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Transporter genes expressed in developing and mature pollen
Male fertility depends on the proper development of the male gametophyte, successful pollen germination, tube growth and delivery of the sperm cells to the ovule. Previous studies have shown that nutrients like boron, and ion gradients or currents of Ca2+, H+, and K+ are critical for pollen tube growth. However, the molecular identities of transporters mediating these fluxes are mostly unknown. As a first step to integrate transport with pollen development and function, a genome-wide analysis of transporter genes expressed in the male gametophyte at four developmental stages was conducted. About 1269 genes encoding classified transporters were collected from the Arabidopsis thaliana genome. Of 757 transporter genes expressed in pollen, 16% or 124 genes, including AHA6, CNGC18, TIP1.3 and CHX08, are specifically or preferentially expressed relative to sporophytic tissues. Some genes are highly expressed in microspores and bicellular pollen (COPT3, STP2, OPT9); while others are activated only in tricellular or mature pollen (STP11, LHT7). Analyses of entire gene families showed that a subset of genes, including those expressed in sporophytic tissues, were developmentally-regulated during pollen maturation. Early and late expression patterns revealed by transcriptome analysis are supported by promoter::GUS analyses of CHX genes and by other methods. Recent genetic studies based on a few transporters, including plasma membrane H+ pump AHA3, Ca2+ pump ACA9, and K+ channel SPIK, further support the expression patterns and the inferred functions revealed by our analyses. Thus, revealing the distinct expression patterns of specific transporters and unknown polytopic proteins during microgametogenesis provides new insights for strategic mutant analyses necessary to integrate the roles of transporters and potential receptors with male gametophyte development.
Summary of Classified Transporter Families in Arabidopsis
Condensed master list (below) that provides the total number of genes in each Transporter Classification (TC) family and how many have gene-specific probes on the ATH1 Affymetrix Gene chip. Families are shown as: TC Code = Transporter Classification system codes, an IUBMB-approved system for membrane transport proteins; TC Class Description = Names of families and subfamilies within the TC system; FAMILY = Abbreviated TC family names; FAM# = Family numbers assigned by Ward (2001), with rare modifications for sorting purposes; and Protein Description = General protein family descriptions from the Aramemnon plant membrane protein database, with included protein names listed at the end of each description. TC code followed by a superscript "a" denotes classifications made by us according to Blastp searches. For each TC Class (in blue) and any subfamilies (normal font), the number of Total Genes and genes on the ATH1 Chip are shown. Start Row refers to the row in the master list (Sup. Table I, link below) in which the family appears. Total summary numbers appear at the top of the spreadsheet in red.
Updated Supplementary Table I (As of 5-March, 2007)
Master list of genes encoding classified transporters and unknown polytopic proteins in Arabidopsis and their expression levels in the developing male gametophyte and in 12 sporophytic tissues. All transcriptome datasets were obtained using the ATH1 Affymetrix Gene chip and normalized. The identity of the genes and the predicted proteins are shown as: AGI = Arabidopsis Genome Initiative gene identification number; TC Code = Transporter Classification system codes, an IUBMB-approved system for membrane transport proteins; TC Class Description = Names of families and subfamilies within the TC system; FAMILY = Abbreviated TC family names; FAM# = Family numbers assigned by Ward (2001), with rare modifications for sorting purposes; Protein Description = Descriptions from the Aramemnon plant membrane protein database, with revisions made for published proteins; Aramemnon Consensus = Predicted transmembrane regions from the Aramemnon database; and PROTEIN = Given protein name, as compiled from Aramemnon and published papers, or the AGI number for unknown proteins. TC code followed by a superscript "a" denotes classifications made by us according to Blastp searches. The normalized expression value is shown in male gametophyte at four stages, MS = Microspore; BC = Bicellular pollen; TC = Tricellular pollen; and MP = Mature pollen; and for sporophytic organ or tissue, SL = Seedlings; WP = Whole plants; SH = Shoots; LF = Leave; GC = Guard cell-enriched leaf extracts; PT = Petioles; ST = Stems; HP = Hypocotyls; XL = Xylem; CR = Cork; RH = Root hair zone; and RT = Roots. Expression is shown as a Cluster number assigned to genes showing similar coexpression patterns during microgametogenesis (Honys and Twell, 2004). To identify genes that show specific or preferential expression in pollen, the Maximum expression from the four pollen stages (MaxPollen); the Maximum expression from the twelve sporophytic tissues (MaxSpor) ; and the ratio of MaxPollen/MaxSpor (FoldChange) are shown. Pollen Pref/Spec mark those genes showing either pollen-specific expression if it is present in pollen, and absent in all 12 sporophyte tissues, or pollen-preferential expression if the ratio of MaxPollen/MaxSpor or FoldChange > 3.0. (See Materials and Methods in below reference for more details.)
Bock, K.W., et al. (2006). Integrating Membrane Transport with Male Gametophyte Development and Function through Transcriptomics. Plant Physiol 140, 1151-1168. [PDF]