Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria

Abstract

The Escherichia coli chromosome is organized into four macrodomains, the function and organisation of which are poorly understood. In this review we focus on the MatP, SeqA, and SlmA proteins that have recently been identified as the first examples of factors with macrodomain-specific DNA-binding properties. In particular, we review the evidence that these factors contribute towards the control of chromosome replication and segregation by specifically targeting subregions of the genome and contributing towards their unique properties. Genome sequence analysis of multiple related bacteria, including pathogenic species, reveals that macrodomain-specific distribution of SeqA, SlmA, and MatP is conserved, suggesting common principles of chromosome organisation in these organisms. This discovery of proteins with macrodomain-specific binding properties hints that there are other proteins with similar specificity yet to be unveiled. We discuss the roles of the proteins identified to date as well as strategies that may be employed to discover new factors.

Figure 1. Hierarchical levels of organization in bacterial chromosomes.

Different levels of organization exist within bacterial chromosomes. (A) At the nm scale nucleoid proteins such as HU, H-NS, CbpA, Dps, and Fis organize the genome by driving events such as DNA bending, bridging, and aggregation. (B) Structures such as seen in (A) likely exist within, and may contribute towards the formation of looped topological domains (on average each ∼10 kbp in size) and transcription foci, where multiple transcribing RNA polymerase molecules are clustered potentially also yielding loops along the genome. (C) All of the above could add to the complexity of the organization within individual macrodomains. The individual macrodomains have a defined localization within the cell throughout the cell cycle. In newborn cells ori and ter are located at mid-cell positions. These sites are located centrally within the Ori and Ter macrodomains. The Left and Right macrodomains occupy positions close to the cell poles. Upon replication, the Ori domains move towards the cell poles. Right before cell division the replicated Ter domains segregate. The chromosome in the daughter cells has again the same Left-Right orientation. MatP preferentially occupies sites in the Ter domain, whereas SlmA and SeqA are absent from this domain.

Figure 2. Distribution of nucleoid-associated proteins across the E. coli chromosome.

(A) A genome atlas where ChIP-chip datasets for IHF (orange), H-NS (purple), and RNA polymerase (black) are plotted against the features of the E. coli chromosome. (B) A genome atlas where ChIP-chip or ChIP-Seq datasets for SeqA (red) , SlmA [purple] (19) and MatP [orange] (20) are plotted against the features of the E. coli chromosome. The locations of ORFs are shown as pink and green lines. The positions of the four macrodomains (MDs) are shown as blue bars and are labelled.

Figure 3. Localization of MatP and SlmA on the E. coli chromosome.

E. coli cells expressing fluorescent derivatives of matP (matP-Cherry) (top panel) and SlmA (GFP-SlmA) (bottom panel). An overlay of phase contrast and fluorescence images is shown for matP, whereas separate fluorescence and DIC images are shown for SlmA. Scale bar, 4 µm. MatP predominantly localizes to the Ter macrodomain, whereas SlmA is absent from this domain.