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Alternative splicing of flowering regulatory gene LFY in Arabidopsis thaliana

拟南芥成花调控LFY基因的选择性剪接



全 文 :广 西 植 物 Guihaia 32(3):371-376                                2012 年 5 月
 
DOI:10.3969/j.issn.1000-3142.2012.05.018
Alternative splicingof floweringregulatory
gene LFYin Arabidopsis thaliana
YU Li-Xia,YAO You-Lin,WU Xiao-Lu,
TANG Xiao-Qian,YAN Bo*
(Faculty of Landscape Architecture,Southwest Forestry University,Kunming 650224,China)
Abstract:To study the expression of flowering regulatory gene LFYgene in Arabidopsis thaliana,we used reverse
transcription-polymerase chain reaction and isolated three alternative splicing(AS)fragments named as LFY1239,
LFY1263,and LFY1275respectively.Sequence analysis confirmed that fragment LFY1263contained an open reading
frame of 1 263bp,and was identical to the previously reported and predicted fragment,while LFY1239lacked 36bp at
the 3′end of the first exon,and LFY1275had an additional 12bp derived from the 3′end of the first intron.Expres-
sion analysis showed that LFY1239was only detected in rosette during the vegetative stage,while LFY1263and
LFY1275presented in both floral organs and rosette during both vegetative and flowering stages.Furthermore,
LFY1263appeared to be the most abundant transcript.The expression ratio of LFY1275to LFY1263was higher in
floral organs than in rosette leaves,which suggested that such ratio might be associated with the flowering regulation.
Key words:LFYgene;floral transition;alternative splicing(AS);differential expression
CLC Number:Q752  Document Code:A  Article ID:1000-3142(2012)03-0371-06

拟南芥成花调控LFY基因的选择性剪接
于丽霞,姚有林,武晓璐,汤晓倩,鄢 波*
(西南林业大学 园林学院,昆明650224)
摘 要:为研究拟南芥成花调控基因LFY,我们采用RT-PCR方法分离克隆了三种选择性剪接的片段,分别
命名为LFY1239,LFY1263和LFY1275。序列分析表明LFY1263包含一个大小为1 263bp的开放阅读框,
与之前报道的LFY基因片段大小相同,而LFY1239在第一外显子的3′端缺失了36bp,LFY1275在第一内含
子的3′末端插入了12bp。对几种片段表达部位的分析显示,LFY1239只能在营养生长期的莲座叶中表达,
而LFY1263和LFY1275在营养生长期和花期的花器官和莲座叶中都可以检测到,并且,LFY1263呈现出主导
地位,LFY1275与LFY1263表达的比例表现为花器官高于莲座叶,该比例的变化可能预示着与成花调控有关。
关键词:LFY基因;成花转变;选择性剪接;差异表达
  LFYgene plays an important role to promote
flower formation by interaction and coordination with
other genes,such as TFL,AP1,AP2,CAL,FT,AP3,
UFO,GA1 et al.In the current model of plant flower-
ing development derived fromArabidopsis,it has been
thought that LFYis central to the integration of floral
signals and regulates flowering.Since Weigel et al.i-
solated LFYgene of A.thaliana(Weigel et al.,1992),
LFYgene has been cloned from other species(Maizel et
al.,2005;Matthewet al.,2005;Qingyi et al.,2005;
* Received date:2011-10-05  Accepted date:2012-03-29
Foundation items:Supported by the National Natural Science Foundation of China(31060042,31160177);Yunnan Province and Minister Key Subject,
University Key Lab and Share Platform
Biography:YU Li-Xia(1981-),女,山东威海人,硕士,助教,主要从事植物分子生物学等研究,(E-mail)yulixia2005@sohu.com。
*Author for correspondence:YAN Bo,男,博士,教授,主要从事植物生物技术等研究,(E-mail)yanbodr@yahoo.com.cn。
Siddhartha et al.,2008).Also,LFYgene is one of the
most wel studied genes and its role in flower develop-
ment has been wel established(Weigel &Coupland,
1995;Pena et al.,2001;He et al.,2001).In flower
meristems,LFY acts as a master regulator orchestra-
ting the whole floral network(Miguel,et al.,2006;
Vivian,2010).LFY is a plant-specific transcription
factor that directly binds to the regulatory region of its
target genes through a helix-turn-helix motif buried
within a unique protein fold(Cécile Hamès,et al.,
2008).To activate AP3in whorls 2and 3,LFY binds
to an F-box protein,known as UFO in Arabidopsis,
which is part of an SCF-type ubiquitin ligase(Euny-
oung et al.,2008).The expression of LFYgene in dif-
ferent plants exist temporality and spatiality.It has
been reported that high levels of expression of LFY
genes are first detected in axilary meristems arising on
the flank of the shoot apex in seed plants,from which
they thought that LFY stil exerts its ancestral role on
the regulation of cel division in gymnosperms and an-
giosperms,but in a territory restricted to axilary meri-
stems.
Alternative splicing(AS)in eukaryotes contributes
to the diversity and the complexity of gene expression
(Michael et al.2008).It may not only change protein
domain organization of activity and localization,but al-
so influence the interaction between protein subunits
and protein post-transcription regulation including pro-
duction of nonfunctional proteins(Craig et al.,2008).
AS has been investigated more comprehensively in hu-
man and animals with about 70%-80%genes of hu-
man with AS shown by microarray assay(Johnson et
al.,2003).Although great eforts have been made in
recent years(Craig et al.,2008;Kemal,2003),AS in
plants stil remain ful of chalenge.It has been repor-
ted that there are several alternative splicing genes in
rice,wheat,Zea mays,orange,populus,sunflower,Vitis
viniferaand leafy spurge in these few years(Yamauchi
et al.,2008;Terashima & Takumi,2009;Howitt et
al.,2009;Lin et al.,2009;Zhang et al.,2009;Srivas-
tava et al.,2009;Lazarescu et al.,2010;Zenoni et al.,
2010;Horvath et al.,2010).And some alternatively
spliced genes in Arabidopsisthaliana has been reported
(Schindler et al.,2008;Yan et al.,2009),including
some genes responsible for floral transition,such as
SEF,GA5,SPY,MAF4,SVP,FT,TOE1 et al.(Reddy
&Golovkin,2008),however,AS of LFYgene has not
been investigated yet.In this paper,alternative splicing
forms of LFYgene in Arabidopsis thaliana were isola-
ted and characterized,named as LFY1239,LFY1263
and LFY1275,respectively.The expression ratio of
three diferent transcripts in rosette leaves and floral
organs was determinated.
1 Material and methods
1.1Plant materials
The plants used in this study were Arabidop-
sis thaliana(L)Heynh,Columbia.
1.2 RNA extraction and synthesis of the first-
strand cDNA
  RNA was extracted from leaves using RNAsimple
Total RNA kit(Tiangen Biotechque Co.Ltd.,China).
The first-strand cDNA synthesis was carried out using
the First-Strand RT-PCR kit(Takara Biotechnology
Co.Ltd.,China).
1.3RT-PCR and sequence analysis
PCR was performed in 96-wel plates with a Bi-
ometer T Gradient thermal cycler.Primers were de-
signed according to the reported cDNA and genomic
DNA sequences of LFYgene in Arabidopsis thaliana
(GenBank accession no.NM_125579,M91208).The
sequences of primers were as the folows,LFYPrimer
Forward: 5′-ATGGATCCTGAAGGTTTCACGAG-
3′, LFY  Primer  Reverse: 5′-CTAGAAACG-
CAAGTCGTCGCCG-3′(the ful-length coding region
of LFYcDNA and DNA sequences);LAS Primer For-
ward: 5′-GAAGAGGAATCTTCTAGACGCCG-3′,
LAS Primer Reverse:5′-CCAGTAACCACTTCCTC-
CTCCG-3′(diferential fragments of diferent tran-
scripts)(Shenggong Biological Engineering Technology
&Services Co.Ltd.,China).The standard PCR con-
ditions were carried out with Taq TMpolymerase(Takara
Biotechnology Co.Ltd.,China).The cycling condi-
tions were with an initial incubation 5min at 94℃fol-
lowed by 35cycles of denaturation lasted 30sat 94
273 广 西 植 物                  32卷
℃,varied annealing temperatures for 30s,and poly-
merization 90sat 72℃.The annealing temperatures
included 66℃in the amplification of complete coding
sequence and 64℃in the amplification of fragments of
180bp or so.PCR products were visualized on a 1%
agarose gel with 0.5μL/mL ethidium bromide.Gel
images were captured using a UVP Imaging System
and documented by VisionWorksLS.RT-PCR prod-
ucts were purified with a DNA Gel Extraction Mini Kit
(Watson Biotechnologies,Inc.,China).The purified
PCR products were cloned into the pMD18-T Easy
vector(Takara Biotechnology Co.Ltd.,China)named
as pTLFY,and then were sequenced in Shenggong Bio-
logical Engineering Technology &Services Co.,Ltd.
1.4Differential expression assay in AS products
Amplifications were carried out under the cycles
of 12,16,28,30,32,34,36,38,40and 42in order to
determine the cycle number of linearity stage.cDNA
from diferent tissues during diferent development sta-
ges were used as templates,which were natural com-
petitive templates and the principal was similar to com-
petitive PCR.The primers were LAS primer F and
LAS primer R.The products of varied sizes were sepa-
rated using 3.5%agarose gel electrophoresis.Optical
density assay on RT-PCR products of diferent AS
transcripts of LFYgene was carried out by means of
VisionWorks LS software of BioSpectrum Imaging
System.
2 Results
2.1Isolation and characterization of different AS
fragments of LFY
  We isolated the ful length of LFYin Arabidopsis
thaliana,which include three transcripts during the
vegetative stage and two transcripts during the repro-
ductive stage.Furthermore,in order to attain more vis-
ual electrophoresis result of diferent transcripts,we i-
solated partial AS fragments of diferent organs during
diferent stage by using LAS primers,which were
shown in Fig.1.There were three AS fragments in ro-
sette leaves during the vegetative stage(Lane 1,Fig.1:
a),and there were two AS fragments both in floral or-
gans(Lane 1,Fig.1:b)and in rosette leaves(Lane 2,
Fig.1:b)during reproductive stage.It was obvious
that the expression patterns of transcripts were difer-
ent during diferent stage.
Fig.1 a.AS fragments in rosette during the vegetative
stage(M:DNA marker);b.AS fragments
in floral organ &rosette during reproductive stage
(M:50bp DNA ladder;1:AS fragments in
floral organ;2:AS fragments in rosette)
2.2Comparison of different transcript sequences
We analyzed these three RT-PCR products of
LFY.Sequence alignment of these three diferential
expression fragments showed that there could be three
alternative splicing transcripts in Arabidopsis thaliana.
Compared with LFY genomic DNA sequence,
LFY1239lacked of 36bp near the 3′end of the first
exon,LFY1263was identical to what was reported
previously with 1 263bp in length,and LFY1275had
additional 12bp in the 3′end of the first intron(Fig.
2).The alternative splicing of LFYleads to either in-
sertion or deletion of the LFYprotein(Fig.3).The al-
ternative spliced transcript,LFY1275,displayed four a-
mino acid(DDWT)insertion compared to LFY1263.In
contrast,the alternatively spliced transcript,LFY1239,
had twelve amino acid(GTHHALDALSQE)deletions
and four amino acid(DDWT)insertion compared
to LFY1263.
2.3Differential expression of AS transcripts
To study if these AS transcripts were diferently
3733期           于丽霞等:拟南芥成花调控LFY基因的选择性剪接
Fig.2 Sequence alignment of three AS fragments
Fig.3 Sequence alignment of amino acid deduced from three AS fragments
expressed during different development stage of
Arabidopsis thaliana,we performed RT-PCR of
LFYgene transcripts in organs at both vegetative
and reproduced stages.The result of optical densi-
ty assay of these transcripts was shown in Fig.4.
Optical density assay showed that the relative ratio
of expression was as folows:a.rosette leaves in
the vegetative stage LFY1275 ∶ LFY1263 ∶
473 广 西 植 物                  32卷
LFY1239=1∶4.784∶1.044,b.rosette leaves in
reproduced stage LFY1275∶LFY1263=1∶4.652,
c.floral organ LFY1275∶LFY1263=1∶3.768.
Over al,LFY1263and LFY1275expression was
consistent in both stages and both rosette leaves
and floral organs,with LFY1263in predominant a-
mount.LFY1239transcript was only detectable in
rosette leaves at vegetative stage.These data sug-
gested that LFYgene alternative splicing was asso-
ciated with different organs at different develop-
ment stages of the plant.
3 Discussion
In the current study,we identified two alternative-
ly spliced transcripts of the Flowering Regulatory Gene
LFY.LFY1239was detected only in rosette leaves at
the vegetative stage,which indicated that LFY1239is
not associated with floral transition of Arabidopsis
thaliana.In contrast,LFY1275and LFY1263ex-
pressed consistently during the vegetative and repro-
ductive stage,which implied that both transcripts were
relevant to floral transition.
Fig.4 Optical density assay on RT-PCR products of
different AS transcripts expression of LFYgene
  LFY1263was the predominant transcript at
different stage,with the ratio of LFY1275to
LFY1263increased slightly in floral organs than
that in rosette leaves,suggesting that LFY1275
may play an important role in floral transition.To-
gether with the result of the reported studies on
the function of LFY1263,who thought increasing
the copy number of endogenous LFY1263reduced
the number of leaves produced before the first
flower is formed(Miguel et al.,1997),transcript
LFY1275may also regulate the growth and floral
transition of Arabidopsis thaliana in addition to
transcript LFY1263.The change of LFYexpres-
sion during the different stage suggested that it
played comprehensive effect in plant development
process,it not only control floral development in-
cluding floral initiation but also played an impor-
tant role in leaf morphogenesis during the vegeta-
tive stage.The biological roles of two spliced vari-
ants(LFY1239and LFY1275)of the LFYgene of
Arabidopsis thaliana remain to be identified,and
we wil develop it in the subsequent research.
In this research,sequence alignment result of
different transcripts showed that they differed in a
short stretch of nucleotide base pairs,with most
coding region identical and no frame shift muta-
tions.Weigel et al.reported that N-terminal(in-
cluding the first exon)of LFY was vital to LFY
protein function.Transcript LFY1239lack of 36
bp in the 3′end near the first exon leading to 12a-
mino acid deletion of the protein,which maybe
there just to make up the number and attribute to
its interfered with floral initiation,and this consist-
ent with our observation that LFY1239transcript
was only detectable in rosette leaves during the vegeta-
tive stage.Transcript LFY1275displayed additional 12
bp in the 3′end of the first intron and result in 4amino
acid insertion in the protein which may enable the gene
product to diferently influence the growth and floral
transition of Arabidopsis thaliana.
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