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Biotechnol Lett (2014) 36:2229–2237

DOI 10.1007/s10529-014-1595-1

ORIGINAL RESEARCH PAPER

Characterization of industrially-valuable xylano-


pectinolytic enzymes produced concurrently by a novel
isolate of Bacillus pumilus
Amanjot Kaur • Avtar Singh • Ritu Mahajan

Received: 19 May 2014 / Accepted: 19 June 2014 / Published online: 22 July 2014
Ó Springer Science+Business Media Dordrecht 2014

Abstract Xylanase and polygalacturonase were Introduction


concurrently produced by a novel alkalo-thermotoler-
ant Bacillus pumilus AJK. They were purified and Xylanases and pectinases are produced by microorgan-
characterized to evaluate their potential for various isms but there are only three reports, two concerning
industrial applications. Xylanase was purified to fungi (Botella et al. 2007; Gomes et al. 1992) and one
19-fold with 67 % recovery and polygalacturonase concerning Streptomyces sp. (Beg et al. 2000), showing
up to 23-fold with 75 % recovery. Existence of the production of these two industrially-valuable
multiple forms of xylanase was indicated by its enzymes in combination from the same isolate, but these
elution-profile through Sephadex G-100 as two peaks, workers have not reported the presence of acidic and
xylanase-I and xylanase-II, with molecular weights of alkaline forms of xylanase. In this study, the industrially-
*24.5 and *13 kDa, respectively, and by the important Bacillus pumilus AJK produces xylanase and
presence of two pH optima, one at pH 6.0 and other polygalacturonase in combination. Purification of these
at pH 8.5. The molecular weight of polygalacturonase enzymes is necessary to know the various characteristics
was *40 kDa by gel-filtration chromatography. Zy- of these enzymes so that they could be efficiently used for
mographic studies confirmed the presence of seven various industrial purposes. This is the first report of the
isozymic forms of xylanase. Xylanase and polygalac- purification of concurrently produced xylanase and
turonase are stable over a broad range of pH and polygalacturonase from a bacterium.
temperature. The unique property of this multifunctional strain
(high concurrent producer of acidic xylanase, alkaline
Keywords Bacillus pumilus  Pectinase  xylanase and pectinase in the same production media,
Polygalacturonase  Purification  Ultrafiltration  is desirable from economic point of view) has not been
Xylanase  Xylano-pectinolytic enzyme  Zymography reported earlier in bacteria. Multiple forms of xylan-
ases (acidic and alkaline) show its suitability for wide
range of industrial applications. The xylanase and
A. Kaur  A. Singh  R. Mahajan (&)
polygalacturonase produced simultaneously were
Department of Biotechnology, Kurukshetra University,
Kurukshetra 136119, India purified and extensively characterized for various
e-mail: ritupanipat@rediffmail.com properties like, pH optima, temperature optima, sta-
A. Kaur bility at different temperature and pH values, kinetic
e-mail: amanjotbiotech@gmail.com properties, molecular weight, activities of these
A. Singh enzymes in the presence of various additives etc. to
e-mail: avtarsingh87@gmail.com find their suitability in various industries.

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2230 Biotechnol Lett (2014) 36:2229–2237

Materials and methods glycine/NaOH buffer (10 mM, pH 8.5) to concen-


trated the retentate in order to get maximum recovery
Microorganism of desired enzymes. In the second step, the permeate
(obtained above) was passed through a 3 kDa NMWC
A concurrent producer of xylanase and pectinase, B. membrane. The extract was concentrated tenfold
pumilus AJK, was isolated from soil contaminated followed by discontinuous diafiltration, so that low
with the effluents of paper and pulp industry (Kaur molecular weight impurities could get maximally
et al. 2011). removed.

Production of xylano-pectinolytic enzymes Ammonium sulphate fractionation

Xylano-pectinolytic enzymes were produced under The ultrafiltered extract was subjected to (NH4)2SO4
submerged fermentation in 50 ml basal medium (g/l: precipitation to different cut-offs (0–25, 25–50, 0–50,
peptone, 5; MgSO47H2O, 2.46; pH 7) supplemented 25–70, 50–70 % saturation). The protein precipitates
with 2 % (w/v) wheat bran and 2 % (w/v) citrus peel. obtained after different cut offs were dissolved in a
The flasks were inoculated with 2 % (v/v) inoculum minimum volume of 10 mM glycine/NaOH buffer
(21 h old, OD * 0.85) and incubated at 37 °C for (pH 8.5). The precipitate sample and supernatant were
60 h at 200 rpm. Crude xylano-pectinolytic enzymes analyzed for xylanase and polygalacturonase activity
were harvested by centrifugation. at each fractionation step. The ammonium sulphate
concentrated xylanase and polygalacturonase samples
Enzyme assay and protein estimation were ultrafiltered using 1 kDa NMWC membrane
followed by discontinuous diafiltration for removing
The enzyme activities were determined using the the salt and then loaded onto gel filtration column.
method of Miller (1959). Birchwood xylan, 2 % (w/v)
(prepared in 0.1 M glycine/NaOH buffer, pH 8.5) and Gel filtration chromatography and molecular weight
polygalacturonic acid, 0.5 % (w/v) (prepared in 0.1 M determination
glycine/NaOH buffer, pH 9.0) were used as substrates
for assaying the activity of xylanase and polygalactu- A Sephadex G-100 column (95 9 0.8 cm) was pre-
ronase, respectively, as described by Kaur et al. equilibrated with 10 mM glycine/NaOH buffer, pH
(2011). Protein was estimated by the Bradford method 8.5. The partially purified xylanase and polygalactu-
using bovine serum albumin as standard. The protein ronase obtained after ammonium sulfate fractionation
content of the chromatographic fractions was also were loaded separately onto this column, which was
measured by monitoring the absorbance at 280 nm. run at 15 ml/h. Fractions 1 ml were collected and
analyzed for protein at 280 nm as well as xylanase or
Purification of xylanase and polygalacturonase polygalacturonase activity. Active fractions were
pooled and concentrated using ultrafiltration (1 kDa
The crude enzymes were purified using fast flow and NMWC) membrane and stored at 4 °C till further use.
conventional purification techniques. All steps of A mixture of gel filtration protein molecular weight
purification were carried out at 4 °C. markers containing (1) cytochrome c (12.4 kDa) (2)
carbonic anhydrase (29 kDa) (3) albumin (66 kDa) (4)
Microfiltration and ultrafiltration of crude extract alcohol dehydrogenase (150 kDa) and (5) b amylase
(200 kDa) was loaded on the Sephadex G-100 column
Clarification of the crude turbid extract was done by a under the above identical conditions and their elution
microfiltration unit (GE Healthcare Biosciences Ltd). volumes were determined. A standard graph was then
The extract obtained after microfiltration was ultrafil- plotted between Ve/Vo on the x-axis and log molec-
tered using 100 kDa nominal molecular weight cutoff ular weight on the y-axis for the calculation of the
(NMWC) membrane. Discontinuous diafiltration was molecular weight of the purified xylanase and
done three times by adding an equal volume of polygalacturonase.

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Biotechnol Lett (2014) 36:2229–2237 2231

Testing of enzymes purity The polygalacturonase clear halo was observed by


overlayering the complete purified polygalacturonase
Purity was checked by native-PAGE. Xylanase and lane of the native PAGE gel onto a 1 % (w/v) agar gel
polygalacturonase samples were run on 10 % native containing 0.1 % (w/v) polygalacturonic acid and
PAGE gel. To avoid the merging of bands of isozymic incubated for 1 h at 37 °C. After incubation, agar-
forms of xylanase, purified xylanase was run on 12 % polygalacturonic acid gel was stained with 1 % (w/v)
native PAGE gel (160 9 200 mm) in a long electro- CTAB (Hadj-Taieb et al. 2011) for 30 min, washed
phoresis gel apparatus. Protein bands were visualized with deionised water, and the zymogram was observed
by silver staining. for clear halos.

Characterization of purified xylanase


Zymography and polygalacturonase

For zymogram analysis, complete purified xylanase The effect of pH on enzymes activity was determined
(run on 12 % native PAGE gel) lane was overlayered by performing assays at different pH values (4–11)
onto 1 % (w/v) agar gel containing 0.1 % (w/v) xylan using the following buffers (100 mM); citrate buffer
and incubated for 20 min at 37 °C. Another purified pH 4–6, phosphate buffer pH 6–8, Tris/HCl buffer pH
xylanase lane of native PAGE gel was cut (corre- 8–9, glycine/NaOH buffer pH 8.5–11 and the stability
sponding to the bands of silver stained purified of enzymes over wide range of pH was investigated by
xylanase lane) into short gel pieces and all gel pieces mixing equal aliquots of purified enzyme and different
were overlayered far away from each other onto 1 % buffers (pH 4–11) followed by incubation at 37 °C.
(w/v) agar gel containing 0.1 % (w/v) xylan, and The effect of temperature on xylanase and polygalac-
incubated for 40 min at 37 °C to detect all the turonase activities was investigated by performing
isozymic forms of xylanase. After incubation, sub- enzymes assay at different temperatures (45, 50, 55,
strate-agar gels were stained with 0.5 % (w/v) Congo 60, 65, and 70 °C) and the temperature stability profile
Red for 15 min, destained with 1 M NaCl, and the was studied after pre-incubating these enzymes at
zymogram was observed for clear halos. To confirm different temperatures (4–55 °C) for variable time
the presence of isozymic forms of xylanase, the intervals. The effect of various metal ions and other
purified xylanase was run on native 12 % PAGE and additives (see Table 2 below) on xylanase and poly-
then the complete purified xylanase lane (cut from rest galacturonase activity was also studied. The Linewe-
of the gel) was rotated and placed at an angle of 908 on aver–Burk plot of the enzyme activity against
another native PAGE gel and again run to get the substrate concentration was plotted to determine the
bands separated in two dimensions. This gel was over- Km and Vmax values. The enzyme activity was
layered onto 1 % (w/v) agar gel containing 0.1 % (w/ estimated after incubating the optimally diluted
v) xylan, and incubated for 2 h at 37 °C. The halos enzyme sample at 55 °C with different concentrations
were observed after treating the gel with congo red. of birchwood xylan (2.5–15 mg/ml) and polygalactu-
The presence of isozymic forms of xylanase was ronic acid (0.3–5 mg/ml) as substrates for xylanase
reconfirmed in another way, the purified xylanase was and polygalacturonase, respectively.
run on native PAGE (12 %) and then the purified
xylanase lane of the polyacrylamide gel was cut
(corresponding to the bands of silver stained purified Results and discussion
xylanase lane) into short gel pieces. All gel pieces
were individually placed in separate wells one after the Enzymes purification
other in the same dimension on another native PAGE
gel and again run to get the well separated bands. This After passing the crude enzyme from microfiltration
gel was overlayered onto 1 % (w/v) agar gel contain- unit, the membrane based process of ultrafiltration,
ing 0.1 % (w/v) xylan, and incubated for 2 h at 37 °C. using 100 and 3 kDa NMWC membrane followed by
The isozymic forms were observed by the same congo discontinuous diafiltration, was used for the purifica-
red method. tion of xylano-pectinolytic enzymes. The ultrafiltration

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Table 1 Summary of the purification of xylanase and polygalacturonase from Bacillus pumilus AJK
Purification steps Enzyme Total activity Total protein Specific activity Yield Fold
(IU) (mg) (IU/mg) (%) purification

Crude microfiltereda Xylanase 560,000 2,000 280 100 1


supernatant Polygalacturonase 180,000 2,000 90 100 1
Ultrafiltrationb (cut off Xylanase 558,330 1,030 542 99.7 1.93
100 kDa) Polygalacturonase 176,794 1,030 172 98.2 1.9
Ultrafiltrationc (cut off Xylanase 552,882 306 1,807 98.7 6.45
3 kDa) Polygalacturonase 171,278 306 560 95.15 6.2
(NH4)2SO4 precipitation Xylanase 459,204 126 3,644 82 13
(0–50 %) Polygalacturonase 154,806 101 1,532 86 17
(50–70 %)
Ultrafiltration (cut off Xylanase 448,004 114 3,929 80 14
1 kDa) Polygalacturonase 149,460 92.4 1,618 83 18
Sephadex G-100 Xylanase 375,212 70 5,360 67 19
Polygalacturonase 135,013 65 2,077 75 23
a
Microfiltration (membrane with a pore size of 0.2 micron) was operated at 0.34 atm transmembrane pressure
b
Ultrafiltration was operated at 0.41 atm transmembrane pressure followed by discontinuous diafiltration
c
Ultrafiltration was operated at 0.51 atm transmembrane pressure followed by discontinuous diafiltration

removed the high and low molecular weight proteins 2008). Gomes et al. (2009) have reported the purifi-
producing the partially purified xylano-pectinolytic cation of an exopolygalacturonase from Penicillium
retentate. Saturation of ultrafiltered enzyme extract viridicatum RFC3 by ultrafiltration, Sephadex G-75
with ammonium sulfate to 0–50 and 50–70 % cut offs gel filtration chromatography and Q Sepharose anion
precipitated xylanase and polygalacturonase, respec- exchanger with 37.7 fold purification and 3.4 %
tively. These precipitates were dissolved individually recovery.
in glycine/NaOH buffer (0.01 M, pH 8.5) and desalted
by 1 kDa NMWC membrane. Partially-purified xy- Molecular weight determination
lanase and polygalacturonase were loaded separately
in Sephadex G-100 column. Xylanase was eluted as Molecular weight of xylanase and polygalacturonase
two peaks from the Sephadex G-100 column, indicat- was determined by gel filtration chromatography using
ing the presence of at least two isozymic forms of standard gel filtration markers. Xylanase I and xylan-
xylanase. Fractions containing xylanase activity were ase II (two peaks of xylanase eluted from Sephadex
pooled and concentrated using a 1 kDa NMWC G-100 column) have a molecular weight of *24.5 and
ultrafiltration membrane. The elution profile of poly- *13 kDa, respectively, while the molecular weight of
galacturonase showed one peak. The polygalacturo- polygalacturonase was *40 kDa, as calculated from
nase fractions were also pooled and concentrated using the standard graph. Many xylanases (Kiddinamoorthy
ultrafiltration (1 kDa NMWC membrane). The purifi- et al. 2008) and pectinases (Kumar et al. 2012; Li et al.
cation fold, recovery and specific activity obtained 2008) produced by the Bacillus genus have molecular
after each purification step are given in Table 1. weights in the range of 20–45 kDa.
Xylanase was purified 19-fold with a 67 % recovery,
while polygalacturonase showed a 75 % recovery with Testing of enzymes purity and zymography
23-fold purification.
Xylanase by Bacillus sp. GRE7 was purified up to Native PAGE (10 %) of xylanase obtained after
28.5-fold with 27 % recovery using ammonium sul- different purification steps is shown in Fig. 1a.
phate precipitation followed by anion exchange and Initially, the two peaks of xylanase eluted from
gel filtration chromatography (Kiddinamoorthy et al. Sephadex G-100 were concentrated and run

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Biotechnol Lett (2014) 36:2229–2237 2233

Fig. 1 Native PAGE of a xylanase:- Lane C Crude xylanase; pooled, concentrated and run as purified xylanase on long
Lane U Ultrafiltered xylanase; Lane A Ammonium sulfate electrophoretic gel apparatus to avoid merging of bands)
concentrated xylanase; Lane F1 Fractions from Sephadex G-100 showing seven bands of xylanase:- Lane A low sample loading
covering peak I of xylanase were pooled, concentrated and run and Lane B heavy sample loading, and c purified polygalactu-
and Lane F2 Fractions from Sephadex G-100 covering peak II of ronase:- Lane C Crude polygalacturonase; Lane U Ultrafiltered
xylanase were pooled, concentrated and run, b purified xylanase polygalacturonase; Lane A Ammonium sulfate concentrated
(all active xylanase fractions covering peak I and peak II were polygalacturonase and Lane P Purified polygalacturonase

separately. The fractions covering peak I of purified long continuous activity band (Fig. 2a), while the
xylanase gave some merged bands of xylanase, while zymogram of short gel pieces from the purified
the fractions covering peak II of xylanase showed two xylanase lane (cut with respect to the bands observed
bands on the native PAGE. Finally, all the fractions of in stained purified xylanase lane) showed the presence
Sephadex G-100 column containing active xylanase of seven prominent activity bands (Fig. 2b). Thirdly,
(covering peak I and peak II) were pooled, concen- by using complete native PAGE gel, in which the
trated and run as purified xylanase on (12 %) native purified xylanase bands separated in one dimension
PAGE in a long electrophoresis gel apparatus to avoid were again separated in second dimension (Fig. 2c),
merging of bands. The gel after staining with silver its zymogram gave seven prominent activity bands
nitrate showed the presence of seven bands of (Fig. 2d) and fourthly, by using complete native
xylanase (Fig. 1b). The purified polygalacturonase PAGE gel, in which the purified xylanase bands were
eluted from Sephadex G-100 column showed a single again separated in same dimension (Fig. 2e). Its
band on (10 %) native PAGE gel (Fig. 1c). zymogram also gave seven prominent activity bands
The seven bands of xylanase were confirmed as (Fig. 2f). Thus, confirming the presence of seven
isozymic forms of xylanase by zymography. Zymog- isozymic forms of xylanase. Separation of xylanase
raphy was performed in four different ways. Firstly, bands in two dimensions and then performing its
by using complete purified xylanase lane and sec- zymography facilitated a more complete examination
ondly, by using purified xylanase lane gel pieces. The and confirmation of xylanase multiplicity. Graciliba-
zymogram of complete purified xylanase lane gave a cillus sp. TSCPVG secreted multiple xylanases in the

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Fig. 2 Zymogram of xylanase obtained by using a complete lane of native PAGE gel and, d its zymogram, e separation of
purified xylanase lane of native PAGE gel, b short gel pieces of purified xylanase bands by using the short gel pieces of purified
the purified xylanase lane (cut with respect to the bands obtained xylanase lane (cut with respect to the bands obtained on similar
on similar stained gel), c Two-dimensional separation of stained gel), and f its zymogram, g zymogram of polygalactu-
purified xylanase bands by using the complete purified xylanase ronase on polygalacturonic acid

extracellular medium and its zymogram analysis on 2010). A zymogram of polygalacturonase showed a
native PAGE gel showed ten multiple bands associ- single prominent activity band at position correspond-
ated with xylanase activity (Giridhar and Chandra ing to that of the band in native PAGE (Fig. 2g).

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Thus, confirmed the presence of a single form of Table 2 Effect of metal ions and other additives on purified
polygalacturonase. xylanase and polygalacturonase produced by Bacillus pumilus
AJK

Characterization of the purified xylanase Metal ion Xylanase Polygalacturonase


and polygalacturonase (1 mM) activity (%) activity (%)

Control 100 100


The purified xylanase showed two pH optima, one at KCl 61 125
pH 6.0 and other at pH 8.5, indicating the presence of NaCl 75 100
isozymic forms of xylanases. Maximum polygalactu- CaCl2 85 80
ronase activity was obtained at pH 9.0. Many MgCl2 153 190
researchers have reported the optimum pH of xylan- CuCl2 89 90
ases in the range of 6.0–9.0 (Nagar et al. 2012), while
CoCl2 70 225
reports on pectinases having optimum pH in the range
BaCl2 106 140
of 8.0–9.0 are also available (Celestino et al. 2006).
HgCl2 16 103
The xylanase was most stable at pH 8.0 and retained
MnSO4 89 295
almost 100 % of its original activity from pH 6.0–11.0
FeSO4 66 103
up to 3 h, while the polygalacturonase was 100 %
ZnCl2 67 203
stable at pH 8–9 even after 48 h of incubation and
Urea 8 80
more than 80 % stable from pH 6.0–11.0 even after
EDTA 96 178
72 h of incubation. The concentrated form of the
SDS 25 34
enzyme was more stable at different pH values (data
b-mercaptoethanola 112 148
not shown). Purified xylanase from B. pumilus SV-85S
Tween 20 150 115
was fully stable from pH 5 to 11 after 1 h of incubation
(Nagar et al. 2012). Pectin lyase from Aspergillus Tween 80 121 243
flavus was stable for 24 h in the pH range 4.0–10.0 Triton X-100a 120 120
(Yadav et al. 2008). To evaluate the effect of various metal ions and additives on
Both purified xylanase and polygalacturonase gave xylanase and polygalacturonase activity, the enzyme sample
was incubated for 1 h at room temperature in the presence of
maximum activities at 55 °C, though they retained
different metal ions and additives. Thereafter, xylanase and
more than 85 % residual activity from 50 to 60 °C. polygalacturonase assays were performed. The 100 % values
Most of xylanolytic (Kamble and Jadhav 2012) and of xylanase and polygalacturonase activities were 280 and
pectinolytic (Celestino et al. 2006; Nadaroglu et al. 90 IU/ml, respectively. Values are given as the mean of three
replicates
2010) enzymes show maximum activity at 50–60 °C. a
The purified xylanase was moderately stable over a Final concentration 1 % (v/v)
wide range of temperatures, while polygalacturonase
showed higher stability. Both the enzymes were purified pectin lyase from B. pumilus (P9) appeared to
100 % stable at 4 °C for more than six months. The be stable and retained its full activity after 1 h
xylanase retained about 100, 85 and 58 % of its incubation from 40 to 50 °C, but the activity was
activity after 1, 2 and 3 days, respectively, whereas reduced to 20 % after 1 h at 60 °C (Nadaroglu et al.
polygalacturonase retained 100 and 56 % of its 2010).
activity after 20 and 25 days, respectively, when kept The effect of various metal ions and additives on
at 37 °C. The xylanase showed nearly 69 % activity at the activity of the purified enzymes was evaluated
50 °C after 1 h of incubation, while polygalacturonase (Table 2). Among the various metal ions tested, Mg2?
showed 98 and 62 % activity at 50 and 55 °C, enhanced the xylanase activity, whereas Ca2?, Mn2?
respectively even after 3 h of incubation. Stability and Cu2? brought slight fall in the activity. All other
was greatly enhanced, when enzyme was stored in metal ions such as Co2?, Zn2?, Hg2?, Fe3?, Na? and
concentrated form at different temperatures (data not K? were inhibitors of xylanase activity. Among the
shown). Xylanase from Cellulosimicrobium sp. various additives tested, b-mercaptoethanol, Tween
retained 86 % of its original activity at 40 °C after 20, Tween 80 and Triton X-100 slightly enhanced
4 h of incubation (Kamble and Jadhav 2012). The xylanase activity, whereas urea decreased the activity.

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Almost all the metal ions, except Ca2? and Cu2?, The present characterization study indicates that these
increased the polygalacturonase activity. Similarly, xylanase and pectinase preparations have great
the majority of the additives such as EDTA, b- potential to be used for various industrial applications
mercaptoethanol, Triton X-100, Tween 20 and Tween at very low cost.
80 increased polygalacturonase activity, whereas urea
decreased activity. In case of both xylanase and Acknowledgments The authors acknowledge the financial
support provided by University Grant Commission, India.
polygalacturonase, SDS was the most potent inhibitor
University Research Scholarship awarded to Amanjot Kaur by
causing almost 75 and 66 % inhibition of activity, Kurukshetra University is also kindly acknowledged.
respectively. The xylanase produced by Bacillus sp.
GRE7 was also inhibited with Cu2? and Fe2? but, Conflict of interest The authors declare that they have no
conflict of interest.
contrary to our data, showed an enhanced activity in
the presence of Mn2? and Co2? (Kiddinamoorthy
et al. 2008). The activities of three endopolygalactu-
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