Εξειδίκευση τύπου :	Άρθρο σε επιστημονικό περιοδικό
Τίτλος:	Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements
Δημιουργός/Συγγραφέας:	Pilalis, Eleftherios [EL] Χατζηιωάννου, Αριστοτέλης[EN] Chatziioannou, Aristotelis Grigoroudis, Asterios I. Panagiotidis, Christos A. [EL] Κολίσης, Φραγκίσκος Ν.[EN] Kolisis, Fragiskos N.‏ [EL] Κυριακίδης, Δ.Α.[EN] Kyriakidis, D.A.
Εκδότης:	Biomed Central Limited
Τόπος έκδοσης:	London
Ημερομηνία:	2011-05-13
Γλώσσα:	Αγγλικά
ISSN:	1471-2164
DOI:	10.1186/1471-2164-12-238
Περίληψη:	Background: Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of E. coli activates the expression of atoDAEB operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that atoSC is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the atoDAEB promoter as the single, cis-regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the E. coli genome. Results: Through the implementation of a computational de novo motif detection workflow, a set of candidate motifs was generated, representing putative AtoC binding targets within the E. coli genome. In order to assess the biological relevance of the motifs and to select for experimental validation of those sequences related robustly with distinct cellular functions, we implemented a novel approach that applies Gene Ontology Term Analysis to the motif hits and selected those that were qualified through this procedure. The computational results were validated using Chromatin Immunoprecipitation assays to assess the in vivo binding of AtoC to the predicted sites. This process verified twenty-two additional AtoC binding sites, located not only within intergenic regions, but also within gene-encoding sequences. Conclusions: This study, by tracing a number of putative AtoC binding sites, has indicated an AtoC-related cross-regulatory function. This highlights the significance of computational genome-wide approaches in elucidating complex patterns of bacterial cell regulation.
Τίτλος πηγής δημοσίευσης:	Bmc Genomics
Τόμος/Κεφάλαιο:	12
Σελίδες:	[17]
Θεματική Κατηγορία:	[EL] Βιοτεχνολογία[EN] Biotechnology [EL] Βιολογία (Γενικά)[EN] Biology (General)
Λέξεις-Κλειδιά:	Genetics & Heredity
Αξιολόγηση από ομότιμους (peer reviewed):	Ναι
Όροι και προϋποθέσεις δικαιωμάτων:	This is an open-access article appearing in: "Pilalis, E., Chatziioannou, A.A., Grigoroudis, A.I. et al. Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements. BMC Genomics 12, 238 (2011)". It can be found at https://doi.org/10.1186/1471-2164-12-238
ΙΒΦΧΒ: αρχειακή συλλογή:	Ινστιτούτο Βιολογικών Ερευνών και Βιοτεχνολογίας (ΙΒΕΒ) (έως 2012)
Εμφανίζεται στις συλλογές:	Ινστιτούτο Χημικής Βιολογίας - Επιστημονικό έργο