ParM-like
Identifiers
Symbol?
PfamPF06406
InterProIPR042051
SCOP21mwm / SCOPe / SUPFAM
CDDCD10227
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

ParM is a prokaryotic actin homologue[1] which provides the force to drive copies of the R1 plasmid to opposite ends of rod shaped bacteria before cytokinesis.

ParM is a monomer that is encoded in the DNA of the R1 plasmid and manufactured by the host cell's ribosomes. In the cytoplasm it spontaneously polymerizes forming short strands that either bind to ParR or hydrolyze. ParR stabilizes ParM and prevents it from hydrolyzing. Once bound by ParR at both ends, monomer units continue to attach to the ends of the ParM and the resulting reaction pushes R1 plasmids to opposite ends of the cell.[2] ParMs from different bacterial plasmids can form astonishingly diverse helical structures comprising two[3][4] or four[5] strands to maintain faithful plasmid inheritance.

Action

In vitro the ParM monomer has been observed polymerizing both with ATP and with GTP, but experiments by Popp et al. seem to indicate that the reaction "prefers" GTP and that GTP is the nucleotide that most likely makes the significant contributions in the cell.[6] For the remainder of this article GTP will be assumed to be the active nucleotide although many experiments have used ATP instead.

ParM binds and hydrolyzes GTP as it polymerizes. The current dominant belief is that a "cap" of GTP is required at the ends of the ParM polymer strands to prevent them from hydrolyzing. Although GTP is hydrolyzed by the ParM units after attachment, it is believed that the energy that drives the plasmids is derived from the Gibbs free energy of the ParM monomer concentrations, and not the energy released from GTP hydrolysis. The concentrations of ParM monomer and polymer must be kept out of equilibrium at the ends where attachment is occurring for the reaction to proceed regardless of GTP concentrations.

Once the ParM has pushed plasmids to opposite ends of the cell the polymer rapidly depolymerizes—returning the monomer units to the cytoplasm.[7]

Structure

The ParM monomer unit is non-functional before binding a GTP nucleotide. Once the GTP has been bound it can attach to the end of a growing filament. At some point after attachment the ParM hydrolyzes GTP which becomes GDP and remains in the ParM subunit as long as the polymer strand remains intact. ParM forms a left-handed helix structure.[6]

A study by Garner and Campbell has suggested that the unit at the end of the ParM strand must have GTP bound to maintain the stability of the polymer. If one of the ends has the GDP bound version the polymer strand depolymerizes very quickly into its constituent monomer units. This is suggested by their experiment in which they cut growing ParM polymer strands exposing ADP bound ends. Once cut the strands quickly hydrolyzed.[7]

Dynamic Instability

Dynamic instability is described as the switching of a polymer between phases of steady elongation and rapid shortening. This process is essential to the function of eukaryotic microtubules. In ParM, dynamic instability "rescue" or the switch from a shortening phase back to the elongation phase has very rarely been observed, and only when the ATP nucleotide is used. Unbound ParM filaments are found with a typical average length of 1.5 – 2 μm, when the ParM monomer concentrations are 2 μM or more. The dynamic instability of ParM and eukaryotic microtubules is believed to be an example of convergent evolution.[8] L ParM spontaneously forms short polymer segments when it is present in the cytoplasm. These segments serve to very efficiently "search" for the R1 plasmids, and also maintains a favorable concentration of ParM monomer units for polymerization.[6]

References

  1. ^ Gunning PW, Ghoshdastider U, Whitaker S, Popp D, Robinson RC (June 2015). "The evolution of compositionally and functionally distinct actin filaments". Journal of Cell Science. 128 (11): 2009–19. doi:10.1242/jcs.165563. PMID 25788699.
  2. ^ Hoischen C, Bussiek M, Langowski J, Diekmann S (February 2008). "Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR". Nucleic Acids Research. 36 (2): 607–15. doi:10.1093/nar/gkm672. PMC 2241845. PMID 18056157.
  3. ^ Popp D, Xu W, Narita A, Brzoska AJ, Skurray RA, Firth N, et al. (March 2010). "Structure and filament dynamics of the pSK41 actin-like ParM protein: implications for plasmid DNA segregation". The Journal of Biological Chemistry. 285 (13): 10130–40. doi:10.1074/jbc.M109.071613. PMC 2843175. PMID 20106979.
  4. ^ Popp D, Narita A, Ghoshdastider U, Maeda K, Maéda Y, Oda T, et al. (April 2010). "Polymeric structures and dynamic properties of the bacterial actin AlfA". Journal of Molecular Biology. 397 (4): 1031–41. doi:10.1016/j.jmb.2010.02.010. PMID 20156449.
  5. ^ Popp D, Narita A, Lee LJ, Ghoshdastider U, Xue B, Srinivasan R, et al. (June 2012). "Novel actin-like filament structure from Clostridium tetani". The Journal of Biological Chemistry. 287 (25): 21121–9. doi:10.1074/jbc.M112.341016. PMC 3375535. PMID 22514279.
  6. ^ a b c Popp D, Narita A, Oda T, Fujisawa T, Matsuo H, Nitanai Y, et al. (February 2008). "Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability". The EMBO Journal. 27 (3): 570–9. doi:10.1038/sj.emboj.7601978. PMC 2241650. PMID 18188150.
  7. ^ a b Garner EC, Campbell CS, Weibel DB, Mullins RD (March 2007). "Reconstitution of DNA segregation driven by assembly of a prokaryotic actin homolog". Science. 315 (5816): 1270–4. Bibcode:2007Sci...315.1270G. doi:10.1126/science.1138527. PMC 2851738. PMID 17332412.
  8. ^ Garner EC, Campbell CS, Mullins RD (November 2004). "Dynamic instability in a DNA-segregating prokaryotic actin homolog". Science. 306 (5698): 1021–5. Bibcode:2004Sci...306.1021G. doi:10.1126/science.1101313. PMID 15528442. S2CID 14032209.
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