Jung Eun Hwang1, Sun-Goo Hwang2, In Jung Jung3, Sung Min Han3, Joon-Woo Ahn3, Jin-Baek Kim3. 1. National Institute of Ecology, Research Center for Endangered Species, Division of Restoration Research, Yeongyang, Republic of Korea. 2. Kangwon Natl University, Department of Applied Plant Sciences, Plant Genomics Lab, Chuncheon, Republic of Korea. 3. Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea.
Abstract
Ionizing radiation has a substantial effect on physiological and biochemical processes in plants via induction of transcriptional changes and diverse genetic alterations. Previous microarray analysis showed that rice OsFBX322, which encodes a rice F-box protein, was downregulated in response to three types of ionizing radiation: gamma irradiation, ion beams, and cosmic rays. In order to characterize the radiation-responsive genes in rice, OsFBX322 was selected for further analysis. OsFBX322 expression patterns in response to radiation were confirmed using quantitative RT-PCR. Transient expression of a GFP-OsFBX322 fusion protein in tobacco leaf epidermis indicated that OsFBX322 is localized to the nucleus. To determine the effect of OsFBX322 expression on radiation response, OsFBX322 was overexpressed in Arabidopsis. Transgenic overexpression lines were more sensitive to gamma irradiation than control plants. These results suggest that OsFBX322 plays a negative role in the defense response to radiation in plants. In addition, we obtained four co-expression genes of OsFBX322 by specific co-expression networks using the ARANCE. Quantitative RT-PCR showed that the four genes were also downregulated after exposure to the three types of radiation. These results imply that the co-expressed genes may serve as key regulators in the radiation response pathway in plants.
Ionizing radiation has a substantial effect on physiological and biochemical processes in plants via induction of transcriptional changes and diverse genetic alterations. Previous microarray analysis showed that riceOsFBX322, which encodes a rice F-box protein, was downregulated in response to three types of ionizing radiation: gamma irradiation, ion beams, and cosmic rays. In order to characterize the radiation-responsive genes in rice, OsFBX322 was selected for further analysis. OsFBX322 expression patterns in response to radiation were confirmed using quantitative RT-PCR. Transient expression of a GFP-OsFBX322 fusion protein in tobacco leaf epidermis indicated that OsFBX322 is localized to the nucleus. To determine the effect of OsFBX322 expression on radiation response, OsFBX322 was overexpressed in Arabidopsis. Transgenic overexpression lines were more sensitive to gamma irradiation than control plants. These results suggest that OsFBX322 plays a negative role in the defense response to radiation in plants. In addition, we obtained four co-expression genes of OsFBX322 by specific co-expression networks using the ARANCE. Quantitative RT-PCR showed that the four genes were also downregulated after exposure to the three types of radiation. These results imply that the co-expressed genes may serve as key regulators in the radiation response pathway in plants.
Abiotic factors such as drought, salinity, temperature, and ultraviolet (UV) light
can influence plant growth and development and limit cultivated plant productivity
worldwide. Plants respond and adapt to these stresses, and achieve stress tolerance
through various biochemical and physiological processes, including those involving
changes in gene expression (Kawasaki ; Seki ; Hazen ).Plants are often exposed to a range of DNA-damaging agents from the extracellular
environment, such as UV light, solar radiation, and ionizing radiation. Ionizing
radiation affects plant growth and development in a variety of ways. These include
stimulatory effects at very low doses, increasingly harmful effects on vegetative
growth as doses increase to medium levels, and pronounced decreases in reproductive
fitness and yield at high radiation levels (Prithivirajsingh ). In radioactively
contaminated environments, plants, due to their sessile nature, are directly
affected by harmful radiation and must adapt to life in ionizing radiation.
Therefore, plants deserve special attention relative to their susceptibility to
ionizing radiation. Ionizing radiations are classified according to their linear
energy transfers (LETs). Alpha particles, neutrons, and heavy ion beams exhibit high
LETs, whereas gamma rays, X-rays, and electron beams exhibit low LETs (Yang and Tobias, 1979). Cosmic rays are
generated by the solar system and are composed of high-energy particle radiation
(Sharma, 2008). These types of ionizing
radiation were reported to affect stress responses in a similar fashion to other
environmental stresses (Hosoki ); however, the mechanisms underlying plant
responses to ionizing radiation remain largely unknown. Our recent microarray study
identified many novel ionizing radiation response genes, including 53 genes that
were expressed specifically in rice (Hwang
). One of these genes,
OsFBX322, which is predicted to encode an F-box domain
containing protein, is investigated further in this study.F-box proteins, which contain a conserved F-box domain (40–50 amino acids), comprise
one of the largest protein families, with approximately 700 members in
Arabidopsis and rice (Gagne
; Jain
). Numerous F-box proteins were
previously identified as components of SCF complexes (SKP1-Cullin-F-box), but
non-SCF-complex F-box proteins were also noted (Clifford ; Galan ; Kim
). Only a small proportion of the known
F-box proteins have been studied in plants to date. These plant F-box proteins were
shown to play important roles in regulating various developmental processes and
mediating stress responses via integration of almost all the phytohormone signaling
pathways (Lechner ; Dreher and Callis, 2007;
Zhang ;
Yan ). The
functions of only three F-box proteins have been described in rice. GID2
(GA-insensitive dwarf 2), the first F-box protein identified in rice, is involved in
positive regulation of gibberellic acid signaling (Sasaki ), D3 (dwarf 3) F-box proteins are
involved in tiller bud activity (Ishikawa ), and MAIF1 (miRNAs
regulated and abiotic stress induced
F-box gene) is proposed to play a negative role in the
response to abiotic stresses by regulating root growth (Yan ). However, despite their
known crucial roles in many aspects of plant development and responses to abiotic
stress, the functions of the majority of F-box proteins in rice remain to be
determined.In this study, we demonstrated that the expression of OsFBX322 was
downregulated in response to different types of ionizing radiation. Transgenic
Arabidopsis lines overexpressing OsFBX322
exhibited increased sensitivity to radiation. We propose that
OsFBX322 is involved in radiation-responsive gene expression in
rice and plays a negative role in tolerance to radiation in plants.
Materials and Methods
Plant materials and radiation treatment conditions
To examine plant responses to radiation, rice seeds (Oryza sativa
cv. Ilpoom) were exposed to gamma- irradiation, ion beams, and
cosmic rays as described by Hwang . Briefly, for gamma-irradiation treatment,
mature seeds were exposed to a dose of 200 Gy generated by a 60Co
gamma irradiator (maximum output, 150 TBq; ACEL, Nordion, Ottawa, ON, Canada) at
the Korea Atomic Energy Research Institute. The ion beam treatment consisted of
irradiation with 220 MeV carbon ions (LET 107 keV/um), at a dose of 40 Gy,
generated by an AVF cyclotron (Japan Atomic Energy Agency, Takasaki, Japan).
Exposure to cosmic rays was achieved by placing samples on “Shijian-8”, an
unmanned breeding spacecraft, for 15 days. For transcriptional expression
analysis, irradiated seeds were cultured on half-strength MS medium and grown
for 9 weeks at 24 °C, photoperiod of 16 h light/8 h dark, and 70% humidity.
Semi-quantitative and quantitative RT-PCR analysis
Total RNA was isolated from transgenic Arabidopsis plants and
from 3-week-old seedlings germinated from rice seeds using TRIzol reagent, as
described by the manufacturer (GibcoBRL, OH, USA). Reverse transcription was
performed for 60 min at 42 °C using a Power cDNA Synthesis Kit (Intron Biotech
Inc., Sungnam, Korea) with 1 μg of oligo(dT)15 primers and 1 μg of total RNA as
template. The resultant cDNA was used as a template for semi-quantitative and
quantitative RT-PCR. Semi-quantitative RT-PCR amplification was performed with
gene-specific primers and 1 μL cDNA as template (Table 1). The resulting RT-PCR products were analyzed on a 1.0%
(w/v) agarose gel with ethidium bromide staining. Quantitative RT-PCR was
performed using an Eco Real-Time PCR system (Illumina, CA, USA) with SYBR Premix
Ex TaqTM (TaKaRa). The PCR cycle was 95 °C for 10 min, followed by 45
cycles of 95 °C for 10 s and 60 °C for 30 s. Primer sequences are listed in
Table 1.
Table 1
Primer and probe sequences used for real-time RT-PCR.
cDNA GenBank Accession Nr.
Description
Forward and reverse primers
Os03g0718100
ACT1(Actin-1)
5’-TGAAGTGCGACGTGGATATTAG
5’-CAGTGATCTCCTTGCTCATCC
Os09g0344400
OsFBX322 (F-Box domain containing protein)
5’-GCTGGTACATGTTCAAACCG
5’-TGTCGAGGACTAGCAAGGTG
Os09g0324300
OsFBX313 (F-box domain containing protein)
5’-CGCTTCTTCTCCCTTGACTT
5’-AGCTCCCATGACCATGAGTT
Os08g0177600
double-strand break repair protein
MRE11, putative
5’-TCTGCAGAACAGGTTTGGTC
5’-TTGCAAGCAGAAAGGATGTC
Os07g0633400
Calmodulin-binding protein
5’-TTGGAGAAGGCAAGGAGATT
5’-ACTTGCCATCCTCAATCACA
Os01g0628000
Cytochrome P450, 72A1
5’-TGTTATCGAGGAGTGCAAGC
5’-CCCAAACAGACCAAGAACCT
Multiple sequence alignment and phylogenetic analysis
The riceOsFBX322 sequence was acquired from the National Center for
Biotechnology Information (NCBI). Phylogenetic analysis was performed by in
MEGA6 software (Tamura ) using the default setting. A phylogenetic tree was constructed
by the Neighbour-joining (NJ) method (Saitou and
Nei, 1987) with 1000 bootstrap replications (Felsenstein, 1985).
Transient expression of OsFBX322 in tobacco epidermal leaf
cells
OsFBX322 cDNA was amplified using the PCR primers
5’-ATGGTGAGGAGGAAGTCGAA-3’ and 5’-TTAAGCATCGTCACAAATAC-3’. The
OsFBX322 fragment was cloned into the pCR/GW/TOPO
(Invitrogen, CA, USA) entry vector and then sub-cloned into the binary vector
pMDC43 for subcellular localization analysis (Curtis and Grossniklaus, 2003). N. benthamiana
leaves were infiltrated with A. tumefaciens GV3101 cells
carrying appropriate plasmids. A. tumefaciens cells that
specifically inhibited plant post-transcriptional gene silencing were
co-infiltrated in order to facilitate high expression of recombinant proteins,
as previously described by Hernández-Sánchez
. A. tumefaciens
cells were grown to ~OD600, collected, and re-suspended in a similar
volume of infiltration buffer (10 mM MgCl2, 10 mM MES (pH 5.6), and
100 μM acetosyringone). An equal mixture of Agrobacterium
strains containing the translational fusion constructs and p19 plasmid was used
for co-infiltration into the abaxial air space of N.
benthamiana leaves. Expression was visualized 3 days after
infiltration. The empty vector was used as a control. The NLS-RFP construct was
utilized as a nuclear marker (Lee ).
Generation of transgenic Arabidopsis
RNA was extracted from OsFBX322 (Os09g0344400) seedlings and
used to generate cDNA. Primers for RT-PCR amplification incorporated
XbaI or KpnI restriction sites and were as
follows: 5’-tctagaATGGTGAGGAGGAAGTCGA AG-3’ and 5’-ggtaccTTAAGCATCGTCACAAATACAT
A-3’. The amplicon was cloned into pGEM-T Easy (Promega, Madison, WI) and
subsequently digested with XbaI and KpnI
(TaKaRa, Tokyo, Japan). The digested fragment was then inserted into pHC21,
which was modified from pCAMBIA2300. The recombinant plasmid was introduced into
Agrobacterium tumefaciens GV3101 and used to transform
Arabidopsis plants (Arabidopsis thaliana
ecotypes Landsberg erecta) via the floral dip method.
Homozygous T3 lines were used for further analyses and transgenic
plants were maintained as described above.
Gamma irradiation of transgenic plants at the seed and seedling stage
To determinate radiation sensitivity of seed, seeds of the T3
generation from different transgenic lines and WT (Arabidopsis
thaliana ecotypes Landsberg erecta) were exposed
to gamma radiation, and then sown on MS medium containing 3% sucrose and 0.25%
phyta-gel (pH 5.8) at 22 oC with 16 h light/8 h dark cycle. For
radiation sensitivity assay at seedling stage, 14-day-old plants grown in soil
were irradiated at 0, 25, 50, and 100 Gy, respectively, for 24 h with a gamma
irradiator (ACEL). At day 4 after gamma irradiation, growth rate was
determined.
In silico analysis of co-expressed genes
Functional gene interactions were identified in OsFBX322 using
weighted gene co-expression network analysis in R package WGCNA (Langfelder and Horvath, 2008), following
the procedure previously described in Hwang
. The module selected as the
OsFBX322 interacting gene cluster was used to reconstruct a
co-expression network in R package ARACNE. The gene-gene interactions detected
by ARACNE were visualized using Cytoscape (Shannon ).
Results
Downregulation of OsFBX322 expression in response to
ionizing radiation
The microarray analysis showed that many FBX genes including
OsFBX322 were differentially regulated in response to three
different types of radiations (Hwang ). We confirmed expression level of
OsFBX322 with the treatments of three different radiations
(gamma radiation, ion beam, and cosmic ray). Results of quantitative reverse
transcription PCR (qRT-PCR) showed that OsFBX322 was
dramatically reduced after exposure to three different types of radiations
(Figure 1), indicating that
OsFBX322 shows radiation responsive expression.
Figure 1
OsFBX322 expression in 3-week-old rice seedlings after
exposure to gamma irradiation, ion beams, or cosmic rays. Quantitative
RT-PCR analysis of OsFBX322 expression after
irradiation. The ACT1 transcript was used for
normalization of mRNA content. Transcript levels are displayed relative
to ACT1 mRNA in non-treated plants (control). Control,
non-irradiated; GA, 200 Gy gamma-irradiation; IB, 40 Gy carbon ions; CR,
exposure on an unmanned spacecraft for 15 days.
Sequence comparison and phylogenetic analysis of OsFBX322 protein
Sequence analysis using BLASTP revealed that OsFBX322 contains an F-box domain in
its N-terminal region, which is a hallmark of F-box proteins from other plant
species. The versatile image from the multiple sequence alignment program
ClustalX highlighted the conserved features (Figure 2A). The results indicate that the F-box domains were
conserved among homologous proteins.
Figure 2
Sequence alignment and phylogenetic tree of OsFBX322 with homologous
proteins. (A) Sequence alignment of the conserved F-box domain in
OsFBX322 and its homologues. Conserved and similar amino acids are shown
in black and grey shading, respectively. (B) Phylogenetic tree analysis
OsFBX322 and its homologues. Accession numbers for the respective
protein sequences are as follows: Oryza sativa japonica
(BAT07596.1), Oryza sativa Indica (EAZ0874.1),
Oryza brachyantha (XP_006661142.1),
Triticum urartu (EMS51354.1), Triticum
aestivum (CDM87191.1), Setaria italica
(XP_022680036.1), Zea mays (PWZ41408.1),
Panicum miliaceum (RLN34519.1), Aegilops
tauschii (XP_020198308.1), Hordeum vulgare
(BAK05154.1), Dichanthelium oligosanthes (OEL21830.1),
Brachypodium distachyon (KQK06273.1),
Sorghum bicolor (EER96573.1). The amino acid
sequences were aligned and the tree was generated using MEGA 6. The
neighbor-joining method with default parameters was used for phylogeny
reconstruction. Statistical support for the tree topology was assessed
by a bootstrap analysis with 1,000 replications. The values at each node
are the bootstrap value.
In order to further elucidate the evolutionary relationship between different
species, we used the Neighbor-joining algorithm to construct a phylogenetic tree
for estimating evolutionary distances and testing evolutionary hypotheses for
OsFBX322 based on amino acid residues (Figure
2B). The phylogenetic analysis showed that OsFBX322 is closely
related to the Oryza sativa indica clade, and this supported
that there is a close relationship of japonica and
indica species.
Nuclear localization of OsFBX322
An N-terminal GFP translational fusion protein was generated to determine the
in vivo subcellular localization of OsFBX322 (Figure 3A). The OsFBX322
open reading frame was cloned into the pCR8 entry vector and sub-cloned into the
pMDC43 gateway binary vector. Transient expression of GFP-OsFBX322 was examined
in N. benthamiana leaves infiltrated with
Agrobacterium carrying the expression plasmid. GFP
fluorescence was observed using a laser-scanning confocal microscope. To reveal
the subcellular localization of OsFBX322, we used a co-transformation protocol
with a GFP-OsFBX322 and NLS-RFP fused construct (NLS-RFP). As shown in Figure 3B, the subcellular distribution of
green and red fluorescent signals overlapped, indicating that OsFBX322 was
localized to the nucleus.
Figure 3
Subcellular localization of OsFBX322 in tobacco epidermal
cells. (A) Schematic representation of the
GFP-OsFBX322 construct. (B) Detection of GFP
fluorescence. OsFBX322 subcellular localization was
investigated using a confocal microscope. Tobacco leaves were
transformed with the pMDC43 vector (GFP alone) (upper panels), NLS-RFP
(middle panels) or GFP-OsFBX322 (lower panels). From
left to right: bright field, GFP, RFP and merged images. Scale bars: 20
μm.
Overexpression of OsFBX322 in transgenic
Arabidopsis
The in vivo functions of OsFBX322 were
investigated in Arabidopsis transformed with a vector carrying
a fusion of the OsFBX322 cDNA and the CaMV35S promoter (Figure 4A). Fourteen independent
T1 plants were selected on media containing kanamycin. To
determine the OsFBX322 copy number in transgenic plants,
T1 plants were self-pollinated and the progeny (T2)
were allowed to segregate on selection media. Following self-pollination of the
T2 lines, two T3 homozygous lines (OX7-4 and OX12-5)
that contained a single T-DNA insertion were selected for analysis (Figure 4B). The presence of
OsFBX322 cDNA (1.353 kb) was verified by genomic DNA PCR
using gene-specific primers (Figure 4B).
RT-PCR analysis of wild-type plants and the overexpression lines OX7-4 and
OX12-5 showed that the integrated OsFBX322 was strongly
detectable only in the OX7-4 and OX12-5 plants (Figure 4C). In order to confirm effect by OsFBX322
overexpression, we used two independent OsFBX322-overexpressing
lines (OX7-4 and OX12-5) for further analyses.
Figure 4
OsFBX322 overexpression in transgenic
Arabidopsis plants. (A) Schematic representation of
the 35S:OsFBX322 overexpression construct.
OsFBX322 was regulated by the CaMV35S promoter
(CaMV35S). (B) Genomic PCR analysis of untransformed wild-type plants
and transgenic Arabidopsis lines. The presence of
OsFBX322 was verified by genomic PCR (Table 1). M, molecular mass marker;
V, pHC21::OsFBX322 vector; WT, untransformed wild-type
plants; OX7-4 and OX12-5, transgenic 35S:OsFBX322
lines. (C) RT-PCR analysis of OsFBX322 transcripts in
WT and transgenic plants. Actin2 was used as a
control.
Enhanced sensitivity of transgenic OsFBX322 overexpressing
lines to radiation
The reduction of OsFBX322 expression after irradiation suggested
that OsFBX322 may play an important role in the radiation
response. Therefore, we evaluated the radiation sensitivity of WT and transgenic
plants. OsFBX322-overexpressing lines, germinated from
gamma-irradiated seeds, displayed different rate of germination and early
seedling growth after 100 Gy gamma irradiation in comparison with a WT control
(data not shown). To determine the direct effect of gamma radiation on the
seedling stage, 14-day-old seedlings of transgenic lines were irradiated with
25, 50 and 100 Gy gamma radiation. OsFBX322 overexpression also
improved the radiation sensitivity at the seedling stage (Figure 5). As shown in Figure
5, there were no apparent differences in growth between unirradiated
wild-type plants and wild-type plants exposed to 25 or 50 Gy of
gamma-irradiation for 24 h. By contrast, growth was inhibited in both the OX7-4
and OX12-5 transgenic lines after the same radiation regime (Figure 5A). The fresh weights of OX7-4 and
OX12-5 were also significantly lower than that of the WT (Figure 5B). OsFBX322-overexpressing
transgenic plants were more sensitive than the WT to radiation. This suggested
that overexpression of OsFBX322 caused increased sensitivity to
gamma irradiation.
Figure 5
Phenotype analysis of transgenic 35S:OsFBX322
plants. (A) Enhanced sensitivity of 35S:OsFBX322
plants. Two-week-old wild-type (WT) and 35S:OsFBX322
(OX7-4 and OX12-5) plants were exposed to gamma irradiation as
indicated. Plants were photographed after 4 days recovery under normal
conditions. Scale bar = 2.5 cm. (B) Fresh weights of irradiated WT and
transgenic plants. Average fresh weight was estimated from 3–5 plants.
Data are means ± SE from at least three independent experiments.
Asterisks indicate statistical significance (p <
0.05, Student’s t-test) of differences between
transgenic lines and WT.
Co-expression network analysis to identify OsFBX322-related
genes
Co-expression network analysis was used to identify genes linked to
OsFBX322 (Figure 6).
Four genes were identified: cytochrome P450 (Os01g0628000), calmodulin-binding
protein (Os07g0633400), double-strand break repair protein
MRE11 (Os08g0177600), and F-box domain containing protein
OsFBX313 (Os09g0324300) (Figure 6A). Expression of these genes after radiation exposure was
examined using real-time PCR (Figure 6B).
Compared to the unirradiated control, all four genes exhibited lower expression
levels in response to gamma-irradiation, ion beams, and cosmic rays. Although
expression of individual genes varied, all four genes exhibited a downregulated
response (Figure 6B). These results
suggested that the co-expressed genes with OsFBX322 had similar
functions in the response to multiple types of irradiation.
Figure 6
Co-expression relationships between OsFBX322 and
related genes. (A) OsFBX322 (Os09g0344400) functional
gene interactions within a co-expression network constructed by R
package ARACNE. Nodes and edges represent the different genes and their
functional interactions, respectively. Genes and interactions
highlighted in red closely interacted with OsFBX322
(Os09g0344400). (B) qRT-PCR analysis of co-expressed genes in rice after
exposure to GA, IB, or CR. Control, non-irradiated; GA, 200 Gy
gamma-irradiation; IB, 40 Gy carbon ions; CR, exposure on an unmanned
spacecraft for 15 days.
Discussion
The mechanisms underlying differential responses to radiation are likely based on
differences at the DNA level. This could include increased mutation rates in
essential genes, which may lead to higher or lower sensitivities to radiation. Our
previous DNA microarray analysis identified 53 candidate genes that were up- or
downregulated in response to radiation exposure, but that were not differentially
regulated by other stresses (Hwang ). One of these genes, OsFBX322,
was substantially downregulated after exposure to gamma-irradiation, ion beams, or
cosmic rays (Hwang ). Attempts have also been made to address the biological functions
of the OsFBX322, we have generated overexpression transgenic plants
in Arabidopsis. Our analysis of this transgenic plant has new and
important information response to radiation condition.F-box domain containing proteins belong to a versatile group and have multiple
functions in degradation of cellular proteins, developmental processes, and
responses to abiotic stress (Lechner ; Dreher and Callis,
2007; Zhang ). However, the molecular mechanisms by which these proteins exert
their functions are not fully known. In our semi-quantitative and quantitative
results, the expression levels of OsFBX322 were found to be
downregulated after gamma-irradiation, ion beam and cosmic-ray exposure (Figure 1). This is consistent with previous
microarray results (Kim ; Hwang ) and indicates that OsFBX322 may play a functional
role in the response to radiation. Additionally, we examined the subcellular
localization of OsFBX322 using a GFP translational fusion. Transiently-expressed
OsFBX322 was found in N. benthamiana epidermal cells (Figure 3). Previous reports showed that F-box
proteins were localized in various intracellular compartments including the nucleus,
cytosol, vacuole, and chloroplasts (Kuroda
). In rice, MOF (a putative F-box
protein) interacted with SKP1-like protein OSK1, suggesting that MOF was a component
of SCF ubiquitin and regulated cellular functions via ubiquitin-mediated protein
degradation or via signaling pathways in the nucleus (He ). OsFBX322 exhibited nuclear
localization and may play a similar role to that of MOF. OsFBX322
was overexpressed in Arabidopsis to further investigate its
radiation sensitivity (Figure 4).
OsFBX322 overexpressing transgenic plants showed increased
sensitivity to gamma irradiation compared to control plants (Figure 5). These results indicate that OsFBX322
is involved in the plant response to radiation and that OsFBX322 is
a radiation responsive gene.Highly correlated gene expression profiles are suggestive of common regulatory
mechanisms and similar biological functions. Detection of gene modules in a
co-expression network can facilitate the discovery of biologically meaningful
clusters, and these methods were successfully used in various biological contexts
(Langfelder and Horvath, 2008; Hwang ). Recent
studies demonstrated that co-expression networks could be used to identify a set of
candidate genes underlying specific phenotypes (Mutwil , Ficklin and Feltus, 2011). In this study, module detection was used to
identify biological systems in rice that changed significantly in response to
ionizing radiation (Figure 6). Four genes
co-expressed with OsFBX322 were identified: Os08g0177600
(double-strand break repair protein MRE11), Os07g0633400 (Calmodulin-binding
protein), Os01g0628000 (Cytochrome P450, 72A1), and an F-box protein, Os09g0324300
(OsFBX313). OsFBX322 was also classified as an
F-box protein. Recent research indicated that F-box domain proteins had important
roles in regulating various developmental processes and stress responses (Lechner ; Dreher and Callis, 2007; Zhang ). Expression of F-box
proteins in rice led to a reduced tolerance of abiotic stresses (Yan ) and F-box
gene expression was downregulated by ionizing radiation (Hwang ). This study provides
evidence that a number of F-box protein-encoding genes are likely to be involved in
radiation responses. Additionally, previous studies showed that MRE11, as part of a
complex with the Rad50 and Xrs2/Nbs1 proteins, functioned in diverse DNA repair and
metabolic mechanisms after induction by ionizing radiation in rice (Hong ; Ji ). The gene
encoding putative OsMRE11-like protein (Os08g01776600) was co-expressed with
OsFBX322 and was downregulated in response to ionizing
radiation (Figure 6). This suggested that
OsMRE11-like protein might perform essential DNA repair and metabolic functions
after ionizing radiation exposure in rice. Calmodulin-binding protein and cytochrome
P450 were shown to be involved in the stress responses (Yang and Poovaiah, 2002; Narusaka ). The presence of multiple
modules with connectivity suggests that the several regulatory networks may be
present in controlling unique and/or overlapping sets of OsFBX322
genes. The high level of connectivity with FBX family gene and several stress
response genes led us to hypothesize a strong likelihood of combinatorial and
synergistic regulation to radiation response by these genes. However, further
research is required to confirm these genes identified by transcriptional
analysis.Our study demonstrates that OsFBX322 plays a significant role in the
radiation responsive pathway, and corresponding genes in other species may be a
valuable resource for producing radiation-sensitive transgenic crop plants. Such
transgenic plants may also be useful for the detection of radiation sensitivity.
Authors: Jennifer M Gagne; Brian P Downes; Shin-Han Shiu; Adam M Durski; Richard D Vierstra Journal: Proc Natl Acad Sci U S A Date: 2002-08-08 Impact factor: 11.205
Authors: Marek Mutwil; Björn Usadel; Moritz Schütte; Ann Loraine; Oliver Ebenhöh; Staffan Persson Journal: Plant Physiol Date: 2009-11-04 Impact factor: 8.340
Authors: Sheela Prithivirajsingh; Michael D Story; Sherry A Bergh; Fady B Geara; K Kian Ang; Sheikh M Ismail; Craig W Stevens; Thomas A Buchholz; William A Brock Journal: FEBS Lett Date: 2004-07-30 Impact factor: 4.124