Data underlying the article: Different RNA recognition by ProQ and FinO depends on the sequence surrounding intrinsic terminator hairpins
Article DOI: 10.1261/rna.080206.124
DATA & FILE OVERVIEW
File List:
Fig.1 - Data presented in Figure 1, Supplemental Figure S4 and Supplemental Figure S5. The Fig.1 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQ, ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Fig.2 - Data presented in Figure 2 and Supplemental Figure S6. The Fig.2 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Fig.3 - Data presented in Figure 3 and Supplemental Figure S7. The Fig.3 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Fig.4 - Data presented in Figure 4 and Supplemental Figure S10. The Fig.4 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Fig.5 - Data presented in Figure 5 and Supplemental Figure S13. The Fig.5 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Fig.6 - Data presented in Figure 6 and Supplemental Figure S15. The Fig.6 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Fig_7_sequences - File contains amino acid sequences of ProQ and FinO proteins used in the modeling of RNA binding surfaces presented in Figure 7
Supplemental_Fig_S1_sequences - The file contains nucleotide sequences of the terminator hairpins of the top 20 ProQ-specific RNA ligands identified in the previous CLIP-seq study in Escherichia coli (Holmqvist et al. 2018), whose peaks map to the regions containing intrinsic transcription terminator. The secondary structures of these hairpins are presented in Supplemental Figure S1.
Supplemental_Fig_S2_sequences - The file contains nucleotide sequences of the terminator hairpins of the top 20 ProQ-specific RNA ligands identified in the previous RIL-seq study in Escherichia coli (Melamed et al. 2020), which were annotated either as 3ʹ-UTRs or sRNAs. The secondary structures of these hairpins are presented in Supplemental Figure S2.
Supplemental_Fig_S3_sequences - The file contains nucleotide sequences of the two main Salmonella enterica FinO-specific RNA ligands, FinP and RepX, which were detected using RIP-seq (El Mouali et al. 2021). The secondary structures of these hairpins are presented in Supplemental Figure S3.
Supplemental_Fig_S8 - Data presented in Supplemental Figure S8. The Supplemental_Fig_S8 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Supplemental_Fig_S9 - Data presented in Supplemental Figure S8. The Supplemental_Fig_S8 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Supplemental_Fig_S11 - Data presented in Supplemental Figure S11. The Supplemental_Fig_S11 folder contains a table file with five columns (RNA name, experiment repetition, protein type used in the binding experiment (Escherichia coli ProQNTD, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-[protein type]-[repetition].
Supplemental_Fig_S12 - Data presented in Supplemental Figure S12. The Supplemental_Fig_S12 folder contains a table file with six columns (RNA name, experiment repetition, lane in the gel, protein type used in the competition experiment (Escherichia coli ProQ, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-competition-[repetition].
Supplemental_Fig_S14 - Data presented in Supplemental Figure S14. The Supplemental_Fig_S14 folder contains a table file with six columns (RNA name, experiment repetition, lane in the gel, protein type used in the competition experiment (Escherichia coli ProQ, or FinO), protein concentration in nanomolar scale, and calculated fraction bound. The folder also contains PNG images of gels for each repetition, named in the format [RNA name]-competition-[repetition].
Supplemental_Fig_S16_sequences - The file contains nucleotide sequences of selected regions including 10 nucleotides upstream of the terminator hairpin on the 5ʹ side and the entire polyU tail on the 3ʹ side of the malM or cspE RNAs from different bacterial species. These sequences were used in the alignment presented in Supplemental Figure S16. The sequences used in the analysis were obtained from the NCBI database.
Information about funding sources that supported the collection of the data: This work was supported by National Science Centre in Poland [grants No. 2020/39/O/NZ1/02448 and No. 2018/31/B/NZ1/02612]. Funding for open access charge: National Science Centre [2020/39/O/NZ1/02448] and Adam Mickiewicz University.
(2025-03)
