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Applied and Environmental Microbiology, November 2006, p. 7238-7245, Vol. 72, No. 11
0099-2240/06/$08.00+0 doi:10.1128/AEM.01494-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
State Key Laboratory of Microbial Resource, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080,1 Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China2
Received 28 June 2006/ Accepted 30 August 2006
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Not only is hydroxyquinol involved in resorcinol degradation; it is also the key intermediate during microbial degradation of a range of aromatic compounds, such as chlorophenol (15), 2,4,6-trichlorophenol (14), dibenzo-p-dioxin (1), 4-aminophenol (27), and 2-aminobenzoate (24). Consequently, the degradation of hydroxyquinol and its derivatives is of importance for the understanding of microbial processes that govern the metabolism of aromatic compounds and for the understanding of the geobiochemical cycling of aromatic compounds. Recently, advances have been made in the understanding of aromatic compound degradation by Corynebacterium glutamicum (7, 25, 26). Here we describe the genetic characterization of the resorcinol catabolic pathway in C. glutamicum.
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TABLE 1. Bacterial strains, plasmids, and primers used in this study
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DNA extraction and manipulation.
The total genomic DNA of C. glutamicum was isolated according to the procedure of Tauch et al. (28). Plasmid isolation, DNA manipulation, and agarose gel electrophoresis were carried out as described by Sambrook et al. (21). DNA restriction enzymes, ligase, and DNA polymerase were used as recommended by the manufacturer. Restricted DNA fragments were separated by agarose gel electrophoresis and were purified by using the agarose gel DNA fragment recovery kit (TIANGEN, Beijing, China).
Amplification of DNA fragments and construction of plasmids.
Target DNA fragments were PCR amplified by using Pyrobest DNA polymerase (TaKaRa) or Taq DNA polymerase (Promega, Madison, Wis.). PCR products were purified using an agarose gel DNA fragment recovery kit. PCR fragments were cloned using the pGEM-T Easy vector system (Promega, Madison, Wis.).
Various plasmids (Table 1) were constructed with pK18mobsacB (22), pXMJ19 (11), or pET28a. The primers used are listed in Table 1. Genes on plasmids were deleted either by gene splicing by overlap extension (10) [NCgl1113 and NCgl(2950-2953)] or by deletions of regions of each gene (NCgl1110, NCgl1111, or NCgl1112) through restriction enzyme digestion (see Fig. 1B). The disrupted genes were fused into pK18mobsacB to generate plasmids pK18mobsacB
NCgl1110, pK18mobsacB
NCgl1111, pK18mobsacB
NCgl1112, pK18mobsacB
NCgl1113, and pK18mobsacB
NCgl(2950-2953). For complementation, plasmids pXMJ19-NCgl1110, pXMJ19-NCgl1111, pXMJ19-NCgl1112, pXMJ19-NCgl1113, pXMJ19-NCgl2951, and pXMJ19-NCgl2952 were created by insertion of each PCR-amplified intact gene into pXMJ19 (11). Plasmids for expression of the target genes in E. coli were constructed from each PCR-amplified gene and pET28a.
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FIG. 1. Physical map and genetic organization (A) of the resorcinol pathway (C) in C. glutamicum and construction of plasmids for gene disruption and complementation (B). Restriction sites are abbreviated as follows: X, XbaI; H, HindIII; E, EcoRI; S, SacI; B, BanI. Right and left triangles with points touching represent deletion by restriction enzyme digestion; wide diamonds represent deletion by gene splicing by overlap extension.
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NCgl1110 to RES167
NCgl1113 and RES167
NCgl(2950-2953) (Table 1). The deletions of the target genes in pK18mobsacB derivatives and in C. glutamicum mutants were verified by PCR and DNA sequencing. The expression of each gene in C. glutamicum was induced by addition of 0.6 mM isopropyl-ß-D-thiogalactopyranoside (IPTG) to the culture broth.
Heterologous expression of genes in E. coli, preparation of cellular lysate, and enzymatic activity assays.
Plasmids (pET28a-NCgl1111 and pET28a-NCgl1112, described above) were electroporated into E. coli BL21(DE3). Synthesis of recombinant proteins was initiated by addition of 0.6 mM IPTG, and cultivation was continued for an additional 3 h. Cells were harvested by centrifugation at 10,000 x g, washed twice with ice-cold 50 mM Tris-HCl buffer (pH 8.0), resuspended in the same buffer, and disrupted by sonification in an ice-water bath. After centrifugation at 20,000 x g for 30 min at 4°C, the clear supernatant was used for enzymatic assays and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. All enzymatic assays were performed in 50 mM Tris-HCl buffer (pH 8.0). Resorcinol hydroxylase activity was measured spectrophotometrically by measuring the decrease in absorption at 340 nm due to oxidation of NADPH and was calculated with an extinction coefficient of 6,220 M1 · cm1 (17). Maleylacetate reductase activities were determined by monitoring NADH/NADPH oxidation as described by Schlömann et al. (23). Hydroxyquinol 1,2-dioxygenase activity was measured by determination of the increase in absorbance at 243 nm that resulted from the formation of maleylacetate, according to the method of Travkin et al. (30). An extinction coefficient of 4,440 M1 · cm1 was used for the calculation of enzymatic activity.
Conversion of resorcinol into maleylacetate via hydroxyquinol.
E. coli BL21(DE3)/pET28-NCgl1111 and E. coli BL21(DE3)/pET28-NCgl1113 were cultivated and induced as described above. Cells were harvested by centrifugation, washed twice with Tris-HCl (50 mM; pH 8.0), and suspended in the same buffer at a final optical density at 600 nm of 2.5. Resorcinol at a final concentration of 2 mM was added to the cell suspensions of E. coli BL21(DE3)/pET28-NCgl1111 and E. coli BL21(DE3)/pET28-NCgl1113, and the mixtures were incubated at 30°C. After 0.5, 1, 2, and 3 h, samples (500 µl each time) were collected, acidified to pH 2.0, extracted with ethyl acetate, and finally dried by N2 blowing. In parallel, cell suspensions of E. coli BL21(DE3)/pET28a and E. coli BL21(DE3)/pET28a-NCgl1113 were used for this conversion (as negative controls).
Operation of MS.
The extracted samples described above were subjected to mass spectrometry (MS) analysis. Mass spectrometry was performed on an electrospray ionization ion trap mass spectrometer (LCQ Deca XPplus; Thermo-Finnigan, San Jose, Calif.) operated in negative-ion mode. Typical parameters were as follows: temperature for ion transfer tube, 160°C; spray voltage, 3.3 kV. The samples were dissolved in methanol. For elucidation of the structure of the product, tandem MS (MS/MS) was performed with 35% normalized collision energy.
SDS-PAGE.
SDS-PAGE was conducted with a 5% stacking gel and a 12% resolving gel and was run in a Mini-PROTEIN II electrophoresis cell (Bio-Rad) according to the manufacturer's instructions. After electrophoresis, the protein bands were visualized by Coomassie brilliant blue staining. Protein concentrations were determined according to the method of Bradford (2), with bovine serum albumin as the standard.
Enzymatic preparation of maleylacetate.
Maleylacetate, the substrate for maleylacetate reductase, was freshly prepared by cleavage of 2 ml of 10 mM hydroxyquinol with hydroxyquinol 1,2-dioxygenase (10 µl) in 50 mM Tris-HCl buffer (pH 6.3) and was monitored by determination of UV absorption at 243 nm. After the conversion was completed (
2 min), the pH of the buffer was adjusted to 8.0. This preparation was used as a substrate without further purification.
RT-PCR.
C. glutamicum was cultivated either with MM broth containing resorcinol or with LB broth. Total RNA was isolated with a TRNzol extraction kit (TIANGEN, Beijing, China). The RNA preparation was first treated with DNase I and then used as a template for reverse transcription with Moloney murine leukemia virus reverse transcriptase (TIANGEN, Beijing, China). The reverse transcription-PCR (RT-PCR) products (cDNAs) were used to amplify approximately 350- to 500-bp fragments of target genes. The primers used in RT-PCR are listed in Table 1. In order to exclude the possibility that residual DNA was amplified, negative controls were run in parallel, except that the Moloney murine leukemia virus reverse transcriptase was omitted from the reaction mixtures.
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FIG. 2. (A through E) Growth curves of various C. glutamicum mutants cultivated with resorcinol; (F) transcriptional analysis by RT-PCR of gene expression during growth in MM broth with resorcinol or in LB broth. According to genome data analysis, NCgl1110 and NCgl2950 encode putative TetR family regulators; NCgl1111 encodes a putative hydroxylase; NCgl1112 and NCgl2952 encode putative maleylacetate reductases; NCgl1113 and NCgl2951 encode putative hydroxyquinol 1,2-dioxygenases; and NCgl2953 encodes a putative transporter. Symbols: , RES167; (A) , RES167 NCgl(2950-2953); (B) , RES167 NCgl1111; , RES167 NCgl1111/pXMJ19-NCgl1111; (C) , RES167 NCgl1112; , RES167 NCgl(2950-2953)/ NCgl1112; , RES167 NCgl(2950-2953)/ NCgl1112/pXMJ19-NCgl1112; , RES167 NCgl(2950-2953)/ NCgl1112/pXMJ19-NCgl2952; (D) , RES167 NCgl1113; , RES167 NCgl(2950-2953)/ NCgl1113; , RES167 NCgl(2950-2953)/ NCgl1113/pXMJ19-NCgl1113; , RES167 NCgl(2950-2953)/ NCgl1113/pXMJ19-NCgl2951; (E) , RES167 NCgl1110; , RES167 NCgl1110/pXMJ19-NCgl1110. (F) Strain RES167 was grown in MM with resorcinol (lanes 1 to 7) or in LB broth (lanes 8 to 11). Total RNAs extracted were used as templates for RT-PCR to detect the transcription of each gene as follows: lane 1, NCgl1110 (420 bp); lane 2, NCgl1111 (464 bp); lane 3, NCgl1112 (550 bp); lane 4, NCgl1113 (410 bp); lane 5, NCgl2950 (no corresponding fragment); lane 6, NCgl2951 (430 bp); lane 7, NCgl2952 (464 bp); lane 8, NCgl1110; lane 9, NCgl1112; lane 10, NCgl2950; lane 11, NCgl2952.
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NCgl1111 lost the ability to grow on resorcinol (Fig. 2B), but its ability to grow on hydroxyquinol was the same as that of the wild-type strain (data not shown). A reasonable explanation for these phenotypes was that the NCgl1111 gene was involved in the conversion of resorcinol into hydroxyquinol through hydroxylation. When the mutant RES167
NCgl1111 was complemented with the NCgl1111 gene, the ability to grow on resorcinol was partially restored (Fig. 2B). RT-PCR showed that NCgl1111 was transcribed in wild-type RES167 when resorcinol was provided in the culture medium (Fig. 2F, lane 2). The translational product of the NCgl1111 gene showed only limited identity to the putative monooxygenase and hydroxylase (Table 2). In order to understand its biochemical properties, NCgl1111 was cloned into E. coli BL21(DE3)/pET28a. The recombinant E. coli cells actively synthesized a protein with a molecular mass of ca. 63 kDa. The cellular lysate of the recombinant E. coli cells showed resorcinol hydroxylase activity (Fig. 3), and this activity depended solely on the presence of NADPH. In addition to the enzyme activity, the cellular conversion of resorcinol also supported the hypothesis that NCgl1111 encodes a hydroxylase (Ncgl1111) that is involved in the conversion of resorcinol to hydroxyquinol. The recombinant cells of E. coli BL21(DE3)/pET28a-NCgl1111 converted resorcinol into hydroxyquinol. When Ncgl1111 was coupled with a hydroxyquinol 1,2-dioxygenase [Ncgl1113, encoded by NCgl1113 and expressed in E. coli BL21(DE3)/pET28a-NCgl1113] (25), resorcinol was converted to a product that was identified as maleylacetate by MS and MS/MS (data not shown).
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TABLE 2. Blast search results and identified functions of genes involved in resorcinol catabolism with Corynebacterium glutamicum
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FIG. 3. (A) Resorcinol hydroxylase activity in recombinant E. coli/pET28a-NCgl1111. (B) E. coli/pET28a was used as a negative control. The absorbances of the reaction mixture at wavelengths of 270 to 400 nm were recorded at time zero (top line) and at 60, 120, and 180 s (bottom line), Hydroxylase activity was also determined with 3-hydroxybenzoate, 3-aminophenol, 3,5-dihydroxytoluene, and 2,4-dihydroxybenzoate, but no activity was detected.
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Both the NCgl1112 gene and the NCgl2952 gene code for maleylacetate reductases.
Disruption of NCgl1112 resulted in the mutant RES167
NCgl1112, which was not able to grow on resorcinol (Fig. 2C). The mutant RES167
(NCgl2950-NCgl2953), in which the NCgl2952 gene was deleted, did not show disturbed assimilation of resorcinol. The double mutant RES167
(NCgl2950-NCgl2953)/
NCgl1112 was created and was used for complementation with NCgl1112 or NCgl2952. The results indicated that either NCgl1112 or NCgl2952 restored the ability to grow on resorcinol (Fig. 2C). Based on BLAST results showing high identities of Ncgl1112 and Ncgl2952 to maleylacetate reductases that had been functionally identified previously (Table 2), both NCgl1112 and NCgl2952 were assumed to code for maleylacetate reductases. When NCgl1112 was heterologously expressed in E. coli, the cellular lysate showed significant maleylacetate reductase activity. The results also indicated that the maleylacetate reductase preferred NADH (0.072 U/mg) to NADPH (0.047 U/mg) as a cofactor. It was also found that both NCgl1112 and NCgl2952 were transcribed in wild-type RES167 when resorcinol was provided in the culture broth (Fig. 2F, lanes 3 and 7).
NCgl1110, but not NCgl2950, codes for a negative transcriptional regulator.
According to the BLAST search results, both NCgl1110 and NCgl2950 encode putative TetR family transcriptional regulators. To determine whether the two genes were functional, NCgl1110 and NCgl2950 were individually disrupted. The resulting mutants, RES
NCgl1110 and RES
NCgl(2950-2953), were not phenotypically affected when resorcinol was provided as a source of carbon and energy. However, when these mutants were cultivated in LB broth, significant hydroxyquinol 1,2-dioxygenase activity (0.305 U/mg) was observed for the mutant RES
NCgl1110 but not for the mutant RES
NCgl(2950-2953) or wild type RES167. When the NCgl1110 gene was introduced (complementation) into the mutant RES167
NCgl1110, hydroxyquinol 1,2-dioxygenase activities disappeared. RT-PCR indicated that only NCgl1110 was transcribed (Fig. 2F, lane 1), and NCgl2950 was not transcribed (Fig. 2F, lane 5), when RES167 was cultivated with resorcinol. Similarly, when RES167 was cultivated in LB broth, only NCgl1110 was transcribed (Fig. 2F, lane 8). These results clearly demonstrate that Ncgl1110 functioned as a repressor and that its repression was neutralized by resorcinol induction. The function of Ncgl2950 was not clear.
The TetR family regulators are usually transcriptional repressors for the biosynthesis of antibiotics, efflux pumps, and osmotic stress (18). There are 15 TetR family members on the genome of C. glutamicum, and 3 were functionally identified (12, 13, 20). But none of the three functioned in aromatic degradation. Our results confirmed that Ncgl1110 was a transcriptional repressor of resorcinol degradation in C. glutamicum. Previously, a TetR family regulator, CymR, was determined to be involved in the regulation of p-cymene (cym) and p-cumate (cmt) degradation in P. putida (6). As far as we know, Ncgl1110 is the second example of a TetR family regulator that is involved in the regulation of aromatic compound catabolism.
The NCgl2953 gene is not necessary for resorcinol assimilation.
According to the results of sequence analysis and BLAST searches, the NCgl2953 gene encodes a protein that is possibly involved in membrane transportation of metabolic substrates or products, and we had deduced that it encoded a resorcinol or hydroxyquinol transporter. However, genetic disruption of the NCgl2953 gene or the whole NCgl2950-NCgl2953 genetic cluster did not affect aromatic compound assimilation. The mutants RES167
NCgl2953 and RES167
NCgl(2950-2953) grew as well as wild-type RES167 did, and this excluded the necessity of NCgl2953 for resorcinol assimilation. The function of this gene needs more investigation.
The two genetic clusters NCgl2950-NCgl2953 and NCgl1110-NCgl1113 function differently for resorcinol assimilation.
As shown above, all the genes at the NCgl1110-NCgl1113 genetic cluster were involved in resorcinol assimilation, but the genes at the NCgl2950-NCgl2953 genetic cluster were different: the mutant RES167
NCgl(2950-2953), in which in the NCgl2950-NCgl2953 genetic cluster was deleted, grew as well as the wild-type strain, RES167, when resorcinol was provided (Fig. 2A), indicating that this genetic cluster was not necessary for resorcinol assimilation. Interestingly, the RT-PCR results showed that NCgl1112 and NCgl1113 at the NCgl1110-NCgl1113 gene cluster, and NCgl2951 and NCgl2952 at the NCgl2950-NCgl2953 gene cluster, were all transcribed when C. glutamicum was cultivated with resorcinol. Apparently, the NCgl2951 and NCgl2952 genes, coding for hydroxyquinol 1,2-dioxygenase and maleylacetate reductase, respectively, were redundant to the NCgl1113 and NCgl1112 genes. Such catabolic redundancy has also been found for A. chlorophenolicus (15) and Pimelobacter simplex (30). One reasonable explanation for this redundancy is that some genes are expressed only under certain conditions: In Burkholderia xenovorans, there are three benzoate-catabolic pathways, and the benzoyl coenzyme A pathways are preferentially active under reduced oxygen tension (5).
This work was supported by grants from the National Natural Science Foundation of China (30230010) and the Chinese Academy of Sciences (KSCX2-SW-113).
Published ahead of print on 8 September 2006. ![]()
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