Molecular Anatomy of ParA-ParA and ParA-ParB Interactions during Plasmid Partitioning

Volante, Andrea; Alonso, Juan C.

doi:10.1074/jbc.m115.649632

Cited by 32 publications

(37 citation statements)

References 42 publications

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“…4A). The formation of the ParB-ParA complex buries ∼450 Å 2 of protein surface from solvent, consistent with data indicating that the ParA-ParB interaction is weak (Vecchiarelli et al 2010;Volante and Alonso 2015). Strikingly, the ParB helices interact specifically with the ParA subunit arrangement found in the nucleotide sandwich dimer state; comparison of the ParA-ParB and ParA-DNA structures shows that ParB cannot dock in the dimer interface of the conformation that ParA adopts when bound to DNA without clash (Fig.…”

Section: Resultssupporting

confidence: 68%

“…Previous biochemical studies identified regions in ParB proteins that are involved in binding to their partner ParA proteins (Bartosik et al 2014;Volante and Alonso 2015). Work by Volante and Alonso (2015) revealed that pSM19035 plasmid ParB (also called ω) interacts with residues 88-119 in its partner, ParA (also called δ).…”

Section: Resultsmentioning

confidence: 99%

“…Thus, the dimer conformation adopted by ParA in the structure appears optimal for engaging these contacts. Although there are no other ParA-nsDNA structures, previous biochemical studies showed that Bacillus subtilis ParA (also called Soj) residue Arg189 (Arg182 in the homologous Thermus thermophilus ParA for which a structure is available) and residues 242-265 in the pSM19035 ParA protein are involved in nsDNA binding (Hester and Lutkenhaus 2007;Volante and Alonso 2015). Superimpositions of the T. thermophilus and pSM19035 ParA structures onto the pNOB8 ParA-AMPPNP-DNA structure reveals that these residues are localized next to pNOB8 ParA nsDNA-binding residues Lys218 and Lys220 (Supplemental Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Work by Volante and Alonso (2015) revealed that pSM19035 plasmid ParB (also called ω) interacts with residues 88-119 in its partner, ParA (also called δ). Comparison of the pNOB8 and pSM19035 ParA structures shows that residues 88-119 of the pSM19035 protein map to the ParB-binding site observed in the TP228 ParA-AMPPNP-ParB structure (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Multiple ParB proteins bind cooperatively to centromere sites on the cargo DNA to form large partition complexes (Rodionov et al 1999;Schumacher and Funnell 2005;Schumacher 2012;Graham et al 2014;Chen et al 2015;Funnell 2016). Data indicate that disordered typically N-terminal regions of ParB proteins displayed on the partition complexes bind their partner ParA proteins to mediate partition dynamics by stimulating ParA-ATP hydrolysis (Barillà et al 2007;Vecchiarelli et al 2013a;Schumacher et al 2015;Volante and Alonso 2015). ParA must be complexed with ATP to bind DNA.…”

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confidence: 99%

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Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation

Zhang

Schumacher

2017

Genes Dev.

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Walker-box partition systems are ubiquitous in nature and mediate the segregation of bacterial and archaeal DNA. Well-studied plasmid Walker-box partition modules require ParA, centromere-DNA, and a centromere-binding protein, ParB. In these systems, ParA-ATP binds nucleoid DNA and uses it as a substratum to deliver ParB-attached cargo DNA, and ParB drives ParA dynamics, allowing ParA progression along the nucleoid. How ParA-ATP binds nonspecific DNA and is regulated by ParB is unclear. Also under debate is whether ParA polymerizes on DNA to mediate segregation. Here we describe structures of key ParA segregation complexes. The ParA-β,γ-imidoadenosine 5 ′ -triphosphate (AMPPNP)-DNA structure revealed no polymers. Instead, ParA-AMPPNP dimerization creates a multifaceted DNA-binding surface, allowing it to preferentially bind high-density DNA regions (HDRs). DNAbound ParA-AMPPNP adopts a dimer conformation distinct from the ATP sandwich dimer, optimized for DNA association. Our ParA-AMPPNP-ParB structure reveals that ParB binds at the ParA dimer interface, stabilizing the ATPase-competent ATP sandwich dimer, ultimately driving ParA DNA dissociation. Thus, the data indicate how harnessing a conformationally adaptive dimer can drive large-scale cargo movement without the requirement for polymers and suggest a segregation mechanism by which ParA-ATP dimers equilibrate to HDRs shown to be localized near cell poles of dividing chromosomes, thus mediating equipartition of attached ParB-DNA substrates.

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Section: Resultssupporting

confidence: 68%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation

Zhang

Schumacher

2017

Genes Dev.

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A novel Vibrio alginolyticus phage and its therapy application in Portunus trituberculatus larvae

Cai,

Li,

Qin

et al. 2024

Aquaculture

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The emergence of phase separation as an organizing principle in bacteria

Azaldegui

Vecchiarelli

Biteen

2021

Biophysical Journal

143

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Recent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This Review assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPS in vivo in bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria. Statement of SignificanceThough membraneless organelles appear to play a crucial role in the subcellular organization and regulation of bacterial cells, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. Furthermore, liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly, but it is difficult to determine subcellular phases in tiny bacterial cells. Thus, we outline the framework to evaluate LLPS in vivo in bacteria and we describe the bacterial systems with proposed LLPS activity in the context of these criteria.

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Molecular Anatomy of ParA-ParA and ParA-ParB Interactions during Plasmid Partitioning

Cited by 32 publications

References 42 publications

Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation

Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation

A novel Vibrio alginolyticus phage and its therapy application in Portunus trituberculatus larvae

The emergence of phase separation as an organizing principle in bacteria

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