MYB transcription factors in Arabidopsis

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http://bartellab.wi.mit.edu/publication_reprints/Rhoades_Cell02.pdf

Prediction of Plant MicroRNA Targets

Micro-RNAs (miRNAs) are regulatory molecules that mediate effects by interacting with messenger RNA (mRNA) targets. Here we show that Arabidopsis thaliana miRNA 39 (also known as miR171), a 21-ribonucleotide species that accumulates predominantly in inflorescence tissues, is produced from an intergenic region in chromosome III and functionally interacts with mRNA targets encoding several members of the Scarecrow-like (SCL) family of putative transcription factors. miRNA 39 is complementary to an internal region of three SCL mRNAs. The interaction results in specific cleavage of target mRNA within the region of complementarity, indicating that this class of miRNA functions like small interfering RNA associated with RNA silencing to guide sequence-specific cleavage in a developmentally controlled manner.

https://science.sciencemag.org/content/sci/297/5589/2053.full.pdf

Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA

Reactive oxygen intermediates (ROI) are strongly associated with plant defense responses. The origin of these ROI has been controversial. Arabidopsis respiratory burst oxidase homologues (rboh genes) have been proposed to play a role in ROI generation. We analyzed lines carrying dSpm insertions in the highly expressed AtrbohD and AtrbohF genes. Both are required for full ROI production observed during incompatible interactions with the bacterial pathogen Pseudomonas syringae pv. tomato DC3000(avrRpm1) and the oomycete parasite Peronospora parasitica. We also observed reduced cell death, visualized by trypan blue stain and reduced electrolyte leakage, in the Atrboh mutants after DC3000(avrRpm1) inoculation. However, enhanced cell death is observed after infection of mutant lines with P. parasitica. Paradoxically, although atrbohD mutation eliminated the majority of total ROI production, atrbohF mutation exhibited the strongest effect on cell death.

/pdf/arabidopsis-gp91phox-homologues-atrbohd-and-atrbohf-are-fr0a4cslkr.pdf

Arabidopsis gp91phox homologues AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response

Far-red light regulates many aspects of seedling development, such as inhibition of hypocotyl elongation and the promotion of greening, acting in part through phytochrome A (phyA). The RING motif protein COP1 is also important because cop1 mutants exhibit constitutive photomorphogenesis in darkness. COP1 is present in the nucleus in darkness but is gradually relocated to the cytoplasm upon illumination. Here we show that COP1 functions as an E3 ligase ubiquitinating both itself and the myb transcription activator LAF1, which is required for complete phyA responses. In transgenic plants, inducible COP1 overexpression leads to a decrease in LAF1 concentrations, but is blocked by the proteasome inhibitor MG132. The coiled-coil domain of SPA1, a negative regulator of phyA signalling, has no effect on COP1 auto-ubiquitination but facilitates LAF1 ubiquitination at low COP1 concentrations. These results indicate that, in darkness, COP1 functions as a repressor of photomorphogenesis by promoting the ubiquitin-mediated proteolysis of a subset of positive regulators, including LAF1. After the activation of phyA, SPA1 stimulates the E3 activity of residual nuclear COP1 to ubiquitinate LAF1, thereby desensitizing phyA signals.

LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1

One of the ways to make consistent progress in a particular field of biology consists in choosing a good model system on which to focus the experimental efforts of the scientific community. It has taken a long time for scientists interested in various aspects of the life of plants to reach some sort of consensus. With the advent and impact of molecular biology, the small weed Arabidopsis is now the object of rapidly growing scientific attention. Since it is reasonable to assume that the general molecular mechanisms that are responsible for the physiological, cellular and biochemical properties of plants will be essentially conserved in all plants, it follows that these mechanisms should also operate in Arabidopsis and hence that its genome should contain most of the genes that we need to know about if we want to understand the genetic determination of the life processes in plants.Arabidopsis has a small genome and well documented genetic studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous or heterologous genes are available. It is therefore realistic and desirable to aim at exploring the genome of this plant in very great detail. As will be illustrated in this book all the elements for such a grand strategy are in place.More and more scientists are therefore willing to accept the obvious and very real practical disadvantages resulting from its small size when experiments call for the isolation of proteins, membranes, subcellular fractions etc, in order to benefit from its extraordinary experimental advantages as a model system in molecular genetics. One can safely predict that in the next decade studies with Arabidopsis will provide major breakthroughs in our understanding of most aspects of plant physiology and developmental biology. The importance of this knowledge for plant breeding and therefore for a sustainable highly productive agriculture cannot be overestimated. We therefore expect that this book will provide valuable guidelines to all those who are planning experiments aimed at understanding various aspects of plant growth, productivity and interactions with the environment. The book offers a wealth of methodical and theoretical information as well as valuable references. It should be of use to students, teachers, as well as advanced researchers and those breeders who want to use molecular techniques in breeding.

Methods in Arabidopsis research.

Desensitization of activated receptors is an important mechanism for terminating signal transduction. Here we show that phytochrome (phy) A, a predominant photoreceptor for seedling deetiolation, colocalizes in nuclear bodies with CONSTITUTIVELY PHOTOMORPHOGENIC (COP) 1, a RING motif-containing E3 ligase. The phyA PAS domain interacts with the COP1 WD40 domain. Both the Pr and the Pfr forms of phyA, as well as the PHYA apoprotein, are ubiquitinated by COP1 in vitro. The phyA destruction rate is decreased in cop1 mutants and by expression of a COP1 RING motif mutant. Our results indicate that COP1 acts as an E3 ligase to regulate phyA signaling by targeting elimination of the phyA photoreceptor itself.

/pdf/photoreceptor-ubiquitination-by-cop1-e3-ligase-desensitizes-979v0ivqpj.pdf

Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling

Light signaling via the phytochrome A (phyA) photoreceptor controls basic plant developmental processes including de-etiolation and hypocotyl elongation. We have identified a new Arabidopsis mutant, pat (phytochrome A signal transduction)1-1, which shows strongly reduced responses in continuous far-red light. Physiological and molecular data indicate that this mutant is disrupted at an early step of phyA signal transduction. The PAT1 gene encodes a cytoplasmic protein of 490 amino acids with sequence homologies to the plant-specific GRAS regulatory protein family. In the pat1-1 mutant, a T-DNA insertion introduces a premature stop codon, which likely results in the production of a truncated PAT1 protein of 341 amino acids. The semidominant phenotype of this mutant can be recapitulated by overexpression of an appropriately truncated PAT1 gene in the wild type. The results indicate that the truncated PAT1 protein acts in a dominant-negative fashion to inhibit phyA signaling.

/pdf/pat1-a-new-member-of-the-gras-family-is-involved-in-29t27bnhcf.pdf

PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction.

Upon activation by far-red light, phytochrome A signals are transduced through several pathways to promote photomorphogenesis. The COP1 E3 ligase represses photomorphogenesis in part by targeting transcription activators such as LAF1 and HY5 for destruction. Another positive regulator of photomorphogenesis is HFR1, a basic helix-loop-helix (bHLH) transcription factor. Here, we show that HFR1 colocalizes with COP1 in nuclear bodies, and that the HFR1 N-terminal region (amino acids 1-131) interacts with the COP1 WD40 domain. HFR1(ΔN), an HFR1 mutant lacking the two N-terminal, COP1-interacting motifs, still localizes in nuclear bodies and retains weak affinity for COP1. Both HFR1 and HFR1(ΔN) can be ubiquitinated by COP1, although with different efficiencies. Expression of 35S-HFR1(ΔN) in wild-type plants confers greater hypersensitivity to FR than 35S-HFR1 expression, and only seedlings expressing 35S-HFR1(ΔN) display constitutive photomorphogenesis. These phenotypic differences can be attributed to the instability of HFR1 compared with HFR1(ΔN). In transgenic plants, HFR1 levels are significantly elevated upon induced expression of a dominant-negative COP1 mutant that interferes with endogenous COP1 E3 activity. Moreover, induced expression of wild-type COP1 in transgenic plants accelerates post-translational degradation of HFR1 under FR light. Taken together, our results show that HFR1 is ubiquitinated by COP1 E3 ligase and marked for post-translational degradation during photomorphogenesis.

/pdf/hfr1-is-targeted-by-cop1-e3-ligase-for-post-translational-jft0e49hru.pdf

Nam-Hai Chua

Papers

LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1

Methods in Arabidopsis research.

Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling

PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction.

HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling