Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis

Yao-Ming Chang, Wen-Yu Liu, Chun-Chieh Shih, Meng-Ni Shen, Chen-Hua Lu, Mei-Yeh Lu, Hui-Wen Yang, Tzi-Yuan Wang, Chun-Chang Chen, Stella Maris Chen, Wen-Hsiung Li, Mauricesb Ku

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121 Citations (Scopus)


To study the regulatory and functional differentiation between the mesophyll (M) and bundle sheath (BS) cells of maize (Zea mays), we isolated large quantities of highly homogeneous M and BS cells from newly matured second leaves for transcriptome profiling by RNA sequencing. A total of 52,421 annotated genes with at least one read were found in the two transcriptomes. Defining a gene with more than one read per kilobase per million mapped reads as expressed, we identified 18,482 expressed genes; 14,972 were expressed in M cells, including 53 M-enriched transcription factor (TF) genes, whereas 17,269 were expressed in BS cells, including 214 BS-enriched TF genes. Interestingly, many TF gene families show a conspicuous BS preference in expression. Pathway analyses reveal differentiation between the two cell types in various functional categories, with the M cells playing more important roles in light reaction, protein synthesis and folding, tetrapyrrole synthesis, and RNA binding, while the BS cells specialize in transport, signaling, protein degradation and posttranslational modification, major carbon, hydrogen, and oxygen metabolism, cell division and organization, and development. Genes coding for several transporters involved in the shuttle of C4 metabolites and BS cell wall development have been identified, to our knowledge, for the first time. This comprehensive data set will be useful for studying M/BS differentiation in regulation and function. © 2012 American Society of Plant Biologists.
Original languageEnglish
Pages (from-to)165-177
Number of pages13
JournalPlant Physiology
Issue number1
Publication statusPublished - 2012
Externally publishedYes


  • plant RNA
  • transcription factor
  • transcriptome
  • vegetable protein
  • article
  • cell differentiation
  • cell wall
  • chromosome map
  • cytology
  • gene expression profiling
  • gene expression regulation
  • genetics
  • maize
  • mesophyll cell
  • metabolism
  • photosynthesis
  • plant cell
  • plant epidermis
  • plant gene
  • plant leaf
  • plasmodesma
  • protein synthesis
  • protein transport
  • protoplast
  • signal transduction
  • vascular bundle (plant)
  • Cell Differentiation
  • Cell Wall
  • Chromosome Mapping
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genes, Plant
  • Mesophyll Cells
  • Photosynthesis
  • Plant Cells
  • Plant Epidermis
  • Plant Leaves
  • Plant Proteins
  • Plant Vascular Bundle
  • Plasmodesmata
  • Protein Biosynthesis
  • Protein Transport
  • Protoplasts
  • RNA, Plant
  • Signal Transduction
  • Transcription Factors
  • Transcriptome
  • Zea mays


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