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Nucleotide Sequence of Plasmid pCNB1 from Comamonas Strain CNB-1 Reveals Novel Genetic Organization and Evolution for 4-Chloronitrobenzene Degradation

State Key Laboratory of Microbial Resource at Institute of Microbiology, Beijing 100080,¹ Chinese National Human Genome Center at Shanghai, Shanghai 201203,² Shanghai Institutes for Biological Sciences, Shanghai 20031, People's Republic of China³

Received 19 March 2007/ Accepted 18 May 2007

	ABSTRACT

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The nucleotide sequence of a new plasmid pCNB1 from Comamonas sp. strain CNB-1 that degrades 4-chloronitrobenzene (4CNB) was determined. pCNB1 belongs to the IncP-1ß group and is 91,181 bp in length. A total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pCNB1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4CNB. The 4CNB degradative genes and arsenate resistance genes were located on an extraordinarily large transposon (44.5 kb), proposed as TnCNB1. TnCNB1 was flanked by two IS1071 elements and represents a new member of the composite I transposon family. The 4CNB degradative genes within TnCNB1 were separated by various truncated genes and genetic homologs from other DNA molecules. Genes for chromate resistance were located on another transposon that was similar to the Tn21 transposon of the class II replicative family that is frequently responsible for the mobilization of mercury resistance genes. Resistance to arsenate and chromate were experimentally confirmed, and transcriptions of arsenate and chromate resistance genes were demonstrated by reverse transcription-PCR. These results described a new member of the IncP-1ß plasmid family, and the findings suggest that gene deletion and acquisition as well as genetic rearrangement of DNA molecules happened during the evolution of the 4CNB degradation pathway on pCNB1.

	INTRODUCTION

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Mobile genetic elements, including plasmids and transposons, play important roles in the generation/evolution of novel catabolic pathways (5, 24, 32, 40, 44, 46, 47). This conclusion is supported by genomic evaluations of degradative plasmids. Examples of such plasmids include pNL1 from Novosphingobium aromaticivorans for biphenyl and naphthalene degradation (36), pADP-1 from Pseudomonas sp. strain ADP for atrazine degradation (26), TOL from Pseudomonas putida for toluene degradation (8), pCAR1 from Pseudomonas resinovorans for carbazole/dioxin degradation (25), pEST4011 from Achromobacter xylosoxidans subsp. denitrificans for 2,4-dichlorophenoxylacetic acid degradation (48), pJP4 from Ralstonia eutropha for 2,4-dichlorophenoxylacetate and 3-chlorobenzoate degradation (45), pND6-1 from Pseudomonas sp. for naphthalene degradation (21), pDTG1 from P. putida for naphthalene degradation (4), and pLB1 from soil that partially degrades -hexachlorocyclohexane (28). Based on current information at the NCBI home page, approximately 900 bacterial plasmids have been sequenced but none of them are involved in the degradation of chlorinated nitroaromatic compounds.

Microbial degradation of nitroaromatic compounds, such as nitrobenzene (NB) and nitrobenzoate, has been extensively studied (10, 17, 20, 31, 34, 38). The degradation of chlorinated nitroaromatic compounds is difficult (37). Chlorinated nitroaromatic compounds, such as 4-chloronitrobenzene (4CNB), are more resistant to microbial attack than are nonchlorinated nitroaromatic compounds due to the electron-withdrawing properties of the chlorine and nitro groups. 4CNB is a relatively new anthropogenic compound and has been widely used for the commercial production of drugs, dyes, pesticides, and other chemicals. Due to its bioresistant nature and the limited amount of time that microbial communities have been exposed to it, 4CNB is an ideal compound for the identification of possible evolutionary events of novel catabolic pathways in microorganisms. Bacterial strain LW1 (18), Comamonas sp. strain CNB-1 (52, 53), P. putida strain ZLW73 (54, 57), and a microbial consortium (35) have been reported to degrade 4CNB, and Escherichia coli and Rhodosporidium have been reported to transform 4CNB (3, 11, 55). Genes involved in 4CNB degradation by strain CNB-1 are located on a large plasmid, pCNB1; however, information on pCNB1 is very limited (52). This work reports the complete nucleotide sequence of pCNB1. This study indicates that pCNB1 harbors a new transposon, TnCNB1, that mediates the 4CNB degradative pathway and additional catabolic functions. pCNB1 also endows its host strain CNB-1 with the ability for chromate and arsenate resistance.

	MATERIALS AND METHODS

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Bacterial strains and cultivation.
Comamonas sp. strain CNB-1 and mutant strain CNB-2 (which lacks pCNB1) were previously described (52, 53). The cultivation medium was Luria-Bertani (LB) broth or agar. LB broth was supplemented with arsenate and chromate under different concentrations when resistance to arsenate or chromate was evaluated.

Plasmid DNA isolation, sequencing, and assembly.
Plasmid DNA was isolated by a modification of the alkaline lysis method (16). Cells of strain CNB-1, grown at 30°C in 100 ml LB broth, were collected by centrifugation at 10,000 x g for 5 min and were resuspended in 0.8 ml of chilled solution I (50 mM glucose, 10 mM EDTA [pH 8.0], 25 mM Tris-HCl [pH 8.0]). Cells were lysed by adding 1.6 ml of freshly prepared solution II (0.2 N NaOH, 1% N-lauryl sarcosine), mixing, and then adding 1.2 ml of solution III (3 M potassium and 5 M acetate with a pH of 4.8) and mixing again. After incubating on ice for 5 min, DNA was extracted by a previously published protocol (52). RNA was removed by RNase digestion. For sequencing, DNA was mechanically broken into small fragments of 1.6 to 4.0 kb by ultrasonic shearing. The fragments were end blunted by T4 DNA polymerase (Fermentas) and ligated into linear vector pUC18. Ligated DNA was used to transform E. coli DH10B (Invitrogen), which was then plated onto LB agar plates containing ampicillin, X-Gal (5-bromo-4-chloro-3-indolyl-ß-D-galactopyranoside), and IPTG (isopropyl-ß-D-thiogalactopyranoside) (Sangon). White colonies were selected for sequencing.

Sequencing from both ends of the plasmid vector was performed by using BigDye, version 3.1, mix (Applied Biosystems) and primers P2 and P4. Reactions were analyzed on an ABI 3730xl DNA analyzer (Applied Biosystems). The Phred/Phrap/Consed software package (www.phrap.org) was applied for quality assessment and sequence assembly. Sequence and/or physical gaps were closed by PCR and primer walking. The final assembly was checked against the physical map of restriction sites.

ORFs, annotation, and sequence analysis.
Open reading frames (ORFs) were predicted online by the software GeneMark (version 2.4; seed sequences, Pseudomonas_syringae_phaseolicola_1448A_plasmid_large), and predicted ORFs were analyzed manually with BLASTP and the NCBI database. G+C contents, multiple sequence alignments, phylogenetic analyses, and phylogenetic tree constructions were determined with DNAMAN (version 5.1; Lynnon Biosoft). The circular plasmid map was drawn with BioEdit (version 7.0.0).

RT-PCR.
Total RNAs were isolated from strain CNB-1 cells grown in LB broth with 120 mM potassium arsenate or 1 mM potassium chromate. DNA contaminants were inactivated by digestion with RNase-free DNase (Takara) for 1 h, and then the DNase was removed by heating at 65°C for 10 min. Reverse transcription (RT) was performed with reverse transcriptase (Takara) for 1 h; 1 µl of the reaction liquid was used as the template for PCR. The primer pair used to target the chromate transporter gene was ChrtF (5'-TAACCTATGCACGGATGG-3') and ChrtR (5'-GCTTGGATGCCTGTATTG-3'). The primer pair used to target the arsenate reductase gene was AserF (5'-CATCACGATCTACCACAAC-3') and AserR (5'-CGTCACTGGAGCTAAATAG-3').

Nucleotide sequence accession number.
The complete sequence of pCNB1 has been deposited in the NCBI GenBank database under accession no. EF079106.

	RESULTS AND DISCUSSION

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Sequence features of pCNB1.
The circular genome of pCNB1 was 91,181 bp in length and had 95 predicted ORFs. BLAST analysis and sequence alignment indicated that ORF products were homologous to functionally known or unknown proteins listed in the NCBI database. The putative functionalities of ORFs are outlined in Table 1. Forty-five ORFs coded for plasmid replication, stability, transfer, and mating pair formation. Thirty-two ORFs coded for the degradation of 4CNB and other aromatic compounds. Nine ORFs coded for transposition or integration. Six ORFs coded for chromate and arsenate resistance. The genetic organization of pCNB1 is shown in Fig. 1A. ORFs on pCNB1 were asymmetrically distributed; 26 ORFs have clockwise orientation, and 69 ORFs have counterclockwise orientation. pCNB1 has remarkably high frequencies of GCCG (944 times) and CGGC (1,008 times), a striking feature that was reported for the IncPß plasmid R751 (43). The average G+C content of pCNB1 is 63.4%, which is close to that of the genome of strain CNB-1 (61.5%). The average G+C content of the 40-kb backbone region of pCNB1 was 65.5%, and G+C variance of this region was minimal. However, the G+C contents of the loading gene regions, which averaged 62.1%, displayed a large variance (e.g., those of the regions of positions 37220 to 39437 and 63777 to 64469 were 72 and 56%, respectively) (Fig. 1B).

View larger version (31K): [in this window] [in a new window]   FIG. 1. Genetic organization (A) and G+C content (B) of pCNB1 from Comamonas sp. strain CNB-1. ORFs are numbered in series, and gene names in the backbone region are indicated. The details of loading regions are shown in Fig. 4. Average G+C contents of various regions are indicated by broken lines in panel B.

Genes for plasmid stability, replication, formation of the mating pair, surface exclusion, relaxosome assembly, and auxiliary transfer were found at the 40-kb-length backbone region of pCNB1 (Fig. 1A). The overall genetic organization of the backbone region of pCNB1 was quite similar to that of prototype IncP-1ß plasmid R751, and their corresponding ORFs shared 64 to 93% identity. However, counterparts of kleG, kleB, trfA2, traC3, traC4, kluA, and kluB of R751 were not found in pCNB1, suggesting that their functions were not necessary or were replaced by other genes.

Genes involved in plasmid replication and transfer.
The putative oriV region of pCNB1 was identified by BLAST search using the oriV sequence of archetype IncP-1 plasmid RK2 (1) and was located at positions 10995 to 11301. The identity of the pCNB1 oriV region to that of R751 is 80%. Eight iterons were found within the oriV region, and the G+C content curve indicated that an AT-rich and GC-rich region follows these iterons (Fig. 2). Although the transferability of pCNB1 is unknown, the deduced amino acid sequences corresponding to 30 ORFs had significant identities (49 to 95%) to the tra and trb products of R751 and the mobilization of a very similar plasmid, pZWL73, between different strains of P. putida has been observed (57). All these facts suggest that pCNB1 is probably transferable. The oriT region, which is important for plasmid transfer between different hosts, was identified at positions 90904 to 91006 on pCNB1 by comparison with that of R751, and the highly conserved nic site was located at positions 90964 to 90965 (Fig. 2).

View larger version (24K): [in this window] [in a new window]   FIG. 2. Analysis of oriV (A) and oriT (B) regions of pCNB1. (A) Triangles represent the binding sites for replication initiation protein. The two rectangles stand for GC-rich and AT-rich regions. The curve shows GC molar content variations of the oriV region, and the arrow indicates the direction of replication. (B) Pairwise alignment of oriT regions from pCNB1 (upper portion) and R751 (lower portion). The sequence in the box is recognized by TraI, and the nic site is identified by the vertical arrow. From right to left, the horizontal arrows show directions of TraK transcription, plasmid transfer, and TraJ transcription.

View larger version (40K): [in this window] [in a new window]   FIG. 3. Features of putatively new transposons at the loading regions from pCNB1. (A) Genetic organization and repeat sequences of the Tn21-like transposon, which carries a chromate-resistant gene (ORF23/CHR). (B) Genes involved in the degradation of 4-chloronitrobenzene. (C) Schematic illustration of the novel TnCNB1 with five interrupted transposase genes. Deleted fragments are indicated by the gray hashed regions in the arrows. (D) Alignment of inverted repeat (IR) sequences flanking IS1071L and IS1071R.

(i) Genes for arsenate resistance.
ORF80 (bp 69047 to 69403), ORF81 (bp 69413 to 70702), and ORF83 (bp 71483 to 71809) of pCNB1 had significant identities to some genes for arsenate resistance proteins. ORF80 had 78% identity to the arsenate reductase (ArsC; ZP_00416371) gene of Azotobacter vinelandii AvOP, ORF81 had 82% identity to the arsenate transmembrane pump (ArsB; AAS45119) gene of Alcaligenes faecalis, ORF82 had 65% identity to a putative phosphatase (ZP_00242261) gene of Rubrivivax gelatinosus PM1, and ORF83 had 67% identity to the regulator (ArsR; CAD18280) gene of Ralstonia solanacearum. To determine whether these ORFs are functional, wild-type strain CNB-1 and mutant strain CNB-2 were cultivated in the presence of various concentrations of arsenate. Strain CNB-1 grew in the presence of 210 mM arsenate, while mutant strain CNB-2 did not grow when arsenate exceeded 20 mM. Moreover, RT-PCR demonstrated that the arsenate reductase gene (arsC) was transcribed when induced with arsenate (data not shown). Two putative transposase-like ORFs flanked the arsenate resistance genes, but they were either truncated (ORF78) or inactivated by insertion (ORF86) (Fig. 3B). Thus, it is unlikely that this genetic element that codes for arsenate resistance is transposable.

(ii) Genes for enzymes that transform/degrade aromatic compounds.
Genes (cnb) coding for enzymes that transform 4CNB and nitrobenzene were located at three genetic fragments that have been reported previously, i.e., the 34-kb fragment coding for a novel aminophenol 1,6-dioxygenase (52), the 6.4-kb fragment coding for nitroreductase and mutase (53, 54), and the 8.2-kb DNA fragment containing a deaminase gene (cnbZ) (23). The three genetic fragments were in TnCNB1 (Fig. 3B). TnCNB1 also carried other putative genes involved in the degradation of aromatic compounds (Table 1). A cat genetic cluster (ORF58 to ORF62) was homologous to the catechol degradation gene cluster, and ORF58 encoded a functional catechol 1,2-dioxygenase, as confirmed by cloning and expression in E. coli (data not shown).

Analysis of ORFs above the cnb and cat regions indicated that genetic deletion, insertion, recombination, and exchange possibly occurred during the evolution of genetic elements involved in the degradation of 4CNB. It has been proposed that truncated genes play important roles in the evolution of new metabolic pathways (33, 50). Truncated genes might have arisen by genetic deletion and/or recombination. Many truncated genes occurred in the 44.5-kb fragment (Table 1 and Fig. 3B). For example, ORF74 and ORF76 that putatively coded for semialdehyde hydrolase and monooxygenase, respectively, were truncated and their parts close to cnbA were lost. Similarly, ORF47 and ORF49 flanking cnbG were truncated, the former having lost both ends and the latter having lost its remote end to cnbG.

(iii) Two IS1071 elements flanked TnCNB1 and were oriented in opposite directions.
IS1071 was initially identified as flanking a composite transposon, Tn5271, carrying genes for 3-chlorobenzoate degradation on the plasmid pBRC60 from Comamonas testosteroni strain BR60 (30). IS1071-like sequences are associated with genes involved in the degradation of xenobiotics (7, 22, 26, 39, 45, 48). TnCNB1 had two IS1071 elements oriented in opposite directions (Fig. 3B and C), which is unlike all known IS1071-flanked transposons. The two putative transposases of IS1071L (ORF44) and IS1071R (ORF87) have only 81% identity, which is significantly lower than the sequence identities of IS1071L and IS1071R transposases from other bacterial hosts. For example, sequence identities between IS1071L and IS1071R transposases from Pseudomonas sp. strain ADP, Ralstonia eutropha JMP134, and Ralstonia metallidurans CH34 are higher than 99%. These analyses suggest that the two IS1071 elements of TnCNB1 evolved divergently.

(iv) TnCNB1 contained five interrupted transposase genes.
Five interrupted transposase genes were identified within TnCNB1 (Fig. 3C). ORF63 encoded a truncated transposase of 165 amino acid residues that was 100% identical to the C terminus of the IS1071 transposase found in R. metallidurans CH34 (NCBI accession no. ZP_00598594); however, the 706 amino acid residues at the N terminus were absent. ORF66, ORF72, ORF78, and ORF86 products are all homologous to IS801-like transposase, and their deduced amino acid sequences had identities of 93, 89, 95, and 100%, respectively, to partial sequences of the transposase from Pseudomonas sp. strain ADP (GenBank accession no. AAK50304). We postulate that ORF66, ORF72, and ORF86 were derived from IS801-like elements by complicated events which probably included gene duplication and deletion. Interestingly, ORF78 had a 100-bp insertion that likely accounted for the inactivation of this ORF (Fig. 3C).

Independent evolution of 4CNB and NB catabolic pathways.
The 4CNB-degrading pathway of Comamonas sp. strain CNB-1 resembles the NB degradation pathway of P. putida HS12 (Fig. 4B). The amino acid sequences of the nitroreductases involved in the partial reduction of 4CNB and NB had significant identities (92%). Moreover, the DNA fragments (100 bp) downstream of the two CnbA genes had 99% identity (Fig. 4A). These facts imply that the CnbA genes evolved from a common ancestor and diverged recently. But other genes, such as those for CnbH and CnbZ (deaminases involved in the degradation of 4CNB) and NbzD (involved in the degradation of NB) were not homologous. Furthermore, the genes involved in the degradation of 4CNB and NB were organized differently. Genes for NB degradation (nbz) in P. putida HS12 are located on two plasmids, pNB1 and pNB2. pNB1 harbors two genetic fragments for NB degradation, namely, nbzCaCbDGFEIH and nbzA, and pNB2 harbors only nbzB (for gene functions, see the legend for Fig. 4) (13, 14, 34, 52). The genetic elements involved in the degradation of 4CNB were found within the large transposon TnCNB1. Unlike genes nbzCaCbDGFEIH, which are consecutive, genes cnbCaCbDEFGHI were separated by various truncated genes (Fig. 3B). Based on these observations, we propose that the cnb and nbz genetic clusters have evolved independently and that the cnb genetic cluster is not derived from the nbz genetic cluster or vice versa.

View larger version (17K): [in this window] [in a new window]   FIG. 4. Comparison of genetic organizations (A) and putative metabolic pathways (B) involved in the degradation of 4-chloronitrobenzene (upper reaction sequence of panel B) and nitrobenzene (lower reaction sequence of panel B) by Comamonas sp. strain CNB-1 and Pseudomonas putida HS12. Homologous genes are filled with the same pattern. I, choloronitrobenzene nitroreductase (CnbA/NbzA); II, hydroxylaminobenzene mutase (CnbB/NbzB); III, 5-chloro/2-aminophenol 1,6-dioxygenase (CnbCaCb/NbzCaCb); IV, aminomuconic semialdehyde dehydrogenase (CnbD/NbzD); V, aminomuconate deaminase (CnbH/NbzE); V', 4-oxalocrotonate tautomerase (CnbG); VI, 4-oxalocrotonate decarboxylase (CnbF/NbzF); VII, 2-oxo-4-pentanoate hydratase (CnbE/NbzG). Unfilled ORFs (i.e., arrows) represent unknown functions or idle genes. Portions of ORFs that are black represent lost parts of truncated genes. The numbers between genetic clusters are the identity values of the corresponding ORFs based on amino acid sequences, and an asterisk indicates that identity was calculated from DNA sequences.

In conclusion, pCNB1 belongs to the IncP-1ß plasmids. An analysis of pCNB1 revealed significant amounts of genetic information that help explain how Comamonas sp. strain CNB-1 adapted itself to newly released 4CNB in the environment. The genes involved in the degradation of 4CNB were located on a novel transposon, TnCNB1. pCNB1 also enables strain CNB-1 to tolerate large amounts of arsenate and chromate. The genes for arsenate resistance were also located on TnCNB1, while those for chromate resistance were located on a different transposon.

	ACKNOWLEDGMENTS

 
This work was supported by grants from the Chinese Academy of Sciences (KSCX2-YW-G-009) and the National Natural Science Foundation of China (30230010).

	FOOTNOTES

 
* Corresponding author. Mailing address for Shuang-Jiang Liu: Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100080, People's Republic of China. Phone: 86-10-64807423. Fax: 86-10-64807421. E-mail: liusj{at}sun.im.ac.cn. Mailing address for Guo-Ping Zhao: Shanghai Institutes for Biological Sciences, Shanghai 200031, People's Republic of China. Phone: 86-21-50801919. Fax: 86-21-50801922. E-mail: gpzhao{at}sibs.ac.cn

Published ahead of print on 25 May 2007.

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