Representative plasmids
Plasmid is typically a circle of DNA that carries genes within a bacterial cell but is distinct from bacterial chromosome and can replicate independently 1, 2. Plasmid-mediated transmission of resistance genes among Enterobacteriaceae and Pseudomonas imposes a major public health concern. Incompatibility (Inc) groups of plasmids are traditionally discriminated on the basis of experimental observations that plasmids with similar replication machinery are often unable to stably co-exist within the same host cell and thus the plasmid shows incompatibility with the same Inc group plasmid. Nowadays, Inc classification is always based on replication initiation protein (Rep) sequences, and it is not necessarily confirmed by conventional conjugation-based incompatibility experiments. It should be noted that there is not any of fully sequenced plasmids for some known Inc groups, and that there are quite a few sequenced plasmids that could not be assigned to any known Inc groups.
Table 1|List of representative plasmids
| Inc group | Inc subgroup | Designation | Host bacterium | Accession number | FASTA sequence | Gene list | GBK-annotation | SQN-annotation | Manual annotation | Gene organization |
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| IncA (=IncP-3) | pRA1 | Aeromonas hydrophila | FJ705807 |  |
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| IncC | Type 1 IncC | pR148 | Aeromonas hydrophila | JX141473 | |
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| IncC | Type 2 IncC | pR55 | Klebsiella pneumoniae | JQ010984 | |
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| IncF | IncFI | Plasmid F | Escherichia coli | AP001918 | |
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| IncF | IncFIIR100 | R100 | Shigella flexneri | AP000342 | |
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| IncF | IncFIIpHN7A8 | pHN7A8 | Escherichia coli | JN232517 | |
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| IncF | IncFIIp0716-KPC | p0716-KPC | Klebsiella pneumoniae | KY270849 | |
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| IncF | IncFIIpKPHS2 | pKPHS2 | Klebsiella pneumoniae | CP003224 | |
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| IncF | IncFIIpP10164-NDM | pP10164-NDM | Leclercia adecarboxylata | KP900016 | |
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| IncF | IncFIIpYPTS01 | pYPTS01 | Yersinia pseudotuberculosis | CP001049 | |
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| IncF | IncFIIpRJ46C | pRJ46C | Raoultella ornithinolytica | KT225580 | |
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| IncF | IncFIIpSPCV50 | pSPCV50 | Salmonella enterica | NC_006855 | |
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| IncF | IncFIIpDSJ09 | pDSJ09 | Pantoea stewartii | CP017590 | |
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| IncF | IncFIIpKOXM1B | pKOXM1B | Klebsiella michiganensis | CP008843 | |
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| IncF | IncFIIpKPN-b0b | pKPN-b0b | Klebsiella pneumoniae | NZ_CP007736 | |
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| IncF | IncFIIpKF727591 | pKF727591 | Enterobacter hormaechei | KF727591 | |
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| IncF | IncFIIpKp_Goe_414-4 | pKp_Goe_414-4 | Klebsiella pneumoniae | CP018341 | |
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| IncG (=IncP-6) | p10265-KPC | Pseudomonas aeruginosa | KU578314 | |
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| IncH | IncHI1 | R27 | Salmonella enterica serovar Typhi | AF250878 | |
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| IncH | IncHI2 (=IncS) | R478 | Serratia marcescens | BX664015 | |
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| IncH | IncHI3 | pNDM-MAR | Klebsiella pneumoniae | JN420336 | |
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| IncH | IncHI4 | pNDM-CIT | Citrobacter freundii | JX182975 | |
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| IncH | IncHI5 | pA324-IMP | Klebsiella pneumoniae | MF344566 | |
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| IncI complex | IncI1/B/O | R64 | Salmonella enterica serovar Typhi | AP005147 | |
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| IncI complex | IncI2 | R721 | Escherichia coli | AP002527 | |
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| IncI complex | IncIγ/K1 | pCT | Escherichia coli | FN868832 | |
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| IncI complex | IncK2/Z | pO26-CRL-125 | Escherichia coli | KC340960 | |
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| IncJ | R391 | Providencia rettgeri | AY090559 | |
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| IncL | R471 | Serratia marcescens | KM406489 | |
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| IncM | R69 | Salmonella paratyphi | KM406488 | |
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| IncN | IncN1 | R46 | Salmonella enterica serovar Typhi | AY046276 | |
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| IncN | IncN2 | pYNKP001-NDM | Raoultella ornithinolytica | KP900017 | |
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| IncN | IncN3 | pN-Cit | Citrobacter freundii | JQ996149 | |
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| IncP | IncP-1α | RK2 | Klebsiella aerogenes | L27758 | |
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| IncP | IncP-1β1 | R751 | Klebsiella aerogenes | U67194 | |
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| IncP | IncP-1β2 | pB4 | Uncultured bacterium | AJ431260 | |
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| IncP | IncP-1γ | pQKH54 | Uncultured bacterium | AM157767 | |
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| IncP | IncP-1δ | pAKD4 | Uncultured bacterium | GQ983559 | |
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| IncP | IncP-1ε | pKJK5 | Uncultured bacterium | AM261282 | |
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| IncP | IncP-1ζ | pMCBF1 | Uncultured bacterium | AY950444 | |
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| IncP | IncP-1η | pP9014 | Photobacterium damselae | AB453229 | |
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| IncP | IncP-1θ | pEP5289 | Neisseria gonorrhoeae | GU479466 | |
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| IncP | IncP-2 | pSx1 | Shewanella xiamenensis | CP013115 | |
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| IncP | IncP-7α | pCAR1 | Pseudomonas resinovorans | AB088420 | |
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| IncP | IncP-7β | pDK1 | Pseudomonas putid | AB434906 | |
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| IncP | IncP-9 | pWW0 | Pseudomonas putida | AJ344068 | |
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| IncP | IncP-9 | pDTG1 | Pseudomonas putida | AF491307 | |
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| IncP | IncP-10 | R91-5 | Pseudomonas aeruginosa | X54695 | |
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| IncQ | IncQ-1α (=IncP-4) | RSF1010 | Escherichia coli | M28829 | |
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| IncQ | IncQ-1β | pIE1107 | Uncultured bacterium | Z74787 | |
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| IncQ | IncQ-1γ | pIE1130 | Uncultured bacterium | AJ271879 | |
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| IncQ | IncQ-1δ | pCHE-A | Enterobacter cloacae | EU266532 | |
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| IncQ | IncQ-2α | pTF-FC2 | Thiobacillus ferrooxidans | M73777+M57717+L37364 | |
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| IncQ | IncQ-2β | pTC-F14 | Acidithiobacillus caldus | AF325537 | |
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| IncQ | IncQ-2γ | pRAS3.1 | Aeromonas salmonicida | AY043298 | |
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| IncQ | IncQ-3 | pGNB2 | Uncultured bacterium | DQ460733 | |
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| IncQ | IncQ-4 | pPNAP08 | Polaromonas naphthalenivorans CJ2 | CP000537 | |
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| IncR | pHN84KPC | Enterobacter cloacae | KY296104 | |
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| IncT | Rts1 | Proteus vulgaris | AP004237 | |
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| IncU | pFBAOT6 | Aeromonas punctata | CR376602 | |
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| IncW | R388 | Escherichia coli | BR000038 | |
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| IncX | IncX1α | pOLA52 | Escherichia coli | EU370913 | |
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| IncX | IncX1β | R485 | Morganella morganii | HE577112 | |
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| IncX | IncX2 | R6K | Escherichia coli | LT827129 | |
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| IncX | IncX3 | pNDM-HN380 | Klebsiella pneumoniae | JX104760 | |
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| IncX | IncX4 | pBS512_33 | Shigella boydii | CP001059 | |
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| IncX | IncX5 | pBK31567 | Klebsiella pneumoniae | JX193302 | |
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| IncX | IncX6 | pKPC3_SZ | Enterobacter cloacae | KU302800 | |
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| IncX | IncX7 | pHI4320 | Proteus mirabilis | AM942760 | |
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| IncX | IncX8 | pCAV1043-58 | Enterobacter asburiae | CP011588 | |
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| IncY | Phage P1 | Escherichia virus P1 | NC_005856 | |
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| IncpKPHS1 | pKPHS1 | Klebsiella pneumoniae | CP003223 | |
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| IncpRBL16 | pRBL16 | Pseudomonas citronellolis | CP015879 | |
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| Incp16005813A | p16005813A | Pseudomonas citronellolis | MK036891 | |
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| IncpNY8709-IMP | pNY8709-IMP | Pseudomonas aeruginosa | CP096823 | |
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| IncpNY4625-IMP | pNY4625-IMP | Aeromonas caviae | MN629346 | |
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| IncpJBCL41 | pJBCL41 | Pseudomonas sp. | MK496050 | |
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| IncpSH5-1 | pSH5-1 | Pseudomonas monteilii | CP022563 | |
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| Incp60512-IMP | p60512-IMP | Pseudomonas aeruginosa | MF3442578 | |
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| IncpPA7790 | pPA7790 | Pseudomonas aeruginosa | CP015000 | |
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| IncpSE5381-aadB | pSE5381-aadB | Pseudomonas aeruginosa | CP121188 | |
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| IncpCHS4.1-3 | pCHS4.1-3 | Providencia | OL908908 | |
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| IncpPROV114-NR | pPROV114-NR | Providencia | CP120529 | |
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Table 2|Key conserved genes in plasmid backbones
| Function category | Function sub-category | Gene name(recommended herein) | Gene name(previously used) | Gene name(P-type homolog) | Product | Reference proteins - plasmid F | Reference proteins - plasmid RP4 |
|---|---|---|---|---|---|---|---|
| Replication | Replication | rep | rep | Replication initiator protein; or helicase; or primase; or regulator | RepB | TrfA | |
| Replication | Replication | Iterons | Iterons | Binding sites for replication initiator protein | |||
| Maintenance | Partitioning | parA | parA | Partitioning protein | SopA | IncC | |
| Maintenance | Partitioning | parB | parB | Centromere-binding protein | SopB | KorB | |
| Maintenance | Partitioning | parC | parC | Centromere, binding sites for ParB | |||
| Conjugal transfer | Conjugative DNA transfer | rlx | traI | Relaxase | TraI | TraI | |
| Conjugal transfer | Conjugative DNA transfer | oriT | nic | Origin region of transfer | |||
| Conjugal transfer | Conjugative DNA transfer | dtr1 | traY | Relaxosome auxiliary protein | TraY | TraH | |
| Conjugal transfer | Conjugative DNA transfer | dtr2 | traM | Relaxosome auxiliary protein | TraM | TraJ | |
| Conjugal transfer | Conjugative DNA transfer | dtr3 | dtr3 | Relaxosome auxiliary protein | TraK | ||
| Conjugal transfer | Conjugative DNA transfer | pri | pri | DNA primase | TraC | ||
| Conjugal transfer | Conjugative DNA transfer | cpl | traD/virD4 | Coupling protein | TraD | TraG | |
| Conjugal transfer | Exclusion | sfx | traT | Surface exclusion protein | TraT | ||
| Conjugal transfer | Exclusion | eex | traS | Entry exclusion protein | TraS | TrbK | |
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB1 | virB1/slt/mpfPN | P-type type IV secretion, transglycosylase/conjugative pilus component | TrbN | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB2 | virB2 | P-type type IV secretion, propilin/conjugative pilus component | TrbC | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB3 | virB3 | P-type type IV secretion, polytopic protein/inner membrane complex component | TrbD | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB4 | virB4 | P-type type IV secretion, ATPase/inner membrane complex component | TrbE | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB5 | virB5 | P-type type IV secretion, pilus-tip protein/conjugative pilus component | TrbF | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB6 | virB6 | P-type type IV secretion, polytopic protein/inner membrane complex component | TrbL | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB7 | virB7 | P-type type IV secretion, outer membrane-associated protein/outer membrane complex component | TrbH | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB8 | virB8 | P-type type IV secretion, bitopic protein/inner membrane complex component | TrbJ | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB9 | virB9 | P-type type IV secretion, outer membrane-associated protein/outer membrane complex component | TrbG | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB10 | virB10 | P-type type IV secretion, cell envelope-spanning subunit/outer membrane complex component | TrbI | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB11 | virB11 | P-type type IV secretion, ATPase/inner membrane complex component | TrbB | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB12 | mpfPM | P-type type IV secretion | TrbM | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB13 | pep | P-type type IV secretion, prepilin cyclization | TraF | ||
| Conjugal transfer | P-type type IV secretion System (TivB) | tivB14 | mpfPO | P-type type IV secretion | TrbO | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF1 | traA | virB2 | F-type type IV secretion, propilin/conjugative pilus component | TraA | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF2 | traF | F-type type IV secretion, pilus extension and retraction protein | TraF | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF3 | traG | virB6 | F-type type IV secretion, mating pair stabilization protein | TraG | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF4 | traH | F-type type IV secretion, pilus extension and retraction protein | TraH | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF5 | trbI | F-type type IV secretion, pilus extension and retraction protein | TrbI | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF6 | traN | F-type type IV secretion, mating pair stabilization protein | TraN | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF7 | traU | F-type type IV secretion, pilus extension and retraction protein | TraU | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF8 | traW | F-type type IV secretion, pilus extension and retraction protein | TraW | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF9 | trbC | F-type type IV secretion, pilus extension and retraction protein | TrbC | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF10 | traL | virB3 | F-type type IV secretion, polytopic protein/inner membrane complex component | TraL | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF11 | traE | virB5 | F-type type IV secretion, pilus-tip protein/conjugative pilus component | TraE | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF12 | traK | virB9 | F-type type IV secretion, outer membrane-associated protein/outer membrane complex component | TraK | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF13 | traB | virB10 | F-type type IV secretion, cell envelope-spanning subunit/outer membrane complex component | TraB | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF14 | traV | virB7 | F-type type IV secretion, outer membrane-associated protein/outer membrane complex component | TraV | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF15 | traC | virB4 | F-type type IV secretion, ATPase/inner membrane complex component | TraC | |
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF16 | traX | F-type type IV secretion, pilin acetylase | TraX | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF17 | orf169 | F-type type IV secretion, transglycosylase/conjugative pilus component | GeneX/Orf169 | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF18 | trbB | F-type type IV secretion, disulfide bond formation | TrbB | ||
| Conjugal transfer | F-type type IV secretion system (TivF) | tivF19 | trhP | F-type type IV secretion, transfer peptidase | TrhP in plasmid R27 |
Modified from a previous publication 2. These gene names and products can also be applied to the other kinds of mobile genetic elements. Accession numbers: plasmid F, NC_002483; RP4, BN_000925; R27, AF250878. Download all the proteins sequences
References
1. Shintani M, Sanchez ZK, Kimbara K. Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy. Front Microbiol 2015; 6: 242.
2. Thomas CM, Thomson NR, Cerdeno-Tarraga AM et al. Annotation of plasmid genes. Plasmid 2017; 91: 61-7.