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Article history: Nitric oxide associated 1 (NOA1) protein is implicated in plant disease resistance and nitric oxide (NO)
Received 5 August 2014 biosynthesis. A full-length cDNA encoding of NOA1 protein from oil palm (Elaeis guineensis) was isolated
Received in revised form 9 October 2014 and designated as EgNOA1. Sequence analysis suggested that EgNOA1 was a circular permutated GTPase
Accepted 9 October 2014
with high similarity to the bacterial YqeH protein of the YawG/YlqF family. The gene expression of EgNOA1
Available online 18 October 2014
and NO production in oil palm root tissues treated with Ganoderma boninense, the causal agent of basal
stem rot (BSR) disease were profiled to investigate the involvement of EgNOA1 during fungal infection and
Keywords:
association with NO biosynthesis. Real-time PCR (qPCR) analysis revealed that the transcript abundance
Circular permutated GTPase
Ganoderma
of EgNOA1 in root tissues was increased by G. boninense treatment. NO burst in Ganoderma-treated root
Nitric oxide tissue was detected using Griess reagent, in advance of the up-regulation of the EgNOA1 transcript. This
NOA1 indicates that NO production was independent of EgNOA1. However, the induced expression of EgNOA1
Oil palm in Ganoderma-treated root tissues implies that it might be involved in plant defense responses against
pathogen infection.
© 2014 Elsevier GmbH. All rights reserved.
http://dx.doi.org/10.1016/j.jplph.2014.10.003
0176-1617/© 2014 Elsevier GmbH. All rights reserved.
132 Y.-M. Kwan et al. / Journal of Plant Physiology 174 (2015) 131–136
AtNOS1 protein and the contradictory NO accumulation responses Materials and methods
in NOA1-silenced mutants have affirmed that AtNOS1 is not an
authentic NOS per se (Van Ree et al., 2011). The involvement of Isolation of full length cDNA sequence
NOA1 in NO biosynthesis is currently identified as sucrose depend-
ent and nitrate reductase (NR)-related (Gas et al., 2009; Van Ree Total RNA was extracted from three month old oil palm (Elaeis
et al., 2011). The indirect regulatory effect of NOA1 in NO pro- guineensis Jacq., Dura × Pisifera, GH500 series) root tissue by adopt-
duction was demonstrated with impaired NO accumulation in ing the protocol outlined in Chan et al. (2007). RNA samples
NOA1-silenced A. thaliana and Nicotiana benthamiana (Guo et al., were treated with DNase I (Fermentas, Lithuania) according to
2003; Asai and Yoshioka, 2009). manufacturer’s instructions to eliminate traces of genomic DNA
Apart from NO biosynthesis, NOA1 is implicated in plastid func- contamination. The integrity of RNA samples was examined using
tion, ribosome biogenesis, and enhanced tolerance to both abiotic agarose gel electrophoresis and purity was assessed using the
and biotic stresses (Flores-Perez et al., 2008; Qiao et al., 2009; Liu NanoDrop ND-1000 UV–Vis Spectrophotometer (NanoDrop Tech-
et al., 2010). Increased susceptibility to pathogens in NOA1 knock- nologies, USA) at absorbance ratio of A260/280 and A260/230.
out A. thaliana and N. benthamiana had demonstrated the role of Gene specific primers were designed according to two expressed
NOA1 in disease resistance (Zeidler et al., 2004; Asai and Yoshioka, sequence tags (ESTs) (i.e. EL694732 and 17871) retrieved from the
2009). The NOA1 mediated defense mechanism was observed be oil palm EST library (Ho et al., 2007) that matched (E-value < 10−5 )
to associated with the induced accumulation of oleic acid, jas- the NOA1 protein in the GenBank non-redundant protein database.
monates and carbon-based secondary metabolites, expression of Gene specific primers were designed using Primer3 Input soft-
salicylic acid (SA)-defense responsive gene and elevated NO pro- ware (version 0.4.0) (www.bioinfopop.ufv.br/sistema/primer3).
duction (Kato et al., 2008; Wünsche et al., 2011; Mandal et al., The primers designed for 5 - and 3 -rapid amplification of cDNA
2012). ends (RACE) PCR were: 17871-R1 (5 -TTC CTG GAA CAA CCC TTG
The African oil palm (Elaeis guineensis) is commercially culti- GTC-3 ) and EL694732-F1 (5 -TTC CTG GAA CAA CCC TTG GTC-
vated for vegetable oil, biofuel and oleochemicals. The outbreak 3 ), respectively. The primers used for nested 5 - and 3 -RACE PCR
of the destructive basal stem rot (BSR) disease in the oil palm were: 17871-R2 (5 -TCC TGG AAC AAC CCT TGG TCC CAT TG-3 )
nursery and plantations, caused by the white rot fungi, Gano- and EL694732-F2 (5 -TCC TGG AAC AAC CCT TGG TCC CAT TG-3 ),
derma species is a major challenge to oil palm cultivation (Paterson respectively. Template for RACE-PCR was synthesized from 10 g of
et al., 2009). BSR disease has resulted in severe economic loss due total RNA using ExactSTART Eukaryotic mRNA 5 - and 3 -RACE kit
to reduction in fresh fruit bunch (FFB) and collapse of standing (Epicentre, USA) according to manufacturer’s instructions. RACE-
palms (Chung, 2011). Ganoderma is spread by airborne basid- PCR products were cloned into the pDrive vector (Qiagen, German)
iospores, insects assisted spore transfer and mycelial root contact and sequenced using T7 and SP6 primers. The resulting full-length
(Sanderson, 2005; Paterson, 2007). The current disease manage- cDNA sequence was designated as EgNOA1.
ment strategies include soil mounding, mechanical removal, clean
clearing, legume cover crops, fungicide application, biological con-
Bioinformatics analysis
trol, fertilizer and biofertilizer input management to prolong the
lifespan of infected palms, but these are not effective in dis-
Sequence similarity and catalytic domain of EgNOA1 was ana-
ease eradication (Chung, 2011). The low effectiveness of these
lyzed using Basic Local Alignment Search Tool (BLASTx) and
approaches is caused by the resistant pseudosclerotia structure of
conserved domain database (www.ncbi.nlm.nih.gov/Structure/
the Ganoderma fungi and the lack of early disease symptoms (Rees
cdd/wrpsb.cgi) at the National Center for Biotechnology Infor-
et al., 2009).
mation (NCBI) (www.ncbi.nlm.nih.gov). Molecular weight and
The different susceptibility to Ganoderma infection exhib-
isoelectric point of the EgNOA1 protein was calculated using ExPASy
ited by planting materials from different geographical origins
ProtParam program (www.expasy.ch/tools/protparam.htm). Sub-
such as Cameroon, Nigeria and Zaire has unraveled the prospect
cellular location of EgNOA1 was predicted using WoLFPSORT
of oil palm genetic improvement programs (Durand-Gasselin
(www.wolfpsort.org). Sequence alignment of different plant
et al., 2005). Breeding of resistant or tolerant planting mate-
NOA homologs was performed using the ClustalW method
rials is effective in disease eradication or delay of disease
(www.ebi.ac.uk/clustalw). The phylogenetic tree was constructed
development. This reduces Ganoderma inoculum for subsequent
using neighbour joining method implemented in Molecular Evo-
replantings. Chitinase, glucanase, isoflavone reductase, metallo-
lutionary Genetics Analysis (MEGA) version 5.1 program (Tamura
thioneins, metallothionein-like protein, early methionine-labeled
et al., 2011).
polypeptides and stearoyl-acyl carrier protein desaturase (SAD)
have been reported to express differentially after Ganoderma
infection (Yeoh et al., 2012; Tan et al., 2013; Tee et al., Plant materials and treatments
2013). Nevertheless, the identification of defense associated
genes against Ganoderma is ongoing. These genes are impor- A total of 70 4-month-old oil palm seedlings (E. guineensis Jacq.,
tant in providing insight into the molecular events during Dura × Pisifera, GH500 series) was purchased from Sime Darby
plant–pathogen interaction and for the development of expressed Seeds & Agricultural Services Sdn. Bhd. (Banting, Malaysia). The
markers for large scale screening of resistant or tolerant planting seedlings were equally divided for two treatments, either treated
materials. with one-month-old Ganoderma boninense PER71 colonized rubber
In the present study, a transcript encoding NOA1 protein from wood blocks (RWB) or sterilized RWBs (served as control). Inocu-
oil palm, designated as EgNOA1, was isolated and characterized. Oil lation was carried out through direct sitting technique by adopting
palm seedlings were artificially inoculated with Ganoderma boni- the protocol outlined by Zaiton (2006). Five seedlings were har-
nense to investigate the expression profile of EgNOA1 in root tissue vested from both treatments at 3, 7, 14, 21, 28, 56 and 96 days after
and its potential as expressed markers for early disease detec- inoculation (DAI). The roots were washed and examined for visible
tion and/or fungal resistance. In addition, the association between symptoms of G. boninense infection, including mycelial coloniza-
EgNOA1 gene expression and NO biosynthesis was also investi- tion on root surfaces and necrotic lesions. Samples of roots were
gated. flash frozen in liquid nitrogen and stored at −80 ◦ C until required.
Y.-M. Kwan et al. / Journal of Plant Physiology 174 (2015) 131–136 133
Fig. 1. Multiple sequence aligment of EgNOA1 with other plant NOA1 homologs. Plant NOA1 proteins have three discrete conserved domains – zinc binding domain (ZBD),
circularly permuted GTPase (CPG) domain arranged in G4-G5-G1-G2-G3 order and the C-terminal domain (CTD). The residues that denote the ZBD are indicated within the
arrows and the four conserved cysteine residues are indicated in the box. The CTD region is indicated within the arrows. The motif residues of the CPG domain are indicated
in the box and the conserved residues are shaded in grey. Gaps are represented by dashes. Numbering of the amino acid is indicated on the right. Protein identification in the
alignment – AtNOA1: A. thaliana NOA1 (NP190329), MtNOA1: Medicago truncatula NOA1 (ADK47527), OsNOA1: O. sativa NOA1 (NP001045614), RcNOA1: R. communis NOA1
(XP002510962) and SbNOA1: S. bicolor NOA1 (XP002451348).
134 Y.-M. Kwan et al. / Journal of Plant Physiology 174 (2015) 131–136
RNA extraction and reverse transcription and qPCR results when ≥1.4 expression fold change was detected
(Morey et al., 2006; Tan et al., 2013).
RNA extraction was performed on root samples pooled from Supplementary Table S1 related to this article can be
five biological replicates harvested from each treatment at respec- found, in the online version, at http://dx.doi.org/10.1016/j.jplph.
tive sampling intervals. Total RNA was isolated from root samples 2014.10.003.
using Total RNA Purification Kit (Norgen Biotek Corporation,
Canada) according to instructions from the manufacturer. On- Griess assay
column DNase I (Fermentas, Lithuania) digestion was carried out
to eliminate traces of genomic DNA. First strand cDNA was synthe- NO concentration in 2 g root samples pooled from equal weight
sized from 1 g of total RNA using Maxima Reverse Transcriptase of five biological replicates harvested from each treatment at
(Fermentas, Lithuania) with combination of oligo-dT and random respective sampling intervals was quantified using Griess assay
primer. according to the protocol outlined by Yucel et al. (2012). The for-
mation of red violet azo compound following nitrite reaction with
Griess reagent (Promega, USA) was measured using a microplate
Real-time PCR (qPCR) reader (Rayto RT-2100C) at 540 nm. Samples were tested in tripli-
cate and data was analyzed using T-test at p = 0.01 level.
The transcript abundance of EgNOA1 in root samples was pro-
filed using qPCR in the BioRad CFX96 real time PCR system (BioRad, Results and discussion
USA). Reaction mixture of 25 L total volume contained 1× Brilliant
III Ultra-Fast SYBR Green Master Mix (Agilent Technologies, USA), Sequence analysis of EgNOA1
100 ng first strand cDNA and 0.2 M forward and reverse primers
(Supplementary Table S1, Ooi et al. 2012). The qPCR reaction was The cDNA sequence contains a 5 -untranslated region (UTR) of
performed under the following temperature regime: initial dena- 47 bp upstream of the predicted start codon (ATG) and the longest
turation at 95 ◦ C for 3 min; 40 cycles of 95 ◦ C for 5 s and 55 ◦ C for 3 -UTR of 219 bp downstream of the translation stop codon (TGA).
10 s. Three technical triplicates were performed from the same RNA EgNOA1 (GenBank accession number KF601427) has an open read-
preparation for each treatment at corresponding sampling intervals ing frame (ORF) of 1674 bp that encodes a polypeptide of 558 amino
and a non-template control (NTC) was included. Melt curve analysis acids with a predicted molecular weight of 61.16 kDa and isoelec-
was performed at 65–95 ◦ C with temperature increment of 0.5 ◦ C tric point of 9.42. The EgNOA1 protein was predicted to be targeted
for every 10 s. The relative transcript abundance of EgNOA1 was to chloroplast and mitochondria by WoLFPSORT.
normalized using manganese superoxide dismutase (MSD), NADH The closest homologs of EgNOA1 were amino acid sequence of
dehydrogenase subunit 5-like (NAD) and ubiquitin according to NOA1 from rice (Oryza sativa NP001045614) (81%), castor bean
the Livak 2−Cq method (Vandesompele et al., 2002). Refer- (Ricinus communis XP002510962) (81%) and mouse-ear cress (Ara-
ence genes for data normalization were selected using NormFinder bidopsis thaliana NP190329) (81%). Besides, the EgNOA1 shares
(Andersen et al., 2004) and BestKeeper (Pfaffl et al., 2004) algo- a rather similar sequence identity with the YqeH protein from
rithms based on gene expression stability. The relative expression Bacillus subtilis (BAA12444) (31%). Multiple sequence alignment of
fold change of EgNOA1 in the G. boninense-treated sample was different plant NOA1 homologs revealed a high level of sequence
obtained by comparison with its transcript abundance in control homology (Fig. 1). Phylogenetic analysis indicated a sequence con-
samples (calibrator) at corresponding sampling intervals. The sig- servation pattern among the NOA1 proteins from monocots/dicots
nificant difference in gene expression was fixed at ≥2 expression and the family (Fig. 2). NOA1 proteins from dicotyledonous and
fold change based on the correlation (0.80) between microarray monocotyledonous plants were grouped into separate clades.
Fig. 2. Phylogenetic analysis of EgNOA1 and NOA1 proteins from plants, bacteria and human. The phylogenetic tree was generated using MEGA 5.1 based on neighbour
joining method. Bootstrap values obtained from 1000 replications are indicated as precentage at tree nodes. The branch length is drawn to scale and in the same unit as
evolutionary distance, number of amino acid sunstituition per site. The scale bar represents 20% of amino acid differences between protein sequences. Protein identification
in the phylogenetic tree – AtNOA1: A. thaliana NOA1 (NP190329), BjNOA1: B. juncea NOA1 (ACX61572), MtNOA1: M. truncatula NOA1 (ADK47527), NbNOA1: N. benthamiana
NOA1 (BAF93184), OsNOA1: O. sativa NOA1 (NP001045614), PsNOA1: P. sitchensis NOA1 (ABR16951), RcNOA1: R. communis NOA1 (XP002510962), SbNOA1: S. bicolor NOA1
(XP002451348), StNOA1: S. tuberosum NOA1 (ADD63989), VvNOA1: V. vinifera NOA1 (XP002268388), ZmNOA1: Z. mays NOA1 (NP001168044), Bacteria YqeH: B. subtilis YqeH
(BAA12444) and Human NOA1: H. sapiens NOA1 (NP115689).
Y.-M. Kwan et al. / Journal of Plant Physiology 174 (2015) 131–136 135
35
30.49
Control Ganoderma-treated
30 27.06
Nitrite concentration (µM)
24.52
24.12
25 22.18
22.60
18.25
20 17.42 16.89
15 12.01
10.86 11.05 10.91 10.82
10
0
3 7 14 21 28 56 96
Day after inoculation
Fig. 4. NO concentration in Ganoderma-treated and control oil palm root tissues at respective sampling intervals. The bars represent means ± standard error (n = 3). The
asterisk (*) indicates significant up-regulation of NO concentration in Ganoderma-treated root tissue compared to that of the control at P < 0.01 as determined by T-test.
136 Y.-M. Kwan et al. / Journal of Plant Physiology 174 (2015) 131–136
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EgNOA1 overexpression and NO production. It has been known that agent of downy mildew and induced defense responses in the host. Serdang:
NOA1-knock out mutants were impaired in NO accumulation dur- Universiti Putra Malaysia; 2011.
Mishra R, Gara SK, Mishra S, Prakash B. Proteins 2005;59:332–8.
ing pathogen invasion, but the mechanism remains unclear (Guo
Misra AN, Misra M, Singh R. J Med Plants Res 2010;4:2729–39.
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Paterson RRM. Crop Prot 2007;26:1369–76.
mitochondria (Moreau et al., 2008; Gas et al., 2009). Paterson RRM, Sariah M, Lima N. J Phytopathol 2009;157:649–56.
Pauly N, Ferrari C, Andrio E, Marino D, Piardi S, Brouquisse R, et al. J Exp Bot
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Conclusions
Pfaffl M, Tichopad A, Prgomet C, Neuvians T. Biotechnol Lett 2004;26:509–15.
Qiao W, Xiao S, Yu L, Fan L. Environ Exp Bot 2009;65:90–8.
In conclusion, a full-length cDNA encoding nitric oxide associ- Rees RW, Flood J, Hasan Y, Potter U, Cooper RM. Plant Pathol 2009;58:982–9.
ated 1 (EgNOA1) protein from oil palm was isolated. The transcript Sanderson FR. Mycopathologia 2005;159:139–41.
Sudhamsu J, Lee GI, Klessig DF, Crane BR. J Biol Chem 2008;283:32968–76.
abundance of EgNOA1 was up-regulated in Ganoderma-treated oil Tada Y, Mori T, Shinogi T, Yao N, Takahashi S, Betsuyaku S. Mol Plant Microbe Interact
palm root tissues at a later stage and did not coincide with NO 2004;17:245–53.
burst. Functional characterization of EgNOA1 protein is useful in Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. Mol Biol Evol
2011;28:2731–9.
elucidating the role of EgNOA1 in plant defense. Tan YC, Yeoh KA, Wong MY, Ho CL. J Plant Physiol 2013;170:1455–60.
Tee SS, Tan YC, Abdullah F, Ong-Abdullah M, Ho CL. Tree Genet Genomes
2013;9:377–86.
Acknowledgements Thakur B, Sohal BS. ISRN Biochem 2013;2013:1–10.
Torres MA, Jones JDG, Dangl JL. Plant Physiol 2006;141:373–8.
The authors would like to acknowledge the Ministry of Science, Uicker WC, Schaefer L, Koenigsknecht M, Britton RA. J Bacteriol 2007;189:2926–9.
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, et al. Genome
Technology and Innovation, Malaysia for funding this research via
Biol 2002;3:1–11 [research0034].
ScienceFund (Project number 05-01-04-SF0950). Y.-M. Kwan was Van Ree K, Gehl B, Chehab EW, Tsai YC, Braam J. Plant J 2011;68:225–33.
supported by scholarship from the Ministry of Higher Education, Wünsche H, Baldwin IT, Wu J. J Integr Plant Biol 2011;53:619–31.
Yeoh KA, Othman A, Meon S, Abdullah F, Ho CL. J Plant Physiol 2012;169:1565–70.
Malaysia. We would also like to thank the GanoDROP Laboratory of
Yucel AA, Gulen S, Dincer S, Yucel AE, Yetkin GI. J Exp Integr Med 2012;2:
Malaysian Palm Oil Board (MPOB) for providing Ganoderma boni- 167–71.
nense PER71 culture. Zaiton S. Bacterial endophytes of oil palm (Elaeis Guineensis) and antagonistic
activity against Ganoderma boninense). Serdang: Universiti Putra Malaysia;
2006.
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