Table of Contents

Reconstruction of the grass genome paleohistory revealed subgenome partitioning of microRNA (miRNA) genes during post-whole-genome duplication diploidization. The evolutionary scenario of miRNAs from the ancestral founder pool to the modern complements displayed dosage balance constrictions on the deletion/retention of miRNAs and associated target genes wherein transposable elements may play a major role in miRNA gene synteny disruption.

Arabidopsis cells expressing either the FLS2 ortholog from Arabidopsis or tomato specifically respond to picomolar concentrations of the flg22 ligand. However, these orthologs exhibit characteristic differences when challenged with flg22 variants. Hybrid forms made from both orthologs allowed attribution of these differences to distinct subsets within the 28 Leucine-rich repeats of their ectodomains.

The genome sequence of Ustilago hordei revealed that transposable elements were involved in restructuring of the genome, which affected fungal reproductive biology and evolution of genes encoding effector proteins. Comparison to other smuts indicated loss of genome defense components in Ustilago maydis and control of repetitive sequences by repeat-induced point mutation in U. hordei.

This work reveals that Flot1 functions in Arabidopsis thaliana seedling development and is involved in a membrane microdomain-dependent, but clathrin-independent, endocytic pathway. Moreover, the dynamic behavior of Flot1-positive puncta differs considerably from that of clathrin light chain–positive puncta.

This research identifies a previously unknown clade of plant-specific proteins whose founding member is shown to facilitate meiotically heritable trans-homologue repression in maize. The findings highlight a diversification of epigenomic control mechanisms in higher plants.

This study reports the isolation of hsr3, an allele of the Arabidopsis ARPC2 locus encoding a subunit of the ARP2/3 complex involved in the regulation of the actin cytoskeleton. In hsr3, reduced abscisic acid–induced stomatal closure is associated with failure of actin reassembly, indicating that modulation of the cytoskeleton through the ARP2/3 complex is crucial for stomatal regulation.

Arabidopsis cells expressing either the FLS2 ortholog from Arabidopsis or tomato specifically respond to picomolar concentrations of the flg22 ligand. However, these orthologs exhibit characteristic differences when challenged with flg22 variants. Hybrid forms made from both orthologs allowed attribution of these differences to distinct subsets within the 28 Leucine-rich repeats of their ectodomains.

This work presents evidence for a novel abscisic acid production pathway involving At-BG2, a β-glucosidase, in the vacuole. This result suggests that abscisic acid is produced in multiple places by multiple pathways in response to abiotic stress.

This work shows that the flv4-flv2 operon provides many β-cyanobacteria with a so far unknown photoprotection mechanism that evolved in parallel with oxygen-evolving photosystem II

This study identifies FHY3 and FAR1 as positive regulators directly affecting chlorophyll biosynthesis through the activation of HEMB1. It shows that FHY3 protein physically interacts with PIF1, a negative regulator in the pathway, and they work coordinately to modulate the plant greening process.

When young plants emerge from the soil or canopy into direct sunlight, they must rapidly adapt to the new light environment containing a higher ratio of red/far-red light. This work reveals the molecular mechanism of how the photoreceptor phyA differentially transduces red and far-red light signals to light-responsive genes for better plant survival in natural environments.

When young plants emerge from the soil or canopy into direct sunlight, they must rapidly adapt to the new light environment containing a higher ratio of red/far-red light. This work reveals the molecular mechanism of how the photoreceptor phyA differentially transduces red and far-red light signals to light-responsive genes for better plant survival in natural environments.

This work reveals that Flot1 functions in Arabidopsis thaliana seedling development and is involved in a membrane microdomain-dependent, but clathrin-independent, endocytic pathway. Moreover, the dynamic behavior of Flot1-positive puncta differs considerably from that of clathrin light chain–positive puncta.

Arabidopsis cells expressing either the FLS2 ortholog from Arabidopsis or tomato specifically respond to picomolar concentrations of the flg22 ligand. However, these orthologs exhibit characteristic differences when challenged with flg22 variants. Hybrid forms made from both orthologs allowed attribution of these differences to distinct subsets within the 28 Leucine-rich repeats of their ectodomains.

This work describes biochemical, biophysical, structural, and genetic analyses of an Arabidopsis homolog of mammalian NEET proteins, which are involved in a wide range of cellular processes. It finds that At-NEET plays a key role in plant development, senescence, reactive oxygen species homeostasis, and iron metabolism.

The quantum yield for CO₂ fixation is wavelength dependent due to (1) light absorption by nonphotosynthetic pigments, (2) inefficient energy transfer, and (3) the excitation balance between the two photosystems. The growth-light spectrum alters the excitation balance by altering the photosystem composition, as shown both in vivo and in vitro. Enhancement effects can increase the quantum yield.

When young plants emerge from the soil or canopy into direct sunlight, they must rapidly adapt to the new light environment containing a higher ratio of red/far-red light. This work reveals the molecular mechanism of how the photoreceptor phyA differentially transduces red and far-red light signals to light-responsive genes for better plant survival in natural environments.

This study identifies a regulatory oxidative pathway, comprised of thioredoxin and peroxiredoxin, in Arabidopsis thaliana chloroplasts. It shows that the pathway is used to sense photosynthetic peroxide formation under low to moderate light intensity and proposes that the oxidative signal adjusts the photosynthetic linear electron flow to fluctuating environmental conditions.

This study reports the isolation of hsr3, an allele of the Arabidopsis ARPC2 locus encoding a subunit of the ARP2/3 complex involved in the regulation of the actin cytoskeleton. In hsr3, reduced abscisic acid–induced stomatal closure is associated with failure of actin reassembly, indicating that modulation of the cytoskeleton through the ARP2/3 complex is crucial for stomatal regulation.

Plants produce hydrogen peroxide (H₂O₂) as a stress signal. This study shows that H₂O₂ promotes the binding of cytosolic, glycolytic enzymes, GAPCs, to the plasma membrane–associated phospholipase PLDδ. The GAPC–PLDδ interaction mediates the plant response to H₂O₂ and provides a molecular link between stress signaling and the alteration of cellular metabolism and growth in the plant response to drought.

Mitogen-activated protein kinase kinase kinase MEKK2 functions as a positive regulator of plant immunity mediated by the nucleotide binding–Leu-rich repeat Resistance protein SUMM2. MEKK2 interacts with MPK4 and is negatively regulated by the MEKK1-MKK1/MKK2-MPK4 kinase cascade.

Mitogen-activated protein kinase kinase kinase MEKK2 functions as a positive regulator of plant immunity mediated by the nucleotide binding–Leu-rich repeat Resistance protein SUMM2. MEKK2 interacts with MPK4 and is negatively regulated by the MEKK1-MKK1/MKK2-MPK4 kinase cascade.

This work examines the role of CYC2 clade genes in floral asymmetry in Primulina heterotricha, finding that CYC1C and CYC1D positively auto- and cross-regulate both themselves and each other in a double positive autoregulatory feedback loop, a regulatory mechanism that may be conserved in other clades with zygomorphic flowers.

Using powerful tools to investigate the regulation of global gene expression in the model microalga Chlamydomonas reinhardtii, we observed an impact of CO₂ and CIA5, a key transcription regulator, on expression of almost 25% of all the genes. We also discovered an array of gene clusters with distinctive expression patterns that provide insight into the regulatory interaction between CIA5 and CO₂.

An Arabidopsis thaliana abscisic acid (ABA) overly sensitive mutant, abo6, was identified, and ABO6 was found to encode a DEXH box RNA helicase that regulates the splicing of genes of complex I in mitochondria. ABA and auxin signaling are shown to regulate primary root growth and seed germination via reactive oxygen species produced in mitochondria.

This work describes biochemical, biophysical, structural, and genetic analyses of an Arabidopsis homolog of mammalian NEET proteins, which are involved in a wide range of cellular processes. It finds that At-NEET plays a key role in plant development, senescence, reactive oxygen species homeostasis, and iron metabolism.

This article presents a method to screen a plant cDNA library for genes encoding proteins that interact with a bait protein directly in plants using bimolecular fluorescence complementation technology. Proof-of-concept experiments identified both known and novel Arabidopsis thaliana proteins important for Agrobacterium-mediated plant transformation.

This work reveals that Flot1 functions in Arabidopsis thaliana seedling development and is involved in a membrane microdomain-dependent, but clathrin-independent, endocytic pathway. Moreover, the dynamic behavior of Flot1-positive puncta differs considerably from that of clathrin light chain–positive puncta.

A Golgi-localized polytopic integral membrane protein, EMP12, was shown to contain an endoplasmic reticulum export signal (FVY) and a Golgi retention signal (KXE/D) that interact with COPII and COPI subunits, respectively, in Arabidopsis cells. These sorting signals are highly conserved in all plant EMP isoforms and, thus, likely represent a general mechanism for EMP targeting in plant cells.

This work examines the role of CYC2 clade genes in floral asymmetry in Primulina heterotricha, finding that CYC1C and CYC1D positively auto- and cross-regulate both themselves and each other in a double positive autoregulatory feedback loop, a regulatory mechanism that may be conserved in other clades with zygomorphic flowers.

The genome sequence of Ustilago hordei revealed that transposable elements were involved in restructuring of the genome, which affected fungal reproductive biology and evolution of genes encoding effector proteins. Comparison to other smuts indicated loss of genome defense components in Ustilago maydis and control of repetitive sequences by repeat-induced point mutation in U. hordei.

The quantum yield for CO₂ fixation is wavelength dependent due to (1) light absorption by nonphotosynthetic pigments, (2) inefficient energy transfer, and (3) the excitation balance between the two photosystems. The growth-light spectrum alters the excitation balance by altering the photosystem composition, as shown both in vivo and in vitro. Enhancement effects can increase the quantum yield.

Group A saponins in soybean are diversified compounds belonging to a group of triterpene saponins and are causal components for bitterness and astringent aftertastes of soy products. This work describes the identification of Sg-1, a UDP-sugar–dependent glycosyltransferase gene that is responsible for the unpleasant tastes due to allelic variation regulating the terminal sugar species in group A saponins.

This study reports the isolation of hsr3, an allele of the Arabidopsis ARPC2 locus encoding a subunit of the ARP2/3 complex involved in the regulation of the actin cytoskeleton. In hsr3, reduced abscisic acid–induced stomatal closure is associated with failure of actin reassembly, indicating that modulation of the cytoskeleton through the ARP2/3 complex is crucial for stomatal regulation.

MAP65-3 contains a distinct C-terminal microtubule binding site that is not shared by other Arabidopsis MAP-65 proteins. This study demonstrates that this C-terminal extension determines the protein’s specific function in cross-linking antiparallel microtubules in the phragmoplast midzone.

This research identifies a previously unknown clade of plant-specific proteins whose founding member is shown to facilitate meiotically heritable trans-homologue repression in maize. The findings highlight a diversification of epigenomic control mechanisms in higher plants.

Group A saponins in soybean are diversified compounds belonging to a group of triterpene saponins and are causal components for bitterness and astringent aftertastes of soy products. This work describes the identification of Sg-1, a UDP-sugar–dependent glycosyltransferase gene that is responsible for the unpleasant tastes due to allelic variation regulating the terminal sugar species in group A saponins.

An Arabidopsis thaliana abscisic acid (ABA) overly sensitive mutant, abo6, was identified, and ABO6 was found to encode a DEXH box RNA helicase that regulates the splicing of genes of complex I in mitochondria. ABA and auxin signaling are shown to regulate primary root growth and seed germination via reactive oxygen species produced in mitochondria.

Predicting the system response to the invading pathogen, dynamic modeling of hormone disease networks explores the effect of cytokinin on immune defense. Together with validation experiments on disease phenotypes and monitoring hormonal responses and gene expression data, this work identified synergistic crosstalk for cytokinin and antagonism between auxin and cytokinin regarding immunity.

This work describes biochemical, biophysical, structural, and genetic analyses of an Arabidopsis homolog of mammalian NEET proteins, which are involved in a wide range of cellular processes. It finds that At-NEET plays a key role in plant development, senescence, reactive oxygen species homeostasis, and iron metabolism.

This study identifies FHY3 and FAR1 as positive regulators directly affecting chlorophyll biosynthesis through the activation of HEMB1. It shows that FHY3 protein physically interacts with PIF1, a negative regulator in the pathway, and they work coordinately to modulate the plant greening process.

A Golgi-localized polytopic integral membrane protein, EMP12, was shown to contain an endoplasmic reticulum export signal (FVY) and a Golgi retention signal (KXE/D) that interact with COPII and COPI subunits, respectively, in Arabidopsis cells. These sorting signals are highly conserved in all plant EMP isoforms and, thus, likely represent a general mechanism for EMP targeting in plant cells.

Biochemical and genetic characterization of two petunia CoA ligases reveals that subcellular compartmentalization of enzymes determines their involvement in the benzenoid metabolic network. Additional evidence shows that formation of cinnamoyl-CoA in peroxisomes is the committed step in the synthesis of benzoyl-CoA via the β-oxidative pathway.

This study shows that the vegetative class of plant actins and the cytoplasmic class of animal actins share conserved functions that were inherited from an ancestral protist actin sequence. Thus, some single-celled protists contain actin that can perform the complex processes required for multicellular development.

Group A saponins in soybean are diversified compounds belonging to a group of triterpene saponins and are causal components for bitterness and astringent aftertastes of soy products. This work describes the identification of Sg-1, a UDP-sugar–dependent glycosyltransferase gene that is responsible for the unpleasant tastes due to allelic variation regulating the terminal sugar species in group A saponins.

This research identifies a previously unknown clade of plant-specific proteins whose founding member is shown to facilitate meiotically heritable trans-homologue repression in maize. The findings highlight a diversification of epigenomic control mechanisms in higher plants.

Group A saponins in soybean are diversified compounds belonging to a group of triterpene saponins and are causal components for bitterness and astringent aftertastes of soy products. This work describes the identification of Sg-1, a UDP-sugar–dependent glycosyltransferase gene that is responsible for the unpleasant tastes due to allelic variation regulating the terminal sugar species in group A saponins.

This work presents evidence for a novel abscisic acid production pathway involving At-BG2, a β-glucosidase, in the vacuole. This result suggests that abscisic acid is produced in multiple places by multiple pathways in response to abiotic stress.

This article provides information about the interaction between the phycobilisomes and the Orange Carotenoid Protein needed for photoprotection. Its red light–activated form has an open structure that allows the interaction of its N-terminal domain, containing the Arg155, with the phycobilisome, permitting a closer interaction between the carotenoid and the phycobilisome chromophores.

MAP65-3 contains a distinct C-terminal microtubule binding site that is not shared by other Arabidopsis MAP-65 proteins. This study demonstrates that this C-terminal extension determines the protein’s specific function in cross-linking antiparallel microtubules in the phragmoplast midzone.

This work examines the reproductive phase transition in rice using laser microdissection and microarrays in addition to biochemical and genetic approaches. The results support that PAP2, a MADS box gene belonging to a grass-specific subclade of the SEP subfamily, and three AP1/FUL-like genes coordinately act in the meristem to specify the identity of the inflorescence meristem downstream of the florigen signal.

This article presents evidence, obtained in Arabidopsis thaliana, that two central DNA repair proteins, the recombinases DMC1 and RAD51, are spatially and functionally separated, respectively, during meiotic DNA repair and shows that a well-known DNA damage response factor, the ATR kinase, is involved in regulating DMC1 deposition.