{"help":"Return the metadata of a dataset (package) and its resources. :param id: the id or name of the dataset :type id: string","success":true,"result":[{"id":"6e91034a-87ad-499e-a6da-813534dccb3e","name":"iron-sulfur-cluster-proteins-present-weak-spot-plasma-treated-escherichia-coli","title":"Iron-sulfur cluster proteins present the weak spot in plasma-treated Escherichia coli","author_email":"julia.bandow@rub.de","maintainer":"Research Data Repository","maintainer_email":"achim.vonkeudell@rub.de","license_title":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/","notes":"\u003Cp\u003ENon-thermal atmospheric pressure plasmas have an antiseptic activity beneficial in different medical applications. In a genome-wide screening, hydrogen peroxide and superoxide were identified as key species contributing to the antibacterial effects of plasma while [FeS] cluster proteins emerged as potential cellular targets. We investigated the impact of plasma treatment on [FeS] cluster homeostasis in Escherichia coli treated for 1 min with the effluent of a microscale atmospheric pressure plasma jet (\u00b5APPJ). Mutants defective in [FeS] cluster synthesis and maintenance lacking the SufBC2D scaffold protein complex or desulfurase IscS were hypersensitive to plasma treatment. Monitoring the activity of [FeS] cluster proteins of the tricarboxylic acid cycle (aconitase, fumarase, succinate dehydrogenase) and malate dehydrogenase (no [FeS] clusters), we identified cysteine, iron, superoxide dismutase, and catalase as determinants of plasma sensitivity. Survival rates, enzyme activity, and restoration of enzyme activity after plasma treatment were superior in mutants with elevated cysteine levels and in the wildtype under iron replete conditions. Mutants with elevated hydrogen peroxide and superoxide detoxification capacity over-expressing sodA and katE showed full protection from plasma-induced enzyme inactivation and survival rates increased from 34% (controls) to 87%. Our study indicates that metabolic and genetic adaptation of bacteria may result in plasma tolerance and resistance, respectively.\u003C\/p\u003E\n","url":"https:\/\/rdpcidat.rub.de\/dataset\/iron-sulfur-cluster-proteins-present-weak-spot-plasma-treated-escherichia-coli","state":"Active","log_message":"Edited by kd.","private":true,"revision_timestamp":"Tue, 06\/10\/2025 - 13:28","metadata_created":"Thu, 02\/06\/2025 - 09:32","metadata_modified":"Tue, 06\/10\/2025 - 13:28","creator_user_id":"fbaa0bb1-6827-46c5-a646-bca2c4ce442a","type":"Dataset","resources":[{"id":"de26eb79-84de-4c6e-99fd-3c7fb8d30718","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%201_characterisation%20deletion%20mutants.xlsx","description":"\u003Cp\u003ECharacterization of strains with gene deletions in the \u003Cem\u003Eisc\u003C\/em\u003E or \u003Cem\u003Esuf\u003C\/em\u003E operon. Plasma survival rate: Deletion strains were exposed to the effluent of the \u00b5APPJ for 30 s and colony forming units were determined. CFU of plasma-treated and gas-treated cells were set in relation to yield the survival rates. Strains with a plasma survival rate different from the wild type were further characterized. Growth rate: Single-gene deletion strains and the wild type were grown in LB medium and growth rates were determined during log-phase (between min 120 to 180 after inoculation) (see Fig. S1). Activity of [FeS] cluster proteins: Logarithmically growing deletion strains were lysed and enzyme assays were performed for aconitase (ACN), fumarase (FUM), succinate dehydrogenase (SDH), and malate dehydrogenase (not containing [FeS] clusters). Means and standard deviation of three independent biological replicates are shown.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:39","name":"Figure1","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"15.54 KB","created":"Thu, 02\/06\/2025 - 09:32","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:39"},{"id":"98d2d312-c549-4bf3-96c7-e9edb57ce2cb","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%202_enzyme%20activity%20wild%20type.xlsx","description":"\u003Cp\u003EEnzyme activity of malate dehydrogenase (MDH), aconitase (ACN), fumarase (FUM), and succinate dehydrogenase (SDH) after \u00b5APPJ treatment for 1 min. \u003Cem\u003EE. coli\u003C\/em\u003E wild type cells were left untreated (gray, set to 1.0), exposed to gas flow (blue), or treated with plasma (orange). Residual enzyme activity was determined either directly after treatment (t0, dark bars) or after a 20 min post-plasma incubation at 37\u00b0C (t20, light bars). Averages and standard deviations represent three independent biological replicates.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:40","name":"Figure2","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"12.14 KB","created":"Thu, 02\/06\/2025 - 09:33","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:40"},{"id":"91ab9188-bd8b-4399-b5b8-e8b6dcf40d07","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%203_cysteine.xlsx","description":"\u003Cp\u003EInfluence of cysteine over-production. (A) Dependency of the plasma survival rate on the intracellular cysteine concentration in the strain \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EcysE\u003C\/em\u003E (blue). Amounts of IPTG for induction [\u00b5M] of \u003Cem\u003EcysE\u003C\/em\u003E are indicated next to each data point. Data for \u003Cem\u003EE. coli\u003C\/em\u003E wild type (without the plasmid) is given as gray triangle. (B) Enzyme activity of malate dehydrogenase (MDH), aconitase (ACN), fumarase (FUM), and succinate dehydrogenase (SDH) after \u00b5APPJ treatment. \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EcysE\u003C\/em\u003E induced with 100 \u00b5M IPTG was left untreated (gray, set to 1.0), exposed to gas flow (blue), or treated with plasma (orange). Residual enzyme activity was determined either directly after treatment (t0, dark bars) or after incubation at 37\u00b0C for 20 min (t20, light bars). Averages and standard deviations represent three independent biological replicates.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:39","name":"Figure3","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"17.57 KB","created":"Thu, 02\/06\/2025 - 09:34","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:39"},{"id":"bf6c5067-23bc-4db2-beaa-e8d3c00776ef","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%204_iron.xlsx","description":"\u003Cp\u003EInfluence of iron supplementation to the minimal medium. (A) Dependency of the plasma survival rate on the intracellular iron concentration in \u003Cem\u003EE. coli\u003C\/em\u003E wild type. Amounts of FeSO4 [\u00b5M] added to the medium are indicated next to each data point. (B) Enzyme activity of malate dehydrogenase (MDH), aconitase (ACN), fumarase (FUM), and succinate dehydrogenase (SDH) after \u00b5APPJ treatment. \u003Cem\u003EE. coli\u003C\/em\u003E wild type supplemented with 10 \u00b5M Fe2+ were left untreated (gray, set to 1.0), exposed to gas flow (blue), or treated with plasma (orange). Residual enzyme activity was determined either directly after treatment (t0, dark bars) or after incubation at 37\u00b0C for 20 min (t20, light bars). Averages and standard deviations represent three independent biological replicates.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:46","name":"Figure4","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"16.43 KB","created":"Thu, 02\/06\/2025 - 09:35","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:46"},{"id":"18a69bf0-cd79-46c8-8d60-e19757c7b8c0","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%205_SOD%20and%20KAT%20mutants%20and%20paraquat.xlsx","description":"\u003Cp\u003E\u003Cem\u003EE. coli\u003C\/em\u003E plasma survival. (A) Plasma resistance of gene-deletion or over-expression strains induced with IPTG [\u00b5M] at different concentrations. The asterisk indicates a survival rate of 0. Western blot analyses were conducted for quantification of the over-expression product shown by orange line graphs. An anti His6 antibody conjugated to a fluorophore was used for detection. (B) \u003Cem\u003EE. coli\u003C\/em\u003E wild type was incubated with paraquat prior plasma treatment to allow for pre-adaptation. ev: empty vector pCA24N. Averages and standard deviations of three biological replicates are shown.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:44","name":"Figure5","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"17.85 KB","created":"Thu, 02\/06\/2025 - 09:36","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:44"},{"id":"2c2d7d72-7012-488f-9847-54aca0bcb3f8","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%206_overexpression%20and%20plasma.xlsx","description":"\u003Cp\u003E[FeS] cluster enzyme activity of \u003Cem\u003EE. coli\u003C\/em\u003E over-expressing \u003Cem\u003EsodA *and\/or *katE\u003C\/em\u003E. Residual enzyme activity was determined either directly after 1 min plasma treatment (t0, dark bars) or after incubation at 37\u00b0C for 20 min (t20, light bars) in the following strains: \u003Cem\u003EE. coli\u003C\/em\u003E wild type harboring the empty vector pCA24N (wt+ev), \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EsodA\u003C\/em\u003E (5 \u00b5M IPTG) (oe sodA), \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EkatE\u003C\/em\u003E (5 \u00b5M IPTG) (oe katE), and \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EsodA\u003C\/em\u003E::\u003Cem\u003EkatE\u003C\/em\u003E (5 \u00b5M IPTG) (oe sodA+katE). Activity of aconitase (A, ACN), fumarase (B, FUM), and succinate dehydrogenase (C, SDH) was determined. The activity of the malate dehydrogenase is shown in Supp. Fig. S4. Averages and standard deviations represent three independent biological replicates.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:44","name":"Figure6","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"16.08 KB","created":"Thu, 02\/06\/2025 - 09:37","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:44"},{"id":"8b10c262-5112-4d74-abda-8ae40059ffa8","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%20S1_growth%20deletion%20mutants.xlsx","description":"\u003Cp\u003EGrowth of \u003Cem\u003EE. coli\u003C\/em\u003E wild type and deletion mutation in LB medium at 37\u00b0C. Averages and standard deviations\u003Cbr \/\u003E\nrepresent three independent biological experiments.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:42","name":"Supplementary Figure1","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"12.63 KB","created":"Thu, 02\/06\/2025 - 09:38","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:42"},{"id":"0cb9ba8b-5309-4661-9265-42d418141173","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%20S2_growth%20cysteine.xlsx","description":"\u003Cp\u003EGrowth of \u003Cem\u003EE. coli\u003C\/em\u003E wild type harboring the empty vector pCA24N (wt+ev) or a \u003Cem\u003EcysE\u003C\/em\u003E over-expression plasmid\u003Cbr \/\u003E\n(pCA24N::\u003Cem\u003EcysE\u003C\/em\u003E) induced with different amounts of IPTG.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:42","name":"Supplementary Figure2","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"12.29 KB","created":"Thu, 02\/06\/2025 - 09:39","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:42"},{"id":"13d8861b-2209-4c28-8fc4-1dd24d1f6795","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%20S3_growth%20iron%20and%20M9.xlsx","description":"\u003Cp\u003EGrowth of \u003Cem\u003EE. coli\u003C\/em\u003E wild type in M9 minimal medium supplemented with FeSO4. (B) Enzyme activity of malate dehydrogenase (MDH), aconitase (ACN), fumarase (FUM), and succinate dehydrogenase (SDH) after \u03bcAPPJ treatment. \u003Cem\u003EE. coli\u003C\/em\u003E wild type grown in M9 medium without any iron supplementation was untreated (gray, set to 1.0), exposed to helium\/oxygen gas flow (blue), or treated with plasma for 1 min (orange). Residual enzyme activity was determined either directly after treatment (t0, dark bars) or after incubation at 37\u00b0C for 20 min (t20, light bars). Averages and standard deviations represent three independent biological replicates.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:44","name":"Supplementary Figure3","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"15.1 KB","created":"Thu, 02\/06\/2025 - 09:40","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:44"},{"id":"d9215117-3812-4ccb-9ae3-f963b04c94ad","revision_id":"","url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/fig%20S4_MDH%20and%20plasma.xlsx","description":"\u003Cp\u003EEnzyme activity of malate dehydrogenase after \u03bcAPPJ treatment. Residual enzyme activity was determined either directly after 1 min plasma treatment (t0, dark bars) or after incubation at 37\u00b0C for 20 min (t20, light bars) in the following strains: \u003Cem\u003EE. coli\u003C\/em\u003E wild type harboring the empty vector pCA24N (wt+ev), \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EsodA\u003C\/em\u003E (5 \u03bcM IPTG) (oe sodA), \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EkatE\u003C\/em\u003E (5 \u03bcM IPTG) (oe katE), and \u003Cem\u003EE. coli\u003C\/em\u003E pCA24N::\u003Cem\u003EsodA\u003C\/em\u003E::\u003Cem\u003EkatE\u003C\/em\u003E (5 \u03bcM IPTG) (oe sodA+katE). Averages and standard deviations represent three independent biological replicates.\u003C\/p\u003E\n","format":"xlsx","state":"Active","revision_timestamp":"Thu, 02\/06\/2025 - 10:43","name":"Supplementary Figure4","mimetype":"application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet","size":"12.89 KB","created":"Thu, 02\/06\/2025 - 09:41","resource_group_id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","last_modified":"Date changed  Thu, 02\/06\/2025 - 10:43"}],"groups":[{"description":"","id":"a7cc37b6-5294-4469-8ad1-7e60df6ea28f","image_display_url":"https:\/\/rdpcidat.rub.de\/sites\/default\/files\/rublogoweiss_0_1.png","title":"Applied Microbiology","name":"group\/applied-microbiology"}]}]}