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Applied and Environmental Microbiology, July 2006, p. 4604-4609, Vol. 72, No. 7
0099-2240/06/$08.00+0 doi:10.1128/AEM.00081-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Biodesulfurization in Biphasic Systems Containing Organic Solvents
Fei Tao,
Bo Yu,
Ping Xu,* and
Cui Qing Ma
State Key Lab of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
Received 12 January 2006/
Accepted 25 April 2006

ABSTRACT
Biphasic systems can overcome the problem of low productivity
in conventional media and have been exploited for biocatalysis.
Solvent-tolerant microorganisms are useful in biotransformation
with whole cells in biphasic reactions. A solvent-tolerant desulfurizing
bacterium,
Pseudomonas putida A4, was constructed by introducing
the biodesulfurizing gene cluster
dszABCD, which was from
Rhodococcus erythropolis XP, into the solvent-tolerant strain
P. putida Idaho. Biphasic reactions were performed to investigate the
desulfurization of various sulfur-containing heterocyclic compounds
in the presence of various organic solvents.
P. putida A4 had
the same substrate range as
R. erythropolis XP and could degrade
dibenzothiophene at a specific rate of 1.29 mM g (dry weight)
of cells
1 h
1 for the first 2 h in the presence
of 10% (vol/vol)
p-xylene.
P. putida A4 was also able to degrade
dibenzothiophene in the presence of many other organic solvents
at a concentration of 10% (vol/vol). This study is a significant
step in the exploration of the biotechnological potential of
novel biocatalysts for developing an efficient biodesulfurization
process in biphasic reaction mixtures containing toxic organic
solvents.

INTRODUCTION
Sulfur oxides generated by the combustion of sulfur-containing
fossil fuel cause severe environmental pollution. Biodesulfurization
is thought to be an interesting alternative for the development
of a new petroleum-refining process (
2,
10,
11,
16,
18,
39).
The derivatives of dibenzothiophene (DBT) and benzothiophene
(BT), as well as other polycyclic aromatic sulfur heterocyclic
compounds (PASHs), are the most abundant heterocyclic compounds
in petroleum. Alkyl DBTs and alkyl BTs are highly recalcitrant
to chemical catalysts, especially when they are alkylated at
positions 4 and 6 (
17,
19,
25). Many researchers have investigated
biological desulfurization systems using DBT or alkyl DBTs as
model compounds, and the metabolic pathway of desulfurization
was proposed to be the so-called "4S" pathway, which removes
sulfur while leaving the carbon backbone intact (
12,
18,
20,
22,
38).
The genes responsible for the "4S" pathway of Rhodococcus erythropolis IGTS8 have been cloned and sequenced. There are three open reading frames, which are transcribed in the same orientation and are designated dszA, dszB, and dszC, as shown in Fig. 1 (28). The reaction catalyzed by the products of dszABC requires addition of reduced flavin (reduced flavin mononucleotide), which cannot be replaced by reduced pyridine nucleotide (NADH) or other flavins (flavin adenine dinucleotide or riboflavin). DszD is a flavin reductase which during NADH oxidation supplies the reducing equivalents to the desulfurizing reaction. The dszD gene encoding DszD, which is located on the chromosome, has been introduced into many strains to enhance the desulfurizing activity (8, 9, 11, 27, 37).
A biphasic system containing water-immiscible organic solvents
has been exploited for biocatalysis because it can overcome
the problem of low productivity in conventional media caused
by poor substrate solubility. A biphasic system can also integrate
bioconversion and product recovery in a single reactor and shift
the chemical equilibrium to enhance yields and selectivity (
21,
34). However, many organic solvents are highly biotoxic and
can kill most microorganisms even at low concentrations (0.1%,
vol/vol), which has made selection of a solvent that combines
adequate physicochemical properties with biocompatibility a
difficult task (
13,
21). Fuel oil has properties similar to
those of an organic solvent and is also toxic to microorganisms.
An immobilized-cell system was used previously to alleviate
the harmful effects of oil in microbial desulfurization of fuels
(
23,
36). However, the mass transfer resistance is enhanced
compared to that in free-cell systems, mainly due to internal
mass transfer limitations (
21). It would be preferable to have
free cells that exhibit high activity in the presence of organic
solvents. Bacteria isolated from an environment contaminated
by organic compounds, such as toluene and xylene, were able
to tolerate organic solvents due to their special structure
and their characteristic physiological mechanisms (
15). Some
of these strains could grow even when the organic solvent concentration
was more than 50% (vol/vol) (
4). Microorganisms with a high
tolerance to organic solvents are useful and important in many
biotechnological fields, such as biodesulfurization and biocatalysis
(
5,
21). However, there have been no reports concerning biodesulfurization
in the presence of high concentrations of toxic organic solvents.
Considering the difficulty of isolating strains having both
solvent tolerance and the desired catalytic activity from the
environment, it may be wise to combine solvent tolerance and
some unique catalytic characteristics using genetic engineering
methods. The aim of this investigation was to introduce the
biodesulfurizing genes into a solvent-tolerant strain in order
to develop a novel biocatalyst that was effective in biphasic
conditions.

MATERIALS AND METHODS
Bacterial strains, plasmid, and growth conditions.
Escherichia coli DH5

was used for general cloning. The genes
responsible for DBT degradation were obtained from
R. erythropolis XP, a DBT-desulfurizing bacterium that uses the "4S" pathway.
R. erythropolis XP was cultivated as previously described (
38).
A solvent-tolerant strain,
Pseudomonas putida Idaho, was used
as the host strain (
4). The broad-host-range expression vector
pMMB66EH was also used in this study (
7).
Pseudomonas cells were initially grown in modified Pseudomonas medium 187 (M187) containing (per liter of distilled water) 10 g of yeast extract, 10 g of Bacto Tryptone (Difco), 5 g of K2HPO4, 10 ml of glycerol, and 5 ml of a metal salts solution. The metal salts solution contained (per liter of distilled water) 0.4 g FeSO4, 0.2 g NaCl, 0.4 g MgSO4 · 7H2O, and 0.2 g MnSO4 · 4H2O, and H2SO4 was added until the pH was less than 3.0. The medium without the salts solution was autoclaved for 20 min; the salts solution was sterilized by passage through a 0.22-µm membrane filter. The cells were cultivated at 30°C on a rotary shaker at 180 rpm. For cultivation of P. putida A4, 1 mM isopropyl-ß-D-thiogalactoside (IPTG) was added to induce expression of dszABCD. For the two-phase reactions, Pseudomonas cells were resuspended and cultivated in M9 minimal medium (24). Growth media were supplemented with ampicillin (100 mg liter1 for E. coli and 1 g liter1 for Pseudomonas) if necessary.
General cloning procedures.
Restriction digestion, agarose gel electrophoresis, isolation of plasmids, and other DNA manipulations were carried out by using standard protocols (26, 31). Primers were designed based on the sequences of dszD and dszABC of R. erythropolis IGTS8. The dszD gene of R. erythropolis XP was amplified with primers dszDf and dszDr using R. erythropolis XP genomic DNA as the template. Similarly, the dszABC gene cluster was amplified with dszf and dszr. The sequences of the four primers were as follows: dszDf, 5'-GAGGAATTCATGTCTGACAAGCCGAATGCC-3' (EcoRI restriction site underlined); dszDr, 5'-CACTCTAGACTATTGACCTAACGGAGTCGG-3' (XbaI restriction site underlined); dszf, 5'-CACTCTAGAAGGACGCATACGCGATGACTC-3' (XbaI restriction site underlined); and dszr, 5'-GATCAAAGCTTCAGATCCTCAGGAGGTGAA-3' (HindIII restriction site underlined). The 0.6-kb dszD PCR product was digested with EcoRI and XbaI, and the 3.7-kb dszABC PCR product was digested with XbaI and HindIII. Then the two fragments were ligated into EcoRI-HindIII-digested pMMB66EH. The resulting plasmid was designated pMMABCD (Fig. 1).
A recombinant Pseudomonas strain harboring pMMABCD was constructed by the triparental mating method (35) with helper plasmid pRK2013 (a gift from David H. Figurski, Department of Microbiology, Columbia University, New York, NY). The cell mass was plated on M9 minimal medium plates supplemented with citrate and 1 g liter1 ampicillin. Colonies were transferred onto M187 agar plates supplemented with 1 g liter1 ampicillin and flooded with pure p-xylene. Then the plates were sealed and incubated at 30°C for 72 h. The solvent-tolerant transformants that appeared were tested for DBT degradation.
Bioavailability analysis.
Seed cultures of P. putida A4, P. putida Idaho, and R. erythropolis XP were diluted 25-fold using basal salts medium (BSM) (38) supplemented with 0.5 mM DBT or Na2SO4 as a sulfur source, with or without 10% (vol/vol) p-xylene. Then incubation was performed in seal-capped 300-ml flasks at 30°C and 180 rpm for 24 h on a rotary shaker; 1 g liter1 ampicillin and 1 mM IPTG were added for cultivation of P. putida A4. Growth was determined by measuring the absorbance at 600 nm using a UV-Vis spectrophotometer.
Southern hybridization analysis.
Southern hybridization experiments were performed using a DIG DNA labeling and detection kit (Roche). Probes were prepared by random primer labeling with digoxigenin according to the manufacturer's instructions. Hybridization was performed overnight at 52°C to detect the dsz gene cluster. Filters (positively charged nylon transfer membranes) were washed under high-stringency conditions twice for 5 min at room temperature in 2x SSC-0.1% sodium dodecyl sulfate and then twice for 15 min at 68°C in 0.1x SSC-0.1% sodium dodecyl sulfate (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate).
Biphasic reaction.
All the reactions involving organic solvents (except the growth of P. putida A4 in the presence of p-xylene) were performed using cell suspensions, and organic solvents were added to a final concentration of 10%. Pseudomonas cells for this type of reaction were grown in M187 supplemented with 1 mM IPTG and 0.1% p-xylene at 30°C for 12 h (1 g liter1 ampicillin was added when P. putida A4 was grown), centrifuged, and resuspended in M9 minimal medium to obtain a concentration of 7.31 g liter1. These experiments were carried out in 250-ml seal-capped flasks which were incubated at 180 rpm for 12 h. At each time, an entire reaction flask was analyzed, which minimized the error due to sampling of an aqueous-organic emulsion. The controls were reaction mixtures without bacteria or with heat-inactivated bacteria as described above.
Analytical methods.
Substrate consumption and product formation were analyzed by gas chromatography with flame ionization detection (CP3380; Varian Associates) using an SPB-5 column (inside diameter, 0.32 mm; length, 30 m; Supelco) after the reaction solution was extracted with 0.5 volume ethyl acetate at a pH less than 2.0. Chromatography was performed with nitrogen gas as the carrier gas, using an oven temperature program in which the temperature started at 50°C and then increased to 300°C at a rate of 20°C min1 and was kept at 300°C for 5 min. The injector and detector temperatures were 275°C and 280°C, respectively. The volume injected was 1 µl.
The molecular structures of the metabolites were analyzed using gas chromatography-mass spectrometry (GCD 1800C; Hewlett-Packard) with a 50-m DB-5 mass spectrometry column (J&W Scientific, Folsom, CA), and the metabolites were identified using the WILEY 275 mass spectral database. Typically, 50 ml of an induced P. putida A4 cell suspension in M9 minimal medium (7.31 g liter1) was incubated with 0.5 mM PASHs, such as DBT, at 30°C and 180 rpm for 24 h on a rotary shaker. Then the broth was extracted with 0.5 volume of ethyl acetate at a pH less than 2.0. The ethyl acetate extract was then concentrated under nitrogen gas before injection. Chromatography was performed with nitrogen as the carrier gas, using an oven temperature program in which the temperature started at 60°C, increased to 150°C at a rate of 10°C min1, and then increased to 280°C at a rate of 15°C min1. The volume injected was 1 µl.
Nucleotide sequence accession numbers.
The nucleotide sequences have been deposited in the GenBank database under accession numbers AY278323 (dszABC) and AY569038 (dszD).

RESULTS
Construction of P. putida A4.
Recombinant plasmid pMMABCD was introduced into the solvent-tolerant
strain
P. putida Idaho by the triparental mating method. Many
transformants were obtained, and some of them were selected
for further study. One, designated
P. putida A4, was selected
from the solvent-tolerant transformants because of its desulfurization
ability. To confirm that
P. putida A4 was the desired transformant,
Southern hybridization analysis was performed, and a 4.3-kb
restriction fragment was detected (see Fig. S1 in the supplemental
material). The partial 16S rRNA gene sequence in the diagnostic
region (nucleotides 1 to 500) of
P. putida A4 was 100% homologous
to sequences of
P. putida strains that have been deposited in
the GenBank database (nucleotide sequence accession numbers
AY772474, AY574282, AY647158, DQ192174, DQ192173, and AE016778).
In addition, bioavailability experiments were performed with
DBT or Na
2SO
4 as the sole sulfur source.
P. putida A4 was able
to grow in BSM supplemented with 0.5 mM DBT, 1 mM IPTG, and
10%(vol/vol)
p-xylene, while no growth of
P. putida Idaho or
R. erythropolis XP was detected under the same conditions (Table
1). All these results indicated that the
dszABCD gene cluster
was successfully expressed in
P. putida A4, which enabled
P. putida A4 to grow with DBT as the sole sulfur source.
Growth of P. putida A4 with 10% (vol/vol) p-xylene.
P. putida A4 was able to grow in M187 supplemented with
p-xylene.
When 10%
p-xylene and a 4% inoculum were added, the absorbance
at 600 nm of the broth reached 3.3 (dry cell weight, 1.77 g
liter
1) after 22 h of shaking at 30°C. The growth
curve in Fig.
2 shows that there was a transient decrease in
biomass and a lag phase after 10%
p-xylene was added.
Desulfurization of heterocyclic sulfur compounds.
To investigate the effect of the host strain on the desulfurizing
enzyme system, induced cells of
P. putida A4 were incubated
in M9 minimal medium (without
p-xylene) supplemented with some
PASHs, such as DBT, methyl DBTs, and methyl BTs, at 30°C
and 180 rpm for 24 h. Then the broth was extracted and analyzed
by gas chromatography-mass spectrometry to detect the metabolites
of PASH degradation by the recombinant strain
P. putida A4.
2-Hydroxybiphenyl and 2-hydroxy-3,3'-dimethyl-biphenyl were
detected as metabolites of DBT and 4,6-dimethyldibenzothiophene
(4,6-DM-DBT), respectively; 2-hydroxy-3'-methyl-biphenyl and
2-hydroxyl-3-methyl-biphenyl were metabolites of 4-methyldibenzothiophene
(4-M-DBT). Moreover, 2-isopropenylphenol was the metabolite
of 3-methylbenzothiophene (3-M-BT), as shown in Fig. S2 in the
supplemental material.
Desulfurization in organic solvent medium.
Free cells of P. putida A4, P. putida Idaho, and R. erythropolis XP were resuspended in M9 minimal medium and shaken in 300-ml seal-capped flasks (20 ml of fluid in each flask) at 30°C and 180 rpm with 10% (vol/vol) p-xylene and 0.5 mM (91.13 mg liter1) DBT in order to investigate the degradation with an organic solvent present. After a 40-h reaction, 97% of the DBT was degraded by P. putida A4, and the majority (86%) was degraded in the initial 6 h; no decrease in the amount of DBT was observed in the reactions performed with R. erythropolis XP, P. putida Idaho, or the controls (Fig. 3). The specific rate of degradation in the first 2 h was 1.29 mM DBT g (dry weight) of cells1 h1.
The PASHs 3-M-BT, DBT, 4-M-DBT, and 4,6-DM-DBT were shaken separately
with cell suspensions of
P. putida A4 in M9 minimal medium supplemented
with 10%
p-xylene to investigate the ability of
P. putida A4
to desulfurize different heterocyclic sulfur compounds in an
organic solvent.
P. putida A4 was able to degrade 97% of the
DBT, 54% of the 4-M-DBT, 71% of the 4,6-DM-DBT, and 53% of the
3-M-BT (Fig.
4). The specific rates of degradation of DBT, 4-M-DBT,
4,6-DM-DBT, and 3-M-BT in the first 2 h were 1.29 mM g (dry
weight) of cells
1 h
1, 0.72 mM g (dry weight) of
cells
1 h
1, 0.69 mM g (dry weight) of cells
1 h
1, and 0.54 mM g (dry weight) of cells
1 h
1,
respectively.
Organic solvents with different values for the common logarithm
of the partition coefficient of a solvent in the
n-octane and
aqueous phases (log P) were used to demonstrate the effects
of different organic solvents on the desulfurizing activity.
Heptanol (log P, 2.4), styrene (log P, 2.9),
p-xylene (log P,
3.1), ethylbenzene (log P, 3.3), cyclohexane (log P, 3.4),
o-dichlorobenzene
(log P, 3.6), diphenylether (log P, 4.2), isooctane (log P,
4.8), and
n-dodecane (log P, 7.0) were added to cell suspensions
(in M9 minimal medium) of induced
P. putida A4 cells at a concentration
of 10% (vol/vol), and the total volume in every 250 ml seal-capped
flask was 20 ml. Then 0.5 mM DBT was added to each flask, and
the flasks were incubated for 12 h with shaking at 30°C
at 180 rpm on a rotary shaker.
P. putida A4 was capable of degrading
DBT with high activity in the presence of organic solvents (Fig.
5).
Additionally, since
P. putida A4, as well as the host strain
P. putida Idaho, was able to tolerate up to 50%
p-xylene, the
biodesulfurization activities in the presence of different concentrations
of
p-xylene were examined. When 20% (vol/vol), 30%(vol/vol),
40%(vol/vol), and 50%(vol/vol)
p-xylene were added to
P. putida A4 cell suspensions in M9 minimal medium in 300-ml seal-capped
flasks and shaken at 30°C for 12 h, the extents of DBT degradation
were 70%, 58%, 48%, and 48%, respectively.

DISCUSSION
Pseudomonas sp. is considered the ideal host for biodesulfurization
because of its high growth rate, its metabolic diversity, its
well-documented ability to carry out biotransformation in biphasic
systems, and the availability of genetic techniques (
29). In
addition, biodesulfurization is an energetically expensive multistep
process that consumes flavin mononucleotide as reducing equivalents
(
11). Cell integrity and viability are necessary for this type
of reaction (
14,
21,
34). Therefore, solvent-tolerant
Pseudomonas strains may be efficient hosts for the desulfurizing enzyme
system, as they are able to supply energy and the necessary
reaction conditions in the presence of organic solvents and
thereby maintain good desulfurizing activity in the oil desulfurization
process. In this study, the
dszABCD genes were introduced into
P. putida Idaho in order to construct a solvent-tolerant desulfurizing
bacterium which could work well with organic solvents. This
study is a significant step in the exploration of the biotechnological
potential of novel biocatalysts for developing an efficient
biodesulfurization process.
There are factors about a host strain, such as the pH of the cytosol, the penetrability of the cell wall and cell membrane, and the respiratory activity, that can affect the efficiency and specificity of the enzyme system introduced into the host strain (3, 33). Thus, different PASHs were used to determine the effect of host strain P. putida Idaho on the specificity of the desulfurizing enzyme system. It should be noted that the metabolite(s) of each PASH produced by P. putida A4 was the same as the metabolite(s) produced by R. erythropolis XP (38). This result indicated that host strain P. putida Idaho did not affect the specificity of the desulfurizing enzyme system from R. erythropolis XP and that the desulfurizing enzyme system worked well in the host strain.
In general, solvents with log P values between 1 and 4 are considered extremely toxic to microorganisms, as the degree of partition into the cell membrane is high, and most microorganisms are not able to survive in organic solvents present in the environment (1, 13, 32). This is a shortcoming for the use of many bacteria in biodesulfurization and biphasic reactions (12). p-Xylene is one of these extremely toxic organic solvents and has log P value of 3.1. P. putida A4 was able to grow well in M187 supplemented with 10% p-xylene, although a transient decrease in biomass and a lag phase were observed after addition of 10% p-xylene (Fig. 2). It is reasonable to suggest that the transient decrease in biomass and the lag phase were due to the organic solvent shock (4). It is notable that there was no growth lag after IPTG was added at 11 h, which indicated that gene expression did not affect the growth of P. putida A4 in organic solvent. It is also notable that P. putida A4 was able to degrade various PASHs, such as DBT, 4-M-DBT, 4,6-DM-DBT, and, 3-M-BT, in the presence of 10% p-xylene and could maintain desulfurizing activity even in the presence of 50% p-xylene. Desulfurization of oils may be more successful with the solvent-tolerant strain P. putida A4.
There are many different organic solvents in oil, polluted environments, and biocatalytic media, and the toxic effects of them on microorganisms correlate with the hydrophobicity, expressed as log P. Thus, solvents with different log P values were examined to determine their effects on desulfurizing activity. P. putida A4 was able to tolerate all the organic solvents used in our study and to maintain the desulfurizing activity of the desulfurizing enzyme system (Fig. 5). de Carvalho et al. investigated the toxicities of dimethylformamide, ethanol, and butanol for Mycobacterium sp., R. erythropolis, and P. putida using fluorescence microscopy technology and found that the toxicities of organic solvents did not correspond to the log P values of solvents (6). Similar results were obtained in this study. It is reasonable to suggest that the unique mechanism of solvent tolerance of P. putida A4 and the unique chemical characteristics of different solvents led to these unexpected results. Cruden et al. suggested that the resistance of P. putida Idaho was due to the ability of this organism to synthesize membranes rapidly to compensate for the membranes damaged by solvents or due to some biochemical difference in the cytoplasmic membrane which makes it more stable in the presence of solvent (4, 30). This unique mechanism of solvent tolerance may be the reason for the broad range of substrates which P. putida A4 can tolerate.
In conclusion, our results suggested that P. putida A4, constructed by introducing dszABCD into P. putida Idaho, could remain viable and exhibit desulfurizing activity with a variety of organic solvents that were present separately. This is the first example of an organism that can efficiently desulfurize in organic solvent-based biphasic media, and this implies that this technology has a future. Currently, the expression of dsz genes is directed by the tac promoter, which makes commercial application of this strain less advisable. For practical application, promoter substitution is necessary, and such work is being performed by members of our group.

ACKNOWLEDGMENTS
This work was supported by the National Natural Science Foundation
of China (grants 20590368 and 29977011).
We thank David T. Gibson for supplying P. putida Idaho, Erich Lanka for supplying plasmid pMMB66EH, David H. Figurski for supplying plasmid pRK2013, and Juan L. Ramos for supplying important literature.

FOOTNOTES
* Corresponding author. Mailing address: State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China. Phone: 86 531 88564003. Fax: 86 531 88567250. E-mail:
pingxu{at}sdu.edu.cn.

Supplemental material for this article may be found at http://aem.asm.org/. 
F.T. and B.Y. contributed equally to this work. 

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Applied and Environmental Microbiology, July 2006, p. 4604-4609, Vol. 72, No. 7
0099-2240/06/$08.00+0 doi:10.1128/AEM.00081-06
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