Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis    

Abstract

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 C 4 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.C 4 plants, with few exceptions, require the coordination of the mesophyll (M) and bundle sheath (BS) cells, arranged in a wreath structure called Kranz leaf anatomy (Hatch and Agostino, 1992), to confer high rates of photosynthesis. The initial carboxylation phase of the C 4 pathway takes place in the M cells, while the decarboxylation phase is restricted to the BS cells. The high photosynthetic capacity of C 4 plants implies a massive efflux of C 4 -related metabolites between M and BS cells and between the cytosol and organelles in each cell type (Weber and von Caemmerer, 2010).Although research in the past few decades has greatly increased our understanding of the biochemical reactions and the enzymes involved in the C 4 pathway of photosynthesis, little is known about the specific genes involved in the development of the Kranz leaf anatomy, the C 4 biochemical pathway, and the underlying regulatory mechanisms for the high-level expression of C 4 -specific genes in a cell-, organ-, or development-specific manner. With the advancement in genomics, the genomic sequences of several C 3 and C 4 model plants have become available. These advances have allowed in-depth comparative proteomic and transcriptomic analyses of the whole leaves of typical C 3 and C 4 plants and their closely related C 3 -C 4 intermediate species of Cleome and Flaveria . These comparative studies allow deduction on how many genes are required to make a C 4 plant and possibly on how they may have been regulated at the genetic level. In addition, attempts have been made recently to characterize...

Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

“…Arabidopsis SHR-SCR complex has been suggested to control the development of vasculature in all tissues, including the Kranz anatomy in C4 leaves (15)(16)(17). Consistent with this hypothesis, the maize SHR and SCR genes not only were highly expressed during the development of Kranz anatomy in embryonic and foliar leaves (7) but also were preferentially expressed in the developing BS strands that contain both BS and vasculature cells (5). Finally, genes in C21 and C22 showed an expression peak at T084 and were overrepresented by many metabolic pathways, including amino acid, lipid, nucleotide, and secondary metabolisms.…”

“…Li et al (4) also obtained the transcriptomes of mesophyll (M) and bundle sheath (BS) cells to study the regulatory and functional differentiation between M and BS cells. A subsequent study by Chang et al (5) led to the identification of genes differentially expressed between M and BS cells, including two metabolite transporter genes and genes for the specialized BS cell wall structure. Liu et al (6) obtained the time-course transcriptomes of embryonic leaves every 6 h, starting from dry seeds to hour 72 post imbibition.…”

Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

“…One count per million or greater was used as a threshold for the detection of transcript (Li et al, 2010a;Chang et al, 2012). Several well-known secondary cell wall genes showed approximately equal high expression in internodes 4 and 5.…”

Evolutionary Convergence of Cell-Specific Gene Expression in Independent Lineages of C4 Grasses

“…This approach has been used to investigate transcript abundance in M and BS cells from maize (Li et al, 2010b;Chang et al, 2012) and led to estimates that in the M between 53 and 78, while in the BS between 102 and 214, transcription factors accumulated preferentially. However, maize represents only one lineage of C 4 plants.…”