Plastid control of abaxial-adaxial patterning

Impaired inosine monophosphate dehydrogenase leads to plant-specific ribosomal stress responses in Arabidopsis thaliana

Nucleotides are the building blocks of living organisms and their biosynthesis must be tightly regulated. Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in GTP synthesis that is essential for biological activities, such as RNA synthesis. In animals, the suppression of IMPDH function causes ribosomal stress (also known as nucleolar stress), a disorder in ribosome biogenesis that results in cell proliferation defects and apoptosis. Despite its importance, plant IMPDH has not been analyzed in detail. Therefore, we analyzed the phenotypes of mutants of the two IMPDH genes in Arabidopsis thaliana and investigated their relationship with ribosomal stress. Double mutants of IMPDH1 and IMPDH2 were lethal, and only the impdh2 mutants showed growth defects and transient chlorophyll deficiency. These results suggested that IMPDH1 and IMPDH2 are redundant and essential, whereas IMPDH2 has a crucial role. In addition, the impdh2 mutants showed a reduction in nucleolus size and resistance to several translation inhibitors, which is a known response to ribosomal stress. Furthermore, the IMPDH1/impdh1 impdh2 mutants showed more severe growth defects and phenotypes such as reduced plastid rRNA levels and abnormal processing patterns than the impdh2 mutants. Finally, multiple mutations of impdh with as2, which has abnormal leaf polarity, caused the development of needle-like leaves because of the enhancement of the as2 phenotype, which is a typical effect observed in mutants of genes involved in ribosome biogenesis. These results indicated that IMPDH is closely related to ribosome biogenesis, and that mutations in the genes lead to not only known responses to ribosomal stress, but also plant-specific responses.

Chloroplasts prevent precocious flowering through a GOLDEN2-LIKE-B-BOX DOMAIN PROTEIN module

The timing of flowering is tightly controlled by signals that integrate environmental and endogenous cues. Sugars produced by carbon fixation in the chloroplast are a crucial endogenous cue for floral initiation. Chloroplasts also convey information directly to the nucleus through retrograde signaling to control plant growth and development. Here, we show that mutants defective in chlorophyll biosynthesis and chloroplast development flowered early, especially under long-day conditions, although low sugar accumulation was seen in some mutants. Plants treated with the bleaching herbicide norflurazon also flowered early, suggesting that chloroplasts have a role in floral repression. Among retrograde signaling mutants, the golden2-like 1 (glk1) glk2 double mutants showed early flowering under long-day conditions. This early flowering was completely suppressed by constans (co) and flowering locus t (ft) mutations. Leaf vascular-specific knockdown of both GLK1 and GLK2 phenocopied the glk1 glk2 mutants. GLK1 and GLK2 repress flowering by directly activating the expression of B-BOX DOMAIN PROTEIN 14 (BBX14), BBX15, and BBX16 via CCAATC cis-elements in the BBX genes. BBX14/15/16 physically interact with CO in the nucleus, and expression of BBXs hampered CO-mediated FT transcription. Simultaneous knockdown of BBX14/15/16 by artificial miRNA (35S::amiR-BBX14/15/16) caused early flowering with increased FT transcript levels, whereas BBX overexpression caused late flowering. Flowering of glk1/2 and 35S::amiR-BBX14/15/16 plants was insensitive to norflurazon treatment. Taking these observations together, we propose that the GLK1/2-BBX14/15/16 module provides a novel mechanism explaining how the chloroplast represses flowering to balance plant growth and reproductive development.

The Arabidopsis ATP-Binding Cassette E protein ABCE2 is a conserved component of the translation machinery

ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 (api7-1), the first viable, hypomorphic allele of ABCE2, which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2, a null, recessive lethal allele of ABCE2. Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support for the first time a conserved role for ABCE proteins in translation in plants, as previously shown for the animal, fungal, and archaeal lineages. In Arabidopsis, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism.

Unveiling the functions of plastid ribosomal proteins in plant development and abiotic stress tolerance

Translation of mRNAs into proteins is a universal process and ribosomes are the molecular machinery that carries it out. In eukaryotic cells, ribosomes can be found in the cytoplasm, mitochondria, and also in the chloroplasts of photosynthetic organisms. A number of genetic studies have been performed to determine the function of plastid ribosomal proteins (PRPs). Tobacco has been frequently used as a system to study the ribosomal proteins encoded by the chloroplast genome. In contrast, Arabidopsis thaliana and rice are preferentially used models to study the function of nuclear-encoded PRPs by using direct or reverse genetics approaches. The results of these works have provided a relatively comprehensive catalogue of the roles of PRPs in different plant biology aspects, which highlight that some PRPs are essential, while others are not. The latter ones are involved in chloroplast biogenesis, lateral root formation, leaf morphogenesis, plant growth, photosynthesis or chlorophyll synthesis. Furthermore, small gene families encode some PRPs. In the last few years, an increasing number of findings have revealed a close association between PRPs and tolerance to adverse environmental conditions. Sometimes, the same PRP can be involved in both developmental processes and the response to abiotic stress. The aim of this review is to compile and update the findings hitherto published on the functional analysis of PRPs. The study of the phenotypic effects caused by the disruption of PRPs from different species reveals the involvement of PRPs in different biological processes and highlights the significant impact of plastid translation on plant biology.

Overexpression of VvPPR1, a DYW-type PPR protein in grape, affects the phenotype of Arabidopsis thaliana leaves

Pentatricopeptide repeat (PPR) proteins play important roles in plant growth and development. However, little is known about their functions in the leaf morphogenesis of Jingxiu grape (Vitis vinifera L.). Here, we explored the function of VvPPR1, which encodes a DYW-type PPR protein in grape. We showed that VvPPR1 is involved in the regulation of leaf rolling, anthocyanin accumulation, and trichome formation in Arabidopsis thaliana. Analysis of structural characteristics showed that VvPPR1 is a DYW-type PPR gene in the PLS subfamily consisting of 15 PPR motifs. The N-terminal had a targeted chloroplast site, and the C-terminal had a DYW domain. Quantitative PCR analysis revealed that the expression level of VvPPR1 was highest in grape leaves. Subcellular localization revealed that VvPPR1 is localized in the cytoplasm and chloroplast. VvPPR1-overexpressing plants had rolled leaves, high degrees of anthocyanin accumulation, and longer trichomes. The expression levels of genes related to these phenotypes were either significantly up-regulated or down-regulated. These results demonstrate that VvPPR1 is involved in leaf rolling, anthocyanin accumulation, and trichome formation in Arabidopsis; more generally, our findings indicate that VvPPR1 could be a target for improving the cultivation of horticultural crops.

RAB GTPASE HOMOLOG 8D is required for the maintenance of both the root stem cell niche and the meristem

Previous studies have suggested that the plastid translation elongation factor, elongation factor thermo unstable (EF-Tu), encoded by RAB GTPASE HOMOLOG 8D (RAB8D) is essential for plant growth. Here, through analyzing the root phenotypes of two knock-down alleles of RAB8D (rab8d-1 and rab8d-2), we further revealed a vital role for RAB8D in primary root development through the maintenance of both the stem cell niche (SCN) and the meristem. Our results showed that RAB8D deficiency affects the root auxin response and SCN maintenance signaling. RAB8D interacts with GENOMES UNCOUPLED 1 (GUN1) in vivo. Further analysis revealed that GUN1 is over-accumulated and is required for both stem cell death and maintenance of root architecture in rab8d Arabidopsis mutants. The ATAXIA-TELANGIECTASIA-MUTATED (ATM)-SUPPRESSOR OF GAMMA RESPONSE 1 pathway is involved in the regulation of root meristem size through upregulating SIAMESE-RELATED 5 expression in the rab8d-2 allele. Moreover, ETHYLENE RESPONSE FACTOR 115 is highly expressed in rab8d-2, which plays a role in further quiescent center division. Our observations not only characterized the role of RAB8D in root development, but also uncovered functions of GUN1 and ATM in response to plastid EF-Tu deficiency.

The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development

Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. The formation of methylated nucleotides is performed by a variety of RNA-methyltransferases. Chloroplasts of plant cells result from an endosymbiotic event and possess their own genome and ribosomes. However, enzymes responsible for rRNA methylation and the function of modified nucleotides in chloroplasts remain to be determined. Here, we identified an rRNA methyltransferase, CMAL (Chloroplast MraW-Like), in the Arabidopsis chloroplast and investigated its function. CMAL is the Arabidopsis ortholog of bacterial MraW/ RsmH proteins and accounts to the N4-methylation of C1352 in chloroplast 16S rRNA, indicating that CMAL orthologs and this methyl-modification nucleotide is conserved between bacteria and the endosymbiont-derived eukaryotic organelle. The knockout of CMAL in Arabidopsis impairs the chloroplast ribosome accumulation and accordingly reduced the efficiency of mRNA translation. Interestingly, the loss of CMAL leads not only to defects in chloroplast function, but also to abnormal leaf and root development and overall plant morphology. Further investigation showed that CMAL is involved in the plant development probably by modulating auxin derived signaling pathways. This study uncovered the important role of 16S rRNA methylation mediated by CMAL in chloroplast ribosome biogenesis and plant development.

Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis

Forward genetic screens have successfully identified many genes and continue to be powerful tools for dissecting biological processes in Arabidopsis and other model species. Next-generation sequencing technologies have revolutionized the time-consuming process of identifying the mutations that cause a phenotype of interest. However, due to the cost of such mapping-by-sequencing experiments, special attention should be paid to experimental design and technical decisions so that the read data allows to map the desired mutation. Here, we simulated different mapping-by-sequencing scenarios. We first evaluated which short-read technology was best suited for analyzing gene-rich genomic regions in Arabidopsis and determined the minimum sequencing depth required to confidently call single nucleotide variants. We also designed ways to discriminate mutagenesis-induced mutations from background Single Nucleotide Polymorphisms in mutants isolated in Arabidopsis non-reference lines. In addition, we simulated bulked segregant mapping populations for identifying point mutations and monitored how the size of the mapping population and the sequencing depth affect mapping precision. Finally, we provide the computational basis of a protocol that we already used to map T-DNA insertions with paired-end Illumina-like reads, using very low sequencing depths and pooling several mutants together; this approach can also be used with single-end reads as well as to map any other insertional mutagen. All these simulations proved useful for designing experiments that allowed us to map several mutations in Arabidopsis.

The Pentatricopeptide Repeat Protein SOT5/EMB2279 Is Required for Plastid rpl2 and trnK Intron Splicing

Chloroplast biogenesis and development are highly complex processes requiring interaction between plastid and nuclear genomic products. Using a high-throughput screen for chloroplast biogenesis suppressors in Arabidopsis (Arabidopsis thaliana), we identified a suppressor of thf1 (sot5) that displays virescent and serrated leaves. Further characterization revealed that sot5 mutants are defective in leaf adaxial and abaxial polarity and act as enhancers of asymmetric leaves2 Map-based cloning identified SOT5 as a gene previously named EMB2279 that encodes a plastid-targeted pentatricopeptide repeat (PPR) protein with 11 PPR motifs. A G-to-A mutation in sot5 leads to a significant decrease in splicing efficiency, generating two additional mRNA variants. As reported previously, the sot5 null mutation is embryo lethal. SOT5 is predicted to bind to specific RNA sequences found in plastid rpl2 and trnK genes, and we found decreased splicing efficiency of the rpl2 and trnK genes in sot5 mutants. Together, our results reveal that the PPR protein SOT5/EMB2279 is required for intron splicing of plastid rpl2 and trnK, providing insights into the role of plastid translation in the coupled development between chloroplasts and leaves.

Plastid translation is essential for lateral root stem cell patterning in Arabidopsis thaliana

The plastid evolved from a symbiotic cyanobacterial ancestor and is an essential organelle for plant life, but its developmental roles in roots have been largely overlooked. Here, we show that plastid translation is connected to the stem cell patterning in lateral root primordia. The RFC3 gene encodes a plastid-localized protein that is a conserved bacterial ribosomal protein S6 of β/γ proteobacterial origin. The rfc3 mutant developed lateral roots with disrupted stem cell patterning and associated with decreased leaf photosynthetic activity, reduced accumulation of plastid rRNAs in roots, altered root plastid gene expression, and changes in expression of several root stem cell regulators. These results suggest that deficiencies in plastid function affect lateral root stem cells. Treatment with the plastid translation inhibitor spectinomycin phenocopied the defective stem cell patterning in lateral roots and altered plastid gene expression observed in the rfc3 mutant. Additionally, when prps17 defective in a plastid ribosomal protein was treated with low concentrations of spectinomycin, it also phenocopied the lateral root phenotypes of rfc3 The spectinomycin treatment and rfc3 mutation also negatively affected symplasmic connectivity between primary root and lateral root primordia. This study highlights previously unrecognized functions of plastid translation in the stem cell patterning in lateral roots.

Retrograde Signals Navigate the Path to Chloroplast Development

Complex signaling networks between the chloroplast and the nucleus mediate the emergence of the seedling into the light and the establishment of photosynthesis.

Arabidopsis mTERF6 is required for leaf patterning

To enhance our understanding of the roles of mitochondrial transcription termination factors (mTERFs) in plants, we have taken a reverse genetic approach in Arabidopsis thaliana. One of the mutants isolated carried a novel allele of the mTERF6 gene, which we named mterf6-5. mTERF6 is a chloroplast and mitochondrial localised protein required for the maturation of chloroplast isoleucine tRNA. The mterf6-5 plants are pale and exhibit markedly reduced growth, and altered leaf and chloroplast development. Our qRT-PCR analyses revealed mis-expression of several plastid, mitochondrial and nuclear genes in mterf6-5 plants. Synergistic phenotypes were observed in double mutant combinations of mterf6-5 with alleles of other mTERF genes as well as with scabra3-2, affected in the plastid RpoTp RNA polymerase; these observations suggest a functional relationship between mTERF6, other mTERFs and SCA3. The mterf6-5 mutation also enhanced the leaf dorsoventral polarity defects of the asymmetric leaves1-1 (as1-1) mutant, which resulted in radial leaves. This interaction seemed specific of the impaired mTERF6 function because mutations in the mTERF genes MDA1 or TWR-1/mTERF9 did not result in radialised leaves. Furthermore, the mterf6-5 mutation dramatically increased the leaf phenotype of as2-1 and caused lethality early in vegetative development. Our results uncover a new role for mTERF6 in leaf patterning and highlight the importance of mTERFs in plant development.

Suitability of two distinct approaches for the high-throughput study of the post-embryonic effects of embryo-lethal mutations in Arabidopsis

Several hundred genes are required for embryonic and gametophytic development in the model plant Arabidopsis thaliana, as inferred from the lethality of their mutations. Despite many of these genes are expressed throughout the plant life cycle, the corresponding mutants arrest at early stages, preventing the study of their post-embryonic functions by conventional methods. Clonal analysis represents an effective solution to this problem by uncovering the effects of embryo-lethal mutations in sectors of mutant cells within an otherwise normal adult plant. In this pilot study, we have evaluated the suitability of two sector induction methods for the large-scale study of the post-embryonic effects of embryo-lethal (emb) mutations in Arabidopsis. In line with the interests of our laboratory, we selected 24 emb mutations that damage genes that are expressed in wild-type vegetative leaves but whose effects on leaf development remain unknown. For the induction of mutant sectors in adult plants, we followed one approach based on the X-ray irradiation of 'cell autonomy' (CAUT) lines, and another based on the site-specific excision of transgenes mediated by Cre recombinase. We conclude that both methods are time-consuming and difficult to scale up, being better suited for the study of emb mutations on a case-by-case basis.

pTAC10, a Key Subunit of Plastid-Encoded RNA Polymerase, Promotes Chloroplast Development

Regulation of photosynthetic gene expression by plastid-encoded RNA polymerase (PEP) is essential for chloroplast development. The activity of PEP largely relies on at least 12 PEP-associated proteins (PAPs) encoded in the nuclear genome of plant cells. A recent model proposed that these PAPs regulate the establishment of the PEP complex through broad PAP-PEP or PAP-PAP interactions. In this study, we identified the Arabidopsis (Arabidopsis thaliana) seedling-lethal mutant ptac10-1, which has defects in chloroplast development, and found that the mutant phenotype is caused by the suppression of PLASTID S1 RNA-BINDING DOMAIN PROTEIN (pTAC10/PAP3). Analysis of the heterozygous mutant and pTAC10-overexpressing transgenic plants indicated that the expression level of pTAC10 is tightly linked to chloroplast development. Characterization of the interaction of pTAC10 with PAPs revealed that pTAC10 interacts with other PAPs, such as FSD2, FSD3, TrxZ, pTAC7, and pTAC14, but it does not interact with PEP core enzymes, such as rpoA and rpoB. Analysis of pTAC10 interactions using truncated pTAC10 proteins showed that the pTAC10 carboxyl-terminal region downstream of the S1 domain is involved in the pTAC10-PAP interaction. Furthermore, overexpression of truncated pTAC10s lacking the C-terminal regions downstream of the S1 domain could not rescue the ptac10-1 mutant phenotype and induced an abnormal whitening phenotype in Columbia-0 plants. Our observations suggested that these pTAC10-PAP interactions are essential for the formation of the PEP complex and chloroplast development.

The ANGULATA7 gene encodes a DnaJ-like zinc finger-domain protein involved in chloroplast function and leaf development in Arabidopsis

The characterization of mutants with altered leaf shape and pigmentation has previously allowed the identification of nuclear genes that encode plastid-localized proteins that perform essential functions in leaf growth and development. A large-scale screen previously allowed us to isolate ethyl methanesulfonate-induced mutants with small rosettes and pale green leaves with prominent marginal teeth, which were assigned to a phenotypic class that we dubbed Angulata. The molecular characterization of the 12 genes assigned to this phenotypic class should help us to advance our understanding of the still poorly understood relationship between chloroplast biogenesis and leaf morphogenesis. In this article, we report the phenotypic and molecular characterization of the angulata7-1 (anu7-1) mutant of Arabidopsis thaliana, which we found to be a hypomorphic allele of the EMB2737 gene, which was previously known only for its embryonic-lethal mutations. ANU7 encodes a plant-specific protein that contains a domain similar to the central cysteine-rich domain of DnaJ proteins. The observed genetic interaction of anu7-1 with a loss-of-function allele of GENOMES UNCOUPLED1 suggests that the anu7-1 mutation triggers a retrograde signal that leads to changes in the expression of many genes that normally function in the chloroplasts. Many such genes are expressed at higher levels in anu7-1 rosettes, with a significant overrepresentation of those required for the expression of plastid genome genes. Like in other mutants with altered expression of plastid-encoded genes, we found that anu7-1 exhibits defects in the arrangement of thylakoidal membranes, which appear locally unappressed.

Proteomic analysis of the mature Brassica stigma reveals proteins with diverse roles in vegetative and reproductive development

The stigma, the specialized apex of the Brassicaceae gynoecium, plays a role in pollen capture, discrimination, hydration, germination, and guidance. Despite this crucial role in reproduction, the global proteome underlying Brassicaceae stigma development and function remains largely unknown. As a contribution towards the characterization of the Brassicaceae dry stigma global proteome, more than 2500 Brassica napus mature stigma proteins were identified using three different gel-based proteomics approaches. Most stigma proteins participated in Metabolic Processes, Responses to Stimulus or Stress, Cellular or Developmental Processes, and Transport. The stigma was found to express a wide variety of proteins with demonstrated roles in cellular and organ development including proteins known to be involved in cellular expansion and morphogenesis, embryo development, as well as gynoecium and stigma development. Comparisons to a corresponding proteome from a very morphologically different Poaceae dry stigma showed a very similar distribution of proteins among different functional categories, but also revealed evident distinctions in protein composition especially in glucosinolate and carotenoid metabolism, photosynthesis, and self-incompatibility. To our knowledge, this study reports the largest Brassicaceae stigma protein dataset described to date.