Does the upstream region possessing MULE-like sequence in rice upregulate PsbS1 gene expression?

Mohammed Nuruzzaman; Tatsuo Kanno; Rika Amada; Yoshiki Habu; Ichiro Kasajima; Toshiki Ishikawa; Maki Kawai-Yamada; Hirofumi Uchimiya

doi:10.1371/journal.pone.0102742

Does the upstream region possessing MULE-like sequence in rice upregulate PsbS1 gene expression?

PLoS One. 2014 Sep 26;9(9):e102742. doi: 10.1371/journal.pone.0102742. eCollection 2014.

Authors

Mohammed Nuruzzaman¹, Tatsuo Kanno², Rika Amada³, Yoshiki Habu⁴, Ichiro Kasajima⁵, Toshiki Ishikawa⁶, Maki Kawai-Yamada¹, Hirofumi Uchimiya³

Affiliations

¹ Institute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan; Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan.
² Japanese Science and Technology Agency, PRESTO, Saitama, Japan; Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Ibaraki, Japan.
³ Institute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan.
⁴ Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Ibaraki, Japan.
⁵ National Agriculture and Food Research Organization, Institute of Floricultural Science, Tsukuba, Japan.
⁶ Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan.

Abstract

The genomic nucleotide sequences of japonica rice (Sasanishiki and Nipponbare) contained about 2.7-kb unique region at the point of 0.4-kb upstream of the OsPsbS1 gene. In this study, we found that japonica rice with a few exceptions possessing such DNA sequences [denoted to OsMULE-japonica specific sequence (JSS)] is distinct by the presence of Mutator-like-element (MULE). Such sequence was absent in most of indica cultivars and Oryza glaberrima. In OsMULE-JSS1, we noted the presence of possible target site duplication (TSD; CTTTTCCAG) and about 80-bp terminal inverted repeat (TIR) near TSD. We also found the enhancement ofOsPsbS1 mRNA accumulation by intensified light, which was not associated with the DNA methylation status in OsMULE/JSS. In addition, O. rufipogon, possible ancestor of modern rice cultivars was found to compose PsbS gene of either japonica (minor) or indica (major) type. Transient gene expression assay showed that the japonica type promoter elevated a reporter gene activity than indica type.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Chromosomes, Plant
DNA Methylation
Gene Dosage
Gene Expression
Gene Expression Regulation, Plant*
Gene Order
Genes, Plant*
Genes, Reporter
Genome, Plant
Molecular Sequence Data
Oryza / genetics*
Promoter Regions, Genetic
Regulatory Sequences, Nucleic Acid*
Terminal Repeat Sequences
Transcription, Genetic
Transcriptional Activation

Grants and funding

This research was supported by a grant from the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN), grants from Ministry of Education, Culture, Sports, Science and Technology (MEXT; (http://www.mext.go.jp/english/)), Japan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.