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Department of Biological and Geological Sciences, Faculty of Education, Alexandria University, El-shatby 21526, Egypt
KEYWORDS Abstract Differential display method was applied to transcripts extracted from leaves of Limonia-
Phytoremediation; strum monopetalum to identify genes that are differentially expressed in response to crude oil pol-
Limoniastrum monopetalum; lution. The results showed that 201 bands with different molecular sizes were differentially
Differential display; expressed in polluted plants. Ten cDNA bands were considered to be consistently over-expressed
Crude oil under crude oil stress and selected for sequencing. Comparative analysis of these cDNA sequences
allowed us to classify them into six categories: (1) enzymes increase its activity under petroleum
stress and were a good marker of petroleum stress (e.g. xanthine dehydrogenase, metallothionein
type 2, and arginine decarboxylase), (2) nitrogen metabolism (e.g. glutamine synthetase and amido-
phosphoribosyltransferase), (3) drought genes (e.g. CPRD2), (4) salinity stress (e.g. retrotransposon
protein), (5) plant growth (e.g. aminocyclopropane-1-carboxylic acid and ribulose-1,5-bisphosphate
carboxylase oxygenase), and (6) transport related genes like proton-dependent oligopeptide trans-
port (POT) family protein. Coincidently with the differential display results, the amount of the total
protein differed signicantly between unpolluted and polluted plants (T = 3.687, P < 0.006). The
electrophoretic patterns (SDSPAGE) for water soluble proteins revealed that 11 peptides with
different molecular masses disappeared and eight different peptides were synthesized in polluted
plants. The results of up-regulated genes identied in this study may explain the way that
L. monopetalum populations established on the crude oil polluted soil and vigorous vegetative
growth of adult plants.
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Total RNA of L. monopetalum were extracted using total Total protein content per gm of dry leaves was determined
RNA kit according to manufactures instruction (Maxim according to the method described by Lowry et al. [40]. The
Biotech INC, USA). The RNA was dissolved in diethylpyro- identication and characterization of different molecular
carbonate (DEPC) treated water, quantitated spectrophoto- weights were obtained using one-dimensional sodium dodecyl
metrically and analyzed on 1% formaldehyde agarose gel. sulfate polyacrylamide gel electrophoresis (SDSPAGE). Poly-
acrylamide slab gel (12.5) was carried out using the discontin-
3.2. Reverse transcription of RNA uous buffer system as described by Laemmli [33]. The banding
pattern, molecular weight, and band percentage were analyzed
Reverse transcription reactions were performed using oligo dT using TotalLab version 1.11 software (Nonlinear Dynamics
primer (5-TTTTTTTTTTTTTTT-3). Each 25 ll reaction mix- Ltd., Durham, USA) in the presence of protein molecular
ture containing 2.5 ll of 5 buffer with 2 MgCl2, 2.5 ll of weight marker.
2.5 mM dNTPs, 1 ll of 10 pmol primer, 2.5 ll RNA of 2 mg/
ml, and 0.5 ll reverse transcriptase enzyme. PCR amplication 4. Results
was performed in a thermal cycler (Eppendorf, Germany) pro-
grammed at 95 C for 5 min, 42 C for 1 h, 72 C for 10 min. 4.1. Differential display
cDNA was then stored at 20 C until used.
Differential display was used to ascertain the genetic variation
3.3. Differential display using 16 primers between unpolluted and polluted populations. Sixteen primers
were used to detect increased gene expression in polluted
Sixteen primers were used in the differential display analysis plants (Table 1). One or more of these bands might be ap-
(Table 1). The reaction mixture for differential display PCR peared as mRNA in the total RNA isolated from the leaves.
was carried out in total volume 25 ll containing 2.5 ll 10 The total number of cDNA bands (genes) resolved in 1.5%
buffer with MgCl, 2 ll 2.5 mM dNTPs, 1 ll 10 pmol, 1.5 ll agarose gel for both unpolluted and polluted plants was 269
cDNA and 0.2 ll (5 units/ll) Taq DNA polymerase (Promega, and 278 respectively (molecular size ranged from10 bp to
Germany). PCR amplication was performed in a thermal 5439 bp) (Appendix Table A1 and Fig. 1). There were 201
140 R. El-Bakatoushi
Figure 1 Differential display using 16 primer for L. monopetalum. Control c1, c2, and c3 and polluted plants 1, 2, and 3. M: 3000 bp
ladder DNA marker (from 3000 to 100 bp), or 1000 (from 1000 to 200). Arrows refer to the expressed bands due to the effect of crude oil.
bands with different molecular sizes differentially expressed in 4.3. Protein analysis
polluted plants (genes were turned on). Meanwhile, 179 bands
were disappeared in polluted plants (a gene was turned off) The amount of the total protein differed signicantly between
(Fig. 2). Four bands with molecular sizes 351 bp (primer 16), unpolluted and polluted plants (T = 3.687, P < 0.006) (Table
791 bp (primer 13), 838 bp (primer 11) and 931 bp (primer 3). Fig. 3 showed that the total protein content increased in all
14) were common in both unpolluted and polluted plants. A polluted plants. The electrophoretic patterns (SDSPAGE) for
band of 255 bp molecular size (primer 1) was detected only water soluble proteins of the two groups unpolluted and
in unpolluted plants. Generally the results of differential dis- polluted plants of L. monopetalum were illustrated in Fig. 4
play revealed that many down-regulated (turned off) and up- and Table 4. A total number of 28 protein bands, with molec-
regulated genes (turned on) were observed in polluted plants. ular weight ranging between 147.18 and 13.66 kDa were
recorded from the electrophenograms of the plants studied.
4.2. Identication of cDNAs at crude oil pollution The electrophoretic patterns of unpolluted and polluted plants
revealed the presence of higher number of peptides (19) in
After differential screening of leaves cDNA from polluted unpolluted plants ranged from 147.18 to 13.66 kDa, while 16
plants, 201 bands were expressed under crude oil pollution. peptides ranged from 141.08 to 14.83 kDa were recorded for
Ten cDNA bands were considered to be consistently expressed polluted plants. The mean percentage of polymorphic bands
under crude oil stress and selected for sequencing. BLAST for unpolluted plants was 30.88, while it was 22.78 in polluted
Identication and characterization of up-regulated genes 141
Table 2 Up-regulated cDNAs in leaves of Limoniastrum monopetalum growing under petroleum stress, identication, and functional
classication.
cDNAs Identity Length Accession No. reference Identity (%) Function
1 Arginine decarboxylase (Citrus trifoliate) 380 JN121995 85 Urea cycle and metabolism of amino
groups and glutamate metabolism
2 Retrotransposon protein (Oryza sativa 280 FR878032 85 Salinity stress responses
Indica Group)
3 Metallothionein type 2 (Limonium 311 FR878033 75 Detoxication of heavy metals
bicolor)
4 1-Aminocyclopropane-1-carboxylate 315 FR878034 71 Plant growth
oxidase (Saccharum ocinarum)
ACC oxidase (Vigna radiate) 71
Aminocylopropane-1-carboxylate oxidase 71
(Vigna radiate)
ACC oxidase 4 (Lepidium sativum) 71
gibberellin receptor 1b (Lepidium sativum) 71
5 Cowpea responsive to dehydration 2 383 FR878035 56 Drought-inducible cowpea gene
(CPRD2)
6 Putative proton-dependent oligopeptide 230 FR878036 87 Transporter activity
transport (POT) family protein (Vigna
unguiculata)
7 Ribulose-1,5-bisphosphate carboxylase/ 249 FR878037 100 Plant growth
oxygenase large subunit (Limoniastrum
monopetalum)
8 Glutamine synthetase (Vigna mungo) FR878038 100 Metabolism of nitrogen
9 Xanthine dehydrogenase (Plumbago FR878039 85 Oxidative metabolism of purines
auriculata)
10 Amidophosphoribosyltransferase, FR878040 88 Catalyzes the rst step of de novo purine
chloroplastic = glutamine nucleotide biosynthesis
phosphoribosylpyrophosphate
amidotransferase (Vigna aconitifolia)
Table 3 t-Test of protein content for unpolluted and polluted plants of Limoniastrum monopetalum.
Paired Dierences t df Sig.
Mean Std. deviation Std. error mean 95% condence interval of the dierence
Lower Upper
Protein content polluted 0.25889 0.21064 0.07021 0.09698 0.42080 3.687 8 0.006
and unpolluted plants
Figure 3 Protein content (mg/g) in L. monopetalum leaves in Figure 4 SDSPAGE prole of leaf proteins extracted from L.
unpolluted plants. Error bars are the standard deviation of three monopetalum. In the left lane M: molecular weight (MW) of
independent replicates. standard protein.
142 R. El-Bakatoushi
Table 5 Rate of ow, molecular weight (M.wt.), and relative concentration (band%) of protein bands of unpolluted and polluted
Limoniastrum monopetalum plants.
Band No. Rf M.wt. (KDa) Band%
Limoniastrum monopetalum
Unpolluted plants Polluted plants
1 2 3 1 2 3
1 0.11 147.18 5.99 13.44 10.64
2 0.12 145.69 2.23
3 0.13 141.08 6.41 16.49
4 0.16 133.72 21.37*
5 0.17 131.60 22.89 24.38
6 0.19 127.85 15.53
7 0.34 91.10 6.12*
8 0.36 85.25
9 0.43 66.28 14.26*
10 0.45 61.88 42.81 15.61 16.29 46.25 33.36 44.29
11 0.47 57.06 31.36 33.52
12 0.59 38.02 12.33 7.15 11.76
13 0.60 36.72 3.35*
14 0.63 35.16 2.56 4.46
15 0.65 34.09 1.37 9.3 11.65 9.37
16 0.66 33.455 6.08 5.16 5.81
17 0.68 32.76 11.03 10.97
18 0.71 31.44 6.26
19 0.72 30.92 6.47*
20 0.75 29.17 1.31
21 0.77 27.78 0.67 0.71 2.96 1.66
22 0.79 26.06 3.44*
23 0.80 25.79 0.86 2.25 0.63 0.82 7.29
24 0.83 22.87 1.46 0.9 2.21
25 0.87 20.67 0.16
26 0.93 16.41 2.56
27 0.96 14.83 4.44 4.89 3.17
28 0.99 13.66 5.82 5.52
Number of individual specic bands 2 0 0 2 1 2
Percentage of polymorphic bands 28.57 39.28 32.14 32.14 28.57 25.00
Mean% of polymorphic bands 33.33 28.57
Total number of bands 19 16
Identication and characterization of up-regulated genes 143
hydroxylases involved in the oxidative metabolism of purines. is of special importance in meristematic cells as it provides
Xanthine dehydrogenase can be converted to xanthine oxidase the building blocks for DNA and RNA in those dividing
by reversible sulfhydryl oxidation or by irreversible proteolytic and elongating tissues [53]. In addition, purine nucleotides
modication [10]. It was reported that the high activity of xan- are precursors in the synthesis of a number of indispensable
thine enzyme in the leaf may be attributed to the involvement of coenzymes such as in NAD biosynthesis (from aspartate)
the enzyme in the metabolism of heterocyclic hydrocarbons [29], avin biosynthesis (bacteria and plants) [6,24]. Moreover,
[25]. Metallothionein type 2 is involved in detoxication of hea- it has been demonstrated in legumes that purine metabolism is
vy metals and provides protection against oxidative stress. employed to assimilate nitrogen in form of ureides that are
Metallothioneins also participate in the uptake, transport, derivatives of inosine 50 -monophosphate (IMP), an branch
and regulation of zinc in biological systems and Zinc, in turn, intermediate in the de novo biosynthesis [48,52].
is a key element for the activation and binding of certain tran- The plants are growing in a petroleum-polluted environ-
scription factors [54]. A cDNA encoding type 3 metallothionein ment, soil particles are covered with a hydrophobic layer that
(PcMT3) was isolated before from the salt stressed leaf cDNA reduces water availability and augments the oxygen demand of
library of Porteresia coarctata (Roxb.) Tateoka, (wild rice) that soil microorganisms which causes anoxic and drought stress
grows well in the heavy metal laden estuarine soils [59] conse- and additionally, the hydrophobic nature of the pollutant also
quently, both cDNAs (3, 9) were good markers of petroleum causes a disruptive chemical stress. The stress signals are
stress in L. monopetalum. Arginine decarboxylase enzyme sensed and communicated by an array of signaling enzymes
belongs to the family of lyases, specically the carboxy-lyases, that induce transcriptional control and protein turnover to fa-
which cleave carboncarbon bonds. This enzyme participates vor the synthesis of enzymes acting to alleviate the harmful ef-
in urea cycle and metabolism of amino groups and glutamate fects induced by petroleum. It was suggested that oil cause
metabolism. It employs one cofactor, pyridoxal phosphate. dehydration in soil and this may be the cause of up-regulated
Recent studies have shown that polyamines (PAs) participate genes of drought and salinity. We identied two cDNAs (5, 2)
in the defense reactions protecting plants against environmen- that support this hypothesis; these are cDNA corresponds to
tal stresses. Increased synthesis of PAs, achieved via increased mRNA coding cowpea responsive to dehydration (CPRD2).
activities of the enzymes arginine decarboxylase (ADC) and The CPRD2 exhibited typical and signicant responses to
S-adenosylmethionine decarboxylase (SAMDC). PA metabo- water stress, induction by dehydration and reduction in the le-
lism and oxidative damage were investigated in the aquatic vel of the transcript upon rehydration [41]. The other cDNA2
form of the liverwort Riccia uitans L. exposed to the polycyclic corresponds to mRNA coding salinity stress retrotransposon
aromatic hydrocarbon (PAH) phenanthrene (PHEN). Expo- protein (Oryza sativa indica Group).
sure of Riccia uitans plants to PHEN induced oxidative stress, Two of the cDNAs (4, 7) isolated in the present work
due to increased synthesis of PAs, achieved via increased activ- showed signicant similarity with proteins and enzymes that
ities of the enzymes arginine decarboxylase (ADC) and S-aden- play an important role at several stages of plant growth like
osylmethionine decarboxylase (SAMDC) [16]. aminocyclopropane-1-carboxylic acid (ACC). ACC plays an
Two cDNAs (8, 10) showed signicant identity with pro- important role in the biosynthesis of the plant hormone ethyl-
teins related to nitrogen metabolism. Glutamine synthetase ene [30,64]. It is synthesized by the enzyme ACC synthase from
(GS) is an enzyme that plays an essential role in the metabo- methionine and converted to ethylene by ACC oxidase [31].
lism of nitrogen by catalyzing the condensation of glutamate ACC oxidase catalyzes the last step in the biosynthesis of the
and ammonia to form glutamine [19]. Glutamine synthetase plant hormone ethylene. Bruce et al. [14] stated that stress eth-
uses ammonia produced by nitrate reduction, amino acid ylene is produced under petroleum and salt impacted land, fre-
degradation, and photorespiration [37]. The amide group of quently leading to diminished plant growth. cDNA7 encoding
glutamate is a nitrogen source for the synthesis of glutamine ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO)
pathway metabolites [36]. The product of its activity, is an enzyme involved in the Calvin cycle that catalyzes the rst
glutamine is donor of amino groups for biosynthesis of other major step of carbon xation, a process by which the atoms of
amino acids, proteins, etc. GDH and GS play key roles in atmospheric carbon dioxide are made available to organisms
maintaining the balance of carbon and nitrogen in plant cell in the form of energy-rich molecules such as glucose. RuBisCO
[43]. Sadunishvili [50] found marked increase in GS activity catalyzes either the carboxylation or the oxygenation of
in the leaves of poplar (Populus deltoids), signicant stimula- ribulose-1,5-bisphosphate with carbon dioxide or oxygen.
tion of GDH and GS activities in the leaves and roots of RuBisCO is very important in terms of biological impact
ryegrass and maize seedlings at benzene highest concentration. because it catalyzes the primary chemical reaction by which
cDNA10 corresponds to amidophosphoribosyltransferase inorganic carbon permanently enters the biosphere and
(Atase) is an enzyme that converts a phosphoribosylpyrophos- increasing the level of expression of RuBisCO subunits im-
phate (a-PRPP) into 5-b-phosphoribosylamine. The enzyme prove photosynthetic efciency. The abundance of RubisCO
uses the ammonia group from the glutamine side-chain. This genes in a particular ecosystem indicates the potential capacity
is the committing step in de novo purine synthesis. ATase is for transcription/translation and subsequent carbon xation
a member of the purine/pyrimidine phosphoribosyltransferase by representatives of the population. RuBisCO enzyme
family. This protein is a regulatory enzyme that catalyzes the controls both the reduction of CO2 and the oxygenolysis of
rst step of de novo purine nucleotide biosynthesis [15]. Purine ribulose-1,5-bisphosphate. Thus, this protein and its catalytic
nucleotides are crucial compounds that are central to primary activity have vast agricultural and environmental signicance
metabolism but are also connected to many facets of and all primary production is linked to the function of this
secondary plant metabolism. They are involved in many vital enzyme [27].
cellular processes which are essential for plant growth and The proton dependent oligopeptide transporters (POTs) are
development [12,65]. De novo purine nucleotide biosynthesis a large family of integral membrane proteins that use the
144
Table A1 Molecular sizes of cDNA bands in base pair of unpolluted (c1, c2, and c3) and polluted (1, 2, and 3) Limoniastrum monopetalum plants.
Primer1 776 720 700 641 619 593 500 488 477 465 443 428. 383 377 341 333 323 310 262 262 255 246 225 213 197 191 182 175 171 164 151 125 119
c1 + + + + + + + +
1 + + + + + + +
c2 + + + + + + + + +
2 + + + + + + + +
c3 + + + + + +
3 + + + + + +
Primer2 258 235 222 191 150 147 106 94 50 38 29 23 20
c1 + +
1 + + +
c2 + +
2 + + +
c3 + + +
3 +
Primer3 751 580 500 429 421 350 340 329 326 323 296 280 235 232 229 223 185 177 172 149 136 126 121
c1 + + + + +
1 + + + + + +
c2 + + + + +
2 + + + + + +
c3 + + + +
3 + + + + + + +
Primer4 507 500 459 337 332 241 165 160 147 98 85 71 64 51 40 35 10
c1 + + + +
1 + + + + +
c2 + + + + + +
2 + + + + + +
c3 + +
3 + + +
Primer5 962 665 508 491 253 235 135 89 75 66 46 24 18.462 10
c1 + + +
1 + + +
c2 + + + +
2 + + +
c3 + +
3 + + + + +
Primer6 734 722 710 700 672 654 624 606 593 545 540 532 496 461 446 437 416 402 384 377 364 325 301 285 279 243 235 221 211 190 167
R. El-Bakatoushi
c1 + + + + + + +
1 + + + + + + + + +
c2 + + + + + + + + + +
2 + + +
c3 + + + + + + + + +
3 + + + + + + + +
Identication and characterization of up-regulated genes
Table A1
Primer7 500 491 474 467 424 412 393 364 353 337 321 310 200
c1 + + +
1 + + + + +
c2 + + +
2 + + + +
c3 + + +
3 + + +
Primer8 830 825 736 507 500 496 406 344 333 325 297 235 233 230 185 173 144 131 98 68 39 27 15
c1 + + + + + + + +
1 + + + + + + +
c2 + + +
2 + + + + + +
c3 + + + + +
3 + + + + + +
Primer9 343 333 324 300 297 276 266 256 225 217 200 191 176 144 121 97 81 66 57 37 26 15
c1 + + + + + + + +
1 + + + + + + +
c2 + + + + + +
2 + + + + + + +
c3 + + + + + +
3 + + + + + + + +
Primer10 1227 1182 1164 862 839 767 733 655 634 600 589 559 540 514 454 450 435 427 409 390 364 359 349 343 327 318 286 281 214 189 182 176 163 155 140 132 122
c1 + + + + +
1 + + + + +
c2 + + + + + +
2 + + + + + + + + + + +
c3 + + + + + + + + + + + +
3 + + + + + + + + + + +
Primer11 1586 1332 1229 1031 1001 950 839 838 812 801 790 770 823 755 718 699 679 597 464 441 346 297 273 249 150 140 130 125 120 100 40 26 11 10
C1 + + + + + + + +
1 + + + + + + + + +
C2 + + + + + + + + + + + + +
2 + + + + + + + + + +
C3 + + + + + + + +
3 + + + + + + + +
Primer12 3917 3549 3549 998 996 977 953 698 651 628 605 395 349 326 186 163 70 23 20 15 10
1 + + + + + + + +
2 + +
3 + + + + + + +
4 + + + + + + + +
5 + + + + + + +
6 + + + + +
145
146
Table A1 (continued)
Primer13 5439 5259 4567 3466 2913 2310 1575 1312 909 810 803 797 791 750 729 708 625 521 500 479 396 354 333 271 229 146 130 120 42 30 20
C1 + + + + +
1 + + + + + + + + + + + +
C2 + + + + + +
2 + + + + + + + + + + +
C3 + + + + + + +
3 + + + + +
Primer14 1669 1489 1339 1275 1217 1121 931 867 800 700 567 533 400 367 333 330 310 300 267 100 33 20 10
1 + + + + + +
2 + + + + + +
3 + + + + + + + +
4 + + + +
5 + + + +
6 + + + + + + +
Primer15 921 842 789 737 632 579 553 447 421 395 316 237 211 158 132 120 79 26 22 20
C1 + + + + +
1 + + + + +
C2 + + + + +
2 + + + + + +
C3 + + + + +
3 + + + + +
Primer16 4047 3863 3682 501 403 387 357 351 345 321 292 276 265 257 228 158 140
C1 + + + + + + +
1 + + + + +
C2 + + + + + +
2 + + + + +
C3 + + + + + +
3 + + + + + +
R. El-Bakatoushi
Identication and characterization of up-regulated genes 147
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