Utilization of selenocysteine in early-branching fungal phyla

Abstract

Selenoproteins are a diverse group of proteins containing selenocysteine (Sec)—the twenty-first amino acid—incorporated during translation via a unique recoding mechanism 1,2 . Selenoproteins fulfil essential roles in many organisms ¹ , yet are not ubiquitous across the tree of life 3–7 . In particular, fungi were deemed devoid of selenoproteins 4,5,8 . However, we show here that Sec is utilized by nine species belonging to diverse early-branching fungal phyla, as evidenced by the genomic presence of both Sec machinery and selenoproteins. Most fungal selenoproteins lack consensus Sec recoding signals (SECIS elements ⁹ ) but exhibit other RNA structures, suggesting altered mechanisms of Sec insertion in fungi. Phylogenetic analyses support a scenario of vertical inheritance of the Sec trait within eukaryotes and fungi. Sec was then lost in numerous independent events in various fungal lineages. Notably, Sec was lost at the base of Dikarya, resulting in the absence of selenoproteins in Saccharomyces cerevisiae and other well-studied fungi. Our results indicate that, despite scattered occurrence, selenoproteins are found in all kingdoms of life. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.

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Letters
https://doi.org/10.1038/s41564-018-0354-9
1Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA. 2Departamento
de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay. 3Worm Biology Laboratory, Institut Pasteur de Montevideo,
Montevideo, Uruguay. 4Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology,
Barcelona, Spain. 5Universitat Pompeu Fabra, Barcelona, Spain. 6Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
*e-mail: mmariotti@bwh.harvard.edu; vgladyshev@rics.bwh.harvard.edu
Selenoproteins are a diverse group of proteins containing
selenocysteine (Sec)—the twenty-first amino acid—incorpo-
rated during translation via a unique recoding mechanism1,2.
Selenoproteins fulfil essential roles in many organisms1, yet
are not ubiquitous across the tree of life3–7. In particular, fungi
were deemed devoid of selenoproteins4,5,8. However, we show
here that Sec is utilized by nine species belonging to diverse
early-branching fungal phyla, as evidenced by the genomic
presence of both Sec machinery and selenoproteins. Most
fungal selenoproteins lack consensus Sec recoding signals
(SECIS elements9) but exhibit other RNA structures, suggest-
ing altered mechanisms of Sec insertion in fungi. Phylogenetic
analyses support a scenario of vertical inheritance of the Sec
trait within eukaryotes and fungi. Sec was then lost in numer-
ous independent events in various fungal lineages. Notably,
Sec was lost at the base of Dikarya, resulting in the absence
of selenoproteins in Saccharomyces cerevisiae and other well-
studied fungi. Our results indicate that, despite scattered
occurrence, selenoproteins are found in all kingdoms of life.
Selenocysteine (Sec)—the twenty-first amino acid—is co-trans-
lationally inserted via an unusual recoding mechanism, wherein
UGA (normally a stop codon) is translated as Sec1. Sec insertion
occurs specifically in selenoprotein genes, due to cis-acting RNA
structures known as SECIS elements9. Sec machinery genes (Sec
transfer RNA (tRNASec), Sec-specific eukaryotic elongation factor
(EFsec), phosphoseryl-tRNA kinase (PSTK), SECIS binding pro-
tein 2 (SBP2), Sec synthase (SecS), and selenophosphate synthe-
tase (SPS)) are trans-factors necessary and sufficient for eukaryotic
Sec synthesis and insertion1,2,10. Sec is believed to confer catalytic
advantage over cysteine (Cys, its sulphur-containing analogue) for
specific oxidoreductase functions11,12. Nevertheless, selenoproteins
are not found in all organisms. Sec usage is scattered across bac-
teria3,4,13 and archaea14. Within eukaryotes, selenoproteins are pres-
ent in most metazoans (including all vertebrates15), some protists
and certain algae4,5,16. They are absent in many insects6, few nema-
todes7, plants5 and various protists4. Notably, fungi were considered
the only kingdom of life entirely devoid of Sec4,5,8. However, here
we provide conclusive genomic evidence for Sec utilization by nine
fungal species belonging to three early-branching phyla.
We downloaded all available fungal genomes from the National
Center for Biotechnology Information (NCBI) (1,201 species;
Supplementary Table 1) and searched them for the presence of
eukaryotic Sec machinery genes (Methods) using Selenoprofiles17
and Secmarker18. These automatically generated predictions
(Supplementary Fig. 1) were analysed for two potential confounders:
the occurrence of protein families with similarity to those of inter-
est, and contaminant sequences in fungal genome assemblies.
For this, we reconstructed gene trees of candidate proteins together
with their most similar annotated sequences (Methods) and
inspected them to distinguish protein families (Supplementary Figs.
2–5). This procedure led to the dismissal of several candidates. After
filtering, Sec machinery proteins (Supplementary Data 1) localized
only in a handful of genomes, and co-occurred with tRNASec (Fig. 1).
After extensive analysis, we filtered out three species with Sec
machinery that we presumed resulted from genome contamination
from Sec-utilizing bacteria (Supplementary Note 1). In contrast, we
concluded that Bifiguratus adelaidae (Mucoromycota), Gonapodya
prolifera (Chytridiomycota), Capniomyces stellatus, Zancudomyces
culisetae, Smittium culicis, Smittium simulii, Smittium megazy-
gosporum, Smittium angustum and Furculomyces boomerangus
(Zoopagomycota) were Sec-utilizing fungi (Fig. 2). These species
formed distinct clades in three early-branching fungal phyla. The
order of Harpellales was particularly well represented: seven of the
eight species analysed had Sec.
We identified selenoproteins in all Sec-utilizing fungi
(Supplementary Data 1), which belonged to seven known seleno-
protein families (gene trees provided in Supplementary Figs. 6–10).
Two of them were found in all Sec-utilizing fungi: SelenoH (a
nuclear oxidoreductase possibly involved in redox homeostasis19)
and SPS (Fig. 3; an essential Sec machinery component4). Other
fungal selenoproteins included SelenoU (an uncharacterized oxi-
doreductase20), AhpC (alkyl hydroperoxide reductase C; found as
selenoprotein in certain bacteria, protists and porifera21), MsrA
(methionine sulfoxide reductase A; identified as selenoprotein
in algae, protists and various non-vertebrate metazoa22), DI-like
(homologous to vertebrate iodothyronine deiodinases23 and present
as selenoprotein in various invertebrates, protists and bacteria16) and
TXNRD (thioredoxin reductase; a selenoprotein present in most
Sec-utilizing eukaryotes24). Notably, this constitutes the first case of
animal-like TXNRD described in fungi, since this kingdom uses a
shorter and Sec-independent form of TXNRD24. G. prolifera was the
species with most selenoproteins, covering all selenoprotein fami-
lies discussed above. Analysis of a publicly available transcriptome
for this species confirmed the expression of all selenoprotein and
Sec machinery genes except tRNASec (Methods). Selenoprotein tran-
scripts appear to occur at high levels in G. prolifera (Supplementary
Fig. 11). SPS was particularly highly expressed, ranking in the top
1–6% transcripts (depending on the background distribution used).
We searched fungal selenoprotein genes for the occurrence of
eukaryotic SECIS elements. Surprisingly, we found canonical SECIS
Utilization of selenocysteine in early-branching
fungal phyla
MarcoMariotti 1*, GustavoSalinas2,3, ToniGabaldón4,5,6 and VadimN.Gladyshev1*
NATURE MICROBIOLOGY | VOL 4 | MAY 2019 | 759–765 | www.nature.com/naturemicrobiology 759
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