Similar Enzymatic Functions in Distinct Bioluminescence Systems: Evolutionary Recruitment of Sulfotransferases in Ostracod Light Organs
Data files
May 03, 2024 version files 24.38 MB
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LST_MS_Dryad_Data.zip
24.37 MB
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README.md
7.90 KB
Abstract
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.
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