RACK1 and the microRNA pathway Speth, Corinna; Laubinger, Sascha
Plant signaling & behavior,
01/2014, Letnik:
9, Številka:
2
Journal Article
Recenzirano
Odprti dostop
MicroRNAs (miRNAs) control many aspects of development and adaption in plants and in animals by post-transcriptional control of mRNA stability and translatability. Over the last years numerous ...proteins have been identified in the miRNA pathway. The versatile scaffold protein RACK1 has been associated with efficient miRNA production and function in plants and metazoans. Here, we briefly summarize the differences of RACK1 function in the plant and animal miRNA pathways and discuss putative mechanisms and functional roles of RACK1 in miRNA biogenesis and action.
Embryogenesis of flowering plants is initiated by polarization of the zygote, a prerequisite for correct axis formation in the embryo. The daughter cells of the asymmetric zygote division form the ...pro-embryo and the mostly extra-embryonic suspensor.1 The suspensor plays a pivotal role in nutrient and hormone transport and rapid growth of the embryo.2,3 Zygote polarization is controlled by a MITOGEN-ACTIVATING PROTEIN (MAP) kinase signaling pathway including the MAPKK kinase (MAP3K) YODA (YDA)4 and the upstream membrane-associated proteins BRASINOSTEROID SIGNALING KINASE 1 (BSK1) and BSK2.5,6 Furthermore, suspensor development is controlled by cysteine-rich peptides of the EMBRYO SURROUNDING FACTOR 1 (ESF1) family.7 While they act genetically upstream of YDA, the corresponding receptor to perceive these potential ligands is unknown. In other developmental processes, such as stomata development, YDA activity is controlled by receptor kinases of the ERECTA family (ERf).8–12 While the receptor kinases upstream of BSK1/2 in the embryo have so far not been identified,1 YDA is in part activated by the sperm cell-derived BSK family member SHORT SUSPENSOR (SSP) that represents a naturally occurring, constitutively active variant of BSK1.5,13 It has been speculated that SSP might be a paternal component of a parental tug-of-war controlling resource allocation toward the embryo.2,13 Here, we show that in addition to SSP, the receptor kinase ERECTA plays a crucial role in zygote polarization as a maternally contributed part of the embryonic YDA pathway. We conclude that two independent parental contributions initiate zygote polarization and control embryo development.
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•Independent maternal and paternal factors influence Arabidopsis zygote polarity•Maternal ERECTA family receptor kinases activate the MAP3K YODA in the zygote•Paternal SHORT SUSPENSOR protein activates YODA independently of maternal ERECTA
Cell polarization and asymmetric division of the zygote initiate axis formation of the embryo in the model plant Arabidopsis. Wang et al. show in this context that a maternal receptor complex and a paternally provided constitutively active signaling protein independently contribute to MAP kinase signaling controlling zygote polarization.
Introns are removed by the spliceosome, a large macromolecular complex composed of five ribonucleoprotein subcomplexes (U snRNPs). The U1 snRNP, which binds to 5ʹ splice sites, plays an essential ...role in early steps of the splicing reaction. Here, we show that Arabidopsis thaliana LETHAL UNLESS CBC7 (LUC7) proteins, which are encoded by a three-member gene family in Arabidopsis, are important for plant development and stress resistance. We show that LUC7 is a U1 snRNP accessory protein by RNA immunoprecipitation experiments and LUC7 protein complex purifications. Transcriptome analyses revealed that LUC7 proteins are not only important for constitutive splicing, but also affect hundreds of alternative splicing events. Interestingly, LUC7 proteins specifically promote splicing of a subset of terminal introns. Splicing of LUC7-dependent introns is a prerequisite for nuclear export, and some splicing events are modulated by stress in a LUC7-dependent manner. Taken together, our results highlight the importance of the U1 snRNP component LUC7 in splicing regulation and suggest a previously unrecognized role of a U1 snRNP accessory factor in terminal intron splicing.
The Arabidopsis thaliana proteins suppressor of phytochrome A-105 1 (SPA1), SPA3, and SPA4 of the four-member SPA1 protein family have been shown to repress photomorphogenesis in light-grown ...seedlings. Here, we demonstrate that spa quadruple mutant seedlings with defects in SPA1, SPA2, SPA3, and SPA4 undergo strong constitutive photomorphogenesis in the dark. Consistent with this finding, adult spa quadruple mutants are extremely small and dwarfed. These extreme phenotypes are only observed when all SPA genes are mutated, indicating functional redundancy among SPA genes. Differential contributions of individual SPA genes were revealed by analysis of spa double and triple mutant genotypes. SPA1 and SPA2 predominate in dark-grown seedlings, whereas SPA3 and SPA4 prevalently regulate the elongation growth in adult plants. Further analysis of SPA2 function indicated that SPA2 is a potent repressor of photomorphogenesis only in the dark but not in the light. The SPA2 protein is constitutively nuclear localized in planta and can physically interact with the repressor COP1. Epistasis analysis between spa2 and cop1 mutations provides strong genetic support for a biological significance of a COP1-SPA2 interaction in the plant. Taken together, our results have identified a new family of proteins that is essential for suppression of photomorphogenesis in darkness.
Information in the genome is not only encoded within sequence or epigenetic modifications, but is also found in how it folds in three-dimensional space. The formation of self-interacting genomic ...regions, named topologically associated domains (TADs), is known as a key feature of genome organization beyond the nucleosomal level. However, our understanding of the formation and function of TADs in plants is extremely limited. Here we show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, exhibits TADs with epigenetic features similar to those of higher plants. By analysing various epigenetic marks across Marchantia TADs, we find that these regions generally represent interstitial heterochromatin and their borders are enriched with Marchantia transcription factor TCP1. We also identify a type of TAD that we name 'TCP1-rich TAD', in which genomic regions are highly accessible and are densely bound by TCP1 proteins. Transcription of TCP1 target genes differs on the basis gene location, and those in TCP1-rich TADs clearly show a lower expression level. In tcp1 mutant lines, neither TCP1-bound TAD borders nor TCP1-rich TADs display drastically altered chromatin organization patterns, suggesting that, in Marchantia, TCP1 is dispensable for TAD formation. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent of expression fold change as opposed to genes that do not belong to these TADs. Our results suggest that, besides standing as spatial chromatin-packing modules, plant TADs function as nuclear microcompartments associated with transcription factor activities.
COP1 (for CONSTITUTIVELY PHOTOMORPHOGENIC1) and the four partially redundant SPA (for SUPPRESSOR OF PHYA) proteins work in concert to repress photomorphogenesis in Arabidopsis thaliana by targeting ...key transcription factors and phytochrome A for degradation via the 26S proteasome. Here, we report a detailed biochemical characterization of the SPA-COP1 complexes. The four endogenous SPA proteins can form stable complexes with COP1 in vivo regardless of light conditions but exhibit distinct expression profiles in different tissues and light conditions. The SPA proteins can self-associate or interact with each other, forming a heterogeneous group of SPA-COP1 complexes in which the exact SPA protein compositions vary depending on the abundance of individual SPA proteins. The four SPA proteins could be divided into two functional groups depending on their interaction affinities, their regulation of ELONGATED HYPOCOTYL5 degradation, and their opposite effects on COP1 protein accumulation. Loss-of-function mutations in a predominant SPA protein may cause a significant reduction in the overall SPA-COP1 E3 ligase activity, resulting in a partial constitutive photomorphogenic phenotype. This study thus provides an in-depth biochemical view of the SPA-COP1 E3 ligase complexes and offers new insights into the molecular basis for their distinct roles in the light control of plant development.
Recent findings suggest that alternative splicing has a critical role in controlling the responses of plants to temperature variations. However, alternative splicing factors in plants are largely ...uncharacterized. Here we establish the putative splice regulator, PORCUPINE (PCP), as temperature-specific regulator of development in Arabidopsis thaliana. Our findings point to the misregulation of WUSCHEL and CLAVATA3 as the possible cause for the meristem defects affecting the pcp-1 loss-of-function mutants at low temperatures.
Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all ...annotated genes present in the reference strain. An alternative are tiling arrays, but previous designs have not allowed the simultaneous analysis of both strands on a single array. We introduce AGRONOMICS1, a new Affymetrix Arabidopsis microarray that contains the complete paths of both genome strands, with on average one 25mer probe per 35-bp genome sequence window. In addition, the new AGRONOMICS1 array contains all perfect match probes from the original ATH1 array, allowing for seamless integration of the very large existing ATH1 knowledge base. The AGRONOMICS1 array can be used for diverse functional genomics applications such as reliable expression profiling of more than 30,000 genes, detection of alternative splicing, and chromatin immunoprecipitation coupled to microarrays (ChIP-chip). Here, we describe the design of the array and compare its performance with that of the ATH1 array. We find results from both microarrays to be of similar quality, but AGRONOMICS1 arrays yield robust expression information for many more genes, as expected. Analysis of the ATH1 probes on AGRONOMICS1 arrays produces results that closely mirror those of ATH1 arrays. Finally, the AGRONOMICS1 array is shown to be useful for ChIP-chip experiments. We show that heterochromatic H3K9me2 is strongly confined to the gene body of target genes in euchromatic chromosome regions, suggesting that spreading of heterochromatin is limited outside of pericentromeric regions.
Summary
MicroRNAs (miRNAs) regulate plant development by post‐transcriptional regulation of target genes. In
Arabidopsis thaliana
, DCL1 processes precursors (pri‐miRNAs) to miRNA duplexes, which ...associate with AGO1. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) or AGO1 to facilitate efficient and precise pri‐miRNA processing and miRNA loading, respectively. In this study, we show that the accumulation of plant microRNAs depends on RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), a scaffold protein that is found in all higher eukaryotes. miRNA levels are reduced in
rack1
mutants, and our data suggest that RACK1 affects the microRNA pathway via several distinct mechanisms involving direct interactions with known microRNA factors: RACK1 ensures the accumulation and processing of some pri‐miRNAs, directly interacts with SERRATE and is part of an AGO1 complex. As a result, mutations in RACK1 lead to over‐accumulation of miRNA target
mRNA
s, which are important for ABA responses and phyllotaxy, for example. In conclusion, our study identified complex functioning of RACK1 proteins in the Arabidopsis miRNA pathway; these proteins are important for miRNA production and therefore plant development.
The four members of the Suppressor of phyA-105 (SPA) gene family function to inhibit photomorphogenesis in dark- and light-grown seedlings. Additionally, SPA1-SPA4 regulate elongation growth of adult ...plants. In these processes, SPA2, SPA3 and SPA4 have overlapping but distinct functions. Here, we have further investigated the role of SPA1 which is partially masked by functional redundancy. We show that SPA1 represses not only red, far-red and blue light responses in a PHYA-dependent fashion, but also acts to suppress light signaling in darkness. We demonstrate that deletion-derivatives of SPA1 lacking the complete N-terminus or part of the kinase-like domain retain SPA1 function in light- and dark-grown seedlings, while deletion of the constitutive photomorphogenesis 1 (COP1)-interacting coiled-coil domain eliminates SPA1 activity. This suggests that the coiled-coil domain and the WD-repeat domain of SPA1 are sufficient for SPA1 function. An analysis of spa2 spa3 spa4 triple mutants demonstrates that SPA1, like SPA2, is sufficient for normal etiolation of dark-grown seedlings. In light-grown seedlings and adult plants, in contrast, SPA1 function is divergent from SPA2 function, with SPA1 playing the predominant role. Levels of SPA1, SPA3 and SPA4 transcript are increased by red, far-red and blue light, consistent with a role of these three SPA genes in light-grown seedlings. The abundance of SPA2 mRNA, in contrast, is not altered by light. Taken together, the analysis of SPA transcript levels suggests that differences in SPA gene expression patterns contribute to divergence in SPA1-SPA4 function.
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