Comparative biology of IncQ and IncQ-like plasmids

Abstract

Plasmids belonging to Escherichia coli incompatibility group Q are relatively small (approximately 5 to 15 kb) and able to replicate in a remarkably broad range of bacterial hosts. These include gram-positive bacteria such as Brevibacterium and Mycobacterium and gram-negative bacteria such as Agrobacterium, Desulfovibrio, and cyanobacteria. These plasmids are mobilized by several self-transmissible plasmids into an even more diverse range of organisms including yeasts, plants, and animal cells. IncQ plasmids are thus highly promiscuous. Recently, several IncQ-like plasmids have been isolated from bacteria found in environments as diverse as piggery manure and highly acidic commercial mineral biooxidation plants. These IncQ-like plasmids belong to different incompatibility groups but have similar broad-host-range replicons and mobilization properties to the IncQ plasmids. This review covers the ecology, classification, and evolution of IncQ and IncQ-like plasmids.

FIG. 1

Genetic maps of plasmids of the IncQ family showing the conserved replicon structure, the regions encoding the mobilization genes, and, where present, the accessory genes. Plasmid pDN1 is represented by a line since its gene map is identical to the backbone region of pIE1107. The genetic map of pTC-F14 is incomplete since only a partial nucleotide sequence is available. Genes and structural features: aph(3′)-I, kanamycin and neomycin aminoglycoside phosphotransferase; cac, control of repA and repC regulator; catIII, chloramphenicol acetyltransferase; grx, glutaredoxin-like gene; linB-like, linB-like lincosamide nucleotyltransferase; merR-like, merR-like regulator gene; mobA, mobB, mobC, mobD, and mobE, mobilization genes; oriV, origin of vegetative replication; orf1, orf4, orf29, orf43, and orfE, open reading frames of unknown function; oriT, origin of transfer; pasA, pasB, and pasC, plasmid addiction system genes; repA, repB, and repC, replication genes; res, site of cointegrate resolution by transposon resolvase; strA and strB, streptomycin aminoglycoside phosphotransferase; sulII, sulfonamide-resistant dihydropteroate synthase; tnpA, transposase; tnpR, resolvase. Genes which have been inactivated by deletions are indicated by asterisks.

FIG. 2

Phylogenetic relationships between Rep proteins of the IncQ plasmid family. Percentages represent percent amino acid sequence identities.

FIG. 3

Schematic diagram of the structural features within the active oriV and nonactive oriV-like regions of IncQ-like plasmids. oriVa and oriVb indicates duplicate oriV regions in the same plasmid. oriVa indicates the nonfunctional but incompatibility active oriV-like region. Arrows pointing in the same direction represent directly repeated sequences and arrows pointing toward each other inverted repeat sequences capable of forming stem-loop structures. Numbers above the arrows indicate the number of bases conserved in imperfectly conserved iterons, and #11/20 indicates a truncated 11bp iteron. A+T, on A+T-rich region; C+G, a G+C-rich region; ssiA and ssiB; single strand initiation sites. DNA synthesis proceeds in a single direction toward the right-hand side from ssiA and toward the left from ssiB. The sequence to the left of the highly conserved 14/15-bp region is more highly conserved than that to to the right.

FIG. 4

Nucleotide sequence alignment of the highly conserved region within the functional oriV of the IncQ-like plasmids. Direct repeats are shown by arrows above the sequence, G+C and A+T regions as shown by solid lines, and the most highly conserved 15-bp region is shown by a broken line above the sequence. Sequences of plasmids pDN1 and pIE1115 have been omitted because they are almost identical to that of pIE1107 within the part of the oriV region shown. Plasmids pDN1 and pIE1115 have 1- and 2-bp mismatches, respectively, compared to pIE1107.

FIG. 5

Phylogenetic relationship between the MobA and MobC proteins of the IncQ-1-type plasmids and their comparison with related relaxases of mobilizable and self-transmissible plasmids. Since in the IncQ-1 plasmids the MobA proteins exist as a MobA-RepB fusion, only the N-terminal 400 aa was considered for comparison with other MobA-related proteins. The protein equivalent to MobC in pTF1 is called MobS. Percentages are percent amino acid sequence identities. GenBank accession numbers are as follows: pMRC01, g3582197; pIP501, L39769; pGO1, g1245474; pSK41, g3676420; pNGR23, P55418; pTi-Sakura, g6498282; pTi-A6NC, g2499023; pTi-C58, g2499022; pTF1, g127224; pIE1107, Z74787; pIE1115, AJ293027; pDN1, Y19120; pIE1130, AJ271879; RSF1010, M28829; pSC101, P14492; pAB6, g4884735.

FIG. 6

Comparison of the regions involved in the mobilization of plasmids pRA2, pTF-FC2, and the IncPα plasmid RP4/RK2. Broken lines linking plasmids show the regions with amino acid sequence similarity.

FIG. 7

Two families of oriT nick regions to which the IncQ-family plasmids belong. Triangles show the positions of strand cleavage in plasmids for which this has been determined.