ORCID

Abstract

In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.

DOI

10.1093/r/gkx860

Publication Date

2017-11-01

Publication Title

Nucleic Acids Research

Volume

45

Issue

20

First Page

11800

Last Page

11820

ISSN

0305-1048

Organisational Unit

School of Biomedical Sciences

Keywords

Synechocystis, Nitrogen, Bacterial Proteins, DNA-Binding Proteins, Transcription Factors, Gene Expression Profiling, Acclimatization, Gene Expression Regulation, Bacterial, Binding Sites, Base Sequence, Protein Binding, Sequence Homology, Amino Acid, Genes, Regulon, Gene Regulatory Networks, Gene Ontology

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