Genome-scale Reconstruction of SoxR Transcriptional Regulatory Network in Methylomonas sp. DH-1

Abstract

Methanotrophs are bacteria that use methane as a sole carbon source and energy source. Since methane takes up almost 90% of natural gas and shale gas and causes global warming, methanotrophs that consume methane are considered as promising industrial strains. Methylomonas sp. DH-1, a novel methanotroph, has a lot of merits such as fast growth, high methanol resistance, innate carotenoid pathway, and so on. However, lack of physiology and genetics about this strain and absence of proper metabolic engineering tools are the bottleneck in industrial application of Methylomonas sp. DH-1. Thus, it is required to understand its genetic and physiologic characteristics and engineering tools tailored to this strain, so that it can be used in diverse industries.

We focused on understanding regulatory networks in Methylomonas sp. DH-1 particularly in response to oxidative stress. SoxR, a known transcriptional regulator that governs transcription against oxidative stress, has different mechanism in enterobacteria and non-enterobacteria. When superoxide, nitric oxide, or redox active compounds exist in enterics, SoxR is activated and genes coding proteins that defend cells against oxidative stress are transcribed. SoxR in non-enterics in known not to regulate superoxide dismutase or else. Understanding SoxR transcriptional regulatory network in methanotroph lets this strain be used in various ways.

In this study, genome-wide SoxR transcriptional regulatory network in Methylomonas sp. DH-1 was elucidated. SoxR of Methylomonas sp. DH-1 was firstly selected from four candidate proteins. Recombination and epitope tagging strategy, and sequencing library protocols were constructed specific to Methylomonas sp. DH-1. Based on RNA-seq of wild-type and SoxR knock-out mutant under both methane and methanol conditions, SoxR-dependent genes were selected. The number of differentially expressed genes in each condition was 522 and 260, respectively. Genome-wide binding sites of SoxR were also identified by Chromatin Immunoprecipitation sequencing (ChIP-seq) under both conditions. By combining transcriptome with genome-wide binding sites, YgiT-type zinc finger protein (AYM39_RS22995) was identified as SoxR regulon.