Os01g0286100

The OsPIL15 gene (Os01g0286100), a phytochromeinteracting factor-like protein gene, is a member of the rice Phytochrome‐interacting factors (PIFs) family, in regulating seedling growth.[1]

Annotated Information

OsPIL15 encodes a basic helix-loop-helix factor localized in the nucleus.Basic helix-loop-helix (bHLH) proteins are the second largest class of plant transcription factors [2]. They comprise two distinct functional regions, a basic region and a helix-loop-helix. The former is required for DNA binding whereas the latter is needed for protein dimerization [3]. Based on DNA-binding ability, the proteins are divided into two groups, 1) DNA-binding bHLH and 2) non-DNA-binding bHLH (HLH) also known as atypical bHLH.

Function

Grain size is a major yield component in rice, and partly controlled by the sizes of the lemma and palea. Molecular mechanisms controlling the sizes of these organs largely remain unknown. In this study, we show that an antagonistic pair of basic helix-loop-helix (bHLH) proteins is involved in determining rice grain length by controlling cell length in the lemma/palea. Overexpression of an atypical bHLH, named POSITIVE REGULATOR OF GRAIN LENGTH 1 (PGL1), in lemma/palea increased grain length and weight in transgenic rice.Proteins with E-values of <4e−12 were selected for analysis; Os12g0610200, Os01g0286100, Os05g0139100, and Os04g0618600. Except for Os04g0618600, all candidates contained amino acids conserved in the basic domain required for binding to DNA. We found expression in the lemma/palea of these candidates. Thus, we chose these four candidates for analysis of interaction with PGL1.

OsPIL15‐OX seedlings exhibit an exaggerated shorter aboveground part and undeveloped root system relative to wild‐type seedlings, suggesting that OsPIL15 represses seedling growth in the dark. Microarray analysis combined with gene ontology analysis revealed that OsPIL15 represses a set of genes involved in auxin pathways and cell wall organization or biogenesis.Given the important roles of the auxin pathway and cell wall properties in controlling plant growth, we speculate that OsPIL15 represses seedling growth likely by regulating the auxin pathway and suppressing cell wall organization in etiolated rice seedlings. Additionally, exposure to red light or far‐red light relieved growth retardation and promoted seedling elongation in the OsPIL15‐OX lines, despite higher levels of OsPIL15 transcripts under red light and far‐red light than in the dark.These results suggest that light regulation of OsPIL15 expression is probably involved in photomorphogenesis in rice.

Expression

To amplify cDNAs from a rice total RNA preparation, an RT-PCR kit was used according to instructions with specific primers. The resulting PCR fragments were cloned and sequenced with an automated DNA sequencer, with the recommended sequencing kits according to instructions[4]. The following primers were used for cDNA amplification:5'-ATGAATTCATGAACCAGTTCGTCCCTGATTGGAGC-3' and 5'-AAGAATTCTTATCCTGATCCTGTGTTGGGTGCATTTTCAGG-3'.

Evolution

An extensive inspection of the entire genome sequence databases of rice (Oryza sativa) revealed six candidate genes (or codingsequences)of PILs, which were esignated OsPIL11 to OsPIL16. A non-rooted neighbor-joining phylogenetic tree was constructed using the amino acid sequence of the bHLH DNA-binding domain.A PIL family is composed of seven members in A. thaliana and six members in O. sativa. (HFR1, GL3, ICE1, and RAP1 are not PIL family, and are used as an out-group.) For these rice OsPIL genes,the annotated ID-code for each coding sequence was adopted from the Rice Annotation Project, and the ID-codes are indicted in parentheses. For the Arabidopsis PIL family members, their characteristics are indicated in parentheses with regard to biological events in which they appear to be implicated: circadian rhythm, elongation of hypocotyls in red light,greening upon the onset of light exposure, shade avoidance, and germination.

Labs working on this gene

[1]Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University,Chikusa-ku, Nagoya 464-8601, Japan

[2]Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China

[3]Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China

[4]Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100190, China

[5]Graduate School of Horticulture, Chiba University, Chiba, Japan

References

[1]Zhou J, Liu Q, Zhang F, et al. Overexpression of OsPIL15, a phytochrome‐interacting factor‐like protein gene, represses etiolated seedling growth in rice[J]. Journal of integrative plant biology, 2014.

[2]Feller A, Machemer K, Braun E L, et al. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors[J]. The Plant Journal, 2011, 66(1): 94-116.

[3]Massari M E, Murre C. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms[J]. Molecular and cellular biology, 2000, 20(2): 429-440.

[4]Nakamura Y, Kato T, Yamashino T, et al. Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa[J]. Bioscience, biotechnology, and biochemistry, 2007, 71(5): 1183-1191.