A ring-polymer model shows how macromolecular crowding controls chromosome-arm organization in Escherichia coli

Chanil Jeon,Youngkyun Jung,Bae-Yeun Ha

doi:10.1038/s41598-017-10421-y

Abstract

Macromolecular crowding influences various cellular processes such as macromolecular association and transcription, and is a key determinant of chromosome organization in bacteria. The entropy of crowders favors compaction of long chain molecules such as chromosomes. To what extent is the circular bacterial chromosome, often viewed as consisting of “two arms”, organized entropically by crowding? Using computer simulations, we examine how a ring polymer is organized in a crowded and cylindrically-confined space, as a coarse-grained bacterial chromosome. Our results suggest that in a wide parameter range of biological relevance crowding is essential for separating the two arms in the way observed with Escherichia coli chromosomes at fast-growth rates, in addition to maintaining the chromosome in an organized collapsed state. Under different conditions, however, the ring polymer is centrally condensed or adsorbed onto the cylindrical wall with the two arms laterally collapsed onto each other. We discuss the relevance of our results to chromosome-membrane interactions.

Highlights

There has been a growing appreciation of entropic effects in organizing chain molecules[1,2,3,4,5,6,7,8,9,10]
As the chain becomes compacted by crowders, the spatial distribution of chain segments is modified in a nontrivial way[9,10]
Here we examine how confinement and molecular crowding orchestrate in organizing a symmetrical ring polymer as a model of the E. coli chromosome under fast growth conditions, resembling a donut

Summary

Introduction

There has been a growing appreciation of entropic effects in organizing chain molecules[1,2,3,4,5,6,7,8,9,10]. A key concept is the entropic (depletion) force between chain segments or monomers induced by crowding[15,16] It is responsible for overall compaction of bacterial chromosomes and governs their local organization by controlling the tendency of internal looping, as desired for such processes as transcription[3,8,9,10]. The spatial distribution of chain segments is governed by the balance between the two effects This has a more profound consequence on a ring polymer or a symmetrically-organized E. coli chromosome (see Fig. 1(A))[5,17,20,21], since the interaction between and relative arrangement of the two arms enter into the picture. The ring polymer problem we consider here provides a rich set of organizational behavior, as evidenced below

Methods

Results

Conclusion