Pyoverdine binding aptamers and label-free electrochemical detection of pseudomonads

Anisuzzaman, Sharif; Alimoradi, Nima; Singappuli-Arachchige, Dilini; Banerjee, Soma; Pogorelko, Gennady V.; Kaiyum, Yunus A.; Johnson, Philip E.; Shrotriya, Pranav; Nilsen-Hamilton, Marit

doi:10.3389/fchem.2024.1438710

Pyoverdine binding aptamers and label-free electrochemical detection of pseudomonads

Journal Article · Thu Aug 01 00:00:00 EDT 2024 · Frontiers in Chemistry

DOI:https://doi.org/10.3389/fchem.2024.1438710· OSTI ID:2434268

Anisuzzaman, Sharif ^[1]; Alimoradi, Nima ^[2]; Singappuli-Arachchige, Dilini ^[3]; Banerjee, Soma ^[4]; Pogorelko, Gennady V. ^[3]; Kaiyum, Yunus A. ^[5]; Johnson, Philip E. ^[5]; Shrotriya, Pranav ^[1]; Nilsen-Hamilton, Marit ^[6]

Ames Laboratory (AMES), Ames, IA (United States); Iowa State Univ., Ames, IA (United States)
Iowa State Univ., Ames, IA (United States)
Ames Laboratory (AMES), Ames, IA (United States); Aptalogic Inc., Ames, IA (United States)
Aptalogic Inc., Ames, IA (United States)
York Univ., Toronto, ON (Canada)
Ames Laboratory (AMES), Ames, IA (United States); Iowa State Univ., Ames, IA (United States); Aptalogic Inc., Ames, IA (United States)

Pyoverdines are iron-chelating siderophores employed by various pseudomonads to promote their growth in iron-limited environments, facilitating both beneficial and detrimental interactions with co-inhabiting microbes or hosts, including plants and animals. The fluorescent pseudomonads produce fluorescent pyoverdines comprised of a conserved central chromophore and a unique strain-specific peptidic side chain produced by non-ribosomal peptide synthetases. Pyoverdine Pf5 (PVD-Pf5) is produced by Pseudomonas protegens Pf-5, a species known for supporting plant growth and its involvement in plant pathogen control. To develop a means of exploring the dynamics of P. protegens activity in soil and in the rhizosphere, we selected DNA aptamers that specifically recognize PVD-Pf5 with high affinities. Two selected aptamers with only 16% identity in sequence were examined for structure and function. We found evidence that both aptamers form structures in their apo-forms and one aptamer has structural features suggesting the presence of a G-quadruplex. Although their tertiary structures are predicted to be different, both aptamers bind the target PVD-Pf5 with similar affinities and do not bind other siderophores, including the related pyoverdine, pseudobactin, produced by Pseudomonas sp. B10. One aptamer binds the pyoverdine peptide component and may also interact with the chromophore. This aptamer was integrated into a nanoporous aluminum oxide biosensor and demonstrated to successfully detect PVD-Pf5 and not to detect other siderophores that do not bind to the aptamer when evaluated in solution. This sensor provides a future opportunity to track the locations of P. protegens around plant roots and to monitor PVD-Pf5 production and movement through the soil.

View Accepted Manuscript (DOE)

Research Organization:: Ames Laboratory (AMES), Ames, IA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-07CH11358

OSTI ID:: 2434268

Report Number(s):: IS-J--11,395

Journal Information:: Frontiers in Chemistry, Journal Name: Frontiers in Chemistry Vol. 12; ISSN 2296-2646

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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References (26)

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