Bioinformatic analysis of the CLE signaling peptide family

Oelkers, Karsten; Goffard, Nicolas; Weiller, Georg F.; Gresshoff, Peter M.; Mathesius, Ulrike; Frickey, Tancred

doi:10.1186/1471-2229-8-1

Cited by 319 publications

(310 citation statements)

References 64 publications

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“…17 MtCLE12/MtCLE13) were constitutively expressed in hairy roots after transformation with Agrobacterium rhizogenes. In both legumes, overexpression of these CLE peptides under the control of the CaMV 35S promoter suppressed nodule formation in nontransgenic parts of the root system.…”

Section: Shoot-controlled Autoregulation Of Nodulationmentioning

confidence: 99%

Long-distance transport of signals during symbiosis

Staehelin

Xie

Illana

et al. 2011

Plant Signaling & Behavior

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Legumes enter nodule symbioses with nitrogen-fixing bacteria (rhizobia), whereas most flowering plants establish symbiotic associations with arbuscular mycorrhizal (AM) fungi. Once first steps of symbiosis are initiated, nodule formation and mycorrhization in legumes is negatively controlled by a shoot-derived inhibitor (SDI), a phenomenon termed autoregulation. According to current views, autoregulation of nodulation and mycorrhization in legumes is regulated in a similar way. CLE peptides induced in response to rhizobial nodulation signals (Nod factors) have been proposed to represent the ascending long-distance signals to the shoot. Although not proven yet, these CLE peptides are likely perceived by leucine-rich repeat (LRR) autoregulation receptor kinases in the shoot. Autoregulation of mycorrhization in non-legumes is reminiscent to the phenomenon of "systemic acquired resistance" in plant-pathogen interactions.

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Section: Shoot-controlled Autoregulation Of Nodulationmentioning

confidence: 99%

Long-distance transport of signals during symbiosis

Staehelin

Xie

Illana

et al. 2011

Plant Signaling & Behavior

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“…In recent years, individual experiments have demonstrated that small proteins (<200 amino acids [aa] in length), encoded by short open reading frames (sORF), play a major role in plant and animal development, e.g., the TAL protein (11 aa) influencing fruit fly development (Galindo et al 2007), the Cg-1 protein (<33 aa) controlling the tomato-nematode interaction (Gleason et al 2008), the CLE family proteins (75-140 aa) (Fletcher et al 1999;Trotochaud et al 2000;Muller et al 2008;Oelkers et al 2008) involved in Arabidopsis meristem development, the galectin-1 protein (;130 aa) associated with the malignant human tumor progression (Camby et al 2006), the lipid-binding protein AZI1 (161 aa) involved in priming plant defenses (Jung et al 2009), and the FLOWERING LOCUS T (FT) protein (175 aa) acting as a long-range signal regulating flowering (Notaguchi et al 2008). …”

mentioning

confidence: 99%

Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

Yang¹,

Tschaplinski²,

Hurst³

et al. 2011

Genome Res.

103

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Small proteins (10-200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained~2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10-200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) codingpotential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

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“…The CLV3 gene is expressed exclusively in stem cells of the aboveground meristems [9,10], and acts as a secreted signalling peptide. All predicted CLE peptides share a conserved C-terminal motif, which forms the core of the active peptide [11,12]. Overexpression of CLE genes in transgenic plants grown in liquid cultures and purification of extracellular peptides from the medium allowed determination of the structure of the active peptide [13,14].…”

Section: The Clavata Pathway As a Paradigm For Intercellular Communicmentioning

confidence: 99%

Peptides and receptors controlling root development

Stahl

Simon

2012

Phil. Trans. R. Soc. B

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The growth of a plant's root system depends on the continued activity of the root meristem, and the generation of new meristems when lateral roots are initiated. Plants have developed intricate signalling systems that employ secreted peptides and plasma membrane-localized receptor kinases for short-and long-range communication. Studies on growth of the vascular system, the generation of lateral roots, the control of cell differentiation in the root meristem and the interaction with invading pathogens or symbionts has unravelled a network of peptides and receptor systems with occasionally shared functions. A common theme is the employment of conserved modules, consisting of a short signalling peptide, a receptor-like kinase and a target transcription factor, that control the fate and proliferation of stem cells during root development. This review intends to give an overview of the recent advances in receptor and peptide ligand-mediated signalling involved in root development.

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Bioinformatic analysis of the CLE signaling peptide family

Cited by 319 publications

References 64 publications

Long-distance transport of signals during symbiosis

Long-distance transport of signals during symbiosis

Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

Peptides and receptors controlling root development

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