Table of Contents

Many plants must reach a certain age before they will flower in response to environmental cues. Perennial Arabis alpina plants are shown not to respond to vernalization until they are 5 weeks old. This effect is found to require the Aa TFL1 gene, which blocks induction of Aa LFY when young plants are exposed to cold.

This work introduces a bioinformatics approach that identifies positive and negative coordination of gene expression between sets of genes, or entire gene networks, in response to environmental or developmental cues. The approach is illustrated by a case study that identifies distinct expression behavior of the energy-associated gene network in response to different biotic and abiotic stresses.

Two different prediction methods for Arabidopsis proteins carrying peroxisome targeting signals type 1 (PTS1) are described. Validation of many novel targeting signals and Arabidopsis PTS1 proteins by in vivo localization experiments demonstrates a high prediction accuracy of the new methods.

In Arabidopsis, the PHOSPHATE TRANSPORTER1 (PHT1) family encodes the high affinity phosphate transporters. This analysis revealed multiple steps of regulation in various cell compartments modulating the level of PHT1 proteins present in the plasma membrane in response to the level of inorganic phosphate.

This work presents the generation of a predictive model describing the DNA recognition specificity of the LEAFY floral transcription factor. The model is used to predict in vivo regulatory interactions between LEAFY and its target genes from mere inspection of various plant genome sequences.

Two different prediction methods for Arabidopsis proteins carrying peroxisome targeting signals type 1 (PTS1) are described. Validation of many novel targeting signals and Arabidopsis PTS1 proteins by in vivo localization experiments demonstrates a high prediction accuracy of the new methods.

Many plants must reach a certain age before they will flower in response to environmental cues. Perennial Arabis alpina plants are shown not to respond to vernalization until they are 5 weeks old. This effect is found to require the Aa TFL1 gene, which blocks induction of Aa LFY when young plants are exposed to cold.

By means of a combination of experimental and modeling approaches applied to the hyperbranching mutant étoile, cell–cell communication, likely mediated by novel transmembrane proteins that share similarities with metazoan Notch receptors, was shown to account for the establishment of filament patterning and cell differentiation in the filamentous brown alga Ectocarpus siliculosus.

Because of their sessile lifestyle, plants need to react promptly to factors that affect meristem integrity. This work shows that the WEE1 checkpoint kinase maintains the root meristem activity under replication stress by controlling S-phase progression, thereby preventing premature onset of vascular cell differentiation.

This study examines the role of the PHYTOCHROME INTERACTING FACTOR3 homolog SPATULA (SPT) in the control of the developing seedling and shows that SPT is a potent regulator of cotyledon size, acting in parallel to DELLAs. As DELLAs negatively regulate SPT abundance, the light regulation of DELLAs drives the DELLA-SPT counterbalance, enforcing growth restraint across a range of ambient light conditions that are prevalent in nature.

RNA-seq assessment of the transcriptome of autotrophic and heterotrophic Chlamydomonas as a function of copper nutrition reveals changes in redox metabolism regulated by CRR1, an SBP domain transcription factor. The changes in RNA abundance impact the abundance of specific plastid-localized proteins and the level of saturation of plastid galactolipids.

RNA-seq assessment of the transcriptome of autotrophic and heterotrophic Chlamydomonas as a function of copper nutrition reveals changes in redox metabolism regulated by CRR1, an SBP domain transcription factor. The changes in RNA abundance impact the abundance of specific plastid-localized proteins and the level of saturation of plastid galactolipids.

This study examines the role of API5, a homolog of animal antiapoptosis proteins, in the degeneration of the tapetum during the formation of male gametophytes in rice. It describes a previously unknown pathway for regulating programmed cell death, one that may be conserved among eukaryotic organisms.

WRKY33 functions downstream of pathogen-responsive MPK3 and MPK6 in reprogramming the expression of camalexin biosynthetic genes; this drives the metabolic flow to camalexin production in Arabidopsis challenged by pathogens. Biochemical and genetic analyses demonstrate that the phosphorylation of WRKY33 by MPK3/MPK6 plays an important role in the process.

HMG-CoA reductase has a key role in the regulation of the mevalonate pathway for isoprenoid biosynthesis and is modulated by many diverse endogenous and environmental stimuli. In this work, protein phosphatase 2A emerges as a positive and negative multilevel regulator of plant HMG-CoA reductase during normal development and in response to a variety of stress conditions.

RNA-seq assessment of the transcriptome of autotrophic and heterotrophic Chlamydomonas as a function of copper nutrition reveals changes in redox metabolism regulated by CRR1, an SBP domain transcription factor. The changes in RNA abundance impact the abundance of specific plastid-localized proteins and the level of saturation of plastid galactolipids.

Many plants must reach a certain age before they will flower in response to environmental cues. Perennial Arabis alpina plants are shown not to respond to vernalization until they are 5 weeks old. This effect is found to require the Aa TFL1 gene, which blocks induction of Aa LFY when young plants are exposed to cold.

This work shows that in the phytopathogenic fungus Ustilago maydis, the genetic pathway involved in the transmission of signals required for the response to DNA damage is also used to control the specific dikaryotic cell cycle that predominates proliferation in planta.

This work identifies MATE2, which transports glycosylated flavonoids into the vacuole, showing higher transport efficiency with anthocyanins than other flavonoid glycosides, and an increase in transport efficiency for malonylated flavonoid glucosides. Null mutants of MATE2 show decreases of anthocyanins and increases in other flavonoids, such as seed proanthocyanidin.

This work reveals that anthocyanin biosynthesis is coupled to floral transition by miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes. SPL negatively regulates anthocyanin accumulation by directly preventing expression of anthocyanin biosynthetic genes through destabilization of a MYB-bHLH-WD40 transcriptional activation complex.

HMG-CoA reductase has a key role in the regulation of the mevalonate pathway for isoprenoid biosynthesis and is modulated by many diverse endogenous and environmental stimuli. In this work, protein phosphatase 2A emerges as a positive and negative multilevel regulator of plant HMG-CoA reductase during normal development and in response to a variety of stress conditions.

This study examines the role of the PHYTOCHROME INTERACTING FACTOR3 homolog SPATULA (SPT) in the control of the developing seedling and shows that SPT is a potent regulator of cotyledon size, acting in parallel to DELLAs. As DELLAs negatively regulate SPT abundance, the light regulation of DELLAs drives the DELLA-SPT counterbalance, enforcing growth restraint across a range of ambient light conditions that are prevalent in nature.

This work identifies cooperative action of ARGONAUTE1 and ARGONAUTE2 in virus resistance conferred by 21-nucleotide virus-derived small interfering RNAs (siRNAs). It also reveals that 22-nucleotide viral siRNAs do not guide efficient antiviral defense, demonstrating a qualitative difference between 21- and 22-nucleotide classes of siRNAs in RNA silencing.

In Arabidopsis, the PHOSPHATE TRANSPORTER1 (PHT1) family encodes the high affinity phosphate transporters. This analysis revealed multiple steps of regulation in various cell compartments modulating the level of PHT1 proteins present in the plasma membrane in response to the level of inorganic phosphate.

This study identifies APEM9 as an essential factor for peroxisomal protein transport in plants. APEM9 proteins have unique amino acid sequences, which are distinct from that of Pex26 functional homologs in mammals.

This study examines the role of the PHYTOCHROME INTERACTING FACTOR3 homolog SPATULA (SPT) in the control of the developing seedling and shows that SPT is a potent regulator of cotyledon size, acting in parallel to DELLAs. As DELLAs negatively regulate SPT abundance, the light regulation of DELLAs drives the DELLA-SPT counterbalance, enforcing growth restraint across a range of ambient light conditions that are prevalent in nature.

This work reveals the significant roles of myo-inositol in Arabidopsis embryogenesis. Experiments show that depletion of myo-inositol by knocking out multiple MIPS genes, which encode d-myo-inositol-3-phosphate synthase, could affect the membrane trafficking via the phosphatidylinositol metabolism by leading to altered auxin distribution in developing embryos.

In this study, the authors find that the expansion of the xylem in Arabidopsis hypocotyls observed upon flowering is directly triggered by signaling through the plant hormone gibberellin. The authors also demonstrate that this involves mobile gibberellin, which therefore can act as a long-distance signal.

This work identifies MATE2, which transports glycosylated flavonoids into the vacuole, showing higher transport efficiency with anthocyanins than other flavonoid glycosides, and an increase in transport efficiency for malonylated flavonoid glucosides. Null mutants of MATE2 show decreases of anthocyanins and increases in other flavonoids, such as seed proanthocyanidin.

Incorporation of arabinose into plant cell wall polysaccharides requires conversion into the furanose form. This conversion is mediated exclusively by UDP-arabinose mutases (RGPs) located in the cytoplasm.

This work shows that in the phytopathogenic fungus Ustilago maydis, the genetic pathway involved in the transmission of signals required for the response to DNA damage is also used to control the specific dikaryotic cell cycle that predominates proliferation in planta.

RNA-seq assessment of the transcriptome of autotrophic and heterotrophic Chlamydomonas as a function of copper nutrition reveals changes in redox metabolism regulated by CRR1, an SBP domain transcription factor. The changes in RNA abundance impact the abundance of specific plastid-localized proteins and the level of saturation of plastid galactolipids.

Incorporation of arabinose into plant cell wall polysaccharides requires conversion into the furanose form. This conversion is mediated exclusively by UDP-arabinose mutases (RGPs) located in the cytoplasm.

The rapidly reversible macrostructural changes in higher-plant chloroplast thylakoid membrane organization accompanying photoprotective energy dissipation (qE) are studied using freeze-fracture electron and laser confocal microscopy. qE is shown to involve the aggregation of light-harvesting complexes and their segregation from photosystem II.

Two different prediction methods for Arabidopsis proteins carrying peroxisome targeting signals type 1 (PTS1) are described. Validation of many novel targeting signals and Arabidopsis PTS1 proteins by in vivo localization experiments demonstrates a high prediction accuracy of the new methods.

This study uses in vivo targeting, subcellular fractionation, and bioinformatics approaches to investigate the signal sequences that determine whether signal-anchored proteins are targeted to the endoplasmic reticulum or to endosymbiotic organelles.

This study uses in vivo targeting, subcellular fractionation, and bioinformatics approaches to investigate the signal sequences that determine whether signal-anchored proteins are targeted to the endoplasmic reticulum or to endosymbiotic organelles.

We show that GUN4-porphyrin complexes help to channel protoporphyrin IX into chlorophyll biosynthesis by binding to the ChlH subunit of Mg-chelatase with a higher affinity than unliganded GUN4 on Arabidopsis chloroplast membranes. GUN4 and ChlH used distinct mechanisms to associate with chloroplast membranes, and mutant alleles of GUN4 and Mg-chelatase subunit genes cause sensitivity to intense light.

By means of a combination of experimental and modeling approaches applied to the hyperbranching mutant étoile, cell–cell communication, likely mediated by novel transmembrane proteins that share similarities with metazoan Notch receptors, was shown to account for the establishment of filament patterning and cell differentiation in the filamentous brown alga Ectocarpus siliculosus.

This study uses in vivo targeting, subcellular fractionation, and bioinformatics approaches to investigate the signal sequences that determine whether signal-anchored proteins are targeted to the endoplasmic reticulum or to endosymbiotic organelles.

This study uses in vivo targeting, subcellular fractionation, and bioinformatics approaches to investigate the signal sequences that determine whether signal-anchored proteins are targeted to the endoplasmic reticulum or to endosymbiotic organelles.

By means of a combination of experimental and modeling approaches applied to the hyperbranching mutant étoile, cell–cell communication, likely mediated by novel transmembrane proteins that share similarities with metazoan Notch receptors, was shown to account for the establishment of filament patterning and cell differentiation in the filamentous brown alga Ectocarpus siliculosus.

This work identifies cooperative action of ARGONAUTE1 and ARGONAUTE2 in virus resistance conferred by 21-nucleotide virus-derived small interfering RNAs (siRNAs). It also reveals that 22-nucleotide viral siRNAs do not guide efficient antiviral defense, demonstrating a qualitative difference between 21- and 22-nucleotide classes of siRNAs in RNA silencing.

This study examines the role of API5, a homolog of animal antiapoptosis proteins, in the degeneration of the tapetum during the formation of male gametophytes in rice. It describes a previously unknown pathway for regulating programmed cell death, one that may be conserved among eukaryotic organisms.

This study examines the regulation of SOMNUS (SOM), which is a key negative regulator of seed germination. ABI3 was found to regulate SOM expression together with PIL5, a previously identified regulator of SOM. PIL5 and ABI3, which interact to form a complex, regulate SOM expression independently in maturing seeds, but collaboratively in imbibed seeds.

This work reveals that anthocyanin biosynthesis is coupled to floral transition by miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes. SPL negatively regulates anthocyanin accumulation by directly preventing expression of anthocyanin biosynthetic genes through destabilization of a MYB-bHLH-WD40 transcriptional activation complex.

This work reveals the significant roles of myo-inositol in Arabidopsis embryogenesis. Experiments show that depletion of myo-inositol by knocking out multiple MIPS genes, which encode d-myo-inositol-3-phosphate synthase, could affect the membrane trafficking via the phosphatidylinositol metabolism by leading to altered auxin distribution in developing embryos.

RNA-seq assessment of the transcriptome of autotrophic and heterotrophic Chlamydomonas as a function of copper nutrition reveals changes in redox metabolism regulated by CRR1, an SBP domain transcription factor. The changes in RNA abundance impact the abundance of specific plastid-localized proteins and the level of saturation of plastid galactolipids.

Two proteins similar to β-amylases (enzymes usually associated with starch breakdown) possess a BZR1-type DNA binding domain and are nuclear localized. They bind a G box-containing motif and regulate the expression of genes, many of which also respond to brassinosteroids, to influence shoot growth. Similar proteins occur in other plants, implying functional conservation.

This study identifies APEM9 as an essential factor for peroxisomal protein transport in plants. APEM9 proteins have unique amino acid sequences, which are distinct from that of Pex26 functional homologs in mammals.