Plasmid partition system

A plasmid partition system is the mechanism that assures the stable transmission of plasmids during bacterial cell division. Each plasmid has its independent replication system which control the number of copy of a plasmid in a cell. The higher the copy number is, the more likely the two daughter cells will contain the plasmid. Each molecule of plasmid diffuses randomly, so the probability of having a plasmid-less cell is 21-N, where N is the number of copies. For instance, if a plasmid has 2 copies of it in a cell, there is 50% of chance of having one plasmid-less daughter cell. However, high-copy number plasmids have a cost for the hosting cell. This metabolic burden is lower for low-copy plasmids, but those have a high probability of loss after few generation. To control vertical transmission of plasmids, in addition to controlled-replication systems, bacterial plasmids use different maintenance strategies, such as multimer resolution systems, post-segregational killing systems or addiction module, and partition systems.[1]

General properties of partition systems

Plasmid copies are paired around a centromere-like site and then separated in the two daughter cell. Partition systems involve three elements, organized in an autoregulated operon[2]

Centromer-like DNA site is required in cis for plasmid stability. It often contains one or more inverted repeats which are recognized by multiple CBPs. This forms a nucleoprotein complex termed partition complex. This complex recruits the motor protein, which is a nucleotide triphosphatase (NTPase). The NTPase uses energy from NTP binding and hydrolysis to directly or indirectly move and attach plasmids to specific host location (e.g. opposite bacterial cell poles).

The partition systems are divided in four types, based primarily on the type of NTPases:[3]

Name of the different elements in the different types
Type Motor protein (NTPase) Centromere binding protein (CBP) Centromere-like binding site Other proteins
Type I ParA ParB or ParG parS (Ia) or parC (Ib)
Type II ParM ParR parC
Type III TubZ TubR tubS TubY

Type I partition system

This system is also used by most bacteria for chromosome segregation.[3] Type I partition system are composed of an ATPase which contains Walker motifs and a CBP which is structurally distinct in type Ia and Ib. ATPases and CBP from type Ia are longer than the one from type Ib, but both CBPs contain an arginine finger in their N-terminal part.[1][4] ParA proteins from different plasmids and bacterial species show 25 to 30% of sequence identity to the protein ParA of the plasmid P1.[5] The partition of type I system uses a "diffusion-ratchet" mechanism. This mechanism works as follows:[6]

  1. Dimers of ParA-ATP dynamically bind to nucleoid DNA[7][8]
  2. ParB bound to parS stimulates the release of ParA from the nucleoid region surrounding the plasmid[9]
  3. The plasmid then chases the resulting ParA gradient on the perimeter of the ParA depleted region of the nucleoid
  4. The ParA that was released from the nucleoid behind the plasmid's movement redistributes to other regions of the nucleoid after a delay [10]
  5. After plasmid replication, the sister copies segregate to opposite cell halves as they chase ParA on the nucleoid in opposite directions

It should be noted that there are likely to be differences in the details of type I mechanisms.[4]

Type 1 partition has been mathematically modelled with variations in the mechanism described above.[11][12][13]

Type Ia

CBP consists in three domains:[4]

Type Ib

CBP (also known as parG) is composed of:[4]

parS is called parC

Type II partition system

This system is the best understood of the plasmid partition system.[4] It is composed of an actin-like ATPAse, ParM, and a CBP called ParR. The centromere like site, parC contains two sets of five 11 base pair direct repeats separated by the parMR promoter. The amino-acid sequence identity can go down to 15% between ParM and other actin-like ATPase.[5][14]

The mechanism of partition involved here is a pushing mechanism:[15]

  1. ParR binds to parC and pairs plasmids which form a nucleoprotein complex, or partition complex
  2. The partition complex serves as nucleation point for the polymerization of ParM; ParM-ATP complex inserts at this point and push plasmids apart
  3. The insertion leads to hydrolysis of ParM-ATP complex, leading to depolymerization of the filament
  4. At cell division, plasmids copies are at each cell extremity, and will end up in future daughter cell

The filament of ParM is regulated by the polymerization allowed by the presence the partition complex (ParR-parC), and by the depolymerization controlled by the ATPase activity of ParM.

Type III partition system

The type III partition system is the most recently discovered partition system. It is composed of tubulin-like GTPase termed TubZ, and the CBP is termed TubR. Amino-acid sequence identity can go down to 21% for TubZ proteins.[5]

The mechanism is similar to a treadmill mechanism:[16]

  1. Multiple TubR dimer binds to the centromere-like region stbDRs of the plasmids.
  2. Contact between TubR and filament of treadmilling TubZ polymer. TubZ subunits are lost from the - end and are added to the + end.
  3. TubR-plasmid complex is pulled along the growing polymer until it reaches the cell pole.
  4. Interaction with membrane is likely to trigger the release of the plasmid.

The net result being transport of partition complex to the cell pole.

Other partition systems

R388 partition system

The partition system of the plasmid R388 has been found within the stb operon. This operon is composed of three genes, stbA, stbB and stbC.[17]

The StbA-stbDRs complex may be used to pair plasmid the host chromosome, using indirectly the bacterial partitioning system.

StbA and StbB have opposite but connected effect related to conjugation.

This system has been proposed to be the type IV partition system.[18] It is thought to be a derivative of the type I partition system, given the similar operon organization. This system represents the first evidence for a mechanistic interplay between plasmid segregation and conjugation processes.[18]

pSK1 partition system (reviewed in [1])

pSK1 is plasmid from Staphylococcus aureus. This plasmid has a partition system determined by a single gene, par, previously known as orf245. This gene has effect neither on the plasmid copy number nor on the grow rate (excluding its implication in a post-segregational killing system). A centromere-like binding sequence is present upstream the par gene, and is composed of seven direct repeats and one inverted repeat.

References

  1. 1 2 3 Dmowski M, Jagura-Burdzy G (2013). "Active stable maintenance functions in low copy-number plasmids of Gram-positive bacteria I. Partition systems" (PDF). Polish Journal of Microbiology / Polskie Towarzystwo Mikrobiologów = the Polish Society of Microbiologists 62 (1): 3–16. PMID 23829072.
  2. ↑ Friedman SA, Austin SJ (1988). "The P1 plasmid-partition system synthesizes two essential proteins from an autoregulated operon". Plasmid 19 (2): 103–12. doi:10.1016/0147-619X(88)90049-2. PMID 3420178.
  3. 1 2 Gerdes K, Møller-Jensen J, Bugge Jensen R (2000). "Plasmid and chromosome partitioning: surprises from phylogeny". Molecular Microbiology 37 (3): 455–66. doi:10.1046/j.1365-2958.2000.01975.x. PMID 10931339.
  4. 1 2 3 4 5 Schumacher MA (2012). "Bacterial plasmid partition machinery: a minimalist approach to survival". Current Opinion in Structural Biology 22 (1): 72–9. doi:10.1016/j.sbi.2011.11.001. PMID 22153351.
  5. 1 2 3 Chen Y, Erickson HP (2008). "In vitro assembly studies of FtsZ/tubulin-like proteins (TubZ) from Bacillus plasmids: evidence for a capping mechanism". The Journal of Biological Chemistry 283 (13): 8102–9. doi:10.1074/jbc.M709163200. PMC 2276378. PMID 18198178.
  6. ↑ Badrinarayanan, Anjana; Le, Tung B. K.; Laub, Michael T. (2015-11-13). "Bacterial Chromosome Organization and Segregation". Annual Review of Cell and Developmental Biology 31: 171–199. doi:10.1146/annurev-cellbio-100814-125211. ISSN 1530-8995. PMID 26566111.
  7. ↑ Hwang, Ling Chin; Vecchiarelli, Anthony G.; Han, Yong-Woon; Mizuuchi, Michiyo; Harada, Yoshie; Funnell, Barbara E.; Mizuuchi, Kiyoshi (2013-05-02). "ParA-mediated plasmid partition driven by protein pattern self-organization". The EMBO Journal 32 (9): 1238–1249. doi:10.1038/emboj.2013.34. ISSN 1460-2075. PMC 3642677. PMID 23443047.
  8. ↑ Vecchiarelli, Anthony G.; Hwang, Ling Chin; Mizuuchi, Kiyoshi (2013-04-09). "Cell-free study of F plasmid partition provides evidence for cargo transport by a diffusion-ratchet mechanism". Proceedings of the National Academy of Sciences of the United States of America 110 (15): E1390–1397. doi:10.1073/pnas.1302745110. ISSN 1091-6490. PMC 3625265. PMID 23479605.
  9. ↑ Vecchiarelli, Anthony G.; Neuman, Keir C.; Mizuuchi, Kiyoshi (2014-04-01). "A propagating ATPase gradient drives transport of surface-confined cellular cargo". Proceedings of the National Academy of Sciences of the United States of America 111 (13): 4880–4885. doi:10.1073/pnas.1401025111. ISSN 1091-6490. PMC 3977271. PMID 24567408.
  10. ↑ Vecchiarelli, Anthony G.; Han, Yong-Woon; Tan, Xin; Mizuuchi, Michiyo; Ghirlando, Rodolfo; Biertümpfel, Christian; Funnell, Barbara E.; Mizuuchi, Kiyoshi (2010-10-01). "ATP control of dynamic P1 ParA-DNA interactions: a key role for the nucleoid in plasmid partition". Molecular Microbiology 78 (1): 78–91. doi:10.1111/j.1365-2958.2010.07314.x. ISSN 1365-2958. PMC 2950902. PMID 20659294.
  11. ↑ Hu, Longhua; Vecchiarelli, Anthony G.; Mizuuchi, Kiyoshi; Neuman, Keir C.; Liu, Jian (2015-12-08). "Directed and persistent movement arises from mechanochemistry of the ParA/ParB system". Proceedings of the National Academy of Sciences of the United States of America 112: E7055–64. doi:10.1073/pnas.1505147112. ISSN 1091-6490. PMC 4697391. PMID 26647183.
  12. ↑ Vecchiarelli, Anthony G.; Seol, Yeonee; Neuman, Keir C.; Mizuuchi, Kiyoshi (2014-01-01). "A moving ParA gradient on the nucleoid directs subcellular cargo transport via a chemophoresis force". Bioarchitecture 4 (4-5): 154–159. doi:10.4161/19490992.2014.987581. ISSN 1949-100X. PMID 25759913.
  13. ↑ Ietswaart, Robert; Szardenings, Florian; Gerdes, Kenn; Howard, Martin (2014-12-01). "Competing ParA structures space bacterial plasmids equally over the nucleoid". PLOS Computational Biology 10 (12): e1004009. doi:10.1371/journal.pcbi.1004009. ISSN 1553-7358. PMC 4270457. PMID 25521716.
  14. ↑ Gunning PW, Ghoshdastider U, Whitaker S, Popp D, Robinson RC (2015). "The evolution of compositionally and functionally distinct actin filaments". J Cell Sci. doi:10.1242/jcs.165563. PMID 25788699.
  15. ↑ Møller-Jensen J, Borch J, Dam M, Jensen RB, Roepstorff P, Gerdes K (2003). "Bacterial mitosis: ParM of plasmid R1 moves plasmid DNA by an actin-like insertional polymerization mechanism". Molecular Cell 12 (6): 1477–87. doi:10.1016/S1097-2765(03)00451-9. PMID 14690601.
  16. ↑ Ni L, Xu W, Kumaraswami M, Schumacher MA (2010). "Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition". Proceedings of the National Academy of Sciences of the United States of America 107 (26): 11763–8. doi:10.1073/pnas.1003817107. PMC 2900659. PMID 20534443.
  17. ↑ Guynet C, Cuevas A, Moncalián G, de la Cruz F (2011). "The stb operon balances the requirements for vegetative stability and conjugative transfer of plasmid R388". PLoS Genetics 7 (5): e1002073. doi:10.1371/journal.pgen.1002073. PMC 3098194. PMID 21625564.
  18. 1 2 Guynet C, de la Cruz F (2011). "Plasmid segregation without partition". Mobile Genetic Elements 1 (3): 236–241. doi:10.4161/mge.1.3.18229. PMC 3271553. PMID 22312593.
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