Table of Contents

The authors combined high-throughput global sequencing targeted to genes and custom-designed bioinformatics tools to catalog and characterize chemically induced mutations in rice and wheat. They demonstrate that this approach can be used to develop large-scale induced mutation resources with relatively small investments and is applicable to resource-limited and polyploid organisms.

Protein quality control mechanisms in the endoplasmic reticulum ensure that only correctly folded proteins are delivered to other compartments of the secretory pathwa, while misfolded proteins are degraded. This study identified and characterized the mannosidases that generate the glycan structure acting as the degradation signal for misfolded glycoproteins in Arabidopsis.

Root architectures of Arabidopsis thaliana were quantified in multiple combinations of N, P, K, S, and light to understand how plants integrate multiple nutritional signals. Combined with mutant phenotypes, transcriptional profiles, and shoot ion contents, the comprehensive data set facilitates the dissection of the nutrient signaling network and identifies roles for receptor-transporters.

In this work, the authors develop a method for simultaneously mapping tens of thousands of insertion sites in the green alga Chlamydomonas reinhardtii. This work reveals insights into the mutagenic insertion process and opens the door to pooled enrichment screens and the generation of indexed mutant libraries.

This work analyzes and elucidates the function of the LHC protein isoform LHCBM9. It provides evidence that the green microalga C. reinhardtii has evolved a LHCII-dependent, medium-term process for photoprotection during environmental stress conditions.

This work analyzes and elucidates the function of the LHC protein isoform LHCBM9. It provides evidence that the green microalga C. reinhardtii has evolved a LHCII-dependent, medium-term process for photoprotection during environmental stress conditions.

This work examines the mechanisms by which Chlamydomonas reinhardtii copes with nitrogen (N) limitation, finding transcriptomic and proteomic changes in multiple metabolic pathways and identifying an N-sparing mechanism that prioritizes respiratory metabolism and shifts the proteomic balance toward proteins with lower N contents, a result with implications for engineering of N-use efficiency.

In this work, the authors develop a method for simultaneously mapping tens of thousands of insertion sites in the green alga Chlamydomonas reinhardtii. This work reveals insights into the mutagenic insertion process and opens the door to pooled enrichment screens and the generation of indexed mutant libraries.

This work used single-particle tracking analysis to detect the dynamics of GFP-RbohD in Arabidopsis. GFP-RbohD spots were found to be mobile with high heterogeneity at the plasma membrane and preferentially assembled into clusters when activated. The results also demonstrated that the internalization of GFP-RbohD occurred via multiple endocytic pathways.

The marine diatom Phaeodactylum tricornutum stores carbon and energy in the form of lipids, predominantly triacylglycerols (TAGs), making it an attractive system for biodiesel production, but the mechanism underlying TAG accumulation is unclear. Using label-free quantitative proteomics and functional analysis, this study shows that the carboxylase MCC2 regulates TAG accumulation in this model diatom.

This study deals with nuclear β-amylase–like proteins, which possess a BZR1-type transcription factor domain and act as transcription factors, showing that their enzymatic-like domain influences DNA binding and ultimately the regulation of gene expression, thereby supporting a role of these proteins in metabolic sensing.

The diversity and dynamics of membrane domains in living plant cells is characterized using imaging-based approaches. Examining the diversity of microdomains that are targeted by members of the large Remorin family revealed that these sites may serve as platforms for interactions between different types of membrane-resident proteins and may contribute to their functions.

This work compares the sequences of five homoeologous centromeres in two closely related species, revealing rapid divergence of centromeric sequences. The results support the idea that centromeric satellite repeats undergo boom-bust cycles before a favorable repeat is fixed in the population.

An analysis of mutants from the compound-leafed model legume Medicago truncatula revealed that the interactions between ARP (PHANTASTICA) and SHOOT MERISTEMLESS (STM)- and BREVIPEDICELLUS (BP)-like KNOXI genes are different from in simple-leafed species, suggesting that the ARP and STM/BP-like KNOXI regulatory module is uncoupled in the formation of compound leaves.

Comparisons of meiosis in near-isogenic allohaploid and euploid lines of B. napus reveal that the mechanism that promotes efficient chromosome sorting in euploids is adjusted to promote crossover formation between homoeologs in allohaploids. This suggests that, in contrast to other polyploid species, in B. napus, chromosome sorting depends on context.

This report identifies the rice bHLH protein TIP2 as a key switch for the meristemoid transition and cell differentiation during early anther development. TIP2 directly triggers the expression of the developmental regulators TDR and EAT1 and interacts with TDR, forming a central cascade regulating differentiation, morphogenesis, and degradation of anther somatic cell layers.

The marine diatom Phaeodactylum tricornutum stores carbon and energy in the form of lipids, predominantly triacylglycerols (TAGs), making it an attractive system for biodiesel production, but the mechanism underlying TAG accumulation is unclear. Using label-free quantitative proteomics and functional analysis, this study shows that the carboxylase MCC2 regulates TAG accumulation in this model diatom.

This report identifies the rice bHLH protein TIP2 as a key switch for the meristemoid transition and cell differentiation during early anther development. TIP2 directly triggers the expression of the developmental regulators TDR and EAT1 and interacts with TDR, forming a central cascade regulating differentiation, morphogenesis, and degradation of anther somatic cell layers.

The auxin efflux carrier PIN2 has a long hydrophilic loop (HL); when transplanted into PIN5 (a short-HL PIN), this HL confers the PIN5:PIN2-HL fusion protein with the capacity for phosphorylation and plasma membrane (PM) targeting but not for PIN2-like polarity. Moreover, depending on cell type, PIN5 can show internal, PM, or polar localization in the PM.

Comparisons of meiosis in near-isogenic allohaploid and euploid lines of B. napus reveal that the mechanism that promotes efficient chromosome sorting in euploids is adjusted to promote crossover formation between homoeologs in allohaploids. This suggests that, in contrast to other polyploid species, in B. napus, chromosome sorting depends on context.

Electrochemical H⁺ gradients are essential to drive active transport of solutes through plant membranes. This work describes plant mutants defective in a proton pump that is specifically located in arbuscule-containing root cells and shows that this proton pump is required for the function of the arbuscular mycorrhizal symbiosis and symbiosis-driven phosphate acquisition and plant growth.

Root architectures of Arabidopsis thaliana were quantified in multiple combinations of N, P, K, S, and light to understand how plants integrate multiple nutritional signals. Combined with mutant phenotypes, transcriptional profiles, and shoot ion contents, the comprehensive data set facilitates the dissection of the nutrient signaling network and identifies roles for receptor-transporters.

The bHLH protein, AMS, acts as a master transcriptional regulator directly modulating the expression of 23 genes related to pollen wall development and sporopollenin biosynthesis in Arabidopsis. These genes are implicated in the separation of microspore mother cells, dissolution of the callose layer of tetrads, and subsequent sporopollenin biosynthesis and pollen coat formation.

This investigation shows that genetic interactions of microtubule function in Arabidopsis trichome differentiation involve ANGUSTIFOLIA1 and F-actin. Detailed analyses of the cytoskeleton of growing trichomes in tortifolia2 distorted1 double mutants indicated that F-actin enhances microtubule dynamics and enables reorientation.

An analysis of mutants from the compound-leafed model legume Medicago truncatula revealed that the interactions between ARP (PHANTASTICA) and SHOOT MERISTEMLESS (STM)- and BREVIPEDICELLUS (BP)-like KNOXI genes are different from in simple-leafed species, suggesting that the ARP and STM/BP-like KNOXI regulatory module is uncoupled in the formation of compound leaves.

The auxin efflux carrier PIN2 has a long hydrophilic loop (HL); when transplanted into PIN5 (a short-HL PIN), this HL confers the PIN5:PIN2-HL fusion protein with the capacity for phosphorylation and plasma membrane (PM) targeting but not for PIN2-like polarity. Moreover, depending on cell type, PIN5 can show internal, PM, or polar localization in the PM.

The marine diatom Phaeodactylum tricornutum stores carbon and energy in the form of lipids, predominantly triacylglycerols (TAGs), making it an attractive system for biodiesel production, but the mechanism underlying TAG accumulation is unclear. Using label-free quantitative proteomics and functional analysis, this study shows that the carboxylase MCC2 regulates TAG accumulation in this model diatom.

This work identifies a negative transcriptional regulator, DEWAX, that represses the expression of genes involved in Arabidopsis cuticular wax biosynthesis. The results suggest that DEWAX-mediated negative regulation of the wax biosynthetic genes might be involved in determining the total wax loads produced in Arabidopsis during daily dark and light cycles.

This report examines ARC1’s role in reconstituting the self-incompatibility trait in Arabidopsis thaliana and demonstrates an important role for ARC1 in promoting a strong and stable pollen rejection response when expressed with two other A. lyrata self-incompatibility factors. The expression of ARC1 conferred another A. lyrata trait for self-pollen avoidance, termed approach herkogamy.

Protein quality control mechanisms in the endoplasmic reticulum ensure that only correctly folded proteins are delivered to other compartments of the secretory pathwa, while misfolded proteins are degraded. This study identified and characterized the mannosidases that generate the glycan structure acting as the degradation signal for misfolded glycoproteins in Arabidopsis.

This work analyzes and elucidates the function of the LHC protein isoform LHCBM9. It provides evidence that the green microalga C. reinhardtii has evolved a LHCII-dependent, medium-term process for photoprotection during environmental stress conditions.

An analysis of mutants from the compound-leafed model legume Medicago truncatula revealed that the interactions between ARP (PHANTASTICA) and SHOOT MERISTEMLESS (STM)- and BREVIPEDICELLUS (BP)-like KNOXI genes are different from in simple-leafed species, suggesting that the ARP and STM/BP-like KNOXI regulatory module is uncoupled in the formation of compound leaves.

This work used single-particle tracking analysis to detect the dynamics of GFP-RbohD in Arabidopsis. GFP-RbohD spots were found to be mobile with high heterogeneity at the plasma membrane and preferentially assembled into clusters when activated. The results also demonstrated that the internalization of GFP-RbohD occurred via multiple endocytic pathways.

This work used single-particle tracking analysis to detect the dynamics of GFP-RbohD in Arabidopsis. GFP-RbohD spots were found to be mobile with high heterogeneity at the plasma membrane and preferentially assembled into clusters when activated. The results also demonstrated that the internalization of GFP-RbohD occurred via multiple endocytic pathways.

This work examines the mechanisms by which Chlamydomonas reinhardtii copes with nitrogen (N) limitation, finding transcriptomic and proteomic changes in multiple metabolic pathways and identifying an N-sparing mechanism that prioritizes respiratory metabolism and shifts the proteomic balance toward proteins with lower N contents, a result with implications for engineering of N-use efficiency.

The authors show that a well-conserved miRNA-transcription factor module implicated previously in developmental control regulates responses to repeated heat stress. They provide a conceptual framework for the integration of environmental stress responses with development to optimize growth under natural conditions.

The marine diatom Phaeodactylum tricornutum stores carbon and energy in the form of lipids, predominantly triacylglycerols (TAGs), making it an attractive system for biodiesel production, but the mechanism underlying TAG accumulation is unclear. Using label-free quantitative proteomics and functional analysis, this study shows that the carboxylase MCC2 regulates TAG accumulation in this model diatom.

To reveal the molecular mechanisms underlying lipid accumulation in microalgae, transcriptomic and lipidomic dynamics of Nannochloropsis oceanica under nitrogen-replete and nitrogen-depleted conditions were simultaneously tracked. The temporal and spatial regulation model established in this study provides a basis for the rational genetic engineering of enhanced oil production.

Comparisons of meiosis in near-isogenic allohaploid and euploid lines of B. napus reveal that the mechanism that promotes efficient chromosome sorting in euploids is adjusted to promote crossover formation between homoeologs in allohaploids. This suggests that, in contrast to other polyploid species, in B. napus, chromosome sorting depends on context.

Comparisons of meiosis in near-isogenic allohaploid and euploid lines of B. napus reveal that the mechanism that promotes efficient chromosome sorting in euploids is adjusted to promote crossover formation between homoeologs in allohaploids. This suggests that, in contrast to other polyploid species, in B. napus, chromosome sorting depends on context.

This work compares the sequences of five homoeologous centromeres in two closely related species, revealing rapid divergence of centromeric sequences. The results support the idea that centromeric satellite repeats undergo boom-bust cycles before a favorable repeat is fixed in the population.

The auxin efflux carrier PIN2 has a long hydrophilic loop (HL); when transplanted into PIN5 (a short-HL PIN), this HL confers the PIN5:PIN2-HL fusion protein with the capacity for phosphorylation and plasma membrane (PM) targeting but not for PIN2-like polarity. Moreover, depending on cell type, PIN5 can show internal, PM, or polar localization in the PM.

This work identifies a negative transcriptional regulator, DEWAX, that represses the expression of genes involved in Arabidopsis cuticular wax biosynthesis. The results suggest that DEWAX-mediated negative regulation of the wax biosynthetic genes might be involved in determining the total wax loads produced in Arabidopsis during daily dark and light cycles.

This work compares the sequences of five homoeologous centromeres in two closely related species, revealing rapid divergence of centromeric sequences. The results support the idea that centromeric satellite repeats undergo boom-bust cycles before a favorable repeat is fixed in the population.

A key feature of arbuscular mycorrhizal symbiosis is improved phosphorus nutrition of the host plant via the mycorrhizal pathway, i.e., fungal uptake of phosphate from the soil and release from arbuscules within root cells. This work shows that the M. truncatula proton ATPase HA1 is required for transfer of phosphate across the periarbuscular membrane that separates the fungus from the host plant.

This work shows that the cyanobacterial photoactive orange carotenoid protein (OCP) protects Synechocystis cells from photoinhibition even under conditions in which it is unable to quench excess energy absorbed by phycobilisomes. OCP plays a dual role under light stress conditions, protecting cells against photooxidative stress by quenching excess energy and singlet oxygen.

This work analyzes and elucidates the function of the LHC protein isoform LHCBM9. It provides evidence that the green microalga C. reinhardtii has evolved a LHCII-dependent, medium-term process for photoprotection during environmental stress conditions.

To reveal the molecular mechanisms underlying lipid accumulation in microalgae, transcriptomic and lipidomic dynamics of Nannochloropsis oceanica under nitrogen-replete and nitrogen-depleted conditions were simultaneously tracked. The temporal and spatial regulation model established in this study provides a basis for the rational genetic engineering of enhanced oil production.

Heat response pathways in plants are regulated by heat stress transcription factors (Hsfs) and perhaps by small interfering RNAs, such as TAS1-derived siRNAs, but the key mediators of these pathways are unclear. This report identified HEAT-INDUCED TAS1 TARGET1 (HTT1) and HTT2, which are targets of TAS1 and are directly activated by HsfA1a, thus mediating thermotolerance pathways.

Heat response pathways in plants are regulated by heat stress transcription factors (Hsfs) and perhaps by small interfering RNAs, such as TAS1-derived siRNAs, but the key mediators of these pathways are unclear. This report identified HEAT-INDUCED TAS1 TARGET1 (HTT1) and HTT2, which are targets of TAS1 and are directly activated by HsfA1a, thus mediating thermotolerance pathways.

This report identifies the rice bHLH protein TIP2 as a key switch for the meristemoid transition and cell differentiation during early anther development. TIP2 directly triggers the expression of the developmental regulators TDR and EAT1 and interacts with TDR, forming a central cascade regulating differentiation, morphogenesis, and degradation of anther somatic cell layers.

The authors combined high-throughput global sequencing targeted to genes and custom-designed bioinformatics tools to catalog and characterize chemically induced mutations in rice and wheat. They demonstrate that this approach can be used to develop large-scale induced mutation resources with relatively small investments and is applicable to resource-limited and polyploid organisms.

This work used single-particle tracking analysis to detect the dynamics of GFP-RbohD in Arabidopsis. GFP-RbohD spots were found to be mobile with high heterogeneity at the plasma membrane and preferentially assembled into clusters when activated. The results also demonstrated that the internalization of GFP-RbohD occurred via multiple endocytic pathways.

Heat response pathways in plants are regulated by heat stress transcription factors (Hsfs) and perhaps by small interfering RNAs, such as TAS1-derived siRNAs, but the key mediators of these pathways are unclear. This report identified HEAT-INDUCED TAS1 TARGET1 (HTT1) and HTT2, which are targets of TAS1 and are directly activated by HsfA1a, thus mediating thermotolerance pathways.