Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs.

Abstract

The most widespread riboswitch class, found in organisms from all three domains of life, is responsive to the vitamin B(1) derivative thiamin pyrophosphate (TPP). We have established that a TPP-sensing riboswitch is present in the 3' untranslated region (UTR) of the thiamin biosynthetic gene THIC of all plant species examined. The THIC TPP riboswitch controls the formation of transcripts with alternative 3' UTR lengths, which affect mRNA accumulation and protein production. We demonstrate that riboswitch-mediated regulation of alternative 3' end processing is critical for TPP-dependent feedback control of THIC expression. Our data reveal a mechanism whereby metabolite-dependent alteration of RNA folding controls splicing and alternative 3' end processing of mRNAs. These findings highlight the importance of metabolite sensing by riboswitches in plants and further reveal the significance of alternative 3' end processing as a mechanism of gene control in eukaryotes.

Full text

Page 1

Riboswitch Control of Gene Expression in Plants by Splicing
and Alternative 39 End Processing of mRNAs
W OA
Andreas Wachter,a,1Meral Tunc-Ozdemir,bBeth C. Grove,cPamela J. Green,dDavid K. Shintani,b
and Ronald R. Breakera,c,e,2
aDepartment of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
bDepartment of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557
cDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
dDepartment of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
eHoward Hughes Medical Institute, Yale University, New Haven, Connecticut 06520
The most widespread riboswitch class, found in organisms from all three domains of life, is responsive to the vitamin B1
derivative thiamin pyrophosphate (TPP). We have established that a TPP-sensing riboswitch is present in the 39 untranslated
region (UTR) of the thiamin biosynthetic gene THIC of all plant species examined. The THIC TPP riboswitch controls the
formation of transcripts with alternative 39 UTR lengths, which affect mRNA accumulation and protein production. We
demonstrate that riboswitch-mediated regulation of alternative 39 end processing is critical for TPP-dependent feedback
control of THIC expression. Our data reveal a mechanism whereby metabolite-dependent alteration of RNA folding controls
splicing and alternative 39 end processing of mRNAs. These findings highlight the importance of metabolite sensing by
riboswitches in plants and further reveal the significance of alternative 39 end processing as a mechanism of gene control in
eukaryotes.
INTRODUCTION
Riboswitches are metabolite-sensing gene control elements
typically located in the noncoding portions of mRNAs. Twelve
structural classes of riboswitches in bacteria have been charac-
terized to date that sense small organic compounds, including
coenzymes, amino acids, and nucleotide bases (Mandal and
Breaker, 2004; Soukup and Soukup, 2004; Winkler and Breaker,
2005; Fuchs et al., 2006; Roth et al., 2007) or magnesium ions
(Cromie et al., 2006). In most instances, riboswitches can be
divided into aptamer and expression platform regions that rep-
resenttwofunctionallydistinctbutusuallyphysicallyoverlapping
domains responsible for ligand binding and gene control, re-
spectively.
Thecomplexity ofthe structures formed byaptamers and their
mechanisms of ligand recognition are evident upon examination
of the atomic resolution models elucidated by x-ray crystallog-
raphy for several riboswitch classes, including those that bind
guanine and adenine (Batey et al., 2004; Serganov et al., 2004),
S-adenosylmethionine(MontangeandBatey,2006),thiaminpyro-
phosphate (TPP) (Edwards and Ferre-D’Amare, 2006; Serganov
et al., 2006; Thore et al., 2006), and glucosamine-6-phosphate
(Kline and Ferre ´-D’Amare ´, 2006; Cochrane et al., 2007). The nu-
cleotide sequences of the ligand binding core and supporting
architectures ofeachaptamerclassarehighlyconservedamong
different species as a result of their need to form a precise re-
ceptor for a specific ligand. By contrast, the expression plat-
forms for riboswitches can vary considerably among species or
even among multiple representatives of a riboswitch class in a
single organism.
The high level of aptamer conservation allows researchers to
employ bioinformatics methods to identify new riboswitch can-
didates (e.g., Grundy and Henkin, 1998; Gelfand et al., 1999;
Barrick et al., 2004; Corbino et al., 2005; Weinberg et al., 2007)
and to determine the distribution of known riboswitch classes in
various organisms (e.g., Rodionov et al., 2002; Vitreschak et al.,
2003; Nahvi et al., 2004; Abreu-Goodger and Merino, 2005). To
date, these searches have revealed that only members of the
TPP-sensing riboswitch class are present in all three domains of
life (Sudarsan et al., 2003). In eukaryotes, TPP aptamers were
found in thiamin metabolic genes from plants and filamentous
fungi,buttheproposalsforthemechanismofriboswitchfunction
remained speculative (Kubodera et al., 2003; Sudarsan et al.,
2003).InthefungusNeurosporacrassa,aTPPaptamerresidesin
an intron within the 59 region of NMT1 mRNA, and recently it has
been shown that TPP binding by the aptamer regulates NMT1
gene expression by controlling alternative splicing (Cheah et al.,
2007). Specifically, TPP binding by the riboswitch prevents
removal of intron sequences carrying upstream open reading
frames (ORFs) that preclude expression of the main ORF.
Herein,wereportthatTPPriboswitchesarepresentinavariety
of plant species where they reside in the 39 untranslated regions
1Current address: Heidelberg Institute for Plant Sciences, University of
Heidelberg, 69120 Heidelberg, Germany.
2Address correspondence to ronald.breaker@yale.edu.
The author responsible for distribution of materials integral to the
findings presented in this article in accordance with the policy described
in the Instructions for Authors (www.plantcell.org) is: Ronald R. Breaker
(ronald.breaker@yale.edu).
WOnline version contains Web-only data.
OAOpen Access articles can be viewed online without a subscription.
www.plantcell.org/cgi/doi/10.1105/tpc.107.053645
The Plant Cell, Vol. 19: 3437–3450, November 2007, www.plantcell.org ª 2007 American Society of Plant Biologists

Page 2

(UTRs) of THIC genes. Formation of THIC transcripts with alter-
native 39 UTR lengths is dependent on riboswitch function and
mediates feedback regulation of THIC expression in response to
changes in cellular TPP levels. Our data indicate that 39 UTR
length correlates with transcript accumulation, thereby estab-
lishing a basis for gene control by alternative 39 end processing.
Weproposeadetailed mechanismfor TPPriboswitchfunctionin
plants, which includes aptamer-mediated control of splicing and
differential 39 end processing of THIC mRNAs. This study further
reveals the versatility of riboswitch control in organisms from
different domains of life and expands our knowledge of previ-
ously unknown aspects of eukaryotic gene regulation.
RESULTS AND DISCUSSION
TPP Aptamers Are Widely Distributed in Plant Species
ThepresenceofhighlyconservedTPPbindingaptamersinthe39
UTRs of the THIC genes from the plant species Arabidopsis
thaliana, Oryza sativa, and Poa secunda had been reported
previously (Sudarsan et al., 2003). The collection of plant TPP
aptamer representatives was expanded by sequencing THIC
genesfromadditionalplantspeciesandbyconductingdatabase
searches for nucleotide sequences that conform to the TPP
aptamer consensus. After cDNA sequences were obtained, the
corresponding regions from genomic DNAs of each species
were cloned and sequenced (see Methods for details), thus
providing the sequences of both the precursor and the pro-
cessed mRNA molecules.
An alignment of all available TPP aptamer sequences from
plants reveals a high level of conservation of nucleotide se-
quence and a secondary structure consisting of stems P1
through P5 (Figure 1A). The major differences of eukaryotic
TPPriboswitchaptamersfromplants(Figure1B)andfilamentous
fungi (Cheah et al., 2007) compared with their bacterial and
archaeal counterparts (Figure 1C) (Rodionov et al., 2002; Winkler
et al., 2002) are the consistent absence of a P3a stem frequently
present in bacterialrepresentatives and thevariable lengthof the
P3 stem in eukaryotes. Neither region is involved directly in TPP
binding (Edwards and Ferre-D’Amare, 2006; Serganov et al.,
2006; Thore et al., 2006; Cheah et al., 2007); therefore, these
differences should not affect ligand binding specificity.
The TPP aptamer is found in the 39 UTR of all known THIC
examples from monocots, dicots, and the conifer Pinus taeda.
Interestingly, in the moss Physcomitrella patens, the TPP ap-
tamer is present in the 39 UTR of THIC (Ppa1) and also resides in
the 39 region of two genes that are homologous to the thiamin
biosynthetic gene THI4 (Ppa2 and Ppa3). This latter observation,
and the observation that fungi also have TPP aptamers associ-
ated with multiple different genes (Cheah et al., 2007), indicate
that eukaryotes likely use representatives of the same riboswitch
class to control multiple genes in response to changing concen-
trations of a key metabolite.
A striking characteristic of TPP aptamers from plants is the
high level of nucleotide sequence conservation. Approximately
80% of the nucleotides (excluding the P3 stem) are conserved in
all plant examples. By contrast, <40% are conserved in filamen-
tous fungi. Most differences among plant TPP aptamers are
found in the P3 stem, which varies both in length and sequence.
Also, the length of the P3 stem varies among TPP aptamer
representatives in the same species, as is observed in P. patens
(Figure 1A). The presence of both an extended P3 stem in the
aptamer present in THIC and very short P3 stems in those
present in THI4 suggests that there is no species-specific re-
quirement for this component of the aptamer.
THIC 39 UTRs Vary in Length and Sequence
We analyzed the nucleotide sequences corresponding to the 39
regions of THIC mRNAs cloned from six plant species or
obtained from GenBank (O. sativa) (see Supplemental Figure
1 online; see also Methods for details). Interestingly, the exon-
intron organization of the 39 regions of THIC genes is conserved
among these seven species, and the formation of three major
types of RNA transcripts with varying 39 UTR lengths is always
observed (Figure 2A). The stop codon for the THIC ORF is
commonlyfollowedbyanintronthatresidesnearaTPPaptamer.
Type I (THIC-I) RNAs represent precursors that carry the com-
pleteaptamerandcan extendtovariablelengths attheir39ends.
THIC-I RNAs can be differentially processed either upstream of
the aptamer to yield type II (THIC-II) RNAs with a shorter 39 UTR
or can be spliced to yield type III (THIC-III) RNAs, which are
missing the 59 portion of the TPP aptamer. THIC-II and THIC-III
RNAs are mutually exclusive fates of THIC-I processing.
Quantitation of the lengths of various regions (designated
1through6)withintheTHIC39UTRsofthesespeciesrevealsthat
some regions (2 through 5) exhibit considerable conservation of
the numbers of nucleotides bridging key features within the UTR
(see Supplemental Figure 2 online). By contrast, the length of the
first intron (region 1) and the length of the 39-most portion of
THIC-I and THIC-III (region 6) are highly variable. For example,
THIC-IandTHIC-IIIcanextendbymorethan1kbattheir39ends.
We speculated that conservation of the distances between
certain 39 UTR features might be important for TPP-mediated
gene regulation.
RT-PCR was used to analyze THIC transcript types. RT-PCR
using a polyT primer (primer b) and a primer specific for the THIC
ORF (primer a; amplifies all THIC transcript types) results pre-
dominantly in amplification of THIC-II (Figure 2B). This indicates
that the short transcript form is most abundant in all species
examined. RNA gel blot analysis of RNA from Arabidopsis with a
probe that binds to the coding region of the THIC mRNA also
results in one major signal corresponding to the size of THIC-II,
which further supports our conclusion that THIC-II is the dom-
inant transcript type (see further discussion below).
THIC-I and THIC-III were detected by RT-PCR using a reverse
primercthatisspecificfortheextended39regionineachspecies
examined but that do not recognize THIC-II RNAs (Figure 2C).
ThesmallestPCRproductbandforeachspeciescorrespondsto
THIC-III, whereas additional bands represent products derived
from THIC-I that still retain one or both introns of the 39 UTR or
represent minor splicing variants. RNA gel blot analysis using a
probe specific for the 39 UTR of THIC-I and THIC-III from
Arabidopsis confirmed that these transcript types are present
in low copy number (see further discussion below) and also
revealed heterogeneity of transcript length.
3438 The Plant Cell

Page 3

To assess whether 39 end processing differs for the various
transcript types in Arabidopsis, RT-PCR was conducted using
primers that permit separate amplification of the various THIC
RNAs. Interestingly, the ratio of amplification products corre-
sponding to THIC-I and THIC-III RNAs differs depending on the
primer used for RT (Figure 2D; see also Figures 4E and 5E).
Amplification products from THIC-III dominate when RT is
conducted with polyT primers, whereas amplification products
from THIC-I are increased relative to THIC-III product amounts
wheneitherrandomhexamers orgene-specific primersareused
for RT. This indicates that a major fraction of THIC-I RNAs is not
polyadenylated at the sites used for 39 end processing of the
other THIC RNA types. Furthermore, amplification product var-
iants of THIC-I with the upstream intron spliced or unspliced
were detected. These findings suggest that THIC-I represents
the unprocessed THIC precursor transcript. By contrast, both
THIC-II and THIC-III RNAs are further processed and polyade-
nylated at the indicated sites, and these RNAs represent the two
alternative processing fates of the precursor transcript.
Also, cDNAs generated with primers binding far downstream
of the aptamer sequence yielded PCR amplification products
(Figure 2D), indicating that THIC-I and THIC-III can extend >1 kb
Figure 1. TPP Aptamers Are Conserved and Widespread in Plant Species.
(A) Alignment of TPP aptamer sequences from various plant species reveals high conservation of sequence and structure. Nucleotides forming stems
P1 through P5 are highlighted in color, and asterisks identify nucleotides that are conserved between all examples. Sequences are derived from
Arabidopsis (Ath, NC003071), Raphanus sativus (Rsa, EF588038), Brassica oleracea (Bol, BH250462), Boechera stricta (Bst, DU681973), Carica papaya
(Cpa, DX471004), Citrus sinensis (Csi, DY305604), Nicotiana tabacum (Nta, EF588039), Nicotiana benthamiana (Nbe, EF588040), Populus trichocarpa
(Ptr, Joint Genome Initiative, Populus genome, LG_IX: 7897690-7897807), Lotus japonicus (Lja, AG247551), Lycopersicon esculentum (Les, EF588041),
Solanum tuberosum (Stu, DN941010), Ocimum basilicum (Oba, EF588042), Ipomoea nil (Ini, BJ566897), Vitisvinifera (Vvi, AM442795), Oryza sativa (Osa,
NC008396), Poa secunda (Pse, AF264021), Triticum aestivum (Tae, CD879967), Hordeum vulgare (Hvu, BM374959), Sorghum bicolor (Sbi, CW250951),
Pinus taeda (Pta, CCGB, Contig116729 RTDS2_8_E12.g1_A021: 551-686), and Physcomitrella patens (Ppa, gnljtij856901678, gnljtij893553357,
gnljtij876297717; Lang et al., 2005). The sequence for I. nil represents a splice variant derived from cDNA and is therefore lacking the 59 end of the
aptamer.
(B) and (C) Consensus sequences and secondary structure models of TPP riboswitch aptamers based on all representatives from plants (B) or bacterial
and archaeal species (C). The mutual information reflects the probability for the occurrence of the boxed base pairs (Barrick and Breaker, 2007).
Gene Control by Plant Riboswitches3439

Page 4

downstream of the annotated end of THIC in Arabidopsis. Full-
length cDNA annotations in GenBank (AK068703, AK065235,
and AK120238) indicate that comparable THIC-III mRNAs with
long 39 UTRs also exist in O. sativa.
Thiamin Affects THIC Transcript Levels
Quantitative RT-PCR (qRT-PCR) was usedto determine whether
THIC transcript levels respond to increased thiamin concentra-
tions. Arabidopsis seedlings were supplemented with various
amounts of thiamin, and the different THIC transcript types were
detected separately using selective primer combinations (see
SupplementalFigure3online).Theprimercombinationamplifying
THIC-II also can bind to a subset of THIC-I RNAs that have
undergonesplicingofthefirst39UTRintron.However,theTHIC-I–
derived amplification products are minor because THIC-I tran-
scripts are far less abundant and are almost undetectable when
cDNAs are generated with polyT primers (Figure 2D).
After growing seedlings on medium containing 1 mM thiamin,
the total amount of THIC transcripts decreases to ;20% of that
measured when seedlings are grown without thiamin supple-
mentation (Figure 3A). THIC-II transcripts exhibit an equivalent
reduction, but both THIC-I and THIC-III transcripts show little or
no change in copy number. Again, the simultaneous decrease of
total and THIC-II transcripts and concomitantly unchanged
levels of THIC-I and THIC-III demonstrate that THIC-II is the
mostabundanttranscriptform.RNAgelblotanalysisofthesame
samples was used to confirm that THIC-II levels decrease and
that THIC-I and THIC-III RNA levels remain relatively unchanged
(Figure 3B).
The time interval in which thiamin-dependent changes in
transcript levels occur was assessed by performing qRT-PCR
Figure 2. The Exon-Intron Organization of THIC 39 UTRs Is Conserved.
(A) Organization of the 39 region of THIC genes and derived transcript types are similar. The first box represents the last exon of the coding region with
the stop codon UAA depicted. The stop codon is followed by an intron (except in L. esculentum, where the intron is located immediately in front of the
stop codon), which is spliced in transcript types II and III (see [B] and [D]). GU and AG notations identify 59 and 39 splice sites, respectively. Arrows
indicate binding sites of primers that were used for RT-PCR amplification of THIC 39 UTRs shown in (B) to (D). Dashed lines indicate splicing events, and
the diamond represents the transcript processing site.
(B) PCR amplification of THIC 39 UTRs with DNA primers a and b from cDNAs generated with polyT primer yields only type II RNAs in all species
examined. RT-PCR products were separated using 1.5% agarose gel electrophoresis and visualized by ethidium bromide staining and UV illumination.
M designates the marker lane containing DNAs of 100-bp increments.
(C) RT-PCR analysis was conducted using the same cDNAs as used in (B) with primers a and c. Primer c is specific for 39 UTRs of types I and III RNAs.
Kbp designates kilobase pairs.
(D) RT-PCR products of 39 UTRs from type I and III RNAs from Arabidopsis cDNAs generated with different RT primers. Primers used for RT were polyT,
random hexamers, or sequence-specific primers that bind near the annotated end of THIC (221 nucleotides downstream of the end of the aptamer) or
further downstream (882 nucleotides downstream of the end of the aptamer) as indicated. PCR amplification was performed with primers a and c for all
cDNAs. I-1 and I-2 represent type I RNAs with the upstream intron following the stop codon unspliced or spliced, respectively. No RT indicates a control
reaction using the RNA without reverse transcription as a template source.
3440The Plant Cell

Page 5

of THIC transcripts from RNA isolated at several time points after
spraying Arabidopsis seedlings with a thiamin solution (Figure
3C). Four hours after thiamin application, total THIC RNA and
THIC-II amounts were reduced to 50% of that measured in the
absence of added thiamin. After 26 h, these levels were de-
creased even further. Interestingly, the modest increase in THIC-
III observed when thiamin is added to the medium (Figure 3A) is
more pronounced in the early phase of the response. Because
thedifferenttranscripttypesshowoppositeresponsestothiamin
treatment, the control mechanism most likely involves RNA 39
end processing, and it is unlikely that the feedback mechanism
acts at the level of promoter regulation. Indeed, expression of a
reporter gene driven by the THIC promoter from Arabidopsis in
transgenic lines was not altered after thiamin supplementation
(see Supplemental Figure 4 online).
Mostofthethiamintakenupbycellsisexpectedtobeconverted
to TPP by successive phosphorylation reactions to yield concen-
trations of this coenzyme that are much higher than the concen-
tration of the unphosphorylated vitamin (I. Ajjawi, M. Rodriguez
Milla, J. Cushman, and D. Shintani, unpublished data). Therefore,
the observed reduction in total THIC RNA levels most probably
reflects a riboswitch-mediated response to increased TPP con-
centration, given that TPP binding to plant aptamers is known to
occur (Sudarsan et al., 2003; Thore et al., 2006). Furthermore, we
speculatedthatdecreasedTPP concentrations should resultin an
opposite response in the levels of THIC transcripts.
Figure 3. THIC Transcript Types Respond Differently to Changes in Thiamin Levels in Arabidopsis.
(A) qRT-PCR analysis was conducted on THIC transcripts from Arabidopsis seedlings grown for 14 d on medium supplemented with 0, 0.1, and 1 mM
thiamin. Total THIC transcripts and types I, II, and III RNAs were separately detected using different primer combinations. cDNAs were generated using
a polyT primer or random hexamers for detection of type I RNAs. Expression was normalized for each primer combination to the value measured using
medium without thiamin (open bars). Values are averages from three independent experiments, and error bars represent SD.
(B) RNA gel blot analysis of THIC transcripts from the same samples described in (A). Twenty micrograms of total RNA was loaded per lane and
analyzed using probes binding to the coding region of THIC, the extended 39 UTR of types I and III RNAs, or the control transcript EIF4A1. The signal of
THIC probes are shown in the size range between 2 and 3 kb. The 39 UTR probe resulted in weak signals, and exposure time was extended to 3 d
compared with 1 d of exposure for the other probes.
(C) qRT-PCR analysis of the time-dependent effects of thiamin treatment on THIC transcripts from Arabidopsis. Seedlings were grown for 14 d on
thiamin-free medium and subsequently sprayed with 50 mM thiamin and 0.25 mg mL?1Tween 80. Control seedlings were treated with a solution
containing only Tween 80. Samples were collected after 4 and 26 h and subjected to qRT-PCR analysis. Amounts of THIC transcripts were analyzed
from cDNAs generated with polyT primer and normalized to the values of the control samples without application of thiamin (open bars). Values are
averages from three independent experiments, and error bars represent SD.
(D) Relative changes of the levels of THIC transcript types in wild-type and TPK-KO Arabidopsis plants. Seedlings were grown for 12 d on thiamin-free
medium, and amounts of THIC transcript types were analyzed by qRT-PCR. Data were normalized to the values for the wild-type samples and reflect
averages from three replicates, with error bars representing SD.
Gene Control by Plant Riboswitches3441

Page 6

To examine this possibility, we compared THIC expression in
wild-type Arabidopsis plants versus those carrying a double
knockout of thiamin pyrophosphokinase (TPK). These mutants
are deficient in both TPK isoforms present in Arabidopsis and
therefore cannot convert thiamin to TPP (I. Ajjawi, M. Rodriguez
Milla, J. Cushman, and D. Shintani, unpublished data). It has
been shown that TPK double knockout (TPK-KO) plants largely
deplete the TPP stored in seeds within 2 weeks of germination
and thatthe plantsdepend onTPPsupplementation to complete
their life cycle (I. Ajjawi, M. Rodriguez Milla, J. Cushman, and D.
Shintani, unpublished data). Interestingly, qRT-PCR analysis of
THIC RNAs from 12-d-old TPK-KO seedlings revealed a pro-
nounced reduction of THIC-III compared with the wild type
(Figure 3D), indicating that the formation of this RNA is triggered
by the presence of TPP. However, total THIC and THIC-II RNAs
do notchange significantly, which might beexplained by the fact
that THIC expression is already close to its maximum under the
conditions tested.
Riboswitch Function in Thiamin Feedback Response
The presence of different THIC RNA types and their changes
in abundance in response to varying thiamin levels suggest that
the TPP aptamer might affect RNA 39 end processing and
thereby control gene expression. This hypothesis was explored
by analyzing the expression of reporter constructs containing
enhanced green fluorescent protein (EGFP) fused with the com-
plete genomic 39 region of THIC (;2.2 kb downstream of the
stop codon) in stably transformed Arabidopsis plants. Thiamin
application resulted in decreased EGFP fluorescence in leaves
from the rosette stage (Figures 4A and 4B). Using qRT-PCR
analysis, we found that total amounts of both EGFP and endog-
enous THIC transcripts were reduced to ;20% of control levels
after thiamin feeding (Figure 4C), which is similar to the extent of
repression observed for Arabidopsis seedlings (Figure 3). Total
THIC and EGFP transcripts were analyzed using primers binding
to the coding regions of the respective cDNAs.
The 39 UTR sequences of EGFP fusion and THIC transcripts
from the transformants were amplified by RT-PCR (Figures 4D
and 4E), cloned, and sequenced. Sequence analyses confirmed
the formation of equivalent transcript processing types for EGFP
and THIC (see also Figure 2). The difference in total transcript
amount of THIC and EGFP can be explained by the action of the
strong promoter used for control of the transgene. Because the
reporter gene construct and the endogenous THIC locus yielded
similar responses to thiamin and similar processed RNAs, we
conclude that no additional sequences upstream of the region
fused to EGFP are involved in the gene control mechanism.
To determine whether the effects of thiamin regulation are
mediated through a TPP riboswitch, we introduced mutations
M1, M2, and M3 into the aptamer (Figure 5A) that reduce TPP
binding affinity. M1 and M3 mutations interfere with formation of
stems P5 and P2 of the TPP aptamer, respectively. With M2,
three nucleotides that are known to be involved in direct inter-
actions with the pyrimidine moiety of TPP (Edwards and Ferre-
D’Amare, 2006; Serganov et al., 2006; Thore et al., 2006) are
mutated. The 39 regions of THIC carrying these variants were
fused to EGFP and stably transformed into Arabidopsis plants.
As expected, plants containing reporter gene constructs car-
rying the mutant aptamers exhibit either reduced (M1) or a
complete loss (M2 and M3) of responsiveness to thiamin appli-
cation compared with plants containing the wild-type construct
(Figure 5B). These findings were confirmed by measuring the
relative levels of transcripts using qRT-PCR (Figure 5C). In
addition, a reporter construct variant of M3 containing compen-
satory mutations that restore formation of P2 (M4) exhibits
activity similar to the wildtype (Figures 5B and 5C). These results
indicate that TPP binding by the aptamer is essential for medi-
ating the response to changing TPP levels in the cell. However,
the modest thiamin responsiveness exhibited by the M1 con-
struct suggests that this mutant might affect riboswitch function
other than just by diminishing the affinity of the aptamer for TPP
(see further discussion below).
RT-PCR analyses of 39 ends of the mRNAs generated from the
EGFP-riboswitch fusions reveal that the mutant constructs
maintain a high level of expression of type II RNAs (Figure 5D),
as is typical of wild-type constructs. However, two major differ-
ences in type I and III RNAs between mutant and wild-type
riboswitches are evident. First, the amount of type III RNA is
substantially reduced in the M1 construct and was not detected
from the M2 construct (Figure 5E). Second, a considerable
decreaseoftranscriptsextendingfardownstreamoftheaptamer
was observed for both mutants (Figure 5E, 882 nts lane; see also
the wild type in Figure 4E). These results reveal that proper
riboswitch function is required for the accumulation of type III
RNAs with extended 39 UTR length.
39 UTR Length Defines Gene Expression Levels
After demonstrating that the riboswitch controls the formation of
different 39 UTRs of RNAs, we sought to determine how the 39
UTRs affect gene expression. The major differences between
THIC-II and THIC-III 39 UTRs are that the THIC-II RNA is shorter
and ends in front of the TPP aptamer. By contrast, THIC-III
includes most of the consensus aptamer sequence, but the first
seven nucleotides at the 59 end are removed due to splicing of
the second intron in the 39 UTR and are replaced with different
nucleotides(Figure6A,shadedsequence).In-lineprobing(Soukup
and Breaker, 1999) was used to determine whether this altered
aptamer retains TPP binding activity. This assay reveals struc-
tural changes of RNAs by monitoring altered patterns of spon-
taneous RNA degradation upon metabolite binding. Briefly, RNA
linkages in unstructured portions of the molecule are generally
more susceptible to spontaneous cleavage by internal phos-
phoester transfer than are linkages in structured portions of an
RNA. Therefore, structural changes brought about by ligand
binding to RNA can be quantitated, mapped, and used to es-
tablish the binding characteristics of aptamers. In-line probing
has beenusedpreviouslytoanalyze TPP aptamers(Winkleretal.,
2002; Sudarsan et al., 2003).
The apparent Kdof the altered aptamer for TPP is ;60 mM
(Figures 6B and 6C) compared with ;50 nM for the full-length
TPP aptamer from Arabidopsis (Sudarsan et al., 2003), which is a
loss of more than three orders of magnitude in ligand binding
affinity. Furthermore, no detectable binding of thiamin occurs
with the altered aptamer (data not shown), and it is unlikely that
3442 The Plant Cell

Page 7

other thiamin derivatives can bind because the region of the
aptamerthatisexchangeduponsplicingisnotdirectlyinvolvedin
ligandrecognition(EdwardsandFerre-D’Amare, 2006;Serganov
et al.,2006;Thore et al.,2006). Thesefindings indicate that, once
splicing of the second intron of the 39 UTR occurs, the altered
version of the TPP aptamer in THIC-III is no longer functional.
To assess possible other effects of the two major THIC 39 UTR
forms on gene expression, the 39 UTR sequences from THIC-II
(188 nucleotides) and THIC-III (408 nucleotides) from Arabidop-
sis were fused to the codingregion of luciferase (LUC), and these
constructs were expressed in plants under control of the con-
stitutive cauliflower mosaic virus 35S promoter and octopine
synthase (OCS) terminator elements (see Supplemental Figure
5A online). THIC-III can extend to a variable length at the 39 end,
but the most abundant, shortest version (corresponding to
GenBank accession number NM179804) was used for our
Figure 4. In Vivo Analysis of Riboswitch Function.
(A) Leaves from stably transformed Arabidopsis lines expressing a reporter fusion of the complete 39 region of AtTHIC fused to the 39 end of EGFP were
abscised and incubated with the petioles in water or in water supplemented with 0.02% thiamin. EGFP fluorescence was assessed at 0, 48, and 72 h
after onset of treatment. One representative set of data from three repeats is shown, and the numbers identify different leaves from one transgenic line.
(B) Quantitation of EGFP fluorescence of leaves depicted in (A) at three time points. The data represent average fluorescence intensity and SD for each
leaf. The plot also depicts average background fluorescence of wild-type leaves.
(C) qRT-PCR analysis of total EGFP and THIC transcripts from leaves incubated for 72 h in water or 0.02% thiamin. Transcript amounts were
standardized to an internal reference transcript and normalized to transcript abundance in water-treated samples. Values are averages from four
independent experiments using different transgenic lines, and error bars represent SD.
(D) and (E) RT-PCR analysis of different 39 UTRs of EGFP and THIC transcript types from Arabidopsis reporter transformants grown in the absence of
exogenous thiamin. For cDNA generation, a polyT primer, random hexamers, or two different gene-specific primers (binding either 221 or 882
nucleotides downstream of the end of the aptamer) were used as indicated. The forward primers (equivalent to primer a in Figure 2A) were specific for
the end of the last exon of the coding region of EGFP (left) or THIC (right), whereas the reverse primer was either a polyT primer ([D]; equivalent to primer
b in Figure 2A) or homologous to a region 221 nucleotides downstream of the end of the aptamer ([E]; equivalent to primer c in Figure 2A). RT-PCR
products were separated and visualized as described in the legend to Figure 2. M designates the marker lanes containing DNAs of 100-bp increments.
No RT indicates a control reaction using the RNA without reverse transcription as a template source. I-1 and I-2 represent type I RNAs with the upstream
intron following the stop codon unspliced or spliced, respectively. The lowest band in the polyT reaction in (E) results from amplification of THIC type II
RNAs with polyT primer remaining from the RT reaction. Additional unmarked bands correspond to nonspecific amplification as confirmed by cloning
and sequencing of all RT-PCR products.
Gene Control by Plant Riboswitches3443

Page 8

expression analyses. Using RT-PCR, we confirmed that reporter
transcripts can extend to and presumably end within the OCS
terminator region (see Supplemental Figures 5B and 5C online).
Afusionconstructcontainingthe39UTRfromTHIC-IIIresulted
in only ;10% of the LUC activity compared with a construct
carrying the 39 UTR from THIC-II (Figure 6D). The possible
involvement of the altered TPP aptamer in the type III construct
was ruled out by introducing mutations M1 and M5 that com-
pletelyabolishTPPbindingbutdonotderepressLUCexpression.
Also, using the reverse complement sequence of the THIC-III
39 UTR sequence did not change LUC activity significantly. These
data indicate that the extended length, and not the altered TPP
aptamer, plays a role in the repression of gene expression from
constructs containing the 39 UTR from type III RNAs. Equivalent
results were obtained with constructs containing the reporter
gene EGFP in place of LUC, and coexpression of the silencing
suppressor P19 excluded the possibility that the observed dif-
ferences are due to silencing effects in the reporter system (see
Supplemental Figure 6 online).
We assessed whether differences in reporter activity are also
reflected in transcript amounts. Using qRT-PCR, the relative
amounts of reporter transcripts containing the 39 UTRs from
THIC-II or THIC-III from either Arabidopsis or Nicotiana ben-
thamiana were determined (Figure 6E). Constructs carrying the
long 39 UTR of type III RNAs from both species were present in
lower abundance compared with those that carried the short
type II 39 UTR. Since all reporter constructs were expressed
under control of identical, constitutive promoters and termina-
tors, the extents of transcription initiation and termination should
be the same for all constructs.
Our findings that reporter transcripts containing the long
THIC-III 39 UTR are present at lower steady state levels than
the respective fusions with the short THIC-II39 UTR and also that
THIC-III RNAs do not accumulate significantly (Figures 2 and 3)
suggest that long 39 UTRs might cause increased transcript
turnover. Thus, riboswitch-mediated redirection of 39 end pro-
cessingtofavortheproductionofmRNAswithextended39UTRs
should reduce THIC expression. One possible mechanism for
Figure 5. Effects of Aptamer Mutations on Riboswitch Function.
(A) Secondary structure model and sequence of the wild-type TPP aptamer from Arabidopsis located in the 39 region of THIC that was fused to EGFP.
Black boxed nucleotides were altered as indicated to generate mutants M1, M2, and M3 with impaired TPP binding and the compensatory mutant M4.
(B) Quantitation of EGFP fluorescence in leaves from Arabidopsis transformants expressing reporter constructs containing the wild-type aptamer
sequence or mutated versions M1, M2, M3, and M4. Leaves were excised and incubated with their petioles in water or 0.02% thiamin for 72 h before
fluorescence analysis. Values are averages from at least three independent experiments using different transgenic lines. Error bars represent SD.
(C) qRT-PCR analyses of EGFP and THIC transcript amounts in Arabidopsis transformants. Thiamin treatment was performed as described in (B).
Transcript amounts (standardized using a reference transcript) were normalized to transcript abundance in water-treated samples. Values are averages
from two to four independent experiments using different transgenic lines. Error bars represent SD.
(D) and (E) RT-PCR analyses of 39 UTRs of EGFP and THIC transcripts from Arabidopsis transformants with mutations M1 or M2. RT-PCR analyses
were performed as described in the legends to Figures 4D and 4E. Forward primers were homologous to the end of the last exon of the coding region of
EGFP or THIC, and the reverse primer was a polyT primer (D) or complementary to a region 221 nucleotides downstream of the end of the aptamer (E).
Kbp designates kilobase pairs.
3444 The Plant Cell

Page 9

the increased transcript turnover of RNAs with long 39 UTRs
might be nonsense-mediated decay (NMD) as previous studies
haveshownthatlong39UTRsinduceNMDinyeast(Muhlradand
Parker, 1999) and plants (Kertesz et al., 2006). In the latter study,
a reduction in the abundance of mRNAs with 39 UTR lengths
>200nucleotides wasobserved,aswasacorrelationbetween39
UTR length and NMD efficiency. However, the extended 39 UTR
could also affect efficiency of 39 end processing at downstream
sites, and future work will be necessary to unravel the underlying
mechanism of the decreased transcript accumulation that we
observed.
Mechanism of Riboswitch Function
The findings described above demonstrate that the riboswitch
affectsgeneexpressionbycontrolling39UTRprocessingtoyield
Figure 6. The Long 39 UTR of THIC Causes Reduced Gene Expression Independent of Aptamer Function.
(A) Secondary structure model of the TPP aptamer generated after splicing in THIC type III RNA from Arabidopsis. Gray shaded nucleotides in stems P1
and P2 identify nucleobase changes compared with the original unspliced aptamer. Black boxed nucleotides were altered as shown to generate
mutants M1 and M5 that do not bind TPP.
(B) In-line probing analysis of TPP binding by the spliced aptamer depicted in (A). Lanes include RNAs loaded after no reaction (NR), after partial
digestion with RNase T1 (T1), or after partial digestion with alkali (?OH). Sites 1 and 2 were quantified to establish the Kdas shown in (C).
(C) Plot indicating the normalized fraction of RNA spontaneously cleaved versus the concentration of TPP for sites 1 and 2 in (B).
(D) In vivo expression analysis of reporter constructs containing the 39 UTR of Arabidopsis type II or III RNAs fused to the 39 end of the coding region of
firefly luciferase (LUC). Constructs M1 and M5 are based on the 39 UTR of type III RNAs but contain the mutations shown in (A). LUC-III M59 contains the
inverted 39 UTR sequence of construct LUC-III M5. Reporter constructs were analyzed in a transient N. benthamiana expression assay and values
standardized to a coexpressed luciferase gene from Renilla. Expression was normalized to the fusion construct containing the 39 UTR of type II RNA.
Data shown are mean values of three independent experiments, and the error bars represent SD.
(E) qRT-PCR analysis of EGFP reporter fusions that contain the 39 UTRs of THIC type II or III RNAs from either Arabidopsis (At) or N. benthamiana (Nb)
after expression in a transient expression assay. Expression was standardized to a coexpressed DsRED reporter gene and normalized to the constructs
containing a type II 39 UTR. Data shown are mean values of two representative experiments, and the error bars reflect SD.
Gene Control by Plant Riboswitches3445

Page 10

either type II or type III RNA. We investigated the mechanism by
which the aptamer regulates these processing events in a TPP-
dependent manner using in-line probing to identify structural
changes in the THIC 39 UTR from Arabidopsis. An aptamer
construct that included 14 nucleotides upstream of the 59 splice
site for the second 39 UTR intron exhibited TPP-dependent
structural modulation of 6 nucleotides immediately upstream of
the splice site and the two nucleotides at the splice site junction
(Figure 7A). Specifically, TPP addition causes an increase in
structural flexibility of the nucleotides near the 59 splice site.
Thus,ligandbindingcouldincreaseaccessibilityofthesplicesite
to the spliceosome, thereby permitting the removal of this intron.
We searched for base-pairing potential between the se-
quences of the modulating 59 splice site nucleotides and the
aptamernucleotidesofTHICgenesfromseveralplantspecies.In
all species examined, sequences on the 59 side of the P4-P5
stems are complementary to the sequences immediately up-
stream (and sometimes inclusive) of the 59 splice site (Figure 7B).
This conservation of base-pairing potential suggests that the
riboswitch controls splicing by the mutually exclusive formation
of structures that either mask the 59 splice site under low TPP
concentrations or expose the splice site under high TPP con-
centrations (Figure 7C).
This model is consistent with the in vitro and in vivo data
generated in this study, including the partial thiamin responsive-
nessobservedwiththeM1variant.M1carriestwomutationsthat
disrupt the P5 stem of the aptamer (Figure 5A), which should
weaken its interaction with TPP and disrupt thiamin responsive-
ness. However, these mutations also weaken base pairing with
the 59 splice site region, which might allow TPP binding to
compete effectively with this alternative pairing, despite the
expected reduction in TPP affinity.
Our findings indicate that TPP binding to the riboswitch makes
accessible a 59 splice site in the 39 UTR; subsequently, splicing
resultsintheformationoftypeIIIRNAs.Todetermineifadditional
effects of TPP binding might contribute to regulation via the 39
splice site, we mutated the 39 splice site in the P2 stem of the
aptamer using nucleotide changes that retained the structure
andTPPbindingactivityoftheRNA(seeSupplementalFigure7A
online). Interestingly, plants containing a reporter gene construct
Figure 7. Mechanism of Riboswitch Function in Plants.
(A) TPP causes changes in RNA structure near to the 59 splice site, which is important for the formation of THIC type III RNA. For in-line probing, a 5932P-
labeled RNA starting 14 nucleotides upstream of the 59 splice site (þ1) and extending to the 39 end of the TPP aptamer (nucleotides ?14 to 261) from
Arabidopsis was incubated in the absence (–) or presence (þ) of 10 mM TPP, and the resulting spontaneous cleavage products were separated by
PAGE. Markers are RNAs partially digested with RNase T1 (T1) or alkali (?OH). The graph depicts the relative band intensities in the lanes indicated.
(B) Base-pairing potential between the 59 splice site region and the P4-P5 stems of the TPP aptamer from Arabidopsis (complementary nucleotides are
shaded). Stretches of complementary nucleotides are also present in all other plant THIC mRNA sequences available.
(C) A model for THIC TPP riboswitch function in plants includes control of splicing and alternative 39 end processing of transcripts. When TPP
concentrationsarelow(left),portionsofstemsP4andP5interactwiththe59splicesiteandtherebypreventsplicing.Thetranscriptprocessingsitelocated
betweenthe59splicesiteandtheTPPaptamerisretained,anditsuseresultsinformationoftranscriptswithshort39UTRsthatpermithighexpression.In
the presence of elevated TPP concentrations (right), TPP binds to the aptamer cotranscriptionally, which leads to a structural change that prevents
interaction with the 59 splice site. Splicing occurs and removes the transcript processing site. Transcription continues and alternative processing sites in
the extended 39 UTR give rise to THIC type III RNAs. The long 39 UTRs lead to increased RNA turnover, causing reduced expression of THIC.
3446The Plant Cell

Page 11

carrying this M6 mutant aptamer still exhibit thiamin responsive-
ness of reporter expression (see Supplemental Figures 7B and
7C online). Analysis of 39 UTRs of M6 reporter transcripts by
sequencing RT-PCR products revealed thatRNAssimilarto type
III can still be formed, but the M6 RNAs are now spliced from a 39
splice site located four nucleotides upstream relative to the
position in the wild-type aptamer (see Supplemental Figure 7D
online).Thisfinding,andthefactthattherelativepositionofthe39
splice site for formation of THIC-III in the TPP aptamer is variable
for different species (see Supplemental Figure 1), indicates that
the 39 splice site is most probably not controlled in a TPP-
dependent manner.
Oneremarkable featureofplantTPPriboswitchesisthatthe59
splice sites under riboswitch control are located >200 nucleo-
tides upstream of the complementary regions in the TPP aptam-
ers (see Supplemental Figure 2 online). The complex structural
organization of the sequences between the complementary
regions (see Supplemental Figure 8 online) might be important
to facilitate their interaction, which might also be one reason for
the conservation of lengths between features of THIC 39 UTRs
from various plants.
Interestingly,TPPriboswitchesalsocontrolalternativesplicing
of the NMT1 genes of fungi, in part by forming ligand-modulated
base pairing between nucleotides near a 59 splice site and the
P4-P5regionofanunoccupiedTPPaptamer(Cheahetal.,2007).
Incontrastwiththeseeukaryoticexamples,bacteriatypicallyuse
nucleotides in P1 stems to interface with expression platforms
located downstream of the aptamer (Winkler et al., 2002;
Sudarsan et al., 2005). Given the substantial changes in the
structure of TPP aptamers upon ligand binding, it is surprising
that only a portion of the P1 and P4-P5 stems are used to control
expression platform function in the TPP riboswitches studied to
date.Onereasonforthismightbetheneedforpreorganizationof
certain aptamer substructures to facilitate rapid ligand sensing.
Model for TPP Riboswitch Function in Plants
Based on our findings, we propose a model for TPP riboswitch
regulation in plants involving the metabolite-mediated control of
splicing and alternative 39 end processing of mRNA transcripts
(Figure 7C). When TPP concentration is low, the aptamer inter-
acts with the 59 splice site and prevents splicing. This intron
carries a major processing site that permits transcript cleavage
and polyadenylation. Processing from this site produces THIC-II
transcripts that carry short 39 UTRs, which yield high expression
of the THIC gene.
When TPP concentrations are high, TPP binding to the
aptamer prevents pairing to the 59 splice site. As a result, the 59
splice site becomes accessible and is used in a splicing event
that removes the major processing site. Transcription subse-
quently can extend up to 1 kb, and the use of cryptic 39 end
processing sites located downstream of the major site gives rise
to THIC-III RNAs that carry much longer 39 UTRs. These findings
are in agreement with previous functional studies of polyadenyl-
ation in plants (e.g., Mogen etal., 1990; Hunt, 1994) showing that
mutation of sequence elements involved in 39 end processing at
acertainsiteresultintheusageofweakandcrypticsitesthatcan
be widely spaced. The 39 end processing at these alternative
sites might be less efficient, or the long 39 UTRs themselves
might cause increased transcript turnover and subsequently
result in reduced THIC expression. Interestingly, a polyuridine
tract immediately follows the aptamer in all known TPP ribo-
switchexamplesinplants(seeSupplementalFigure1online),and
its conservation indicates a possible role in riboswitch control.
Our findings reveal a mechanism for how TPP-sensing ribo-
switches can control gene expression in plants and how feed-
back control maintains TPP levels. In addition, this study further
expands the known diversity of mechanisms that riboswitches
use to regulate gene expression. The TPP riboswitch in Arabi-
dopsis harnesses metabolite binding to control RNA splicing,
which determines alternative 39 end processing fate and ulti-
mately defines the steady state levels of mRNAs. The extensive
conservation of sequences, structural elements, and spacing
between key 39 UTR features within the THIC genes of various
plants indicates that this riboswitch mechanism is maintained in
diverseplantspecies.Althoughitwaspreviouslyestablishedthat
alternative polyadenylation is employed by eukaryotic cells to
produce variant products from the same gene, for example,
either calciton or calcitonin gene-related peptides (Lou et al.,
1998) or variants of immunoglobulin M heavy chain (Takagaki
et al., 1996), our study extends this mechanism to include
quantitative gene control. Independent of riboswitch-mediated
regulation, the potential for the control of genes by regulating
splicing and subsequently alternative 39 end processing appears
to be large; therefore, this general mechanism might be far more
widespread in eukaryotes.
The unique location of TPP riboswitches in the 39 regions of
plant genes compared with their locations in fungi and bacteria
mightreflectadaptations to specificregulatoryneedsofdifferent
organisms.Nearlyallknownriboswitchesresideinthe59UTRsof
bacterial mRNAs (Mandal and Breaker, 2004; Soukup and
Soukup, 2004; Winkler and Breaker, 2005) or in introns of 59
UTRsorcodingregionsoffungi(Cheahetal.,2007)andoftencan
suppress gene expression almost completely. However, a more
subtle level of riboswitch regulation is observed in plants. Al-
thoughplantscantakeupthiaminefficiently,mostofthedemand
must be supplied by endogenous synthesis. In contrast with the
autotrophic lifestyle of plants, fungi and bacteria sometimes
grow under rich conditions that allow them to satisfy their entire
requirements for compounds like thiamin by import, thus pro-
viding some rationale for different extents of regulation found in
various groups of organisms.
METHODS
Plants and Plant Tissues
Arabidopsis thaliana ecotype Columbia-0 plants were grown on soil at
238C in a growth chamber under a 16-h-light/8-h-dark photoperiod with
60% humidity unless otherwise stated. For seedling experiments, plants
were grown on basal MS medium (Murashige and Skoog, 1962) supple-
mentedwith2%sucroseandvaryingconcentrationsofthiaminandunder
continuous light unless otherwise specified. Nicotiana benthamiana
plants for leaf infiltration assays were grown on soil for 3 to 5 weeks
under continuous light. Plant material from other species was derived
from seedlings grown from commercially available seeds.
Gene Control by Plant Riboswitches3447

Page 12

Oligonucleotides and DNA Constructs
All synthetic DNAs and the details of cloning of DNA constructs are
described in Supplemental Table 1 online.
RNA Isolation and RT-PCR Analyses
TotalRNAwasextractedfromfrozenplanttissuesusingtheRNeasyplant
mini kit (Qiagen) following the manufacturer’s instructions. Two to five
micrograms of total RNA were subjected to DNase treatment and sub-
sequently reverse transcribed using SuperScript II reverse transcriptase
(Invitrogen) according to the manufacturer’s instructions. For cDNA gen-
eration,gene-specificprimersor(ifnototherwisespecified)apolyTprimer
(DNA1) were used. cDNAs were used as templates for PCR amplification
ofTHICandEGFPreportertranscripts.Allproductsobtainedwerecloned
into TOPO-TA cloning vector (Invitrogen) and analyzed by sequencing
(Howard Hughes Medical Institute Keck Foundation Biotechnology Re-
source Center at Yale University).
qRT-PCR was performed using the Applied Biosystems 7500 real-time
PCR system and Power SYBR Green Master Mix (Applied Biosystems).
Serial dilutions of the templates were conducted to determine primer
efficiencies for all primer combinations. Each reaction was performed in
triplicate, and the amplification products were examined by agarose gel
electrophoresis and melting curveanalysis.Datawereanalyzed using the
relative standard curve method, and the abundance of target transcripts
was normalized to reference transcripts reported previously (Czechowski
et al., 2005) from genes At1g13320 (PP2A catalytic subunit), At5g60390
(EF-1a), and At1g13440 (GAPDH).
Amplification of THIC Transcripts and Genomic Sequences
from Plants
The 39 UTRs from THIC-II RNAs were cloned using RT-PCR with a polyT
primer and a degenerate primer that targets a conserved portion of the
coding sequence near the stop codon. For THIC-III transcripts, 39 UTRs
were amplified in two fragments from polyT-generated cDNA using
specific primer combinations. The 59 portion of each 39 UTR was PCR
amplified using a degenerate primer targeting the coding region and a
primer that targets the TPP aptamer. The 39 portion of each 39 UTR was
obtained using a primer targeting the aptamer and a polyT primer. PCR
products were cloned (TOPO-TA), and several independent clones were
sequenced. The combined sequence information was used to design
primer pairs for amplification of the corresponding genomic sequences.
Genomic DNA was isolated using Plant DNAzol reagent (Gibco BRL)
according to the manufacturer’s instructions, and the resulting PCR
products were cloned and sequenced.
RNA Gel Blot Analysis
Transcripts from Arabidopsis seedlings were analyzed by RNA gel blot
analysis as described previously (Newman et al., 1993). Probes were
specificagainstregionsinthecodingregionofTHIC,theextended39UTR
of THIC types I and III RNAs, or the control transcript EIF4A1.
In-Line Probing of RNA
In-line probing assays were conducted essentially as described previ-
ously (Winkler et al., 2002; Sudarsan et al., 2003). Details are described in
Supplemental Methods online.
Agrobacterium-Mediated Leaf Infiltration Assay
For transient gene expression analysis, N. benthamiana leaves were
transformed by a leaf infiltration assay as described by Cazzonelli and
Velten (2006). Agrobacterium tumefaciens lines harboring the various
reporter constructs were grown overnight in Luria-Bertani medium and
centrifuged,andthepelletedcellswereresuspendedinwater.OD600was
adjusted to the same value (;0.8) for cells harboring the different con-
structs, and Agrobacteria were mixed in equal amounts for cotransfor-
mation of constructs. Either luciferases from firefly (Photinus pyralis) or
sea pansy (Renilla reniformis), or the fluorescent proteins EGFP and
DsRed2, were used as reporter proteins. Additional details regarding
reporter gene quantitation are described in Supplemental Methods
online.
Stable Transformation of Arabidopsis by the Floral Dip Method
Arabidopsis was transformed by a floral dip method described previously
(Clough and Bent, 1998). After transformation, seeds were grown under
sterile conditions on medium containing 50 mg mL?1kanamycin to select
for transformants and 200 mg mL?1cefotaxime to prevent bacterial
growth. Surviving plants were transferred after 2 to 3 weeks to soil and
expression of the transgene was determined after further growth.
Accession Numbers
Sequence data from this article can be found in the GenBank/EMBL data
libraries under accession numbers EF588038 to EF588042. The Arabi-
dopsis Genome Initiative locus identifier for THIC is At2g29630, and
accessionnumbersforTHICsequencesfromadditionalspeciesarelisted
in the legend to Figure 1.
Supplemental Data
The following materials are available in the online version of this article.
Supplemental Figure 1. Genomic DNA Sequence Contexts of TPP
Riboswitches in THIC Genes from Different Plant Species.
Supplemental Figure 2. The Exon-Intron Organization of THIC 39
UTRs Is Conserved, and Relative Distances of Key Features Are
Similar among Different Species.
Supplemental Figure 3. Binding Sites and Sequences of DNA
Primers Used for qRT-PCR Analysis of the Various THIC RNAs from
Arabidopsis.
Supplemental Figure 4. The THIC Promoter from Arabidopsis Does
Not Appear to be Responsible for Downregulation of THIC Expression
after Thiamin Supplementation.
Supplemental Figure 5. Schematic Representation of Reporter
Constructs and RT-PCR Detection of RNA Products Containing
Two Different 39 UTRs of At THIC.
Supplemental Figure 6. Effect of 39 UTRs from Different Types of
THIC Transcripts on Reporter Gene Expression.
Supplemental Figure 7. The Relative Position of the 39 Splice Site for
Formation of Type III RNAs Can Be Variable.
Supplemental Figure 8. TPP-Induced Modulation in the 59 Flanking
Sequence of the Aptamer.
Supplemental Table 1. Sequences of DNA Primers.
Supplemental Methods.
ACKNOWLEDGMENTS
We thank Monica Accerbi for technical assistance with the RNA gel blot
analyses and Fred Souret and Justin Faletek for access to unpublished
work. We thank Imad Ajjawi for providing us seeds of the TPK double
3448 The Plant Cell

Page 13

knockout Arabidopsis plants, Jeff Velten for the gift of a plasmid
containing Renilla luciferase, and S.P. Dinesh-Kumar for providing the
P19 vector and access to plant growth facilities. We also thank Elena
Puerta-Fernandez and other members of the Breaker lab for helpful
comments. A.W. was supported by a postdoctoral fellowship from the
German Research Foundation, M.T. was funded by National Science
Foundation Grant MCB-0236210, and B.C.G. received support from
National Institutes of Health training grant GM07223. R.R.B. is sup-
ported by the Howard Hughes Medical Institute and received support
for this project from National Institutes of Health Grants GM 068819 and
DK070270.
ReceivedJune14,2007;revisedOctober16,2007;acceptedOctober18,
2007; published November 9, 2007.
REFERENCES
Abreu-Goodger, C., and Merino, E. (2005). RibEx: A web server for
locating riboswitches and other conserved bacterial regulatory ele-
ments. Nucleic Acids Res. 33: W690–692.
Barrick, J.E., and Breaker, R.R. (2007). The distributions, mechanisms,
and structures of metabolite-binding riboswitches. Genome Biol., in
press.
Barrick, J.E., Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M.,
Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., Wickiser, J.K.,
and Breaker, R.R. (2004). New RNA motifs suggest an expanded
scope for riboswitches in bacterial genetic control. Proc. Natl. Acad.
Sci. USA 101: 6421–6426.
Batey, R.T., Gilbert, S.D., and Montange, R.K. (2004). Structure of a
natural guanine-responsive riboswitch complexed with the metabolite
hypoxanthine. Nature 432: 411–415.
Cazzonelli, C.I., and Velten, J. (2006). An in vivo, luciferase-based,
Agrobacterium-infiltrationassay
transcriptional gene silencing. Planta 224: 582–597.
Cheah, M.T., Wachter, A., Sudarsan, N., and Breaker, R.R. (2007).
Control of alternative RNA splicing and gene expression by eukaryotic
riboswitches. Nature 447: 497–500.
Clough, S.J., and Bent, A.F. (1998). Floral dip: A simplified method for
Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant
J. 16: 735–743.
Cochrane, J.C., Lipchock, S.V., and Strobel, S.A. (2007). Structural
investigation of the glmS ribozyme bound to its catalytic cofactor.
Chem. Biol. 14: 97–105.
Corbino, K.A., Barrick, J.E., Lim, J., Welz, R., Tucker, B.J.,
Puskarz, I., Mandal, M., Rudnick, N.D., and Breaker, R.R.
(2005). Evidence for a second class of S-adenosylmethionine ribo-
switches and other regulatory RNA motifs in alpha-proteobacteria.
Genome Biol. 6: R70.
Cromie, M.J., Shi, Y., Latifi, T., and Groisman, E.A. (2006). An RNA
sensor for intracellular Mg(2þ). Cell 125: 71–84.
Czechowski, T., Stitt, M., Altmann, T., Udvardi, M.K., and Scheible,
W.R. (2005). Genome-wide identification and testing of superior
reference genes for transcript normalization in Arabidopsis. Plant
Physiol. 139: 5–17.
Edwards, T.E., and Ferre-D’Amare, A.R. (2006). Crystal structures of
the thi-box riboswitch bound to thiamine pyrophosphate analogs
reveal adaptive RNA-small molecule recognition. Structure 14: 1459–
1468.
Fuchs, R.T., Grundy, F.J., and Henkin, T.M. (2006). The S(MK) box is a
new SAM-binding RNA for translational regulation of SAM synthetase.
Nat. Struct. Mol. Biol. 13: 226–233.
system:Implications forpost-
Gelfand, M.S., Mironov, A.A., Jomantas, J., Kozlov, Y.I., and Perumov,
D.A. (1999). A conserved RNA structure element involved in the
regulation of bacterial riboflavin synthesis genes. Trends Genet. 15:
439–442.
Grundy, F.J., and Henkin, T.M. (1998). The S-box regulon: A new
global transcription termination control system for methionine and
cysteine biosynthesis genes in gram-positive bacteria. Mol. Microbiol.
30: 737–749.
Hunt, A.G. (1994). Messenger 39 end formation in plants. Annu. Rev.
Plant Physiol. Plant Mol. Biol. 45: 47–60.
Kertesz, S., Kerenyi, Z., Merai, Z., Bartos, I., Palfy, T., Barta, E., and
Silhavy, D. (2006). Both introns and long 39-UTRs operate as cis-
acting elements to trigger nonsense-mediated decay in plants.
Nucleic Acids Res. 34: 6147–6157.
Kline, D.J., and Ferre ´-D’Amare ´, A.R. (2006). Structural basis of glmS
ribozyme activation by glucosamine-6-phosphate. Science 313:
1752–1756.
Kubodera, T., Watanabe, M., Yoshiuchi, K., Yamashita, N., Nishimura,
A., Nakai, S., Gomi, K., and Hanamoto, H. (2003). Thiamine-regulated
gene expression of Aspergillus oryzae thiA requires splicing of the in-
tron containing a riboswitch-like domain in the 59-UTR. FEBS Lett. 555:
516–520.
Lang, D., Eisinger, J., Reski, R., and Rensing, S.A. (2005). Represen-
tation and high-quality annotation of the Physcomitrella patens tran-
scriptome demonstrates a high proportion of proteins involved in
metabolism in mosses. Plant Biol. (Stuttg) 7: 238–250.
Lou, H., Neugebauer, K.M., Gagel, R.F., and Berget, S.M. (1998).
Regulation of alternative polyadenylation by U1 snRNPs and SRp20.
Mol. Cell. Biol. 18: 4977–4985.
Mandal, M., and Breaker, R.R. (2004). Gene regulation by riboswitches.
Nat. Rev. Mol. Cell Biol. 5: 451–463.
Mogen, B.D., MacDonald, M.H., Graybosch, R., and Hunt, A.G.
(1990). Upstream sequences other than AAUAAA are required for
efficient messenger RNA 39-end formation in plants. Plant Cell 2:
1261–1272.
Montange, R.K., and Batey, R.T. (2006). Structure of the S-adenosyl-
methionine riboswitch regulatory mRNA element. Nature 441: 1172–
1175.
Muhlrad, D., and Parker, R. (1999). Aberrant mRNAs with extended 39
UTRs are substrates for rapid degradation by mRNA surveillance.
RNA 5: 1299–1307.
Murashige, T., and Skoog, F. (1962). A revised medium for rapid
growth and bioassays with tobacco tissue cultures. Physiol. Plant. 15:
473–497.
Nahvi, A., Barrick, J.E., and Breaker, R.R. (2004). Coenzyme B12
riboswitches are widespread genetic control elements in prokaryotes.
Nucleic Acids Res. 32: 143–150.
Newman, T.C., Ohme-Takagi, M., Taylor, C.B., and Green, P.J.
(1993). DST sequences, highly conserved among plant SAUR genes,
target reporter transcripts for rapid decay in tobacco. Plant Cell 5:
701–714.
Rodionov, D.A., Vitreschak, A.G., Mironov, A.A., and Gelfand, M.S.
(2002). Comparative genomics of thiamin biosynthesis in prokaryotes.
New genes and regulatory mechanisms. J. Biol. Chem. 13: 48949–
48959.
Roth, A., Winkler, W.C., Regulski, E.E., Lee, B.W., Lim, J., Jona, I.,
Barrick, J.E., Ritwik, A., Kim, J.N., Welz, R., Iwata-Reuyl, D., and
Breaker, R.R. (2007). A riboswitch selective for the queuosine pre-
cursor preQ1 contains an unusually small aptamer domain. Nat.
Struct. Mol. Biol. 14: 308–317.
Serganov,A.,Polonskaia,A.,Phan,A.T.,Breaker,R.R.,andPatel,D.J.
(2006). Structural basis for gene regulation by a thiamine pyrophosphate-
sensing riboswitch. Nature 441: 1167–1171.
Gene Control by Plant Riboswitches3449

Page 14

Serganov, A., Yuan, Y.R., Pikovskaya, O., Polonskaia, A., Malinina,
L., Phan, A.T., Hobartner, C., Micura, R., Breaker, R.R., and Patel,
D.J. (2004). Structural basis for discriminative regulation of gene
expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11:
1729–1741.
Soukup, G.A., and Breaker, R.R. (1999). Relationship between inter-
nucleotide linkage geometry and the stability of RNA. RNA 5: 1308–
1325.
Soukup, J.K., and Soukup, G.A. (2004). Riboswitches exert genetic
control through metabolite-induced conformational change. Curr.
Opin. Struct. Biol. 14: 344–349.
Sudarsan, N., Barrick, J.E., and Breaker, R.R. (2003). Metabolite-
binding RNA domains are present in the genes of eukaryotes. RNA 9:
644–647.
Sudarsan, N., Cohen-Chalamish, S., Nakamura, S., Emilsson, G.M.,
and Breaker, R.R. (2005). Thiamine pyrophosphate riboswitches are
targets for the antimicrobial compound pyrithiamine. Chem. Biol. 12:
1325–1335.
Takagaki, Y., Seipelt, R.L., Peterson, M.L., and Manley, J.L. (1996).
The polyadenylation factor CstF-64 regulates alternative processing
of IgM heavy chain pre-mRNA during B cell differentiation. Cell 87:
941–952.
Thore, S., Leibundgut, M., and Ban, N. (2006). Structure of the
eukaryotic thiamine pyrophosphate riboswitch with its regulatory
ligand. Science 312: 1208–1211.
Vitreschak, A.G., Rodionov, D.A., Mironov, A.A., and Gelfand, M.S.
(2003). Regulation of the vitamin B12metabolism and transport in
bacteria by a conserved RNA structural element. RNA 9: 1084–1097.
Weinberg, Z., et al. (2007). Identification of 22 candidate structured
RNAs in bacteria using Cmfinder comparative genomics pipline.
Nucleic Acids Res. 35: 4809–4819.
Winkler, W., Nahvi, A., and Breaker, R.R. (2002). Thiamine derivatives
bind messenger RNAs directly to regulate bacterial gene expression.
Nature 419: 952–956.
Winkler, W.C., and Breaker, R.R. (2005). Regulation of bacterial gene
expression by riboswitches. Annu. Rev. Microbiol. 59: 487–517.
3450 The Plant Cell