Os09g0401100 - Revision history

Rice2012: /* Structured Information */

2015-06-12T09:41:38Z

‎Structured Information

Victoria: /* Expression */

2014-05-25T08:50:14Z

‎Expression

Victoria: /* Expression */

2014-05-25T08:47:55Z

‎Expression

Victoria: /* Expression */

2014-05-25T08:46:48Z

‎Expression

Victoria: /* Expression */

2014-05-25T08:45:38Z

‎Expression

Victoria: /* Expression */

2014-05-25T08:42:11Z

‎Expression

Victoria: /* Expression */

2014-05-25T08:28:29Z

‎Expression

Victoria: /* Expression */

2014-05-25T08:27:49Z

‎Expression

Victoria: /* References */

2014-05-25T08:21:29Z

‎References

Victoria: /* Expression */

2014-05-25T08:02:51Z

‎Expression

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 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

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 The central structureof thesymbiotic association betweenplants and arbuscularmycorrhizal (AM) fungi is the fungal arbuscule that delivers minerals to the plant. Our earlier transcriptome analyses identiﬁed two half-size ABCG transporters that displayed enhanced mRNA levels in mycorrhizal roots. We now show speciﬁc transcript accumulation in arbusculated cells of both genes during symbiosis. Presently, arbuscule-relevant factors from monocotyledons have not been reported. Mutation of either of the Oryza sativa (rice) ABCG transporters blocked arbuscule growth of different AM fungi at a small and stunted stage, recapitulating the phenotype of Medicago truncatula stunted arbuscule 1 and 2 (str1 and str2) mutants that are deﬁcient in homologous ABCG genes. This phenotypic resemblance and phylogenetic analysis suggest functional conservation of STR1 and STR2 across the angiosperms. Malnutrition of the fungus underlying limited arbuscular growth was excluded by the absence of complementation of the str1 phenotype by wild-type nurse plants. Furthermore, plant AM signaling was found to be intact, as arbuscule-induced marker transcript accumulation was not affected in str1 mutants. Strigolactones have previously been hypothesized to operate as intracellular hyphal branching signals and possible substrates of STR1 and STR2. However, full arbuscule development in the strigolactone biosynthesis mutants d10 and d17 suggested strigolactones to be unlikely substrates of STR1/STR2. Interestingly, rice STR1 is associated with a cis-natural antisense transcript (antiSTR1). Analogous to STR1 and STR2, at the root cortex level, the antiSTR1 transcript is speciﬁcally detected in arbusculated cells, suggesting unexpected modes of STR1 regulation in rice.
-===Expression===
+[[File:2222.png|200px|thumb|left|alt text]]===Expression===
 Please input expression information here.
 Transcripts of STR1, STR2 and antiSTR1 accumulate in arbusculated cells

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 exon by 819 nt (Figure 1a). The ﬁrst exon of antiSTR1 matches 131 nt of another gene adjacent to STR1 (RAP ID, Os09t0401200-01; data not shown) in sense orientation. AntiSTR1 is predicted (http://www.rapdb.dna.affrc.go.jp) to encode a protein of 94 amino acids. However, no corre- sponding protein sequence has been reported from any organism, as determined by BLAST searches. Therefore, antiSTR1 is not likely to encode for a protein but instead represents a bona ﬁde cis-NAT. Computational searches for similar cis-NAT sequences from other plant species did not yield any match. The presence of antiSTR1 was conﬁrmed by real-time RT-PCR, with primers speciﬁcally targeting antiSTR1 and with cDNA synthesized by an antiSTR1- speciﬁc primer (Tables S1 and S3). Natural antisense transcripts have been proposed to regulate complementary mRNA in many different ways, such as transcriptional interference, RNA masking, chro- matin remodelling, RNA editing and RNA interference (Lapidot and Pilpel, 2006). For RNA interference, small interfering (si) RNAs of mostly 21–25 nt in length are produced from the antisense transcript, and lead to Argo- naut-dependent degradation of mRNAs (Okamura and Lai, 2008). We considered the possibility that siRNAs might be produced from antiSTR1 and could also target other genes in trans. Applying a cut-off of 21-nt sequence complemen- tarity revealed a matching sequence of 121 nt in length contained within the ﬁrst exon of the STR2 open reading frame, indicating the possibility that STR2 could be targeted by antiSTR1 in trans. However, as antiSTR1 originates from the same locus as STR1 we kept the name antiSTR1. Small complementary stretches of 23–34 nucleotides were also found in three other genes located on chromosomes 4 and 7, and encoding an inorganic pyrophosphatase, a glycosyl- transferase and a hypothetical protein (Table S2). However, these genes are not regulated by AM colonization (Gu ¨imil et al., 2005; C. Gutjahr, R. J. H. Sawers, H. Angliker, T. Roloff, E. Oakeley, U. Paszkowski unpublished data). Next, to conﬁrm the AM-responsive induction of STR1, and to assess AM induction of STR2 and antiSTR1, real-time RT-PCR analysis was performed on cDNA from non-colo- nized and Glomus intraradices-colonized roots. High levels of STR1 and STR2 mRNA were detected in mycorrhizal roots, thereby conﬁrming previous microarray data, whereas expression was at the background level in non- colonized roots (Gu ¨imil et al., 2005; C. Gutjahr, R. J. H. Sawers, H. Angliker, T. Roloff, E. Oakekly, U. Paszkowski, unpublished data). antiSTR1 mRNA also accumulated in roots, but the level did not change upon AM colonization (Figure 1b). Examination of the transcript levels of STR1, STR2 and antiSTR1 in panicle, leaf, stem and embryo revealed only background levels of expression in these organs for all three genes. As STR1 and STR2 were induced in mycorrhizal roots we next examined their expression in arbusculated cells collected by laser microdissection (Figure 1c). Transcript levels were compared between arbusculated and non- arbusculated cortex cells from mycorrhizal roots (hereafter called systemic cortex cells) and cortex cells from mock- inoculated roots. To ensure the speciﬁcity of the samples, we ﬁrst recorded the expression of the arbuscule marker PT11. PT11 was speciﬁcally expressed in arbusculated cells, but not in systemic or mock control cells, as reported earlier (Gutjahr et al., 2008). Similarly, STR1 and STR2 were
 speciﬁcally expressed in arbusculated cortex cells. Arbus- cule-speciﬁc expression was also observed for antiSTR1. This cell-speciﬁc expression pattern was unexpected as the expression level of antiSTR1 was similar between mock and Glomus intraradices-inoculated root systems (Figure 1b). antiSTR1 transcript accumulation might therefore differ spatially between colonized and non-colonized roots, but the total level of antiSTR1 transcripts in the root system might not differ between the two treatments. In summary,
-all three transcripts accumulate in arbusculated cells, suggesting they play a role in arbuscule development, maintenance or function.[[File:1111.jpg]]
+all three transcripts accumulate in arbusculated cells, suggesting they play a role in arbuscule development, maintenance or function.[[File:1111.png|200px|thumb|left|alt text]]
 ===Evolution===

@@ Line 13: / Line 13: @@
 exon by 819 nt (Figure 1a). The ﬁrst exon of antiSTR1 matches 131 nt of another gene adjacent to STR1 (RAP ID, Os09t0401200-01; data not shown) in sense orientation. AntiSTR1 is predicted (http://www.rapdb.dna.affrc.go.jp) to encode a protein of 94 amino acids. However, no corre- sponding protein sequence has been reported from any organism, as determined by BLAST searches. Therefore, antiSTR1 is not likely to encode for a protein but instead represents a bona ﬁde cis-NAT. Computational searches for similar cis-NAT sequences from other plant species did not yield any match. The presence of antiSTR1 was conﬁrmed by real-time RT-PCR, with primers speciﬁcally targeting antiSTR1 and with cDNA synthesized by an antiSTR1- speciﬁc primer (Tables S1 and S3). Natural antisense transcripts have been proposed to regulate complementary mRNA in many different ways, such as transcriptional interference, RNA masking, chro- matin remodelling, RNA editing and RNA interference (Lapidot and Pilpel, 2006). For RNA interference, small interfering (si) RNAs of mostly 21–25 nt in length are produced from the antisense transcript, and lead to Argo- naut-dependent degradation of mRNAs (Okamura and Lai, 2008). We considered the possibility that siRNAs might be produced from antiSTR1 and could also target other genes in trans. Applying a cut-off of 21-nt sequence complemen- tarity revealed a matching sequence of 121 nt in length contained within the ﬁrst exon of the STR2 open reading frame, indicating the possibility that STR2 could be targeted by antiSTR1 in trans. However, as antiSTR1 originates from the same locus as STR1 we kept the name antiSTR1. Small complementary stretches of 23–34 nucleotides were also found in three other genes located on chromosomes 4 and 7, and encoding an inorganic pyrophosphatase, a glycosyl- transferase and a hypothetical protein (Table S2). However, these genes are not regulated by AM colonization (Gu ¨imil et al., 2005; C. Gutjahr, R. J. H. Sawers, H. Angliker, T. Roloff, E. Oakeley, U. Paszkowski unpublished data). Next, to conﬁrm the AM-responsive induction of STR1, and to assess AM induction of STR2 and antiSTR1, real-time RT-PCR analysis was performed on cDNA from non-colo- nized and Glomus intraradices-colonized roots. High levels of STR1 and STR2 mRNA were detected in mycorrhizal roots, thereby conﬁrming previous microarray data, whereas expression was at the background level in non- colonized roots (Gu ¨imil et al., 2005; C. Gutjahr, R. J. H. Sawers, H. Angliker, T. Roloff, E. Oakekly, U. Paszkowski, unpublished data). antiSTR1 mRNA also accumulated in roots, but the level did not change upon AM colonization (Figure 1b). Examination of the transcript levels of STR1, STR2 and antiSTR1 in panicle, leaf, stem and embryo revealed only background levels of expression in these organs for all three genes. As STR1 and STR2 were induced in mycorrhizal roots we next examined their expression in arbusculated cells collected by laser microdissection (Figure 1c). Transcript levels were compared between arbusculated and non- arbusculated cortex cells from mycorrhizal roots (hereafter called systemic cortex cells) and cortex cells from mock- inoculated roots. To ensure the speciﬁcity of the samples, we ﬁrst recorded the expression of the arbuscule marker PT11. PT11 was speciﬁcally expressed in arbusculated cells, but not in systemic or mock control cells, as reported earlier (Gutjahr et al., 2008). Similarly, STR1 and STR2 were
 speciﬁcally expressed in arbusculated cortex cells. Arbus- cule-speciﬁc expression was also observed for antiSTR1. This cell-speciﬁc expression pattern was unexpected as the expression level of antiSTR1 was similar between mock and Glomus intraradices-inoculated root systems (Figure 1b). antiSTR1 transcript accumulation might therefore differ spatially between colonized and non-colonized roots, but the total level of antiSTR1 transcripts in the root system might not differ between the two treatments. In summary,
-all three transcripts accumulate in arbusculated cells, suggesting they play a role in arbuscule development, maintenance or function.[[File:[[File:File.png|200px|thumb|left|alt text]] ]]
+all three transcripts accumulate in arbusculated cells, suggesting they play a role in arbuscule development, maintenance or function.[[File:1111.jpg]]
 ===Evolution===

@@ Line 13: / Line 13: @@
 exon by 819 nt (Figure 1a). The ﬁrst exon of antiSTR1 matches 131 nt of another gene adjacent to STR1 (RAP ID, Os09t0401200-01; data not shown) in sense orientation. AntiSTR1 is predicted (http://www.rapdb.dna.affrc.go.jp) to encode a protein of 94 amino acids. However, no corre- sponding protein sequence has been reported from any organism, as determined by BLAST searches. Therefore, antiSTR1 is not likely to encode for a protein but instead represents a bona ﬁde cis-NAT. Computational searches for similar cis-NAT sequences from other plant species did not yield any match. The presence of antiSTR1 was conﬁrmed by real-time RT-PCR, with primers speciﬁcally targeting antiSTR1 and with cDNA synthesized by an antiSTR1- speciﬁc primer (Tables S1 and S3). Natural antisense transcripts have been proposed to regulate complementary mRNA in many different ways, such as transcriptional interference, RNA masking, chro- matin remodelling, RNA editing and RNA interference (Lapidot and Pilpel, 2006). For RNA interference, small interfering (si) RNAs of mostly 21–25 nt in length are produced from the antisense transcript, and lead to Argo- naut-dependent degradation of mRNAs (Okamura and Lai, 2008). We considered the possibility that siRNAs might be produced from antiSTR1 and could also target other genes in trans. Applying a cut-off of 21-nt sequence complemen- tarity revealed a matching sequence of 121 nt in length contained within the ﬁrst exon of the STR2 open reading frame, indicating the possibility that STR2 could be targeted by antiSTR1 in trans. However, as antiSTR1 originates from the same locus as STR1 we kept the name antiSTR1. Small complementary stretches of 23–34 nucleotides were also found in three other genes located on chromosomes 4 and 7, and encoding an inorganic pyrophosphatase, a glycosyl- transferase and a hypothetical protein (Table S2). However, these genes are not regulated by AM colonization (Gu ¨imil et al., 2005; C. Gutjahr, R. J. H. Sawers, H. Angliker, T. Roloff, E. Oakeley, U. Paszkowski unpublished data). Next, to conﬁrm the AM-responsive induction of STR1, and to assess AM induction of STR2 and antiSTR1, real-time RT-PCR analysis was performed on cDNA from non-colo- nized and Glomus intraradices-colonized roots. High levels of STR1 and STR2 mRNA were detected in mycorrhizal roots, thereby conﬁrming previous microarray data, whereas expression was at the background level in non- colonized roots (Gu ¨imil et al., 2005; C. Gutjahr, R. J. H. Sawers, H. Angliker, T. Roloff, E. Oakekly, U. Paszkowski, unpublished data). antiSTR1 mRNA also accumulated in roots, but the level did not change upon AM colonization (Figure 1b). Examination of the transcript levels of STR1, STR2 and antiSTR1 in panicle, leaf, stem and embryo revealed only background levels of expression in these organs for all three genes. As STR1 and STR2 were induced in mycorrhizal roots we next examined their expression in arbusculated cells collected by laser microdissection (Figure 1c). Transcript levels were compared between arbusculated and non- arbusculated cortex cells from mycorrhizal roots (hereafter called systemic cortex cells) and cortex cells from mock- inoculated roots. To ensure the speciﬁcity of the samples, we ﬁrst recorded the expression of the arbuscule marker PT11. PT11 was speciﬁcally expressed in arbusculated cells, but not in systemic or mock control cells, as reported earlier (Gutjahr et al., 2008). Similarly, STR1 and STR2 were
 speciﬁcally expressed in arbusculated cortex cells. Arbus- cule-speciﬁc expression was also observed for antiSTR1. This cell-speciﬁc expression pattern was unexpected as the expression level of antiSTR1 was similar between mock and Glomus intraradices-inoculated root systems (Figure 1b). antiSTR1 transcript accumulation might therefore differ spatially between colonized and non-colonized roots, but the total level of antiSTR1 transcripts in the root system might not differ between the two treatments. In summary,
-all three transcripts accumulate in arbusculated cells, suggesting they play a role in arbuscule development, maintenance or function.[[File:1111.jpg]]
+all three transcripts accumulate in arbusculated cells, suggesting they play a role in arbuscule development, maintenance or function.[[File:[[File:File.png|200px|thumb|left|alt text]] ]]
 ===Evolution===

@@ Line 25: / Line 25: @@
 ==References==
 Please input cited references here.
 ==Structured Information==