Browse
Submit Data
Databases
API
Help

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The structure of bacterial ParM filaments.

ABSTRACT: Bacterial ParM is a homolog of eukaryotic actin and is involved in moving plasmids so that they segregate properly during cell division. Using cryo-EM and three-dimensional reconstruction, we show that ParM filaments have a different structure from F-actin, with very different subunit-subunit interfaces. These interfaces result in the helical handedness of the ParM filament being opposite to that of F-actin. Like F-actin, ParM filaments have a variable twist, and we show that this involves domain-domain rotations within the ParM subunit. The present results yield new insights into polymorphisms within F-actin, as well as the evolution of polymer families.

SUBMITTER: Orlova A

PROVIDER: S-EPMC3541950 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The structure of bacterial ParM filaments.

Orlova Albina A Garner Ethan C EC Galkin Vitold E VE Heuser John J Mullins R Dyche RD Egelman Edward H EH

Nature structural & molecular biology 20070916 10

Bacterial ParM is a homolog of eukaryotic actin and is involved in moving plasmids so that they segregate properly during cell division. Using cryo-EM and three-dimensional reconstruction, we show that ParM filaments have a different structure from F-actin, with very different subunit-subunit interfaces. These interfaces result in the helical handedness of the ParM filament being opposite to that of F-actin. Like F-actin, ParM filaments have a variable twist, and we show that this involves domai ...[more]

PMID: 17873883

Similar Datasets

A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation.

Project description:To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between sister plasmids. In the ParMRC system of the Escherichia coli R1 plasmid, ParM, an actinlike protein, forms the spindle between ParRC complexes on sister plasmids. By using a combination of structural work and total internal reflection fluorescence microscopy, we show that ParRC bound and could accelerate growth at only one end of polar ParM filaments, mechanistically resembling eukaryotic formins. The architecture of ParM filaments enabled two ParRC-bound filaments to associate in an antiparallel orientation, forming a bipolar spindle. The spindle elongated as a bundle of at least two antiparallel filaments, thereby pushing two plasmid clusters toward the poles.

| S-EPMC3694215 | biostudies-literature

Are ParM filaments polar or bipolar?

Project description:A recent perspective [Erickson, H. (2012). Bacterial actin homolog ParM: arguments for an apolar, antiparallel double helix. J. Mol. Biol., 422, 461-463] by Harold Erickson has suggested that published reconstructions of bacterial ParM filaments from three different laboratories may have artifactually imposed polarity upon a filament that is really bipolar, with the two strands running in opposite directions. We show that Erickson's model of a bipolar filament can be easily distinguished from a polar filament by helical diffraction, since the asymmetric unit in a bipolar filament would be twice the size as that in a polar filament. Existing data from both electron cryo-microscopy and X-ray diffraction exclude a bipolar model. We adopt the suggestion put forward by Erickson to process filaments, assuming that they are bipolar, and show that the resulting filaments are polar.

| S-EPMC3467344 | biostudies-literature

F-actin-like filaments formed by plasmid segregation protein ParM.

Project description:It was the general belief that DNA partitioning in prokaryotes is independent of a cytoskeletal structure, which in eukaryotic cells is indispensable for DNA segregation. Recently, however, immunofluorescence microscopy revealed highly dynamic, filamentous structures along the longitudinal axis of Escherichia coli formed by ParM, a plasmid-encoded protein required for accurate segregation of low-copy-number plasmid R1. We show here that ParM polymerizes into double helical protofilaments with a longitudinal repeat similar to filamentous actin (F-actin) and MreB filaments that maintain the cell shape of non-spherical bacteria. The crystal structure of ParM with and without ADP demonstrates that it is a member of the actin family of proteins and shows a domain movement of 25 degrees upon nucleotide binding. Furthermore, the crystal structure of ParM reveals major differences in the protofilament interface compared with F-actin, despite the similar arrangement of the subunits within the filaments. Thus, there is now evidence for cytoskeletal structures, formed by actin-like filaments that are involved in plasmid partitioning in E.coli.

| S-EPMC139093 | biostudies-literature

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles.

Project description:Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.

| S-EPMC4493928 | biostudies-literature

Structure of the ParM filament at 8.5A resolution.

Project description:The actin-like protein ParM forms the cytomotive filament of the ParMRC system, a type II plasmid segregation system encoded by Escherichia coli R1 plasmid. We report an 8.5Å resolution reconstruction of the ParM filament, obtained using cryo-electron microscopy. Fitting of the 3D density reconstruction with monomeric crystal structures of ParM provides insights into dynamic instability of ParM filaments. The structural analysis suggests that a ParM conformation, corresponding to a metastable state, is held within the filament by intrafilament contacts. This filament conformation of ParM can be attained only from the ATP-bound state, and induces a change in conformation of the bound nucleotide. The structural analysis also provides a rationale for the observed stimulation of hydrolysis upon polymerisation into the filament.

| S-EPMC3794156 | biostudies-literature

Dynamic Filament Formation by a Divergent Bacterial Actin-Like ParM Protein.

Project description:Actin-like proteins (Alps) are a diverse family of proteins whose genes are abundant in the chromosomes and mobile genetic elements of many bacteria. The low-copy-number staphylococcal multiresistance plasmid pSK41 encodes ParM, an Alp involved in efficient plasmid partitioning. pSK41 ParM has previously been shown to form filaments in vitro that are structurally dissimilar to those formed by other bacterial Alps. The mechanistic implications of these differences are not known. In order to gain insights into the properties and behavior of the pSK41 ParM Alp in vivo, we reconstituted the parMRC system in the ectopic rod-shaped host, E. coli, which is larger and more genetically amenable than the native host, Staphylococcus aureus. Fluorescence microscopy showed a functional fusion protein, ParM-YFP, formed straight filaments in vivo when expressed in isolation. Strikingly, however, in the presence of ParR and parC, ParM-YFP adopted a dramatically different structure, instead forming axial curved filaments. Time-lapse imaging and selective photobleaching experiments revealed that, in the presence of all components of the parMRC system, ParM-YFP filaments were dynamic in nature. Finally, molecular dissection of the parMRC operon revealed that all components of the system are essential for the generation of dynamic filaments.

| S-EPMC4911067 | biostudies-literature

Multimodal multiscale analysis reveals flexible DNA contacts of bacterial nucleoprotein filaments

Project description:Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the overall structures, arrangements of DNA-binding domains (DBDs), positions of DBD–DNA contacts, and determinants of genomic distribution for these linear and bridged filaments are uncertain. To connect H-NS structures that silence genes in vivo with features elucidated in vitro, we developed a multimodal multiscale analysis that combines a new method for chromatin reconstitution and mapping (Nitro-seq), ChIP-seq, tethered-nuclease mapping of DBD–DNA contacts (TEN-map), ·OH footprinting, molecular dynamics, and bioinformatics. We find that DNA sequence principally governs H-NS-filament location with indistinguishable sequence specificity in bridged or linear forms with or without the H-NS modifiers StpA and Hha and that DBD–DNA contacts vary in orientation and position with ~10-bp average spacing. Our results support a hemi-sequestration model of linear-to-bridged filament switching.

2023-09-01 | GSE157512 | GEO

Asymmetric chromosome segregation and cell division in DNA damage-induced bacterial filaments

Project description:We performed RNA seq analysis on Escherichia coli MG1655 recovering from DNA damage induced by mitomycin C Escherichia coli was grown overnight in luria broth at 37°C with shaking at 200 rpm. The culture was back diluted to ~OD600 0.01 and allowed to grow to OD600 ~0.1. It was then treated with 1 μg/ml mitomycin C for 60 min. Cells were pelleted, washed with fresh media, resuspended to OD600 ~0.1 and then allowed to recover from damage treatment. Samples were collected before addition of damage as control. Samples were also collected every 20 min for 3 hrs during recovery and then every 1 hr for 3 hrs after that. Cultures were maintained in log phase (OD600 ~0.1 - 0.4) throughout the experiment. RNA was extracted using the Direct-zol™ RNA MiniPrep (Zymo, Cat no. R2052A81) and RNA Clean & Concentrator™-25 (Zymo, Cat no. R1018A82). RNA libraries were prepared using the TruSeq Stranded mRNA Library Preparation kit. Libraries were sequenced using Illumina MiSeq sequencing platform. Samples were collected from 2 independent experiments.

2020-11-15 | E-MTAB-9696 | biostudies-arrayexpress

Bacterial actin MreB forms antiparallel double filaments.

Project description:Filaments of all actin-like proteins known to date are assembled from pairs of protofilaments that are arranged in a parallel fashion, generating polarity. In this study, we show that the prokaryotic actin homologue MreB forms pairs of protofilaments that adopt an antiparallel arrangement in vitro and in vivo. We provide an atomic view of antiparallel protofilaments of Caulobacter MreB as apparent from crystal structures. We show that a protofilament doublet is essential for MreB's function in cell shape maintenance and demonstrate by in vivo site-specific cross-linking the antiparallel orientation of MreB protofilaments in E. coli. 3D cryo-EM shows that pairs of protofilaments of Caulobacter MreB tightly bind to membranes. Crystal structures of different nucleotide and polymerisation states of Caulobacter MreB reveal conserved conformational changes accompanying antiparallel filament formation. Finally, the antimicrobial agents A22/MP265 are shown to bind close to the bound nucleotide of MreB, presumably preventing nucleotide hydrolysis and destabilising double protofilaments.DOI: http://dx.doi.org/10.7554/eLife.02634.001.

| S-EPMC4051119 | biostudies-literature

The bacterial cytoskeleton: more than twisted filaments.

Project description:Far from being simple 'bags' of enzymes, bacteria are richly endowed with ultrastructures that challenge and expand standard definitions of the cytoskeleton. Here we review rods, rings, twisted pairs, tubes, sheets, spirals, moving patches, meshes and composites, and suggest defining the term 'bacterial cytoskeleton' as all cytoplasmic protein filaments and their superstructures that move or scaffold (stabilize/position/recruit) other cellular materials. The evolution of each superstructure has been driven by specific functional requirements. As a result, while homologous proteins with different functions have evolved to form surprisingly divergent superstructures, those of unrelated proteins with similar functions have converged.

| S-EPMC3597445 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data