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OPEN Luciferase gene of a Caribbean

fireworm (Syllidae) from Puerto
Rico
Received: 10 June 2019 Yasuo Mitani1, Rie Yasuno2, Ryo Futahashi   3, Todd H. Oakley4 & Yoshihiro Ohmiya2,5
Accepted: 27 August 2019
Published: xx xx xxxx The fireworms Odontosyllis spp. are globally distributed and well-known for their characteristic and
fascinating mating behavior, with secreted mucus emitting bluish-green light. However, knowledge
about the molecules involved in the light emission are still scarce. The fireworms are believed to emit
light with a luciferin-luciferase reaction, but biochemical evidence of the luciferase is established for
only one species living in Japan and no information is available for its luciferin structure. In this study,
we identified a luciferase gene from a related Puerto Rican fireworm. We identified eight luciferase-
like genes in this Puerto Rican fireworm, finding amino acid identities between Japanese and Puerto
Rican luciferase-like genes to be less than 60%. We confirmed cross reactivity of extracts of the
Japanese fireworm luciferin with a recombinant Puerto Rican luciferase (PR1). The emission spectrum
of recombinant PR1 was similar to the crude extract of the native luciferase, suggesting that PR1 is a
functional luciferase of this Puerto Rican fireworm. Our results indicate that the molecular mechanism
of luminescence is widely conserved among fireworms.

A wide variety of luminous animals are distributed on the earth. Some of them are terrestrial, many are marine,
while only one species is known from fresh water1,2. Since the first cloning of a luciferase gene involved in light
emission from the firefly Photinus pyralis3, a diversity of luciferase genes has been reported, mainly from ter-
restrial organisms2,4. While terrestrial beetles basically use the same light emission system with D-luciferin as
a substrate among different families, luminous marine animals use various luciferins including coelenterazine,
Cypridinid luciferin, and dinoflagellate luciferin2,5.
The fireworms Odontosyllis spp., including O. enopla, O. phosphorea, O. undecimdonta, O. octodentata, and O.
luminosa, are distributed sporadically in locations around the world including the Caribbean Sea, West Coast of
the United States, and Japan6–11. Despite many observations of their characteristic mating behavior, the molecular
mechanisms underlying light emission is not well understood1,2. Luciferin structure has not been determined
although more than 50 years ago Shimomura et al. partially purified luciferin and luciferase from more than
50,000 individuals of O. enopla12.
Recently, we identified a fireworm luciferase gene using unpurified luminous mucus from the Japanese
species, Odontosyllis undecimdonta13,14. This luciferase gene was independently identified by another group
using protein purification procedures15. The recombinant luciferase protein produced the same characteristic
bluish-green emission peak as the wild fireworms14,15. It should be noted that the fireworm luciferase gene has
an evolutionarily different origin from other known luciferase genes because the fireworm system did not show
any cross reactivity to known systems including coelenterazine and Cypridinid luciferin14. In a third study, tran-
scriptome analyses of the Bermuda fireworm O. enopla identified luciferase-like genes16, although its biochemical
function has not been confirmed.
In this study, we focused on a fireworm from Puerto Rico. A species living in Puerto Rico was originally
described as O. octodentata17 with behavior similar to O. enopla18. Although we have not determined the species
in detail, we confirmed the cross reaction between the recombinant luciferase of Japanese fireworm and the etha-
nol extract of a Puerto Rican fireworm which probably contains fireworm luciferin. RNA sequencing (RNA-Seq)
and subsequent analyses identified 8 possible luciferase paralogous genes (PR1-PR8), among which PR1 shows

1
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST),
Sapporo, 062-8517, Japan. 2Biomedical Research Institute, AIST, Tsukuba, 305-8566, Japan. 3Bioproduction Research
Institute, AIST, Tsukuba, 305-8566, Japan. 4Marine Science Institute, University of California, Santa Barbara, CA,
93106, USA. 5DAILAB, Biomedical Research Institute, AIST, Tsukuba, 305-8566, Japan. Correspondence and requests
for materials should be addressed to Y.M. (email: [email protected])

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Figure 1.  The Puerto Rican fireworm. (a) Bright field image of anterior part. (b) Luminous mucus from a worm
that was pressed on paper. The bluish-green color appeared similar to that observed in their natural secretion
during the mating behavior on the sea surface. Scale bar = 2 mm. (c) i to v are a series of assays using different
combination of substrate extract (PRs and JPs) using the native PRe. A 10 μL of PRe was measured in 100 μL RB
in total (i) and left for 3 hours (ii). Then, 1 μL JPs was added to this solution to check the cross reaction (iii). The
activity went down to almost background level after 1 hour of the reaction (iv) and 10 μL PRs was added to the
mixture (v). The activity using 1 μL JPre and 10 μL PRs is shown in (vi).

the highest expression level. The recombinant PR1 exhibited light emitting activity in the presence of crude lucif-
erin extract from the Japanese species. These data strongly suggested that the Japanese O. undecimdonta and the
Puerto Rican species share molecular mechanisms of bioluminescence through luciferin-luciferase (LL) reaction.

Results and Discussion

Collection of the fireworm in Caribbean Sea and the LL reaction.  We collected the fireworm in
the Caribbean Sea, off Puerto Rico (Fig. 1a). The fireworms came to the sea surface 30 to 40 min after sunset
and disappeared suddenly approximately 30 min after the appearance of the first visible displays, as described
previously18. Their appearance peaked a couple of days after the full moon, when more than one hundred females
were observed to make luminous circles. Although it was not difficult to collect them, we could not keep them
alive for long periods, even in a sea table with fresh seawater flowing. After they were collected, they did not emit
light even after strong stimulation; however, when they were pressed against a paper towel, a similar bluish-green
light as observed on the sea surface was confirmed (Fig. 1b). This feature was different from the Japanese species
because the they emit strong light when stimulated by a needle tip14. This is probably because the Caribbean indi-
viduals already secreted most of their luciferase and luciferin outside the body as a mating signal.
To conduct cross-reactivity tests, a single specimen of the Caribbean fireworm was crushed to obtain crude
luciferase extract (PRe) while another specimen was soaked in ethanol to obtain crude luciferin (PRs). We used
some animals for the cross reaction tests, but it was difficult to obtain clear numerical data because their activities
were different from worm to worm due to the residual level of luciferase and luciferin in the body. Thus, we pre-
sented typical cross reaction data in Fig. 1. The luminous activity of the luciferase extract was confirmed visually
just after crushing (Fig. 1c,i). This extract was left in a refrigerator for 3 hours to consume the luciferin (Fig. 1c,ii).
The addition of the crude luciferin obtained from O. undecimdonta (JPs) recovered the luminescent activity
(Fig. 1c,iii). Then, this solution was left in a refrigerator for 1 hour to exhaust the added luciferin (Fig. 1c,iv). The
addition of PRs recovered the luminescent activity (Fig. 1c,v). Finally, the light emission activity was confirmed
for the mixture of recombinant luciferase of the Japanese fireworm O. undecimdonta (JPre) and PRs (Fig. 1c,vi).
Thus, cross-reactions between these two species were confirmed. These results suggested that the light emission
mechanisms underlining these two different fireworms are the same, although we were not able to obtain quanti-
tative data due to difficulties of collecting enough active animals.

Luciferase homolog of a fireworm from Puerto Rico.  To obtain the luciferase genes, we performed
RNA-Seq analysis using a single individual of Puerto Rican fireworm to exclude genetic diversity derived from
polymorphism. After manual assembly, we identified 8 possible paralogous genes (PR1-PR8) with significant
sequence similarity to Japanese and Bermuda fireworm luciferase genes (Fig. 2a). We numbered the genes in
descending order of expression level with PR1 as the gene with the highest expression (Fig. 2b). From the molecu-
lar phylogenetic tree, three paralogous genes from the Japanese fireworm luciferase formed a single clade with the
Puerto Rican fireworm luciferase PR2 and Bermuda fireworm luciferase BM1 together forming a sister clade. This

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Figure 2.  Molecular phylogeny and expression analysis of the Caribbean fireworm luciferase paralogs. (a)
Molecular phylogenetic analysis of fireworm luciferases. A maximum likelihood phylogeny is shown, while
neighbor-joining phylogeny exhibit the same topologies. Statistical supporting values are indicated on each
node in the order of (bootstrap value of maximum likelihood)/(bootstrap value of neighbor-joining). (b)
Relative expression level of eight luciferase-like gene in whole body of single individual calculated based on
RNA-Seq analysis.

Identities Positives Gaps

JP1 vs PR1 184/330 (56%) 228/330 (69%) 3/330 (0.01%)

Table 1.  Percent of identities, positives, and gaps between Japanese and Puerto Rican fireworm luciferase
homologues. The number of identical amino acid residues and those with similar properties are shown as
Identities and Positives, respectively.

molecular phylogenetic tree indicates that the luciferase gene duplication occurred independently in Japanese
and Puerto Rican fireworms. The identity of amino acids between Japanese fireworm luciferase and Puerto Rican
fireworm luciferase was less than 60% (Table 1), but the positions of 10 cysteine residues in all luciferase-like
genes were conserved (Fig. 3). The Bermuda fireworm luciferase-like gene (BM1) was almost identical to PR2
with only a single amino acid substitution (99% identities). The high similarity of these genes suggests our Puerto
Rican species is very similar or the same species as that analyzed previously from Bermuda. Although several
luciferase-like paralogs were reported in the Bermuda fireworm16, there was no biochemical data of their activity
as luciferase. All these luciferase-like proteins contained probable secretion signal peptides at each N-terminus
(Fig. 3). As shown for Cypridina luciferase19,20, at least one N-glycosylation motif characteristic of secreted pro-
teins was found in 10 genes of 12 fireworm luciferase-like genes except PR6 and PR8 (Fig. 3, boxes).

Recombinant PR1 protein expression and its secretion property.  In order to clarify the function
of a Puerto Rican fireworm luciferase-like gene, we synthesized recombinant protein of PR1 which showed the
highest expression level among Puerto Rican luciferase-like genes in Fig. 2. We produced recombinant PR1 by
mammalian expression systems using COS1 and HEK293 cells. Luciferase activity was measured separately for
supernatant of culture media (Fig. 4a, sup) and whole cell lysate (Fig. 4a, lys) after collection of the cells by cen-
trifugation, because recombinant protein was expected to be secreted into the culture media. The recombinant
protein exhibited significant light emitting activity for both supernatant and lysate fractions compared to negative
control (Fig. 4a), and the ratio of the secretion fraction was higher than that of Japanese fireworm luciferase JP1
(Table 2)14. Importantly, like the Japanese fireworm luciferase14, the emission spectrum of recombinant PR1 was
similar to the native luciferase crude extract with a possible peak around 510–530 nm (Fig. 4b), suggesting that
PR1 is a functional luciferase gene. Improvement of recombinant PR1 protein production is necessary to obtain
a clear emission spectrum to clarify its emission peak. Unfortunately, we were not able to obtain the emission
spectrum using native luciferin extract from the Caribbean species due to low amount of samples.

Methods
Animal collection.  Fireworms were collected in La Parguera (17.95N, 67.05W), Puerto Rico on July. 22–29,
2016. The fireworm length ranged from 5 to 30 mm. Animals were kept frozen for a long-term storage or soaked
in RNAlater (Thermo Fisher Scientific) solution and kept frozen for RNA extraction.

LL reaction.  Fifty worms of the Japanese species were put into 1.5 mL of 99.5% ethanol, and the supernatant
after short centrifugation was used as the crude luciferin solution (JPs). A single specimen of the Caribbean
species was crushed in 100 μL of the reaction buffer (RB) containing 50 mM Tris-HCl (pH 7.5), 300 mM NaCl,
and 20 mM MgCl2 and the supernatant collected after centrifugation at 20,000 × g for 10 min was used as a crude

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Figure 3.  Comparison of amino acid sequences among fireworm luciferase-like genes. JP, BM, and PR mean
Japanese O. undecimdonta (Mitani et al.14), Bermuda O. enopla (Brugler et al.16), and Puerto Rican (this study)
genes, respectively. Identical or conserved amino acid residues are shaded by red and pink, respectively. N-
terminal secretion signal sequence is indicated by arrows. N-glycosylation motifs are indicated by boxes.
Conserved cysteine residues are indicated by asterisks.

Figure 4.  Recombinant luciferase expression using mammalian cells COS1 and HEK293. (a) Expression vector
containing luciferase gene PR1 or empty vector as negative control (NC) was expressed and their activities
were monitored. In each case, supernatant (sup) and lysate (lys) were analyzed to detect secretion and cytosolic
recombinant protein, respectively. (b) Spectrum analysis of a mixture of recombinant PR1 protein and crude
luciferin extract.

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Host cell Clone Secretion rate (Std. dv.)/%

JP1 0.918 (0.238)
COS1
PR1 41.7 (9.54)
JP1 18.4 (3.09)
HEK293
PR1 33.9 (4.14)

Table 2.  Secretion rate of the recombinant luciferases. Estimated secretion rate is shown with standard
deviation (std. dv.) of three independent experiments. COS1 and HEK293 were used as host cells and JP1 and
PR1 were expressed.

luciferase solution (PRe) while another specimen was soaked in 100 μL of ethanol and the supernatant was used
as a crude luciferin extract (PRs). The recombinant luciferase for O. undecimdonta (JPre) was described previ-
ously14. In the light emission activity assays, normally 1 μL JPs, 1 μL JPre, 10 μL PRe, and 10 μL PRs were used
with an appropriate combination in 100 μL RB in total. The activity was monitored using luminometer, Phelios
AB-2350 (ATTO) and recorded as relative light unit (RLU) for 10 s accumulation of the measurement. Emission
spectrum was measured using a high sensitivity CCD spectrophotometer, AB-1850S (ATTO).

RNA-Seq and gene analysis.  Total RNA was extracted from one whole individual using Maxwell 16 LEV
Simply RNA Tissue kit (Promega). RNA-Seq analysis was performed as described previously14,21. cDNA libraries
were constructed using TruSeq RNA Sample Preparation Kits v2 (Illumina) and sequenced by MiSeq (Illumina).
The raw reads were subjected to de novo assembly by using Trinity22 implemented in the MASER pipeline23. After
automatic assembling, we checked and manually corrected the putative luciferase sequences as reported previ-
ously24. After manual assembly, sequence read mapping was performed using the BWA-mem software25 imple-
mented in the MASER pipeline, whereby the transcript expression levels were estimated to calculate the fragments
per kilobase of exon per million (FPKM) values. Signal peptide sequences were predicted by using SignalP26.
Multiple alignment was performed using ClustalW (DNA Data Bank of Japan). Protein similarity was estimated
using BlastP program (NCBI) to find identical and similar character amino acid sequences. To construct the
molecular phylogeny of fireworm luciferase genes, deduced amino-acid sequences were aligned using the Clustal
W program implemented in MEGA727. Molecular phylogenetic analyses were conducted by the neighbor-joining
method and the maximum-likelihood method using MEGA7. Bootstrap values for neighbor-joining and max-
imum likelihood phylogenies were obtained by 1000 resampling. Maximum Composite Likelihood model and
Tamura Nei model were used for neighbor-joining and maximum likelihood analysis, respectively28. Bootstrap
values for neighbor-joining and maximum likelihood phylogenies were obtained by 1000 bootstrap replications.

Recombinant protein expression in mammalian cells.  Gene sequence coding PR1 optimized
to human codon usage was synthesized and inserted into a pcDNA3.1- vector by an outsourcing company
(Genscript). COS1 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Wako) supplemented
with 10% fetal bovine serum (FBS) at 37 °C in a humidified incubator exposed to 5% CO2. COS1 cells were
transfected with expression plasmids using Lipofectamine 3000 (Invitrogen). On the following day, the culture
medium was replaced with serum-free DMEM. The culture medium was collected 24 h after medium exchange
and used as the supernatant fraction (sup). Cells were lysed with 10 mM Tris-HCl (pH 7.4) using sonication. The
lysate was centrifuged at 20,000 × g for 5 min, and the resulting supernatant was used as the cell extract fraction
(lys). The activity of recombinant PR1 in each fraction was measured by adding NaCl and MgCl2 solutions to
a final concentration of 300 mM and 20 mM each, and adding crude luciferin extract obtained from O. undec-
imdonta14. The luminescence of the mixture was immediately measured using a Phelios AB-2350 luminometer
(ATTO). Secretion ratio was determined as the activity ratio of sup to total (sup plus lys) activity.

References
1. Harvey, E. N. Bioluminescence. Academic Press, New York (1952).
2. Shimomura, O. Bioluminescence: Chemical principals and methods. World Scientific (2006)
3. de Wet, J. R., Wood, K. V., Helinski, D. R. & DeLuca, M. Cloning of firefly luciferase cDNA and the expression of active luciferase in
Escherichia coli. Proc. Natl. Acad. Sci. USA 82, 7870–7873 (1985).
4. Viviani, V. R. The origin, diversity, and structure function relationships of insect luciferases. Cell. Mol. Life Sci. 59, 1833–1850 (2002).
5. Widder, E. A. Bioluminescence in the ocean: origins of biological, chemical, and ecological diversity. Science 328, 704–708 (2010).
6. Galloway, T. W. & Welch, P. S. Studies on a phosphorescent Bermudan annelid, Odontosyllis enopla Verrill. Trans. Am. Micosc. Soc.
30, 13–39 (1911).
7. Fischer, A. & Fisher, U. On the life-style and life-cycle of the luminous polychaete Odontosyllis enopla (Annelida: Polychaeta). Inv.
Biol. 114, 236–247 (1995).
8. Markert, R. E., Markert, B. J. & Vertrees, N. J. Lunar periodicity in spawning and luminescence in Odontosyllis enopla. Ecology. 42,
414–415 (1961).
9. Tsuji, F. I. & Hill, E. Repetitive cycles of bioluminescence and spawning in the polychaete, Odontosyllis phosphorea. Biol. Bull. 165,
444–449 (1983).
10. Imajima, M. & Hartman, O. The polychaetous annelids of Japan. Allan Hancock Found. Pub. Los Angeles, http://digitallibrary.usc.
edu/cdm/ref/collection/p15799coll82/id/18494 (1964).
11. Gaston, G. R. & Hall, J. Lunar periodicity and bioluminescence of swarming Odontosyllis luminosa (Polychaeta: Syllidae) in Belize.
Gulf Carib. Res. 12, 47–51 (2000).
12. Shimomura, O., Johnson, F. H. & Saiga, Y. Partial purification and properties of the Odontosyllis luminescence system. J. Cell. Phys.
61, 275–292 (1963).
13. Ohmiya, Y., Mitani, Y. & Yasuno, R. Light-emitting enzyme protein. Patent Application WO/2017/155036 (2017).
14. Mitani, Y. et al. Novel gene encoding a unique luciferase from the fireworm Odontosyllis undecimdonta. Sci. Rep. 8, 12789 (2018).

Scientific Reports | (2019) 9:13015 | https://doi.org/10.1038/s41598-019-49538-7 5

www.nature.com/scientificreports/ www.nature.com/scientificreports

15. Schultz, D. T. et al. Luciferase of the Japanese syllid polychaete Odontosyllis undecimdonta. Biochem. Biophys. Res. Commun. 502,
318–323 (2018).
16. Brugler, M. R., Aguado, M. T., Tessler, M. & Siddall, M. E. The transcriptome of Bermuda fireworm Odontosyllis enopla (Annelida:
Syllidae): A unique luciferase gene family and putative epitoky-related genes. PLoS ONE 13(8), e0200944 (2018).
17. Treadwell, A. L. Polychaetous annelids from Florida, Porto Rico, Bermuda and the Bahamas. Carnegie Institute of Washington
Publication. 251, 255–272 (1917).
18. Erdman, D. S. Lunar periodicity in the swarming of luminescent worms, Odontosyllis octodentata Treadwell (Annelida) off La
Parguera, P.R. Caribb J Sci 5, 103–107 (1965).
19. Mitani, Y. et al. Efficient production of glycosylated Cypridina luciferase using plant cells. Protein Expr. Purif. 133, 102–109 (2017).
20. Yasuno, R., Mitani, Y. & Ohmiya, Y. Effects of N-Glycosylation deletion on Cypridina luciferase activity. Photochem. Photobiol. 94,
338–342 (2018).
21. Futahashi, R. Molecular Mechanisms Underlying Color Vision and Color Formation in Dragonflies. Diversity and Evolution of
Butterfly Wing Patterns: An Integrative Approach, eds Sekimura, T, Nijhout, H. F. (Springer, Singapore), pp 303–321 (2017).
22. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 29,
644–652 (2011).
23. Kinjo, S. et al. Maser: one-stop platform for NGS big data from analysis to visualization. Database (Oxford). 2018 Jan 1;2018, https://
doi.org/10.1093/database/bay027 (2018).
24. Futahashi, R. et al. Extraordinay diversity of visual opsin genes in dragonflies. Proc. Natl. Acad. Sci. USA 112, E1247–1256 (2015).
25. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio.GN] (2013).
26. Nielsen, H. Predicting secretory proteins with SignalP. Methods Mol. Biol. 1611, 59–73 (2017).
27. Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol.
33, 1870–1874 (2016).
28. Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans
and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993).

Acknowledgements
We are very grateful to people in Isla Magueyes laboratory, university of Puerto Rico, Emily Ellis (UCSB),
and Niko Nensley (UCSB) for assistance with collecting animals. This work was partially supported by JSPS
KAKENHI Grant Numbers 26560440 and 16K01929 (to Y.M.).

Author Contributions
Y.M. conducted the experiments using natural animals. R.Y. conducted the mammalian expression experiments.
R.F. conducted the RNA-Seq and informatics analysis. T.H.O. organized the animal collection. Y.M. and Y.O.
wrote and all the authors modified the paper.

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