CyAbrB2 is a nucleoid-associated protein inSynechocystiscontrolling hydrogenase expression during fermentation

Abstract

AbstractThehoxoperon inSynechocystissp. PCC 6803, encoding bidirectional hydrogenase responsible for H2 production, is transcriptionally upregulated under microoxic conditions. Although several regulators forhoxtranscription have been identified, their dynamics and higher-order DNA structure ofhoxregion in microoxic conditions remain elusive. We focused on key regulators for thehoxoperon: cyAbrB2, a conserved regulator in cyanobacteria, and SigE, an alternative sigma factor. Chromatin immunoprecipitation-sequencing revealed that cyAbrB2 binds to thehoxpromoter region under aerobic conditions, with its binding being flattened in microoxic conditions. Concurrently, SigE exhibited increased localization to thehoxpromoter under microoxic conditions. Genome-wide analysis revealed that cyAbrB2 binds broadly to AT-rich genome regions and represses gene expression. Moreover, we demonstrated the physical interactions of thehoxpromoter region with its distal genomic loci, and the interactions are lowered in microoxic conditions. In the absence of cyAbrB2, the interactions stayed low both in aerobic and microoxic conditions. From these results, we propose that cyAbrB2 is a cyanobacterial nucleoid- associated protein (NAP), modulating chromosomal conformation, which blocks RNA polymerase from thehoxpromoter in aerobic conditions. We further infer that cyAbrB2, with altered localization pattern upon microoxic conditions, modifies chromosomal conformation in microoxic conditions, which allows SigE-containing RNA polymerase to access thehoxpromoter. The coordinated actions of this NAP and the alternative sigma factor are crucial for the properhoxexpression in microoxic conditions. Our results highlight the impact of cyanobacterial chromosome conformation and NAPs on transcription, which have been insufficiently investigated.