August 2012, 12:154,
Open Access This content is freely available online to anyone, anywhere at any time.
Date: 30 Aug 2012
A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq
The majority of nitrogen accumulating in cereal grains originates from proteins remobilised from vegetative organs. However, interactions between grain filling and remobilisation are poorly understood. We used transcriptome large-scale pyrosequencing of flag leaves, glumes and developing grains to identify cysteine peptidase and N transporter genes playing a role in remobilisation and accumulation of nitrogen in barley.
Combination of already known and newly derived sequence information reduced redundancy, increased contig length and identified new members of cysteine peptidase and N transporter gene families. The dataset for N transporter genes was aligned with N transporter amino acid sequences of rice and Arabidopsis derived from Aramemnon database. 57 AAT, 45 NRT1/PTR and 22 OPT unigenes identified by this approach cluster to defined subgroups in the respective phylogenetic trees, among them 25 AAT, 8 NRT1/PTR and 5 OPT full-length sequences. Besides, 59 unigenes encoding cysteine peptidases were identified and subdivided into different families of the papain cysteine peptidase clade. Expression profiling of full-length AAT genes highlighted amino acid permeases as the group showing highest transcriptional activity. HvAAP2 and HvAAP6 are highly expressed in vegetative organs whereas HvAAP3 is grain-specific. Sequence similarities cluster HvAAP2 and the putative transporter HvAAP6 together with Arabidopsis transporters, which are involved in long-distance transfer of amino acids. HvAAP3 is closely related to AtAAP1 and AtAAP8 playing a role in supplying N to developing seeds. An important role in amino acid re-translocation can be considered for HvLHT1 and HvLHT2 which are specifically expressed in glumes and flag leaves, respectively. PCA and K-means clustering of AAT transcript data revealed coordinate developmental stages in flag leaves, glumes and grains. Phloem-specific metabolic compounds are proposed that might signal high grain demands for N to distantly located plant organs.
The approach identified cysteine peptidases and specific N transporters of the AAT family as obviously relevant for grain filling and thus, grain yield and quality in barley. Up to now, information is based only on transcript data. To make it relevant for application, the role of identified candidates in sink-source communication has to be analysed in more detail.
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Peoples MBDM: The interlplay between proteolysis and amino acid metabolism during senescence and aging in plants. New York: AcademicPress Inc; 1988.
Peeters KMU, Van Laere AJ: Amino acid metabolism associated with N-mobilization from the flag leaf of wheat ( Triticum aestivum L .) during grain development. Plant Cell Environ 1994,17(2):131–141.CrossRef
Parrott DL, Martin JM, Fischer AM: Analysis of barley ( Hordeum vulgare ) leaf senescence and protease gene expression: a family C1A cysteine protease is specifically induced under conditions characterized by high carbohydrate, but low to moderate nitrogen levels. New Phytol 2010,187(2):313–331.PubMedCrossRef
ARAMEMNON - Plant Membrane Protein Database. [http://aramemnon.uni-koeln.de]
Ouyang J, Cai Z, Xia K, Wang Y, Duan J, Zhang M: Identification and analysis of eight peptide transporter homologs in rice. Plant Science 2010,179(4):374–382.CrossRef
von Wiren N, Mori S, Marschner H, Romheld V: Iron Inefficiency in Maize Mutant ys1 ( Zea mays L . cv Yellow-Stripe) Is Caused by a Defect in Uptake of Iron Phytosiderophores. Plant Physiol 1994,106(1):71–77.PubMed
Inoue H, Kobayashi T, Nozoye T, Takahashi M, Kakei Y, Suzuki K, Nakazono M, Nakanishi H, Mori S, Nishizawa NK: Rice OsYSL15 Is an Iron-regulated Iron(III)-Deoxymugineic Acid Transporter Expressed in the Roots and Is Essential for Iron Uptake in Early Growth of the Seedlings. J Biol Chem 2009,284(6):3470–3479.PubMedCrossRef
Yen M-R, Tseng Y-H, Saier MH: Maize Yellow Stripe1, an iron-phytosiderophore uptake transporter, is a member of the oligopeptide transporter (OPT) family. Microbiology 2001,147(11):2881–2883.PubMed
Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, et al.: Unlocking the Barley Genome by Chromosomal and Comparative Genomics. The Plant Cell Online 2011,23(4):1249–1263.CrossRef
NCBI non-redundant dataset. [ftp://ftp.ncbi.nlm.nih.gov/blast/db/]
MEROPS - The Peptidase Database. [http://merops.sanger.ac.uk/]
Wookey PJ, Pittard J, Forrest SM, Davidson BE: Cloning of the tyrP gene and further characterization of the tyrosine-specific transport system in Escherichia coli K-12. J Bacteriol 1984,160(1):169–174.PubMed
The TIGR Rice Genome Annotation Resource: improvements and new features. [http://rice.plantbiology.msu.edu/index.shtml]
IPK Barley Viroblast. [http://webblast.ipk-gatersleben.de/barley/viroblast.php]
Waters SP, Peoples MB, Simpson RJ, Dalling MJ: Nitrogen redistribution during grain growth in wheat ( Triticum aestivum L .). Planta 1980,148(5):422–428.
Araus JL, Brown HR, Febrero A, Bort J, Serret MD: Ear photosynthesis, carbon isotope discrimination and the contribution of respiratory CO2 to differences in grain mass in durum wheat. Plant Cell Environ 1993,16(4):383–392.CrossRef
Jukanti AK, Heidlebaugh NM, Parrott DL, Fischer IA, McInnerney K, Fischer AM: Comparative transcriptome profiling of near-isogenic barley ( Hordeum vulgare ) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation. New Phytol 2008,177(2):333–349.PubMed
Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, Lin J-F, Wu S-H, Swidzinski J, Ishizaki K, et al.: Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. The Plant Journal 2005,42(4):567–585.PubMedCrossRef
Van Bel AJE: Quantification of the xylem-to-phloem transfer of amino acids by use of inulin [14C]carboxylic acid as xylem transport marker. Plant Science Letters 1984,35(1):81–85.CrossRef
Liu D, Gong W, Bai Y, Luo J-C, Zhu Y-X: OsHT, a Rice Gene Encoding for a Plasma-Membrane Localized Histidine Transporter. Journal of Integrative Plant Biology 2005,47(1):92–99.CrossRef
Weigelt K, Küster H, Radchuk R, Müller M, Weichert H, Fait A, Fernie AR, Saalbach I, Weber H: Increasing amino acid supply in pea embryos reveals specific interactions of N and C metabolism, and highlights the importance of mitochondrial metabolism. The Plant Journal 2008,55(6):909–926.PubMedCrossRef
Xiang X, Bao Y: Relationship between embryo and endosperm development and accumulation of storage reserves in barley. Acta Botanica Sinica 1997, 39:905–913.
The European Nucleotide Archive (ENA). [http://www.ebi.ac.uk/ena/]
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990,215(3):403–410.PubMed
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005,437(7057):376–380.PubMed
Perl - version 5.8.8. [http://perl.org]
BioPerl version 1.6.0. [http://bioperl.org/]
Swofford DL: PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta. Florida State University: Sinauer Associates, Inc., Publishers; 2002.
Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J: TM4 Microarray Software Suite. In Methods in Enzymology. Edited by: Alan K, Brian O. San Diego, Calif: Elsevier/Academic Press; 2006:134–193.
MacQueen J: Some methods for classification and analysis of multivariate observations. In: Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability: June 21-July 18, 1965 and December 27, 1965-January 7, 1966 1965; Berkeley, California, USA. Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability. Berkeley, California: Statistics: University of California Press; 1967:281–297.
OriginPro 8.1. [http://www.originlab.com/]
- A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq
- Open Access
- Available under Open Access This content is freely available online to anyone, anywhere at any time.
BMC Plant Biology
- Online Date
- August 2012
- Online ISSN
- BioMed Central
- Additional Links
- Vegetative organs
- Developing grains
- N remobilisation
- N accumulation
- Cysteine peptidases
- N transporter genes
- Source-sink communication
- Author Affiliations
- 1. Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Gatersleben, D-06466, Germany
- 2. Christian-Albrechts-Universität (CAU), Kiel, D-24118, Germany