title: TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches.
abstract: Riboswitches are located in non-coding areas of mRNAs and act as sensors of cellular small molecules, regulating gene expression in response to ligand binding. The TPP riboswitch is the most widespread riboswitch occurring in all three domains of life. However, it has been rarely characterized in environmental bacteria other than Escherichia coli and Bacillus subtilis. In this study, TPP riboswitches located in the 5' UTR of thiC operon from Alishewanella tabrizica and Alishewanella aestuarii were identified and characterized. Moreover, affinity analysis of TPP binding to the TPP aptamer domains originated from A. tabrizica, A. aestuarii, E.coli, and B. subtilis were studied and compared using In-line probing and Surface Plasmon Resonance (SPR). TPP binding to the studied RNAs from A. tabrizica and A. aestuarii caused distinctive changes of the In-line cleavage pattern, demonstrating them as functional TPP riboswitches. With dissociation constant of 2-4nM (depending on the method utilized), the affinity of TPP binding was highest in A. tabrizica, followed by the motifs sourced from A. aestuarii, E. coli, and B. subtilis. The observed variation in their TPP-binding affinity might be associated with adaptation to the different environments of the studied bacteria.
authors.affiliation: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
authors.forename: Elnaz
authors.initials: E
authors.lastname: Mehdizadeh Aghdam
authors.affiliation: Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
authors.forename: Malte
authors.initials: M
authors.lastname: Sinn
authors.affiliation: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
authors.forename: Vahideh
authors.initials: V
authors.lastname: Tarhriz
authors.affiliation: Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran.
authors.forename: Abolfazl
authors.initials: A
authors.lastname: Barzegar
authors.affiliation: Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany. Electronic address: joerg.hartig@uni-konstanz.de.
authors.forename: Jörg S
authors.initials: JS
authors.lastname: Hartig
authors.affiliation: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. Electronic address: saeidhejazi@tbzmed.ac.ir.
authors.forename: Mohammad Saeid
authors.initials: MS
authors.lastname: Hejazi
mesh_terms: D034241:Alteromonadaceae / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D058928:Riboswitch / Q000235:genetics*; D020349:Surface Plasmon Resonance
chemical_list: D001426:Bacterial Proteins; D058928:Riboswitch; C105797:ThiC protein, Bacteria
keywords: Alishewanella tabrizica; In-line probing; Riboswitch; SPR; Thiamine pyrophosphate