Plasmids of carotenoid-producing strains of Paracoccus spp.

At the initial stage of this study we analyzed the plasmid content of 22 strains representing 20 Paracoccus spp. (listed in Methods section). Plasmid screening revealed that the majority of the tested strains contained megaplasmids (above 100 kb) (data not shown). Only four of the strains (P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22 – all able to produce beta-carotenoid pigments) contained numerous smaller replicons ranging in size from approx. 2.5 kb to 85 kb.

To analyze plasmid diversity in these strains we obtained the nucleotide sequences of 14 randomly selected replicons (listed in Table 1): (i) 5 pAES plasmids of P. aestuarii DSM 19484, (ii) 2 pHAE plasmids of P. haeundaensis LMG P-21903, (iii) 4 pMARC plasmids of P. marcusii DSM 11574 and (iv) 3 pMOS plasmids of P. marcusii OS22.

The results of the overall characterization of the plasmids are presented in Table 1. A summary of the distinguished open reading frames (ORFs), including their position, the size of the putative proteins they encode and their closest homologs, is presented in Table S1 in the supplemental material.

Comparative bioinformatic analysis was used to distinguish the plasmid backbones, composed of different combinations of genetic modules responsible for plasmid replication (REP), stabilization (toxin-antitoxin – TA; partitioning – PAR) and mobilization for conjugal transfer (MOB), and accessory genetic information, which may potentially influence the phenotype of the host (Figure 1). Detailed characterization of the predicted modules is presented below.

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Figure 1. The genetic organization of the Paracoccus spp. plasmids analyzed in this study.

Arrows indicate the transcriptional orientation of the ORF2. The color-coded keys show the species and strain of origin of each plasmid (circles) and the likely plasmid maintenance/transfer processes in which the genes are involved (squares). Plasmid islets (PI) of lower than average G+C content, insertion sequences (IS) and restriction and modification systems (R-M) are indicated by the use of different boxes (see figure). Shaded areas connect genes of plasmids that encode orthologous proteins. For comparative analysis, two other related plasmids of Paracoccus spp. have been included: pAMI3 of P. aminophilus JCM 7686 [10] and pWKS1 of P. pantotrophus DSM 11072 [12].

https://doi.org/10.1371/journal.pone.0080258.g001

Replication modules

Replication systems of the vast majority of plasmids residing in gram-negative bacteria consist of two elements: (i) a gene encoding a Rep protein, which initiates DNA replication, and (ii) the cis-required origin (oriV; equivalent to chromosomal oriC) where replication begins. Most Rep proteins are highly conserved and they can be grouped into several families on the basis of amino acid (aa) sequence similarities. In contrast, oriVs are more divergent and they are usually placed in close proximity to the rep genes. In many cases, the location of the oriVs can be predicted in silico by the presence of (i) directly repeated sequences (including iterons), which constitute the Rep protein binding sites (iterons, being key elements in the control of replication initiation, determine plasmid incompatibility [13]), (ii) A+T-rich DNA regions, where strand opening and assembly of host replication initiation factors occurs, and (iii) conserved DNA boxes representing sites of interaction with chromosomally-encoded proteins, e.g. DnaA or integration host factor (IHF) [14].

Comparative sequence analysis revealed that the analyzed plasmids of Paracoccus spp. contain different types of replication systems. Based on aa sequence similarities of the predicted Rep proteins, the presence of conserved motifs and the oriV structures, the REP modules could be classified into four groups, some representing novel replication system types. The genetic structure of these REP modules is illustrated in Figure 2 and the nucleotide sequences of the predicted oriVs are presented in Additional file 2: Figure S1.

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Figure 2. Schematic structure of the REP modules analyzed in this study.

The color-coded keys show the species and strain of origin of each plasmid (circles) and identified direct repeats (DRs), inverted repeats (IRs) as well as predicted DnaA and IHF binding sites (mixed shapes). The sequences of the iteron-like DRs are presented next to the relevant diagrams with a consensus sequence shown for DRs of plasmids with related REP modules. Blue arrows indicate the rep genes and their transcriptional orientation. Specific motifs identified within the aa sequences of the Rep proteins are indicated by colored rounded bars. A+T and G+C indicate DNA regions of lower or higher than average G+C content, respectively. The components of the REP modules are not shown to scale.

https://doi.org/10.1371/journal.pone.0080258.g002

REP modules of pAES2, pAES3, pHAE1, pHAE2, pMARC1, pMARC4 and pMOS7

The REP modules of plasmids pAES2, pAES3 (P. aestuarii DSM 19484), pHAE1, pHAE2 (P. haeundaensis LMG P-21903), pMARC1, pMARC4 (P. marcusii DSM 11574) and pMOS7 (P. marcusii OS22) encode replication initiation proteins (Rep) of the Rep_3 superfamily (PFAM: PF01051), which show significant level of aa sequence identity with RepB-type proteins from Rhodobacterales, whose phylogenetic analysis was presented by Petersen et al. [15]. Comparative analysis of the sequences and structures of these modules identified three distinct subgroups, present in the following plasmids: (i) pAES2, pAES3, pHAE1, pMARC4, (ii) pMARC1, pMOS7 and (iii) pHAE2.

REP modules of pAES1, pAES7, pMARC3 and pMOS2

Another group of REP modules (present in plasmids pAES1, pAES7, pMARC3 and pMOS2) encode replication initiation proteins containing predicted helix-turn-helix (HTH) domains (HTH_36) conserved in many transcription regulators (PFAM: 13730). Based on aa sequence comparisons, these REP modules were divided into two subclasses comprising (i) pAES7, pMARC3, pMOS2, and (ii) pAES1.

REP modules of plasmids pAES4 and pMARC2

The highly homologous REP modules of pAES4 and pMARC2 do not possess iteron-like DRs. Upstream of the rep genes they contain only long inverted repeats, covering the predicted rep promoters (Figure 2 and Figure S1). The IRs of pAES4 form a long (46 bp) imperfect (3 mismatches) palindromic sequence, while those of pMARC2 (18 bp) are identical and are separated by a 4-bp spacer sequence (Figure S1).

The Rep proteins of these plasmids show 92% aa sequence identity. Both contain a predicted HTH motif typical of transcriptional regulators of the MarR family. Homologous Rep proteins are not common in other bacteria. Only four proteins with significant aa sequence identity (47-55%) (annotated as hypothetical proteins) were identified in the NCBI databases – all from strains belonging to the Alphaproteobacteria. These are encoded by (i-ii) plasmids pACMV6 and pACMV8 of Acidiphilium multivorum AIU301 (accession nos YP_004277313 and YP_004277317, respectively), (iii) plasmid pAPA01-060 of Acetobacter pasteurianus IFO 3283-01 (accession no YP_003189587) and (iv) Rhodospirillum photometricum DSM 122 (sequence contig; accession no YP_005418451). All the aforementioned proteins are annotated as hypothetical proteins and they do not show sequence similarity to any other plasmid encoded Rep proteins. Therefore, the results of the comparative analysis strongly suggest that the Rep proteins of pAES4 and pMARC2 may be considered as the archetypes of a novel group of plasmid replication initiators.

REP module of pMOS6

The REP module of pMOS6 encodes a predicted Rep protein (Rep_pMOS6), which is related to proteins encoded by strains belonging to the Alpha-, Beta- and Gammaproteobacteria as well as the CFB group of bacteria (genus Bacteroides). The majority of these proteins are annotated as conserved hypothetical proteins of unknown function. However, more detailed analysis revealed that all of them contain domains conserved in the plasmid replication proteins of the RepL family from Firmicutes (PFAM: PF05732). Closely related Rep protein sequences were identified within a few plasmids, i.e. pTINT02 of Thiomonas intermedia K12, pML of Bartonella schoenbuchensis m07a (accession no ENN90461) and pPsv48C of Pseudomonas savastanoi, and some chromosomes, e.g. Bartonella vinsonii (accession no YP_007462201). Interestingly, besides Rep_pMOS6 homologs, the three aforementioned plasmids encode other proteins that may be involved in replication initiation (RepC in pML and a replication protein with a primase domain in pTINT02 and pPsv48C). Plasmid pMOS6 encodes only a single Rep protein, which is sufficient for initiation of replication, as proved by the construction of a pMOS6 minimal replicon (data not shown).

The oriV-containing region of pMOS6, identified upstream of the rep gene, contains a sequence (5’-gAACcTCTGTCTTG-3’) with similarity to the IHF-box distinguished in Paracoccus methylutens DM12 plasmid pMTH4 [19] and two identical 18-bp iteron-like repeated sequences, separated by 3 bp (Figure 2 and Figure S1).

Toxin-antitoxin modules

Toxin-antitoxin modules confer plasmid stabilization in a population by eliminating plasmid-less cells at the post segregational level. Such genetic modules are composed of two elements: (i) a toxin protein that binds a specific cellular target and (ii) an antitoxin (protein or antisense RNA), which counteracts the toxin. BLAST searches revealed that seven of the analyzed plasmids (pAES4, pAES7, pMARC1, pMARC3, pMARC4, pMOS6 and pMOS7) contain putative toxin-antitoxin modules representing five TA groups: (i) relBE/parDE, (ii) tad-ata, (iii) higBA, (iv) mazEF and (v) toxBA.

Plasmids pAES3 and pAES7 (P. aestuarii DSM 19484) contain highly related TA modules (94% nucleotide sequence identity) of the RelBE/parDE superfamily [20], composed of two short overlapping ORFs (4 bp overlap). The first ORFs of the predicted operons (orf6 of pAES3 and orf3 of pAES7) encode putative proteins with significant similarity to a number of plasmid-encoded antitoxins, classified within a large family of transcriptional regulators containing a CopG/Arc/MetJ DNA-binding domain (cluster of orthologous groups COG3609). The highest similarity was to the TA module antitoxin of plasmid pAMI3 of Paracoccus aminophilus JCM 7686 [10] (78 and 79% aa sequence identity, respectively). The downstream ORFs (orf5 of pAES3 and orf4 of pAES7) encode putative proteins with substantial homology to toxins of the ParE family (COG3668), with the highest similarity to the toxin of the aforementioned pAMI3 TA module [10] (72 and 75% aa sequence identity, respectively).

Interestingly, plasmid pAES7 also carries another TA module (orf14-orf15) representing the tad-ata group, whose archetype was identified in plasmid pAMI2 of Paracoccus aminophilus JCM 7686 [21]. A related module is also present within plasmid pMOS6 of P. marcusii OS22 (orf11-orf12) (Figure 1). The Tad-related toxins are encoded by the first genes of the predicted TA operons. They belong to a large family of proteins (COG4679), exhibiting significant sequence similarity to the RelE toxins (relBE-type TA modules), which act as mRNA-cleaving RNAses [22]. Comparative sequence analysis of the antitoxins of pAES7 and pMOS6 (encoded downstream of the tad-homologs) revealed that these proteins belong to COG5606 and COG1396, respectively, and they contain a HTH motif typical of the Xre/Cro family.

An analogous genetic organization (toxin gene upstream of the antitoxin gene) was also observed in the TA system of pAES4 (P. aestuarii DSM 19484), classified within the higBA family [23]. This TA module is composed of two ORFs (orf8 and orf9), separated by a 10-bp intergenic region, encoding proteins with the highest level of aa identity to the killer chromosomal protein of Rhodopseudomonas palustris CGA009 (accession no NP_947628) (68%) and the antitoxin of the Xre family encoded by another strain of R. palustris – BisB18 (accession no YP_534586) (70%), respectively.

Plasmid pMARC4 of P. marcusii DSM 11574 carries two overlapping (4 bp) ORFs: orf3 and orf4. The latter encodes a predicted toxin with substantial similarity (63% aa sequence identity) to the PemK-like protein of Chlorobium phaeobacteroides BS1 (mazEF family of TA systems). Interestingly, the orf3-encoded protein displays 65% identity to a hypothetical protein of plasmid pDSHI01 of Dinoroseobacter shibae DFL 12, and is quite different from typical MazE-type antitoxins. BLAST searches revealed that gene pairs homologous to orf3-orf4 are conserved in many bacterial genomes (mainly in plasmids). Our analysis suggests that the TA hybrid module of pMARC4 might be considered the prototype of a new subgroup within the MazEF TA family.

Plasmids pMARC1, pMARC3 (P. marcusii DSM 11574) and pMOS7 (P. marcusii OS22) contain related pairs of genes (orf5-orf6, orf8-orf9, orf6-orf7, respectively), which represent a novel group of TA modules, that we designate the toxAB family (Figure 1). Homologous loci were distinguished by Leplae et al. [24], but none of them were analyzed at the molecular level. The first genes of the predicted TA operons encode DUF497 proteins (predicted toxin; ToxB), while the genes in the second position were classified into the COG3680 (pMOS7 and pMARC1) or COG3514 (pMARC3) orthologous groups (putative antitoxins; ToxA). The predicted secondary structure of the COG3680 and COG3514 antitoxins is highly conserved. Proteins of both groups contain, in their C-terminal regions, a RHH_1 domain related to a domain of the CcdA antitoxin of the ccdAB TA system [25]. The most closely related TA module was identified within Desulfomicrobium baculatum DSM 4028 (accession nos YP_003157266 and YP_003157267).

Restriction-modification module

One of the analyzed plasmids (pAES2 of P. aestuarii DSM 19484) contains a putative type II restriction-modification (R-M) system (Figure 1). Similarly to TA, such systems may increase the stability of plasmids by killing plasmid-less cells [26]. The RM module of pAES2 is composed of overlapping orf3 and orf4 (1-bp overlap). The orf3 protein shares substantial similarity with a large number of proteins annotated as m5C methyltransferases (MTases) (PFAM: PF00145). The predicted pAES2 MTase contains six (I, IV, VI, VIII, IX and X) of the ten amino acid sequence motifs (placed in conserved order) characteristic of m5C MTases, including an invariant Pro-Cys dipeptide in the catalytic motif IV [27] (data not shown). The orf4-encoded protein is similar to restriction endonuclease NgoMIV, which recognizes the sequence 5’-GCCGGC-3’. The most closely related R-M module was identified in plasmid pAOVO02 of Acidovorax sp. JS42 (accession nos YP_974088 and YP_974088) with 89% and 93% aa sequence identity of the MTases and endonucleases, respectively.

Partitioning module

Partitioning systems (PAR), which allow proper segregation of plasmid copies upon cell division, are components of the vast majority of large low copy number plasmids. Only one of the plasmids analyzed in this study (pMARC3 of P. marcusii DSM 11574; 10,672 bp) contains a predicted PAR module of typical structure, composed of two par genes (orf2 and orf3) and a centromere-like partitioning site (Figure 1).

BLAST searches revealed that the deduced aa sequence of Orf2 is similar over its entire length to a large number of partitioning ATPases (ParA), with highest identity (44%) to the putative ParA protein of plasmid pMRAD03 of the alphaproteobacterium Methylobacterium radiotolerans JCM 2831 (accession no YP_001776801).

Detailed analysis of Orf2/ParA revealed the presence of a sequence motif [KGGSGKS] matching the canonical sequence [KGG(T/N/V)GKT] of a deviant Walker A motif, which is characteristic for ATPases of type I partitioning modules [28]. The orf3-encoded polypeptide of pMARC3 (putative ParB) displays only slight homology to a hypothetical protein of Bacillus sp. 2_A_57_CT2 (accession no ZP_08007698) (30% aa sequence identity), whose gene (as in pMARC3) is associated with that encoding a partitioning ATPase.

The putative centromere-like site (parS) of the pMARC3 PAR module is located within the promoter region of parA, which consists of three non-identical 13-bp-long repeated sequences.

Taking into account its structure (i.e. the presence of a small parB gene and the location of the parS site) and the results of detailed comparative analyses, the predicted PAR module of pMARC3 was classified into the Ib group of partitioning systems [28].

Modules for mobilization for conjugal transfer

Many plasmids are capable of horizontal transfer by conjugation. According to their transfer ability, they may be grouped into two categories comprising self-transmissible and mobilizable replicons. The latter grouping contains MOB DNA regions, which carry genetic information essential for the processing of conjugative DNA. The MOBs are usually composed of two elements: an origin of transfer (oriT) and a gene coding for relaxase, which nicks DNA at the oriT sites. The transfer of mobilizable plasmids requires a membrane-associated mating pair formation complex, which may be provided by self-transmissible plasmids or integrative and conjugative elements (ICE) co-residing in the cell [29].

None of the 14 Paracoccus spp. plasmids was a self-transmissible replicon, but nine of them contained predicted MOB modules (Figure 1). Based on comparative analysis of the relaxase aa sequences, these proteins (and the MOB modules encoding them) were classified within the Mob_Q, Mob_P or Mob_V families [30].

Additional genetic load

Besides the REP, TA, PAR, R-M and MOB modules, the analyzed plasmids contain diverse accessory genetic information, including two insertion sequences (ISs) in pAES7 and pMARC3 (Figure 1). Plasmid pAES7 carries the functional element ISPaes2 (IS427 group, IS5 family), which was identified previously by its transposition into the trap plasmid pMAT1 [5]. ISPaes2 is bordered by dinucleotide (TA) direct repeats (DR), which represent the duplicated target site of transposition.

The IS of pMARC3 is a novel element that we have designated as ISPmar4 (1343 bp). It contains 12-bp-long imperfect terminal IR sequences (5'-ATGGc/tCCGCCCC-3') and carries a single ORF (orf5), encoding a predicted protein with similarity to transposases of the IS110 family (IS1111 group). ISPmar4 is not flanked by DRs in the pMARC3 genome, which is a typical feature of members of the IS110 family.

An intriguing feature of all but one of the plasmids (pMARC3) is the presence of related ORFs (orf2), placed downstream of the predicted rep genes (Figure 1). These ORFs encode putative proteins (Orf2) with low, but significant similarity [at least 30% aa identity (E value 1e-04)] to entry exclusion-like proteins 1 (Exc1). All of these predicted proteins contain a conserved helix-turn-helix domain (HTH_17) in their N-terminal region (Figure S3 in the supplemental material).

Entry exclusion (EEX) systems prevent the entry of exogenous plasmids into a host cell carrying an identical or related EEX system. It is thought that EEX is a specific feature of all conjugative plasmids [32]. The exclusion phenotype has been observed for mobilizable plasmid ColE1, whose exc1 and exc2 genes were predicted to encode the EEX system [33]. Although subsequent studies [34] excluded the possibility of exc1 and exc2 involvement in plasmid exclusion, homologous genes are still being annotated and described in the literature as entry exclusion components, e.g. [35].

The examined plasmids of Paracoccus spp. were found to contain only one of these genes – exc1. This is not a unique feature, since related “orphan” exc1-like genes have been identified in several other plasmids, including pKlebB-K17/80 of Klebsiella pneumoniae [36] and pMWHK1 of Pedobacter cryoconitis BG5 [35]. The conserved position of this gene, accompanying different REP modules, strongly suggests that the Exc1 proteins may play an important role in the biology of these plasmids. However, their specific function has yet to be determined.

Downstream of the exc1 genes in several plasmids (pAES3, pAES4, pHAE1, pHAE2, pMARC1, pMARC2, pMOS2 and pMOS7), putative plasmids islets (PI) were identified, i.e. horizontally-acquired DNA regions of lower than average GC content (Figure 1). The ORFs encoded within these PI (listed in Table 2) show similarity to genes (mainly of unknown function) conserved in the chromosomes of many bacteria.

The significant role of PI in shaping plasmid genomes was revealed by comparative analysis of the related plasmids pMARC1 and pMOS7 of P. marcusii (strains DSM 11574 and OS22, respectively). These plasmids have highly conserved backbones (REP and TA modules showing approx. 86% nucleotide sequence identity), but they contain different PIs (Figure 3). Plasmids pMARC2 and pHAE4 represent an analogous pair of related replicons containing different PIs (Figure 1). The PI of pMOS7 carries two ORFs, including orf4 encoding a predicted retron-type reverse transcriptase, while that of pMARC1 is composed of orf3, encoding a putative DUF805 transmembrane protein and orf4, encoding a protein containing a conserved domain of RelA and SpoT proteins (both proteins are involved in the metabolism of the regulatory compound guanosine 3',5'-bis-pyrophosphate, ppGpp, which plays a crucial role in the bacterial stringent response).

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Figure 3. Comparison of the structure and G+C sequence profile of P. marcusii plasmids pMARC1 and pMOS7.

Arrows show the transcriptional orientation of the genes and the color code indicates their predicted functions (as shown in Figure 1). Shaded areas connect homologous DNA regions. The PI regions (with indicated G+C content) are marked by yellow rectangles and dashed lines. The plot shows the G+C content of pMARC1 and pMOS7 sequences (the average values are given to the right).

https://doi.org/10.1371/journal.pone.0080258.g003

The PI of pMARC2, another plasmid of P. marcusii (strain DSM 11574), contains a pair of overlapping genes (1-bp overlap), orf3 and orf4, conserved (in synteny) in several bacterial chromosomes. The first gene of this predicted module encodes a putative ATPase with significant similarity to the SMC proteins, which play an important role in chromosome condensation, packaging, partitioning and DNA repair [37]. The downstream orf4 encodes a hypothetical protein of unknown function. The closest homologs of orf3 and orf4 were identified within the chromosome of Pedobacter heparinus DSM 2366 (accession nos YP_003093112 and YP_003093113, respectively).

The largest of the plasmids analyzed in this study, pMARC4, does not contain a PI, but it does encode proteins possibly involved in carbohydrate metabolism. The predicted proteins show significant similarity to (i-ii) acyltransferases (Orf5 and Orf7), (iii) polysaccharide biosynthesis protein (Orf10), (iv) phosphoribosyltransferase (Orf11), (v) dolichyl-phosphate mannose synthase (Orf12), and (vi) glycosyltransferase (Orf13). Two other ORFs (orf6 and orf14) encode a putative undecaprenyl-diphosphate phosphatase and UDP-glucose 6-dehydrogenase (EC 1.1.1.22), respectively. It has been demonstrated that Orf6 homologs are involved in the synthesis and recycling of undecaprenyl phosphate (Und-P), a lipid carrier of glycan biosynthetic intermediates of carbohydrate polymers exported to the bacterial cell envelope [38], while Orf14 relatives are responsible for the NAD-dependent oxidation of UDP-glucose to UDP-glucuronic acid, a key component in the biosynthesis of gellan (extracellular polysaccharide of biotechnological value) [39]. Based on these similarities, it is likely that the pMARC4-encoded gene cluster may be involved in the biosynthesis of envelope-associated polysaccharides.

Another plasmid, pMOS6 of P. marcusii OS22, besides several ORFs of unknown function, carries orf4 encoding a putative zinc-dependent alcohol dehydrogenase (ADH_ZINC), containing a conserved signature sequence: G-H-E-x(2)-G-x(5)-[GA]-x(2)-[IVSAC] (where x indicates any amino acid; H is a zinc ligand) [40]. Related enzymes catalyze the oxidation of alcohols, with the concomitant reduction of nicotinamide adenine dinucleotide (NAD) [41]. The most similar alcohol dehydrogenase (99% aa sequence identity) is encoded by Methylobacterium chloromethanicum CM4 (accession no YP_002424246).

Distribution of related plasmids in genus Paracoccus

We analyzed the distribution of the replication modules of the pAES, pHAE, pMARC and pMOS plasmids in the genomes of 20 strains representing 19 species of Paracoccus spp. To do this, a specific DNA probe for each plasmid (rep gene fragment amplified by PCR and DIG-labeled) was used in dot blot hybridization to screen total DNAs isolated from the paracoccal strains.

This analysis revealed that the majority of the analyzed plasmids occur exclusively in the multireplicon carotenoid-producing species (LMG P-21093, OS22, DSM 11574, DSM 19484), although none of the replicons was present in all four strains (Figure 4). The strains P. haeundaensis LMG P-21093 and P. aestuarii DSM 19484 displayed an almost identical hybridization pattern (7 common replicons), which was also similar to that of P. marcusii OS22 (4 common plasmids). In contrast, the hybridization pattern of two strains of P. marcusii (OS22 and DSM 11574) was significantly different, indicating the presence of four strain-specific replicons (pMARC2, pMARC3, pMARC4 and pMOS2), which were unique among Paracoccus spp. (Figure 4).

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Figure 4. Distribution of the REP modules analyzed in this study in the Paracoccus spp. genomes.

A specific DNA probe (fragment of a rep gene amplified by PCR and DIG-labeled) was prepared for each analyzed REP module and used in dot blot hybridization analysis with total DNA isolated from 20 strains of Paracoccus spp. The results are presented as a matrix. The relatedness of the tested Paracoccus strains is shown beneath by a phylogenetic tree based on their 16S rDNA sequences. The tree was constructed by the neighbor-joining algorithm with Kimura corrected distances. The statistical support for the internal nodes was determined by 1000 bootstrap replicates and values of >50% are shown. The Paracoccus strains from which the plasmids were isolated are denoted by red text.

https://doi.org/10.1371/journal.pone.0080258.g004

A few related plasmids were also detected in other species, located on distant branches of the phylogenetic tree, which points to the role of horizontal gene transfer in the dissemination of these replicons. The most ubiquitous replicons were plasmids related to pAES4, which were detected in 6 strains, including P. zeaxanthinifaciens ATCC 21588T, P. thiocyanatus JCM 20756 and P. yeei CCUG 46822 (Figure 4).

Host range of the Paracoccus spp. plasmids

The host range of the paracoccal plasmids in several bacterial strains belonging to the Alpha-, Beta- or Gammaproteobacteria was examined. For this analysis we employed REP regions representing different groups of plasmids (Figure 2): (i-ii) pAES1 and pMOS7, (iii) pAES7, (iv) pMARC2 and (v) pMOS6. The REPs were cloned within the multiple cloning site (MCS) of the mobilizable vector pABW1 (Km^r, oriV ColE1, oriT RK2) (see Methods for details) and the resulting plasmids were introduced into 9 strains of Alphaproteobacteria (Rif^r derivatives of Paracoccus spp. strains P. alcaliphilus JCM 7364, P. aminophilus JCM 7686, P. aminovorans JCM 7685, P. kondratievae NCIMB 13773, P. pantotrophus DSM 11072, P. versutus UW225, as well as Rhizobium etli CE3 and Ochrobactrum sp. LM19R, one strain of Betaproteobacteria (Alcaligenes sp. LM16R) and two strains of Gammaproteobacteria (Pseudomonas sp. LM7R and E. coli BR825

The constructed shuttle plasmids contained an E. coli-specific pMB1 (ColE1-type) replication system, which is functional in neither Alpha- and Betaproteobacteria nor in Pseudomonas sp. LM7R and E. coli BR825 (Gammaproteobacteria; the BR825 strain carries a mutation within the DNA polymerase I gene that blocks pMB1 replication). Therefore, the functions required for replication and maintenance of these plasmids in the tested hosts have to be provided by the paracoccal REP modules. It is important to mention that the Paracoccus spp. strains, in which the plasmids were tested for their ability to replicate, were not the original hosts of any of these plasmids, and most of these strains did not render a positive hybridization with the REP probes of such plasmids (Figure 4).

All of the shuttle plasmids were found to replicate exclusively in strains of Alphaproteobacteria, which indicates the relatively narrow host range of the tested REP modules. This is in agreement with the results of our previous studies, which showed that the plasmids of Paracoccus spp. are not promiscuous (e.g. [10]).

Members of the genus Paracoccus are not naturally competent for transformation, therefore conjugal transfer is the only efficient way of introducing of foreign DNA into their cells. Unfortunately, conjugative plasmids (or ICE elements) have not yet been identified in these bacteria. We also do not know whether such replicons are present in the natural host strains of the plasmids analyzed in this study (P. aestuarii, P. haeundensis and P. marcusii). However all of them (as well as many other Paracoccus spp. and numerous Alphaproteobacteria) carry mega-sized replicons, some of which could be self-transmissible.

Until now, the complete nucleotide sequences of only three Paracoccus spp. genomes (with defined physical maps of chromosomes and plasmids) have been deposited in the NCBI database (P. denitrificans PD1222, P. aminophilus JCM 7686 and Paracoccus sp. N5). Our detailed in silico analysis revealed that each of the strains carries one replicon (chromosome II, megaplasmid pAMI8 and a replicon referred to as contig 3, respectively) containing a complete predicted type IV secretion system, with a potential to support the conjugal transfer of mobilizable plasmids. Plasmid mobilization might be therefore a frequent phenomenon in Paracoccus spp., especially when the fact that the majority of the plasmids characterized in this study (9 replicons) contained the MOB modules is taken into account.

Vector cassette construction

To facilitate genetic manipulation of the carotenoid-producing strains of Paracoccus spp. two vector cassettes were constructed (see Methods for details). We used REP regions of plasmids pMOS6 (P. marcusii OS22) and pAES7 (P. aestuarii DSM 19484), which were free of the majority of restriction sites commonly found in the MCSs of many cloning vectors. The construction of these cassettes was performed according to the general scheme used for the generation of the DIY (Do It Yourself) cassettes, described in our previous study [10].

The cassettes contain (i) the REP regions, (ii) a kanamycin resistance gene, providing a selectable marker convenient for Paracoccus spp. (and other Alphaproteobacteria), and (iii) a MOB module, which enables conjugal transfer of the plasmids in the presence of a helper, functional transfer system (the MOB module originated from BHR conjugative plasmid RK2, commonly used in the construction of vectors for gram-negative bacteria). Both cassettes, designated DIY_pMOS6 and DIY_pAES7, also contain polylinkers with a number of restriction sites to facilitate their insertion into different locations (plasmids pKRP-DYI_pMOS6 and pKRP-DIY_pAES7; Figure 5). The pKRP-DIY plasmids are not cloning vectors and they serve exclusively as a source of the DIY cassettes. Insertion of a single cassette into any E. coli plasmid can create a mobilizable shuttle vector.

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Figure 5. The plasmids containing the DIY cassettes constructed in this study.

A. pKRP-DIY plasmids. B. pVIV mobilizable shuttle vectors. The plasmids contain DIY_AES7 and DIY_MOS6 cassettes composed of REP modules (of plasmids pAES7 and pMOS6, respectively), a Km^r gene and a MOB module derived from BHR plasmid RK2. B – BamHI, E – EcoRI, H – HindIII, K – KpnI, P – PstI, Sc – SacI, Sh – SphI, Sl – SalI, Sm – SmaI, X – XbaI.

https://doi.org/10.1371/journal.pone.0080258.g005

The cassettes were used to construct two mobilizable E. coli-Paracoccus spp. shuttle vectors pVIV6 and pVIV7, whose genetic organization is shown in Figure 5. These vectors also carry a MluI restriction fragment of E. coli-specific plasmid pBGS18 containing (i) a replication system originating from pMB1 (non functional in Paracoccus spp.) and (ii) a selection cassette (MCS and the lacZ’ gene) enabling the identification of recombinant molecules by "blue-white" screening. These shuttle vectors proved to be good cloning vectors with specific features determined by the DIY cassettes (data not shown).

There are also available some other cloning vectors based on the REP modules of Paracoccus spp. plasmids. They contain replication systems of pTAV1 (P. versutus UW1) [42] or pAMI plasmids of P. aminophilus JCM 7686 [10]. Although all of them are functional in Alphaproteobacteria, their stability significantly varies in different hosts [10]. Therefore there is a need to enrich the pool of such vectors, which will enable selection of the most convenient one for a given host and task.

Bacterial strains and culture conditions

The following strains of the genus Paracoccus were used in this study: (i) P. aestuarii [43], (ii) P. haeundaensis LG P-21903 [44], (iii) P. marcusii [45], (iv) P. marcusii OS22 [46] as well as (v-xviii) P. alcaliphilus JCM 7364 [47], P. aminophilus JCM 7686 [48], P. aminovorans JCM 7685 [48], P. halophilus JCM 14014 [49], P. homiensis DSM 17862 [50], P. kondratievae NCIMB 13773 [51], P. koreensis JCM 21670 [52], P. methylutens DM12 [53], P. pantotrophus DSM 11072 [54], P. pantotrophus KL100 [6], P. seriniphilus DSM 14827 [55], P. solventivorans DSM 11592 [56], P. sulfuroxidans DSM 14013 [57], P. thiocyanatus JCM 7364 [58], P. versutus UW1 [59], P. versutus UW225 [60], P. yeei CCUG 46822 [61] and P. zeaxanthinifaciens ATCC 21588 [62]. Other strains used in this study were (i) Rhizobium etli CE3 [63], Ochrobactrum sp. LM19R [10], (Alphaproteobacteria) (ii) Alcaligenes sp. LM16R [10] (Betaproteobacteria), and (iii) Eschericha coli – strains TG1 [64], BR825 [65] and Pseudomonas sp. LM7R [66] (Gammaproteobacteria). As recipients in triparental matings, rifampicin-resistant (Rif^r) derivatives of the wild-type strains were used. Bacteria were grown in LB (Luria Bertani) medium [67], at 37°C (E. coli) or 30°C (other strains). P. homiensis DSM 17862 was cultivated in Marine Broth (Difco) and R. etli CE3 in TY medium [68]. Where necessary, the medium was supplemented with kanamycin (50 μg/ml), streptomycin (50 μg/ml) and rifampicin (50 μg/ml).

Plasmids used and constructed in this study

The following plasmid vectors were used: (i) pABW1 (Km^r; ori pMB1; oriT RK2; MCS-lacZ') [69], pBGS18 (Km^r; ori pMB1; MCS) [70], pBluescript KSII (Ap^r; ori pMB1; MCS-lacZ') [71], pGEM-T Easy (Promega), pKRP12 (Ap^r; Km^r; ori pMB1) [72], pDIY-KM (Ap^r; Km^r; ori pMB1) [10]. Plasmids constructed in this study were (i-v) pABW-AES1, pABW-AES7, pABW-MARC2, pABW-MOS6 and pABW-MOS7 – shuttle plasmids used for host range analysis, (vi-ix) pKRP-DIY_AES7, pKRP-DIY_MOS6, pBS-DIY_AES7 and pBS-DIY_MOS6 – containing DIY cassettes, and (x-xi) shuttle vectors pVIV6 and pVIV7.

Shuttle plasmids pABW-AES1, pABW-AES7, pABW-MARC2, pABW-MOS6 and pABW-MOS7 (containing REP regions of plasmids pAES1, pAES7, pMARC2, pMOS6 and pMOS7, respectively) were constructed by cloning of REP-containing plasmid restriction fragments (pAES7, pMARC2, pMOS6 and pMOS7) or DNA fragment amplified by PCR (pAES1; primers used are listed in Table S2 in the supplemental material) into the MCS of mobilizable vector pABW1.

The plasmids representing the source of the DIY cassettes were constructed in several steps. First, the REP modules of pAES7 and pMOS6 were amplified by PCR (pMOS6; primers listed in Table S2) or recovered within 1.9 kb SacI-NotI restriction fragment (pAES7) and cloned into vector pGEM-T Easy. These modules were then excised from the recombinant plasmids with restriction endonuclease NotI and cloned into compatible sites of plasmid pBS-MOBKm (pBluescript SKII containing the Km^r cassette from pMBS1 and the BHR plasmid RK2 MOB module within its MCS). The REP-Km^r-MOB cassettes were excised from the recombinant plasmids and inserted (i) between HindIII sites of plasmid pKRP12 (HindIII digestion of pKRP12 removed the original resistance gene cassette of this plasmid), yielding plasmids pKRP-DIY_AES7 and pKRP-DIY_MOS6, or (ii) cloned into the MCS of Bluescript SKII, yielding plasmids pBS-DIY_AES7 and pBS-DIY_MOS6.

The mobilizable E. coli-Paracoccus spp. shuttle plasmids pVIV6 and pVIV7 were constructed by ligation of the DIY_pAES7 or DIY_pMOS6 cassettes (excised from pBS-DIY_AES7 and pBS-DIY_MOS6, respectively) with MluI-cleaved pBGS18.

Plasmid DNA isolation, genetic manipulations and PCR conditions

Plasmid DNA was isolated using a standard alkaline lysis procedure [73] and when required, purified by CsCl-ethidium bromide density gradient centrifugation. Total DNA was isolated from Paracoccus spp. using the procedure described by Chen and Kuo [74]. Southern hybridization analysis and common DNA manipulation methods were performed according to Sambrook and Russell [67]. Oligonucleotides used to generate molecular probes are listed in Table S2. PCR was performed in a Mastercycler (Eppendorf) using HiFi polymerase (Qiagen; with supplied buffer), dNTP mixture and total DNA of Paracoccus spp. with appropriate primer pairs (listed in Table S2).

Introduction of plasmid DNA into bacterial cells and plasmid stability assay

DNA was introduced into Rif^r (Alcaligenes sp. LM16R, Ochrobactrum sp. LM19R, Paracoccus spp. and Pseudomonas sp. LM7R) or Str^r (R. etli CE3) recipient strains by triparental mating as previously described [42]. Chemical transformation of E. coli cells was performed according to the method of Kushner [75]. The stability of plasmids was tested during growth under non-selective conditions. Stationary-phase cultures of plasmid-containing strains were diluted in fresh medium without antibiotic selection and cultivated for approximately 10, 20 and 30 generations. Samples were diluted and plated onto solid medium lacking selective antibiotics. One hundred colonies were tested for the presence of the Km^r marker by replica plating. Plasmid retention was determined from the percentage of kanamycin-resistant colonies.

DNA sequencing

The nucleotide sequences of plasmids pMARC and pMOS were determined in the DNA Sequencing and Oligonucleotide Synthesis Laboratory at the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, using a dye terminator sequencing kit and an automated sequencer (ABI 377 Perkin Elmer). Primer walking was used to complete the sequences. In the case of pMARC2, pMARC3 and pMOS2, unidirectional nested deletions within the cloned plasmid restriction fragments were generated by the use of exonuclease III and S1 nuclease (ExoIII/S1 deletion kit; MBI Fermentas). The nucleotide sequences of plasmids pAES and pHAE were determined by pyrosequencing performed by Genomed.

Bioinformatic analysis

Plasmid nucleotide sequences were analyzed using Clone Manager (Sci-Ed8) and Artemis software [76]. Similarity searches were performed using the BLAST programs [77] provided by the National Center for Biotechnology Information (NCBI) (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Comparison searches of insertion sequences were performed with ISfinder [78]. Protein homology detection and structure prediction were performed using the HHpred program [79]. Protein families were identified using the PFAM database [80]. Helix-turn-helix motifs were predicted using the HELIX-TURN-HELIX MOTIF PREDICTION program [81]. Phylogenetic analyses were performed using the Phylogeny Inference Package – PHYLIP v3.69 [82], applying the neighbor-joining algorithm with Kimura corrected distances and 1000 bootstrap replicates. DNA sequence alignments obtained using ClustalW [83] were manually refined using the T-Coffee Multiple Sequence Alignment program [84]. The tree was rendered with TreeView version 1.6.6 [85].

Nucleotide sequence accession numbers

Plasmid nucleotide sequences have been annotated and deposited in the GenBank database (accession numbers are given in parenthesis): pAES1 (JQ041633), pAES2 (JQ065021), pAES3 (JQ066766), pAES4 (JQ684025), pAES7 (JQ796370), pHAE1 (JQ066767), pHAE2 (JQ684024), pMARC1 (KC542384), pMARC2 (KC561053), pMARC3 (KC561054), pMARC4 (KC561055), pMOS2 (JQ664550), pMOS6 (JQ678602) and pMOS7 (JQ684023).