DOI: 10.25349/d94w5n
title: Similar Enzymatic Functions in Distinct Bioluminescence Systems: Evolutionary Recruitment of Sulfotransferases in Ostracod Light Organs

description: Genes from ancient families are sometimes involved in the convergent
 evolutionary origins of similar traits, even across vast phylogenetic
 distances. Sulfotransferases are an ancient family of enzymes that
 transfer sulfate from a donor to a wide variety of substrates, including
 probable roles in some bioluminescence systems. Here we demonstrate
 multiple sulfotransferases, highly expressed in light organs of the
 bioluminescent ostracod Vargula tsujii, transfer sulfate in vitro to the
 luciferin substrate, vargulin. We find luciferin sulfotransferases of
 ostracods are not orthologous to known luciferin sulfotransferases of
 fireflies or sea pansies; animals with distinct and convergently evolved
 bioluminescence systems compared to ostracods. Therefore, distantly
 related sulfotransferases were independently recruited at least three
 times, leading to parallel evolution of luciferin metabolism in three
 highly diverged organisms. Re-use of homologous genes is surprising in
 these bioluminescence systems because the other components, including
 luciferins and luciferases, are completely distinct. Whether convergently
 evolved traits incorporate ancient genes with similar functions or instead
 use distinct, often newer, genes may be constrained by how many genetic
 solutions exist for a particular function. When fewer solutions exist, as
 in genetic sulfation of small molecules, evolution may be more constrained
 to use the same genes time and again.
description: # Similar enzymatic functions in distinct bioluminescence systems:
 Evolutionary recruitment of sulfotransferases in ostracod light organs
 #### Emily S Lau1, Jessica A Goodheart1,2, Nolan T Anderson3, Vannie L
 Liu3, Arnab Mukherjee3,4,5,6, Todd H Oakley1 #### 1 Department of Ecology,
 Evolution, and Marine Biology, University of California Santa Barbara,
 Santa Barbara, CA 93106 #### 2 Division of Invertebrate Zoology, American
 Museum of Natural History, New York, NY 10025 #### 3 Department of
 Chemical Engineering, University of California Santa Barbara, Santa
 Barbara, CA 93106 #### 4 Department of Biological Engineering, University
 of California Santa Barbara, Santa Barbara, CA 93106 #### 5 Department of
 Chemistry, University of California Santa Barbara, Santa Barbara, CA 93106
 #### 6 Neuroscience Research Institute, University of California Santa
 Barbara, Santa Barbara, CA 93106 --- ## Directory structure and file list
 ``` README.md Lau_etal_Rcode_supplement.Rmd Lau_etal_Rcode_supplement.html
 Rmarkdown_csv_files/ full_uni_sulfo_abs.csv uni_sulfo_corr_abs.csv
 luciferase_assay.csv luciferase_inhibition_no_background.csv
 pNitrophenol_abs.csv uni_sulfo_dunnett.csv luciferase_inhibition.csv
 purified_luciferase.csv Bioinformatic_analyses/ Fig2_data/
 compiled_sulfotransferases_midpoint_rooted.txt
 sulfotransferases_compiled_aligned.fa
 sulfotransferases_compiled_aligned.fa.log
 sulfotransferases_compiled_aligned.treefile sulfotransferases_compiled.fa
 FigS10_data/ Vtsujii_cd95_st_clean_aligned.fa.log
 Vtsujii_sulfotransferase_midpoint_rooted_tree.txt
 Vtsujii_sulfotransferases_aligned.fa
 Vtsujii_sulfotransferases_aligned.treefile
 Vtsujii_sulfotransferases_counts.csv Vtsujii_sulfotransferases.fa
 FigS11_data/ compiled_sulfotransferases_trimmed_midpoint_rooted.txt
 sulfotransferases_compiled_aligned_trimmed.fa
 sulfotransferases_compiled_aligned_trimmed.fa.log
 sulfotransferases_compiled_aligned_trimmed.treefile FigS13_data/
 sulfotransferase_domain_hmmer.xlsx sulfotransferases_aligned.fa
 Isoseq_reference_transcriptome/ Vargula_tsujii_cdhit_95.fasta
 Plasmid_sequences/ Luciferase/ pcmv-cypridinaluc-flag-6his.gb
 Sulfotransferases/ pet6his-sumo-st1.gb pet6his-sumo-st2.gb
 pet6his-sumo-st5.gb pqe80l_st3.gb pqe80l_st4.gb ``` --- ## File
 descriptions ``` LST_MS_Dryad_Data/Lau_etal_Rcode_supplement.Rmd: R
 markdown file containing code used for data analysis and generating
 figures ``` ``` LST_MS_Dryad_Data/Lau_etal_Rcode_supplement.html: html
 file containing code and output of the R markdown file ``` ```
 LST_MS_Dryad_Data/Rmarkdown_csv_files/: Contains data files for the
 functional assays full_uni_sulfo_abs.csv: Full dataset for the universal
 sulfotransferase assay Fig. 1b uni_sulfo_corr_abs.csv: Dataset for the
 universal sulfotransferase assay Fig. 1b with average blank values
 subtracted luciferase_assay.csv: Data for the luciferase assay Fig. 1c
 pNitrophenol_abs.csv: Data for the pNitrophenol sulfation assay Fig. S9
 uni_sulfo_dunnett.csv: Subset of data from the universal sulfotransferase
 assay, used to perform Dunnett's test Fig 1b
 luciferase_inhibition.csv: Complete dataset for ostracod luciferase
 kinetics luciferase_inhibition_no_background.csv: Data for ostracod
 luciferase kinetics Fig. S12 with average background reading at 0 uM
 subtracted purified_luciferase.csv: Data for ostracod luciferase
 purification Supp. Fig. S8 ``` ```
 LST_MS_Dryad_Data/Bioinformatic_analyses/: Contains transcriptomic, gene
 expression, and phylogenetic data Fig2_data/: Contains .fa files of
 unaligned and aligned sulfotransferases that have been functionally tested
 in the literature, newick file of tree, and IQTREE log file
 compiled_sulfotransferases_midpoint_rooted.txt: Newick file of the
 midpoint rooted maximum likelihood tree of functionally tested
 sulfotransferases sulfotransferases_compiled_aligned.fa: Multiple sequence
 alignment of sulfotransferases functionally tested
 sulfotransferases_compiled_aligned.fa.log: IQTREE log file
 sulfotransferases_compiled_aligned.treefile: Newick file of the maximum
 likelihood Fig. 2 tree, containing ultrafast bootstrap support values at
 each node sulfotransferases_compiled.fa: Sequences of sulfotransferases
 that have been functionally tested FigS10_data/: Contains data used to
 identify highly expressed sulfotransferases in the light-organ of Vargula
 tsujii Vtsujii_cd95_st_clean_aligned.fa.log: IQTREE log file
 Vtsujii_sulfotransferase_midpoint_rooted_tree.txt: Newick file of the
 midpoint rooted maximum likelihood tree of sulfotransferases from V.
 tsujii Vtsujii_sulfotransferases_aligned.fa: Multiple sequence alignment
 of sulfotransferases identified from the reference transcriptome of V.
 tsujii Vtsujii_sulfotransferases_aligned.treefile: Newick file of the
 maximum likelihood Fig. 2 tree, containing ultrafast bootstrap support
 values at each node Vtsujii_sulfotransferases_counts.csv: Counts file
 containing sulfotransferase gene expression data in the light-organ of N=9
 individual Vtsujii_sulfotransferases.fa: Sequences of sulfotransferases
 identified from the reference transcriptome of V. tsujii FigS11_data/:
 Contains files to infer a phylogeny of functionally tested
 sulfotransferases, using a trimmed alignment
 compiled_sulfotransferases_trimmed_midpoint_rooted.txt: Newick file of
 midpoint rooted maximum likelihood tree using trimmed alignment of
 functionally tested sulfotransferases
 sulfotransferases_compiled_aligned_trimmed.fa: Trimmed multiple sequence
 alignment of sulfotransferases that have been functionally tested
 sulfotransferases_compiled_aligned_trimmed.fa.log: IQTREE log file
 sulfotransferases_compiled_aligned_trimmed.treefile: Newick file of the
 maximum likelihood Fig. S11 tree, inferred using a trimmed alignment,
 containing ultrafast bootstrap support values at each node FigS13_data/:
 Contains files used to identify sulfotransferase domains in LSTs
 sulfotransferase_domain_hmmer.xlsx: Excel file containing HMMER results,
 used to identify sulfotransferase domains as shown in Fig. S13
 sulfotransferases_aligned.fa: Multiple sequence alignment of Vargula
 tsujii STs, firefly LST, Renilla coelenterazine ST, and human SULT1A1
 Isoseq_reference_transcriptome/: Contains the Vargula tsujii reference
 transcriptome Vargula_tsujii_cdhit_95.fasta: Vargula tsujii's
 reference Iso-seq transcriptome after using cd-hit to cluster sequences
 greater than or equal to 95% ``` ``` LST_MS_Dryad_Data/Plasmid_sequences/:
 Contains plasmid sequence .gb files Luciferase/: Contains plasmid sequence
 for Cypridina noctiluca luciferase pcmv-cypridinaluc-flag-6his.gb: Plasmid
 sequence for Cypridna noctiluca luciferase with 3X FLAG and 6His tag
 Sulfotransferases/: Contains plasmid sequences for recombinant
 sulfotransferases pet6his-sumo-st1.gb: Plasmid sequence for ST1 with SUMO
 solubility tag and 6His tag pet6his-sumo-st2.gb: Plasmid sequence for ST2
 with SUMO solubility tag and 6His tag pet6his-sumo-st5.gb: Plasmid
 sequence for ST5 with SUMO solubility tag and 6His tag pqe80l_st3.gb:
 Plasmid sequence for ST3 with 6His tag pqe80l_st4.gb: Plasmid sequence for
 ST4 with 6His tag ``` --- ## NOTE: All raw sequencing data are available
 on NCBI (BioProject: PRJNA935772) #### Sulfotransferase sequences are
 available on GenBank (Accessions: OQ626349, OQ626350, OQ626351, OQ626352,
 OQ626353)