Defining the Bacteroides Ribosomal Binding Site

Abstract

ABSTRACTThe human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genusBacteroidesare among the most abundant bacterial species in the human colon.Bacteroidetesdiverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals inBacteroides, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use ofpepIfromLactobacillus delbrueckiisubsp.lactisas a novel reporter gene forBacteroides. Furthermore, we report the identification of the 3′ end of the 16S rRNA ofBacteroides ovatusand analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5′ untranslated region of otherBacteroidalesribosomal protein genes, we conclude that our findings are relevant to all members of this order.