duplicated again and the two copies diverged in their luminescent color and expression pattern.

Functional conversion of fatty acyl-CoA synthetase to firefly luciferase by site-directed mutagenesis: a key substitution responsible for luminescence activity

We demonstrated that firefly luciferase has a catalytic function of fatty acyl-CoA synthesis [Oba, Y., Ojika, M. and Inouye, S. (2003) Firefly luciferase is a bifunctional enzyme: ATP-dependent monooxygenase and a long chain fatty acyl-CoA synthetase. FEBS Lett. 540, 251-254] and proposed that the evolutionary origin of beetle luciferase is a fatty acyl-CoA synthetase (FACS) in insect. In this study, we performed the functional conversion of FACS to luciferase by replacing a single amino acid to serine. This serine residue is conserved in luciferases and possibly interacts with luciferin. The mutants of FACSs in non-luminous click beetle Agrypnus binodulus (AbLL) and Drosophila melanogaster (CG6178) gave luminescence enhancement, suggesting that the serine residue is a key substitution responsible for luminescence activity.

Firefly bioluminescence: a mechanistic approach of luciferase catalyzed reactions

Luciferase is a general term for enzymes catalyzing visible light emission by living organisms (bioluminescence). The studies carried out with Photinus pyralis (firefly) luciferase allowed the discovery of the reaction leading to light production. It can be regarded as a two-step process: the first corresponds to the reaction of luciferase's substrate, luciferin (LH(2)), with ATP-Mg(2+) generating inorganic pyrophosphate and an intermediate luciferyl-adenylate (LH(2)-AMP); the second is the oxidation and decarboxylation of LH(2)-AMP to oxyluciferin, the light emitter, producing CO(2), AMP, and photons of yellow-green light (550- 570 nm). In a dark reaction LH(2)-AMP is oxidized to dehydroluciferyl-adenylate (L-AMP). Luciferase also shows acyl-coenzyme A synthetase activity, which leads to the formation of dehydroluciferyl-coenzyme A (L-CoA), luciferyl-coenzyme A (LH(2)-CoA), and fatty acyl-CoAs. Moreover luciferase catalyzes the synthesis of dinucleoside polyphosphates from nucleosides with at least a 3'-phosphate chain plus an intact terminal pyrophosphate moiety. The LH(2) stereospecificity is a particular feature of the bioluminescent reaction where each isomer, D-LH(2) or L-LH(2), has a specific function. Practical applications of the luciferase system, either in its native form or with engineered proteins, encloses the analytical assay of metabolites like ATP and molecular biology studies with luc as a reporter gene, including the most recent and increasing field of bioimaging.

Characterization of a phenylacetate-CoA ligase from Penicillium chrysogenum

Enzymatic activation of PAA (phenylacetic acid) to phenylacetyl-CoA is an important step in the biosynthesis of the beta-lactam antibiotic penicillin G by the fungus Penicillium chrysogenum. CoA esters of PAA and POA (phenoxyacetic acid) act as acyl donors in the exchange of the aminoadipyl side chain of isopenicillin N to produce penicillin G or penicillin V. The phl gene, encoding a PCL (phenylacetate-CoA ligase), was cloned in Escherichia coli as a maltose-binding protein fusion and the biochemical properties of the enzyme were characterized. The recombinant fusion protein converted PAA into phenylacetyl-CoA in an ATP- and magnesium-dependent reaction. PCL could also activate POA, but the catalytic efficiency of the enzyme was rather low with k(cat)/K(m) values of 0.23+/-0.06 and 7.8+/-1.2 mM(-1).s(-1) for PAA and POA respectively. Surprisingly, PCL was very efficient in catalysing the conversion of trans-cinnamic acids to the corresponding CoA thioesters [k(cat)/K(m)=(3.1+/-0.4)x10(2) mM(-1).s(-1) for trans-cinnamic acid]. Of all the substrates screened, medium-chain fatty acids, which also occur as the side chains of the natural penicillins F, DF, H and K, were the best substrates for PCL. The high preference for fatty acids could be explained by a homology model of PCL that was constructed on the basis of sequence similarity with the Japanese firefly luciferase. The results suggest that PCL has evolved from a fatty-acid-activating ancestral enzyme that may have been involved in the beta-oxidation of fatty acids.

An ancestral luciferase in the Malpighi tubules of a non-bioluminescent beetle!

The evolutionary origin of beetle bioluminescence is enigmatic. Previously, weak luciferase activity was found in the non-bioluminescent larvae of Tenebrio molitor (Coleoptera: Tenebrionidae), but the detailed tissular origin and identity of the luciferase-like enzyme remained unknown. Using a closely related giant mealworm, Zophobas morio, here we show that the luciferase-like enzyme is located in the Malpighi tubules. cDNA cloning of this luciferase like enzyme, showed that it is a short AMP-ligase with weak luciferase activity which diverged long ago from beetle luciferases. The results indicate that the potential for bioluminescence in AMP-ligases is very ancient and provide a first reasonable protoluciferase model to investigate the origin and evolution of beetle luciferases.

Firefly luminescence: a historical perspective and recent developments

Significant advances have occurred regarding our knowledge of firefly luciferase mechanisms. Although most of this progress was an outcome of molecular biology and structural studies, important achievements have also occurred on its fundamental chemistry. Those developments are here summarized and presented in a historical perspective.

The evolutionary process of bioluminescence and aposematism in cantharoid beetles (Coleoptera: Elateroidea) inferred by the analysis of 18S ribosomal DNA

Cantharoid beetles are distinctive for their leathery soft elytra and conspicuous color or bioluminescence, and many of the members are equipped with chemical defenses. Thus, the vivid coloration of Cantharidae and Lycidae and the bioluminescence in Lampyridae and Phengodidae appear to be aposematic signals. However, the evolutionary aspect of their aposematism is not well understood, because the classification of the families remains controversial. In this study, we performed molecular phylogenetic analyses of species from cantharoid families, based on nucleotide sequence comparisons of nuclear 18S ribosomal DNA. The results shows that the luminous species Rhagophthalmus ohbai, which had sometimes been classified in Lampyridae, is excluded from a lampyrid clade and associates with the taxa of Phengodidae. The molecular data also suggests that four major subfamilies of Cantharidae (Cantharinae, Chauliognathinae, Malthininae, and Silinae) form a clade. The six subfamilies of Lampyridae are grouped and classified into two sublineages: Amydetinae+Lampyrinae+Photurinae and Cyphonocerinae+Luciolinae+Ototretinae. Genera Drilaster and Stenocladius are the members of Ototretinae in Lampyridae. These results conform to traditional taxonomy but disagree with more recent cladistic analyses. Based on these findings, we propose an evolutionary process of bioluminescence and aposematism in cantharoids: the clades of Cantharidae, Lampyridae, Lycidae, and Phengodidae have evolved aposematic coloration; subsequently Lampyridae and Phengodidae acquired bioluminescence; and these four major cantharoid families achieved their current adaptive diversities.