School of Biological Sciences, Life Science Building, The University of Liverpool, PO Box 147, Liverpool L69 7ZB, UK1
Department of Medical Biochemistry2 and Department of Medical Microbiology3, Medical School, University of Cape Town, Observatory 7925, Cape Town, South Africa
Department of Biochemistry, University of Otago, Dunedin, New Zealand4
Institute of Freshwater Ecology, Windermere Laboratories, The Ferry House, Ambleside, Cumbria LA22 0LP, UK5
Author for correspondence: A. Mark Osborn. Tel: +44 1206 87 3763. Fax: +44 1206 87 2592. e-mail: osborn{at}essex.ac.uk
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ABSTRACT |
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Keywords: plasmid, incompatibility, evolution, replicon, pGSH500
The EMBL accession numbers for the sequences reported in this paper are AJ009980 (pGSH500 alpha replicon) and AJ009981 (pLV1402 alpha replicon).
a Present address: Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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INTRODUCTION |
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The replicons from plasmids of many of the Inc groups have been extensively characterized, in terms both of DNA and protein structure, and of the mechanism of their replication and replication control. The replicons from plasmids belonging to IncB, IncFII, IncFIC, IncI1, IncK, IncL/M and IncZ have been shown to share a common replication control mechanism, namely antisense control, and to share some homology between both DNA and protein sequences (Athanasopoulos et al., 1995 ; Hama et al., 1990
; Praszkier et al., 1991
; Saadi et al., 1987
). In the IncFII replicon of R1 an antisense RNA molecule (CopA) inhibits synthesis of the replication protein (RepA) by binding to the leader region of the repA mRNA (CopT). RepA synthesis is dependent upon translation of a short leader peptide (TapA) that is not expressed when CopA binds to CopT, thereby preventing translation of RepA and consequently preventing replication of the plasmid (Blomberg et al., 1992
). Replication of R1 is unidirectional and is initiated by the binding of RepA to the minimal replication origin (oriR) (Diaz & Staudenbauer, 1982
) with leading strand DNA synthesis starting about 380 bp downstream of oriR (Bernander et al., 1992
; Masai & Arai, 1989
).
A number of plasmids possess more than one replicon, e.g. the F plasmid (Lane & Gardner, 1979 ; Saadi et al., 1984
), the Streptococcus plasmid pAM
1 (Perkins & Youngman, 1983
) and the Bacillus plasmid pTB19 (Imanaka et al., 1984
). More recently, the moderately promiscuous plasmid pGSH500 from a South African clinical isolate of Klebsiella pneumoniae has been found to carry two replicons: alpha (cloned as pFDT100) and beta (cloned as pFDT200). The latter displays a mosaic character and is related to, but compatible with, both the IncN replicon of pCU1 and the ori-2 of F (da Silva Tatley & Steyn, 1993
). Two mercury-resistant environmental isolates, AH14 and AH16, from freshwater sediments of Windermere, Cumbria, UK, have subsequently been identified that both carry a plasmid (pLV1402 and pLV1403, respectively) with sequences homologous to both alpha and beta replicons. Analysis of partial sequences from the beta replicons of these plasmids showed them to be virtually identical (99·2% identity across 910 bp and 98·6% identity across 888 bp, respectively) to the beta replicon from pGSH500 (Osborn et al., 2000
).
In this paper we describe the nucleotide sequences of the alpha replicons from pGSH500 and pLV1402, their relationship to each other and their relationship to a group of replicons belonging to, or related to, those of the IncFII family. In addition, we describe the relationship of these IncFII-related replicons to those from other antisense-control-regulated replicons and discuss the mechanisms involved in the evolution of this broader family.
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METHODS |
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PCR amplification and determination of DNA sequence of IncFII-like sequences.
Primers were designed to consensus sequences in the copB and repA genes, and the oriR region of replicons from plasmids pFM82139 (Rodríguez-Peña et al., 1997 ), pYVe439-80 (Vanooteghem & Cornelis, 1990
), pSU316 (Lopez et al., 1989
), NR1 (Womble et al., 1985
), R100 and R1 (Ryder et al., 1982
). Template DNA was prepared as described previously (Osborn et al., 1993
). PCR products were amplified using Taq DNA polymerase (2·5 U) with the primer pairs: CA1 and RA1, RA2 and OR1, and CA1 and OR1. Reactions were performed for 30 cycles [94 °C for 1 min, 53 °C (CA1/RA1) or 54 °C (RA2/OR1 and CA1/OR1) for 1 min, 72 °C for 2 min] followed by 1 cycle of 72 °C for 10 min. Primer and dNTP concentrations were 30 pmol and 50 µM, respectively. PCR products were visualized following electrophoresis on 0·8% agarose TAE gels containing ethidium bromide (1 µg ml-1). PCR products were sequenced as described above using custom synthesized primers.
Computer analysis.
Sequences were analysed using the GCG set of programs (version 8, August 1994, Genetics Computer Group, Madison, Wisconsin, USA). The structures of the major hairpin loops of RNA molecules were predicted by the method of Zuker (1989) , with free energy values calculated according to the energy parameters of Walter et al. (1994)
. RepA protein sequences were aligned using CLUSTAL W (Thompson et al., 1994
). A neighbour-joining tree (Saitou & Nei, 1987
) was constructed showing bootstrap values (1000 replicates) (Felsenstein, 1985
).
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RESULTS |
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An extended family of RepA proteins from IncFII-related replicons
The predicted sequence of the 286 aa RepA protein from pFDT100 was most closely related to those from pLV1402 (86·4% identity), the Salmonella enteritidis plasmid pFM82139 (85·8% identity; Rodríguez-Peña et al., 1997 ) and the virulence plasmids pYVe439-80 from Yersinia enterocolitica (Vanooteghem & Cornelis, 1990
) and pCD1 (Hu et al., 1998
) from Yersinia pestis (82·5% identity). TFASTA searches using the pFDT100 RepA sequence identified further similarity with a number of RepA proteins from both IncFII replicons and those from more distantly related replicons, such as the IncZ replicon on pIE545 (Praszkier et al., 1991
) and the RepA proteins from a number of plasmids isolated from Buchnera sp. (Bracho et al., 1995
; van Ham et al., 1997
; Silva et al., 1998
). TFASTA searches using RepA proteins from these Buchnera plasmids further extended this family of RepA proteins to include those from replicons of the IncB, FIC, I1, K and L/M groups. A neighbour-joining tree (Saitou & Nei, 1987
) of RepA sequences was constructed (Fig. 2
) and revealed the presence of three distinct subgroups of RepA proteins from the extended family of RepFIIA antisense-control-regulated replicons (Saadi et al., 1987
). On this basis, we now propose that the extended RepFIIA family should describe and include the replicons of the I complex (IncI1, IncB/O, IncK and IncL/M).
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The site of leading strand synthesis in plasmid R1 has been located at a point about 380 bp downstream of the minimal oriR in in vivo (Bernander et al., 1992 ) and in vitro (Masai & Arai, 1989
) studies. Comparison of the pFDT100 sequence with that of R1 in this region reveals a single base pair difference between the proposed in vitro start sites, whilst the proposed in vivo start sites are identical (Fig. 1
, box C).
To further define the limit of the minimal alpha replicon of pGSH500, the subclones pFDT101 and pFDT102 (Fig. 1) were transformed into the E. coli polA1 mutant strain GW125a (Dorrington & Rawlings, 1989
). Replication from the DNA polymerase I-dependent ColE1 replicon from the vector regions of pFDT101 and pFDT102 is prevented in this strain. Both constructs were able to replicate in GW125a, showing that both subclones of pFDT100 still carry functional replicons. The SstI site that defines the 3' end of pFDT101 lies upstream of both the TerR sequences and the proposed start site for leading strand synthesis in pFDT100, showing that these regions are not required for replication. Similarly, sequences equivalent to the R1 and R100 initiation sites (Bernander et al., 1992
) are located outside of the minimal origin. Interestingly, in pFDT101, a region of vector sequence (3'-agCCCCgACaCcC-5') which lies 336 bp downstream of oriR bears some similarity to the pFDT100 start site (see Fig. 1
, box C). This region may function as the start site for leading strand synthesis in pFDT101, and perhaps significantly, the CCCC motif, which has been shown to be the in vivo start site in R1, is conserved in this region.
pGSH500 carries sequences homologous to the E. coli chromosome
FASTA searches of the region downstream of the alpha replicon revealed a region of 707 bp which showed 72·6% identity to a region on the E. coli chromosome (43·3'). Raha et al. (1993) had previously proposed that this region is non-coding in both the E. coli and Salmonella typhimurium chromosomes. However, translation of the pFDT100 DNA sequence in this region revealed two putative ORFs, ORF1 (138 aa) and ORF2 (171 aa). TFASTA searches revealed homology (80·3% identity across 132 aa) between ORF1 and the 217 aa gene product of the hypothetical E. coli gene yedG (Blattner et al., 1997
). Further homology to yedG was found upstream of ORF1, suggesting ORF1 is a truncated version of yedG. In the E. coli chromosome the initiation codon of yedG is found at a position that would lie upstream of the E. coli-homologous region of pLV1402.
Role of Chi sites in the formation of mosaic structures in antisense-control-regulated replicons
The replicons from the Inc groups B, FII, FIC, I1, K, L/M and Z encode related replication proteins (Fig. 2) and their replication is controlled by a common mechanism involving antisense control by a small RNA molecule. Comparison of the DNA sequences of replicons from these Inc groups reveals that a number of these replicons are mosaic in structure (Fig. 4
). Alignment of these replicons suggests that the IncFIC replicon consists of a rep gene that is closely related to those from the IncB, K and I1 replicons, whilst the upstream inc region containing copA is closely related to those from IncFII replicons. Conversely, the IncZ replicon is a mosaic structure consisting of a rep gene closely related to that of IncFII replicons, whilst its inc region is closely related to that of the IncB, K and I1 replicons. The breakpoint of these mosaic structures is found where tapA overlaps with the rep gene.
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DISCUSSION |
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It is clear from DNA and protein sequence comparisons that the pYVe439-80, pCD1 and pFM82139 replicons and the alpha replicons from pGSH500 and pLV1402 are related to IncFII plasmids and their close relatives, the IncFIII and IncFVI replicons. However, it is also apparent that they are outliers of the IncFII family and it is likely that many other replicons exist in plasmids from members of the Enterobacteriaceae that will be related to this plasmid family, yet similarly divergent. The divergence of the replicons from pYVe439-80 and pCD1, pFM82139 and pGSH500 may also be a consequence of these plasmids being found in hosts other than E. coli (i.e. species of Yersinia, Salmonella and Klebsiella, respectively) and may represent adaptation of such plasmids to their hosts.
Compatibility between R100 and pYVe439-80 results from sequence variation in the stem region of CopA (Vanooteghem & Cornelis, 1990 ). Similarly, compatibility between members of the extended RepFIIA family is also a consequence of sequence variation in both loop and upper stem sequences in CopA (Athanasopoulos et al., 1995
). Given the variation between stem sequences of CopA, from the other IncFII-related replicons shown in Fig. 3
, including those of the pGSH500 and pLV1402 alpha replicons and from pFM82139, it is likely that some or all of these replicons may be compatible with each other. The sequence CGCCAA that forms the proposed loop in CopA is conserved across the majority of replicons from the extended RepFIIA family. Furthermore, some conservation of this loop sequence is seen across a range of other antisense-controlled replicons. This is most notable in ColE2 replicons (CCGCCAA), but also to some extent in the RNA I molecules of ColE1 (CUACCAA) and pT181 (UGACCAA) (Hiraga et al., 1994
), suggesting that this sequence and consequently the replication control regions themselves may have a common evolutionary origin.
The mosaic nature of plasmids is broadly recognized, with a range of mobile genetic elements, e.g. transposons, integrons, gene cassettes and IS elements, commonly found inserted into the plasmid backbone (Hall & Vockler, 1987 ; Pansegrau et al., 1994
). In pGSH500, the presence of an E. coli-homologous region, immediately downstream of the alpha replicon in pGSH500, provides evidence for the acquisition of chromosomal regions by plasmids, possibly during recombination events.
The beta replicons of pGSH500 and pLV1402 are very closely related (99·2% identity at the DNA level; Osborn et al., 2000 ). Determination of plasmid copy number for pGSH500 and its derived minireplicons, alpha (pFDT100) and beta (pFDT200), indicates that replication of pGSH500 proceeds from the beta replicon (da Silva Tatley & Steyn, 1993
). Given the divergence between the alpha replicons of pGSH500 and pLV1402, it is attractive to propose that these replicons have been free to diverge, perhaps during recombination events with other IncFII-related replicons. Such a hypothesis is in agreement with the model of Sykora (1992)
for non-selective divergence of plasmid replicons in co-integrate (i.e. multi-replicon) plasmids, where one replicon is strongly conserved due to selective pressure (i.e. the beta replicon), whilst the second replicon (the alpha replicon) is free to diverge.
Comparison of the IncFIC replicon P307 with those of the IncFII replicons of R1 and R100 has shown the presence of a number of homologous and non-homologous regions, which has been proposed to result from recombination events (Saadi et al., 1987 ). Our comparison of the DNA sequences of members of the extended RepFIIA family of antisense-controlled replicons has revealed the presence of mosaic replicons. The presence of Chi-like sequences at the junction of these mosaics suggests that Chi-related recombination events have played an important role in the evolution of this replicon family. Smith et al. (1981)
have demonstrated that a number of single base pair mutations within the Chi sequence can abolish its activity. However, three sequences in wild-type
phage that differ at the first (G to A), second (C to T) and fourth (G to A) positions have partial Chi activity (6, 11 and 38%, respectively; Cheng & Smith, 1984
). The imperfect Chi sequences at the start of the repA genes may similarly have partial Chi activity and have been involved in recombination events between replicons. Alternatively, the Chi-like sequences seen in these replicons may have since diverged from the archetypal E. coli Chi sequence. The presence of Chi-related sequences in replicons from other Inc groups related to IncFII, e.g. IncFIII and IncFVI, would suggest that there is great potential for the evolution of new replicons by Chi-mediated recombination events. Chi-related sequences have been similarly implicated in recombination events in the formation of mosaic RepFIB-related repA genes in plasmids from natural populations of E. coli (Boyd et al., 1996
). Mosaic regions have also been identified in the ColE2 family of antisense-control-regulated replicons, with one breakpoint between segments again found between the inc and rep regions (Hiraga et al., 1994
). However, no Chi sites could be identified in this region, excluding the possibility of Chi-mediated homologous recombination in mosaic formation for the ColE2 replicons.
The existence of mosaic replicons causes additional complications for the classification of bacterial plasmids and for attempts to assess the evolutionary relationships between plasmids and their replicons. Plasmids are often classified on the basis of their incompatibility relationships and a series of replicon (rep) probes have been developed for a number of incompatibility groups to facilitate the classification of new plasmids by hybridization analysis. However, the individual rep probes of the RepFIIA family of antisense-controlled replicons show considerable cross-hybridization (Couturier et al., 1988 ), which limits their effective use in demonstrating membership of this broad family. Classification of plasmids of this group is further complicated as incompatibility relationships between these replicons can result from single base pair changes. Consequently, any attempt to characterize new members of this family should be made with these considerations in mind. Moreover, descriptions of replicon evolution should in some cases consider inc and rep regions as separate evolutionary units. The problems of plasmid classification are further complicated by the occurrence of multi-replicon elements where replication may proceed from different replicons on the plasmid in different hosts. We suggest that replicons from such plasmids are themselves treated and classified as separately evolving systems.
In conclusion, comparative analysis of members of the extended RepFIIA family has provided evidence supporting the roles both of non-selective divergence in multi-replicon plasmids and of Chi-mediated homologous recombination in the evolution of plasmid replicons. Finally, this work underlines the considerable value of such systematic analyses of the wealth of hitherto under-utilized sequence data that is available to further our understanding of the evolution of bacterial plasmids.
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ACKNOWLEDGEMENTS |
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Received 15 March 2000;
revised 13 June 2000;
accepted 19 June 2000.