Competitive binding of MatP and topoisomerase IV to the MukB hinge domain

Fisher, Gemma Lm; Bolla, Jani Reddy; Rajasekar, Karthik V.; Mäkelä, Jarno; Baker, Richard; Zhou, Maosheng; Prince, Josh P; Stracy, Mathew; Robinson, Carol V.; Arciszewska, Lidia K.; Sherratt, David J.

doi:10.7554/elife.70444

Cited by 14 publications

(10 citation statements)

References 69 publications

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“…An interaction of MatP with the MukB hinge, at least in the absence of DNA, has been reported ( Fisher et al, 2021 ; Nolivos et al., 2016 ) but is not seen in our structures. It is conceivable that this occurs at a different stage during unloading and could suggest subunit and DNA transport within the complex.…”

Section: Discussioncontrasting

confidence: 53%

Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

et al. 2021

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Summary The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo . Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.

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Section: Discussioncontrasting

confidence: 53%

Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

et al. 2021

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“…4f). For example, loss of the ability to fully segregate chromosomes in ⊿ mukB can at least in part be understood through the inherent loss of MukBEF’s ability to recruit chromosomal TopoIV, leading to reduced sister untangling throughout segregation 22 . Further, MatP was found to be essential for DNA translocation by the FtsK protein 47 , which is another component that processes DNA in the late stages of cell division 48 .…”

Section: Discussionmentioning

confidence: 99%

“…Another important direct interaction partner of both MukBEF and MatP is the topoisomerase IV 20–22 . Topo IV influences the linking number of the nucleoid primarily in the ori region, where MukBEF is predominantly localized.…”

Section: Introductionmentioning

confidence: 99%

MukBEF-dependent chromosomal organization in widened Escherichia coli

Japaridze

Wee

Gogou

et al. 2022

Preprint

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The bacterial chromosome is spatially organized through protein-mediated compaction, supercoiling, and cell-boundary confinement. Structural Maintenance of Chromosomes (SMC) complexes are a major class of chromosome-organizing proteins present throughout all domains of life. Here, we study the role of the Escherichia coli SMC complex MukBEF in chromosome architecture and segregation. Using quantitative live-cell imaging of shape-manipulated cells, we show that MukBEF is crucial to preserve the toroidal topology of the E. coli chromosome and that it is non-uniformly distributed along the chromosome: it prefers locations towards the origin and away from the terminus of replication, and it is unevenly distributed over the origin of replication along the two chromosome arms. Using an ATP hydrolysis-deficient MukB mutant, we find that MukBEF translocation along the chromosome is ATP-dependent, in contrast to its loading onto DNA. MukBEF and MatP are furthermore found to be essential for sister chromosome decatenation. We propose a model that explains how MukBEF, MatP, and their interacting partners organize the chromosome and contribute to sister segregation and recombination. The combination of bacterial cell-shape modification and quantitative fluorescence microscopy paves way to investigating chromosome-organization factors in vivo.

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“…Interaction of SMC proteins and topoisomerases is common. The direct interaction of a Topo IV and MukB is well established (29,51,52). Thus, the interaction of MksBEF and MksG may not come as a surprise.…”

Section: Discussionmentioning

confidence: 99%

“…IV and MukB is well established (29,51,52). Thus, the interaction of MksBEF and MksG may not come as a surprise.…”

Section: Interaction Of Smc Proteins and Topoisomerases Is Common The...mentioning

confidence: 95%

A novel nuclease is the executing part of a bacterial plasmid defense system

Weiss

Giacomelli

Assaya

et al. 2022

Preprint

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Cells are continuously facing the risk of taking up foreign DNA that can compromise genomic and cellular integrity. Therefore, bacteria are in a constant arms race with mobile genetic elements such as phages, transposons and plasmids. They have developed several active strategies against invading DNA molecules that can be seen as a bacterial innate immune system. Anti-phage systems are usually organized in defense islands and can consist of restriction-modification (R-M) systems, CRISPR-Cas, and abortive infection (Abi) systems. Despite recent advances in the field, much less is known about plasmid defense systems. We have recently identified the MksBEFG system in Corynebacterium glutamicum as a novel plasmid defense system which comprises homologues of the condensin system MukFEB. Here, we investigated the molecular arrangement of the MksBEFG complex. Importantly, we identified MksG as a novel nuclease that degrades plasmid DNA and is, thus, the executing part of the system. The crystal structure of MksG revealed a dimeric assembly through its DUF2220 C-terminal domains. This domain is homologous to the TOPRIM domain of the topoisomerase II family of enzymes and contains the corresponding divalent ion binding site that is essential for DNA cleavage in topoisomerases, explaining the in vitro nuclease activity of MksG. We further show that the MksBEF subunits exhibit an ATPase cycle similar to MukBEF in vitro and we reason that this reaction cycle, in combination with the nuclease activity provided by MksG, allows for processive degradation of invading plasmids. Super-resolution localization microscopy revealed that the Mks system is spatially regulated via to the polar scaffold protein DivIVA. Introduction of plasmids increases the diffusion rate and alters the localization of MksG, indicating an activation of the system in vivo

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Competitive binding of MatP and topoisomerase IV to the MukB hinge domain

Cited by 14 publications

References 69 publications

Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

MukBEF-dependent chromosomal organization in widened Escherichia coli

A novel nuclease is the executing part of a bacterial plasmid defense system

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