Are there any eukaryotic algae that degrade EDTA?

Question

EDTA is a frequently-used chelator in molecular biology experiments and medical applications. Buchelia-Witschel et al 2001 discuss certain bacteria have monooxygenases that are capable of degrading EDTA, so there is a basic precedent that living things can biodegrade EDTA.

The chemical properties between eukaryotes and bacteria are sometimes similar, but also frequently quite different. It isn't obvious to me that algae could not degrade EDTA, but has anyone demonstrated that there exists a species of eukaryotic algae that can break down EDTA?

Answer 1

I can find no published evidence for the degradation of EDTA by eukaryotic algae. I found only one publication where algal metabolism of an aminopolycarboxylic acid was tested, specifically whether NTA could be used as a nitrogen source by different marine microalgae.¹ Their results, summarized in Table VII, were that the tested organisms could not use NTA as a nitrogen source.

_{The possibility that NTA could serve as a nitrogen source was investigated using SS-1 medium in which NTA was substituted for the nitrogen. None of the four species of phytoplankton (Table VII) was able to use NTA as a nitrogen source. The slight stimulation shown by S. costatum at 0.073 mg/L N as NTA and I. galbana at 7.3 mg/L N as NTA does not seem to be related to NTA metabolism.}

Of course, the organisms listed in the table above are just a small subset of the massive polyphyletic group that can be described as eukaryotic algae.² Instead of directly asking whether algae degrade EDTA, we can take a naïve approach and ask do any algae encode proteins that are similar to bacterial proteins known to degrade EDTA? Section 5.2 of the review article linked by Galen ³ lists two proteobacterial strains for which the biochemical determinants of EDTA catabolism have been studied: BNC1 (Chelativorans sp. BNC1) and DSM 9103 (Chelativorans multitrophicus). For DSM 9103, a two-enzyme system consisting of a monooxygenase and an oxidoreductase was shown to be sufficient to cleave two acetyl groups from EDTA, though the monooxygenase seems to be the vital component given that the activity of the oxidoreductase could be substituted by paralogous enzyme from the NTA degradation pathway.⁴

Since that review, additional work has been done to characterize the catalytic mechanism of EDTA monooxygenase (EmoA) and identify structural homologs across bacteria.⁵ Searching the NCBI Identical Protein Group database for "EDTA monooxygenase" returns 25 hits (as of 6 July 2021) to unique proteobacterial proteins. Multiple sequence alignment of these proteins reveals a highly conserved catalytic core (red regions):

If we then find a consensus sequence from the MSA, we can use that sequence to perform a blastp search against the subset of NCBI nonredundant protein sequences corresponding to taxa annotated as eukaryotic algae by Wikipedia.

Name	Taxonomic Identifier
Mesostigmatophyceae	96475
Chlorokybophyceae	131213
Chlorophyta	3041
Rhodophyta	2763
Glaucophyta	38254
Chlorarachniophytes	29197
Euglenids	3035
Bacillariophyceae	33849
Cryptophyta	3027
Dinoflagellata	2864
Haptophyta	2830
Bolidomonas	91990
Eustigmatophyceae	5747
Phaeophyceae	2870
Chrysophyceae	2825
Raphidophyceae	38410
Synurophyceae	33859
Xanthophyceae	2833

With default blastp parameters, we get a whopping 2 hits, one to a dimethyl-sulfide monooxygenase from the endosymbiotic dinoflagellate Symbiodinium pilosum and one to a protein containing a monooxygenase-like region from Ostreococcus tauri, the smallest free-living eukaryote.⁶ (The same hits were obtained after blasting each bacterial protein individually to the same algal protein set.)

Description	Scientific Name	Query Cover	E value	Per. ident	Accession
dmoA	Symbiodinium pilosum	87%	1.00E-54	32.21	CAE7149325.1
luciferase-like domain-containing protein	Ostreococcus tauri	82%	1.00E-14	25.72	OUS44788.1

While both of these hits have good query coverage, the sequence identities are low, and both organisms lack (per a separate blastp) good hits to the NADH-dependent FMN reductase needed to supply the FMNH₂ cofactor for the monooxygenase, though another enzyme could fill that role.

So, if algae degrade EDTA, they likely do it using enzymes that are structurally different from known EDTA-catabolizing bacterial enzymes, or by a biochemical mechanism yet to be deduced.

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References

1. Erickson SJ, Maloney TE, Gentile JH. Effect of nitrilotriacetic acid on the growth and metabolism of estuarine phytoplankton. J Water Pollut Control Fed. 1970 Aug;42(8):Suppl:+329+.
2. Keeling PJ. Diversity and evolutionary history of plastids and their hosts. Am J Bot. 2004 Oct;91(10):1481-93.
3. Bucheli-Witschel M, Egli T. Environmental fate and microbial degradation of aminopolycarboxylic acids. FEMS Microbiol Rev. 2001 Jan;25(1):69-106.
4. Witschel M, Nagel S, Egli T. Identification and characterization of the two-enzyme system catalyzing oxidation of EDTA in the EDTA-degrading bacterial strain DSM 9103. J Bacteriol. 1997 Nov;179(22):6937-43.
5. Jun SY, Lewis KM, Youn B, Xun L, Kang C. Structural and biochemical characterization of EDTA monooxygenase and its physical interaction with a partner flavin reductase. Mol Microbiol. 2016 Jun;100(6):989-1003.
6. Palenik B et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A. 2007 May 1;104(18):7705-10.