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PLA2 encodes MEI2-like RNA binding protein that is likely to be a rice orthologue of te1.The primary function of PLA2resides in regulating leaf maturation, which in turn plays a major role in regulating plastochron in rice.

Annotated Information


Taken together, our results indicated that the patatin-like PLA2 might play a significant role in the formation of vascular bundles, and that the dep3 mutant may provide another EP resource for rice breeding programs[1].

Phospholipase A(2)s (PLA(2)s) constitute a large superfamily of enzymes whose products are important for a multitude of signal transduction processes, lipid mediator release, lipid metabolism, development, plant stress responses, and host defense[2].

CSL1 may represent a novel gene, which functions downstream of PLA1 and/or PLA2, or alternatively functions in a separate pathway, involved in the regulation of leaf initiation and developmental transition via plant hormones or other mobile signals[3].

Mutants with abnormal leaf developmental patterns not only provide a great insight into understanding the regulatory mechanism of plant architecture, but also enrich the ways to its modification by which crop yield could be improved[4].

Instead, it produced a leafy panicle, in which all primary rachis-branches were converted to vegetative shoots[3].

These results indicate that both PLA1 and PLA2 act downstream of the GA signal transduction pathway to regulate leaf development[5].

Architecture of the rice inflorescence, which is determined mainly by the morphology, number and length of primary and secondary inflorescence branches, is an important agronomical trait[1].

Detailed analyses indicate that the primary function of PLA2 resides in regulating leaf maturation, which in turn plays a major role in regulating plastochron in rice.[6].


To gain more insight into the biological function of PLA2, we examined the PLA2 expression in detail. We first examined PLA2 expression by RT-PCR analysis. RNA was isolated from 3-weekold vegetative shoot apices, the inflorescence apex, the leaf blade, the leaf sheath, and the root. PLA2 was strongly expressed in shoot apex and inflorescence apex and intermediately in root, while low expression was detected in leaf blade and leaf sheath (see Supplemental Figure 6 online).To obtain more detailed information on the spatial pattern of PLA2 expression, we performed in situ hybridization experiments.By this method, PLA2 expression was seen throughout the life cycle. In the embryo, transcripts were detected in leaf primordia, vascular bundles, and the radicle (Figure 6A). In the vegetative phase, PLA2 was expressed in crown root apices(Figure 6B) and shoot apices (Figures 6C to 6F). Although Paquet et al. (2005) reported that PLA2/Ostel1/OML1 was expressed in shoot apices but not in roots and leaves, we detected obvious expression in roots, though no mutant phenotypes were apparent in this organ. In the shoot apex, PLA2 expression was first detected in the entire early P1 primordium that later developed into midrib (Figure 6C) and then became extended to the marginal region (Figure 6C). In P2-P4 primordia, the expression was localized to marginal and distal regions and was then downregulated from basal midrib region (Figures 6D to 6F). In older leaves than P4, PLA2 transcripts could not be detected. Almost no or only low levels of PLA2 transcripts could be detected in the SAM (Figure 6C). In the early reproductive phase, PLA2 was expressed in bracts and several external layers of the rachis meristem (Figure 6G), suggesting that at this stage, PLA2 may regulate meristem identity directly. At the later stages, PLA2 was expressed in branch meristems, floral meristems, and floral organs (Figures 6H and 6I). In the control experiment hybridized with sense RNA probe, no hybridization signals were detected(Figure 6J).[6].

Figure6.jpg In Situ Localization of PLA2 Transcripts (A) to (I) Antisense probe. (J) Sense probe. (A) Longitudinal section of embryo at 10 d after pollination. sm, SAM; vb, vascular bundle; ra, radicle. (B) Crown root at 1 week after germination. (C) Longitudinal section of 3-week-old shoot apex. (D) to (F) Serial transverse sections of 3-week-old shoot apex. Panels are from the bottom to the top. PLA2 signals are strong in marginal regions. (G) Inflorescence apex at stage In2. Two primary rachis branches (asterisks) are formed. b1 and b2 indicate first and second bracts, respectively. (H) Inflorescence apex at stage In5. Asterisks indicate spikelet primordia.

(I) Spikelet at stage Sp6. le, lemma; pa, palea; lo, lodicule; st, stamen.

(J) Longitudinal section of shoot apex. No hybridization signals are observed with sense probe.

Bars = 500 μm in (A), 250 μm in (B) and (H), 100 μm in (C), (G), and (J), and 150 μm in (D) to (F) and (I). ]

Phenotypes of pla2 Mutants

Plastochron and Leaf Size Rice plants normally initiate leaves from the SAM at regular intervals in 1/2 alternate phyllotaxy and, like many grasses, form several juvenile leaves in embryo before dormancy. In both the wild type and pla2, three leaves were present in mature embryos.After germination, both pla2-1 and pla2-2 showed an increased rate of leaf emergence compared with the wild type (Figures 1A and 1C). Since mature wild-type and pla2 embryos have the same number of leaf primordia, the more frequent leaf emergence indicates a shorter plastochron for subsequently formed leaves in the pla2 mutant. Given the similarity of pla2-1 and pla2-2 phenotypes, we chose to focus on pla2-1 .Plastochrons of the wild type and pla2-1 were nearly constant throughout the vegetative phase at 5.0 and 1.8 d, respectively (Figure 1C). For comparison, we examined phenotypes of pla1 mutants, which were reported previously (Itoh et al., 1998;Miyoshi et al., 2004). The plastochron of pla2 is significantly shorter than pla1 (1.8 versus 2.3). Furthermore, in contrast with pla1, in which the angle between the blade and sheath is increased for all leaves, the third leaf of pla2 appears erect due to an irregular blade-sheath boundary (see Supplemental Figure 1 online). The transition of vegetative to reproductive phase was also delayed in pla2-1 and pla2-2. Together with an extended vegetative period, pla2 produced threefold as many leaves as the wild type (49 versus 16 leaves). Assuming that this increase reflects loss of normal PLA2 function, these results suggest that the PLA2 gene normally acts to inhibit leaf initiation. In addition to a shortened plastochron, pla2 plants exhibited significantly smaller leaves than the wild type with respect to the length of blade and sheath and also the width of leaf blade(Figure 1B; see Supplemental Figures 2A to 2C online). As the size of epidermal cells of the third leaf in pla2 was almost comparable to that in the wild type, this size reduction was exclusively due to the reduction in the number of cells . The possibility of a causal relationship between leaf size and plastochron is reinforced by the phenotype of pla1, which also shows reduced leaf size and plastochron but not as severe as seen for pla2 (Figure 1B; see Supplemental Figures 2A to 2C online). Thus, there exists a positive correlation between plastochron and leaf size in the wild type, pla1, and pla2.Figure1.0.jpgFigure2222.jpg


With respect to plastochron, several genes have been identified: PLASTOCHRON1 (PLA1) in rice (Oryza sativa; Miyoshi et al., 2004), terminal ear1 (te1) in maize (Zea mays; Veit et al., 1998), and ALTEREDMERISTEM PROGRAM1 (AMP1), PHYTOCHROME B (PHYB), and SERRATE (SE) in Arabidopsis thaliana (Reed et al., 1993;Helliwell et al., 2001; Prigge andWagner, 2001). pla1, te1, and amp1 show shorter plastochron. By contrast, phyB and se show longer plastochron than the wild type. With each of these genes encoding a distinct class of protein and showing distinct loss-offunction phenotypes, the regulation of plastochron appears complex. The predicted PLA2 protein contains three RNA recognition motifs (RRM1, RRM2, and RRM3) and shows high similarity to the maize TE1 and the fission yeast MEI2 proteins (Figures 5B and 5C). The amino acid identities between PLA2 and TE1 in the three RRMs were 75.4, 74.6, and 89.5%, respectively, and those between PLA2 and MEI2 were 24.6, 29.9, and 52.6%, respectively (Figures 5B and 5C). Anderson et al. (2004) have reported six MEI2-like proteins in rice and nine in Arabidopsis and divided them into two subfamilies: a MEI2-like subfamily and a TE1-like subfamily. PLA2 is identical to OML1 of the TE1-like subfamily. By BLAST search, we have identified an additional MEI2-like protein in rice, OML7, which like OML6, has only the C-terminal RRM. A phylogenetic tree based on a comparison of the highly conserved RRM3 domain indicates that PLA2 is likely to be the orthologue of TE1 (Figure 5D; see Supplemental Figure 5 online).Figure5.0.jpg Structures of PLA2 and Related Genes.[6]. (A) Exon/intron structure of the PLA2 gene. Six boxes indicate exons. RNA recognition motifs (RRMs) are shaded. Locations of the two pla2 mutations are indicated: base and amino acid substitutions in exon 6 in pla2-1 and base substitution and non-sense mutation in pla2-2. (B) Deduced amino acid sequence of PLA2 protein. Underlining indicates RRMs. (C) Comparison of PLA2, TE1, and MEI2 proteins. RRMs are shaded. Numbers above TE1 and below MEI2 represent amino acid identity between TE1 and PLA2 and MEI2 and PLA2, respectively. Numbers at the right side indicate the number of amino acids. (D) Phylogenetic tree of MEI2-like RNA binding proteins. Numbers at each branch point indicate bootstrap values. PLA2, OML2, OML3, OML4, OML5, OML6, and OML7 are from O. sativa, TE1 from Z. mays, TEL1, TEL2, AML1, AML2, AML3, AML4, AML5, MCT1, and MCT2 from Arabidopsis, and MEI2 from Schizosaccharomyces pombe.

Labs working on this gene

1Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan 2National Institute of Genetics, Mishima 411-8540, Japan 3AgResearch, Private Bag 11008, Palmerston North, New Zealand


<references> [1] [2] [3] [4] [5] [6]

Structured Information

Gene Name



Similar to Terminal ear1


NM_001051674.1 GI:115441718 GeneID:4324983


3557 bp


Oryza sativa Japonica Group Os01g0907900, complete gene.


Oryza sativa Japonica Group

 ORGANISM  Oryza sativa Japonica Group
           Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
           Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
           clade; Ehrhartoideae; Oryzeae; Oryza.

Chromosome 1


Chromosome 1:41279485..41283041

Sequence Coding Region



GEO Profiles:Os01g0907900

Genome Context

<gbrowseImage1> name=NC_008394:41279485..41283041 source=RiceChromosome01 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008394:41279485..41283041 source=RiceChromosome01 preset=GeneLocation </gbrowseImage2>

Coding Sequence


Protein Sequence


Gene Sequence


External Link(s)

NCBI Gene:Os01g0907900, RefSeq:Os01g0907900

  1. 1.0 1.1 1.2 Qiao, Y; Piao, R; Shi, J; Lee, SI; Jiang, W; Kim, BK; Lee, J; Han, L; Ma, W; Koh, HJ. (2011) Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 122: 7.
  2. 2.0 2.1 Guy, JE; Ståhl, U; Lindqvist, Y. (2009) Crystal structure of a class XIB phospholipase A2 (PLA2): rice (oryza sativa) isoform-2 pla2 and an octanoate complex.The Journal of biological chemistry 284: 29.
  3. 3.0 3.1 3.2 Zhu, QH; Dennis, ES; Upadhyaya, NM. (2007) Compact shoot and leafy head 1, a mutation affects leaf initiation and developmental transition in rice (Oryza sativa L).Plant cell reports 26: 4.
  4. 4.0 4.1 Xiong, GS; Hu, XM; Jiao, YQ; Yu, YC; Chu, CC; Li, JY; Qian, Q; Wang, YH. (2006) Leafy head2, which encodes a putative RNA-binding protein, regulates shoot development of rice.Cell research 16: 3.
  5. 5.0 5.1 Mimura, M; Nagato, Y; Itoh, J. (2012) Rice PLASTOCHRON genes regulate leaf maturation downstream of the gibberellin signal transduction pathway.Planta 235: 5.
  6. 6.0 6.1 6.2 6.3 Kawakatsu T1, Itoh J, Miyoshi K, Kurata N, Alvarez N, Veit B, Nagato Y.PLASTOCHRON2 regulates leaf initiation and maturation in rice.Plant Cell. 2006 Mar;18(3):612-25. Epub 2006 Feb 3.