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Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6: 2 fluorotelomer sulfonamidoalkyl betaine or 6: 2 fluorotelomer sulfonate as sole sulfur source

Bottos, Eric M., AL-shabib, Ebtihal Y., Shaw, Dayton M. J., McAmmond, Breanne M., Sharma, Aditi, Suchan, Danae M., Cameron, Andrew D. S., Van Hamme, Jonathan D.·2020·Biodegradation
DOI 10.1007/s10532-020-09917-8PMC PMC7661421
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Abstract

Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are environmental contaminants of concern. We previously described biodegradation of two PFAS that represent components and transformation products of aqueous film-forming foams (AFFF), 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) and 6:2 fluorotelomer sulfonate (6:2 FTSA), by Gordonia sp. strain NB4-1Y. To identify genes involved in the breakdown of these compounds, the transcriptomic response of NB4-1Y was examined when grown on 6:2 FTAB, 6:2 FTSA, a non-fluorinated analog of 6:2 FTSA (1-octanesulfonate), or MgSO 4 , as sole sulfur source. Differentially expressed genes were identified as those with ± 1.5 log 2 -fold-differences (± 1.5 log 2 FD) in transcript abundances in pairwise comparisons. Transcriptomes of cells grown on 6:2 FTAB and 6:2 FTSA were most similar (7.9% of genes expressed ± 1.5 log 2 FD); however, several genes that were expressed in greater abundance in 6:2 FTAB treated cells compared to 6:2 FTSA treated cells were noted for their potential role in carbon–nitrogen bond cleavage in 6:2 FTAB. Responses to sulfur limitation were observed in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments, as 20 genes relating to global sulfate stress response were more highly expressed under these conditions compared to the MgSO 4 treatment. More highly expressed oxygenase genes in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments were found to code for proteins with lower percent sulfur-containing amino acids compared to both the total proteome and to oxygenases showing decreased expression. This work identifies genetic targets for further characterization and will inform studies aimed at evaluating the biodegradation potential of environmental samples through applied genomics. Graphic Abstract:

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Fig. 1 Differences in genome wide gene expression changes when NB4-1Y was provided with 6:2 FTAB, 6:2 FTSA, octanesulfonate (OCT) or MgSO4 as sole added sulfur source
Fig. 1 Differences in genome wide gene expression changes when NB4-1Y was provided with 6:2 FTAB, 6:2 FTSA, octanesulfonate (OCT) or MgSO4 as sole added sulfur sourceCC BY · PubMed Central
Fig. 2 Structures of a 6:2 FTAB, b 6:2 FTSA, c octanesulfonate (OCT)
Fig. 2 Structures of a 6:2 FTAB, b 6:2 FTSA, c octanesulfonate (OCT)CC BY · PubMed Central
Fig. 3 Shared a upregulated and b downregulated genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4
Fig. 3 Shared a upregulated and b downregulated genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4CC BY · PubMed Central
Fig. 4 Differential expression levels of sulfur metabolism genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4. Letters following accession numbers indicate grouping corresponding to those shown in Fig. 3: (a) FTAB; (b) FTSA; (c) FTAB and OCT; (d) FTAB and FTSA; (e) FTSA and OCT; (f) FTAB, FTSA and OCT
Fig. 4 Differential expression levels of sulfur metabolism genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4. Letters following accession numbers indicate grouping corresponding to those shown in Fig. 3: (a) FTAB; (b) FTSA; (c) FTAB and OCT; (d) FTAB and FTSA; (e) FTSA and OCT; (f) FTAB, FTSA and OCTCC BY · PubMed Central
Fig. 5 Expression levels of oxygenase genes for 6:2 FTAB, 6:2 FTSA, octanesulfonate (OCT) and MgSO4. Letters following accession numbers indicate grouping corresponding to those shown in Fig. 3: (a) FTAB; (b) FTSA; (c) FTAB and OCT; (d) FTAB and FTSA; (e) FTSA and OCT; (f) FTAB, FTSA and OCT
Fig. 5 Expression levels of oxygenase genes for 6:2 FTAB, 6:2 FTSA, octanesulfonate (OCT) and MgSO4. Letters following accession numbers indicate grouping corresponding to those shown in Fig. 3: (a) FTAB; (b) FTSA; (c) FTAB and OCT; (d) FTAB and FTSA; (e) FTSA and OCT; (f) FTAB, FTSA and OCTCC BY · PubMed Central
Fig. 6 Percent sulfur-containing amino acids in the predicted proteome for up- and down-regulated genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4
Fig. 6 Percent sulfur-containing amino acids in the predicted proteome for up- and down-regulated genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4CC BY · PubMed Central
Fig. 7 Differential expression levels of dehydrogenase, oxidoreductase, reductase and CoA transferase genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4. Letters following accession numbers indicate grouping corresponding to those shown in Fig. 3: (a) FTAB; (b) FTSA; (c) FTAB and OCT; (d) FTAB and FTSA; (e) FTSA and OCT; (f) FTAB, FTSA and OCT
Fig. 7 Differential expression levels of dehydrogenase, oxidoreductase, reductase and CoA transferase genes for 6:2 FTAB, 6:2 FTSA and octanesulfonate (OCT) as compared to MgSO4. Letters following accession numbers indicate grouping corresponding to those shown in Fig. 3: (a) FTAB; (b) FTSA; (c) FTAB and OCT; (d) FTAB and FTSA; (e) FTSA and OCT; (f) FTAB, FTSA and OCTCC BY · PubMed Central

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Sorted by citations

Metadata

Authors
Bottos, E. M., AL-shabib, E. Y., Shaw, D. M. J., McAmmond, B. M., Sharma, A., Suchan, D. M., Cameron, A. D. S., & Van Hamme, J. D.
ORCID
Venue
Biodegradation
Publisher
Springer Science and Business Media LLC
Published
2020-11-05
Volume
31
Issue
4-6
Pages
407-422
ISSN
  • 0923-9820
  • 1572-9729
DOI
10.1007/s10532-020-09917-8
PMC
PMC7661421
Cited by
23
References
13
Language
en
Licence
Funders
  • Natural Sciences and Engineering Research Council of Canada (RGPIN-435784-2013)
  • Canada Foundation for Innovation
  • University of Regina

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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