The vitamin B12-dependent photoreceptor AerR relieves photosystem gene repression by extending the interaction of CrtJ with photosystem promoters

Abstract

Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is Crt J, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B12 binding antirepressor of Crt J called Aer R is required for anaerobic expression of the photosystem. However, the mechanism whereby Aer R regulates Crt J activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of Crt J and the role of Aer R in controlling this regulation. Our results indicate that Crt J has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (Ch IP-seq) and Ch IP-seq and exonuclease digestion (Ch IP-exo) studies and in vitro biochemical studies demonstrate that Aer R forms a 1:2 complex with Crt J (Aer R-Crt J2) and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that Aer R-Crt J2 anaerobically forms an extended interaction with the bacteriochlorophyll bch C promoter to relieve repression by Crt J. This is contrasted by aerobic growth conditions where Crt J alone functions as an aerobic repressor of bch C expression. These results indicate that the DNA binding activity of Crt J is modified by interacting with Aer R in a redox-regulated manner and that this interaction alters Crt J’s function. IMPORTANCE Photoreceptors control a wide range of physiology often by regulating downstream gene expression in response to light absorption via a bound chromophore. Different photoreceptors are known to utilize a number of different compounds for light absorption, including the use of such compounds as flavins, linearized tetrapyrroles (bilins), and carotenoids. Recently, a novel class of photoreceptors that use vitamin B12 (cobalamin) as a blue-light-absorbing chromophore have been described. In this study, we analyzed the mechanism by which the vitamin B12 binding photoreceptor Aer R controls the DNA binding activity of the photosystem regulator Crt J. This study shows that a direct interaction between the vitamin B12 binding photoreceptor Aer R with Crt J modulates Crt J binding to DNA and importantly, the regulatory outcome of gene expression, as shown here with photosystem promoters.