Table of Contents

This study provides evidence that two laccases, LAC4 and LAC17, participate in the polymerization of lignins in Arabidopsis stems. These findings suggest that the genetic engineering of lignin-specific laccases is a potentially innovative and promising tool for the fine-tuning of lignin content and structure.

Plants synthesize the growth hormone indole-3-acetic acid using a variety of incompletely understood pathways. This work demonstrates that the conversion of indole-3-butyric acid to indole-3-acetic acid contributes to wide-ranging auxin-regulated processes in Arabidopsis seedlings and that shutting off this auxin supply renders seedlings less able to respond to exogenous auxin.

Sphingolipids are a diverse group of essential membrane lipids thought to play important roles in both membrane function and cellular signaling. By identifying an Arabidopsis thaliana mutant lacking 3-ketodihydrosphinganine reductase, a critical enzyme in sphingolipid biosynthesis, this work uncovers a connection between sphingolipid metabolism in roots and whole-plant mineral ion homeostasis.

This study shows that geminivirus C2/L2 protein interferes with the derubylation of CUL1. Responses regulated by the CUL1-based SCF ubiquitin ligases, and particularly the response to jasmonates, are altered in transgenic Arabidopsis thaliana expressing C2/L2. The capability to selectively interfere with SCF complexes may define a novel and powerful strategy in viral infections.

Patatin-related phospholipase pPLAIIIβ lacks the canonical esterase catalytic center but possesses acyl-hydrolyzing and acyl-CoA thioesterase activities. Knockout and overexpression of pPLAIIIβ have opposite effects on the levels of membrane lipids, cellulose content, mechanical strength, and cell length. Thus, membrane lipid metabolism may be linked to cellulose production in Arabidopsis.

This study provides evidence that two laccases, LAC4 and LAC17, participate in the polymerization of lignins in Arabidopsis stems. These findings suggest that the genetic engineering of lignin-specific laccases is a potentially innovative and promising tool for the fine-tuning of lignin content and structure.

This study provides evidence that two laccases, LAC4 and LAC17, participate in the polymerization of lignins in Arabidopsis stems. These findings suggest that the genetic engineering of lignin-specific laccases is a potentially innovative and promising tool for the fine-tuning of lignin content and structure.

This work presents a high-resolution time-course analysis of gene expression during development of a leaf from expansion through senescence. Enrichment in ontologies, sequence motifs, and transcription factor families within genes showing altered expression over time identified both metabolic pathways and potential regulators active at different stages of leaf development and senescence.

This study defines a previously unknown combinatorial interaction between transcription factors in plants and provides a better understanding of how plants integrate signals to regulate petal development. It also highlights the role of a motif in the bHLH transcription factor that resembles a motif that was previously shown to be important in auxin signaling.

This study demonstrates that the tomato APETALA2a (AP2a) transcription factor modulates fruit ripening by negatively regulating ethylene biosynthesis and signaling. Various ripening regulators are shown to act upstream of AP2a. Gene expression analysis reveals that AP2a is involved in chloroplast to chromoplast transition.

Genes that are similarly expressed, or coexpressed, are often involved in related biological processes. Such coexpressed relationships also appear to be conserved across species. The PlaNet platform enables comparative analysis of genome-wide coexpression networks across seven plant species, thus enabling prediction of gene function and elucidation of the identity of functional homologs.

Sphingolipids are a diverse group of essential membrane lipids thought to play important roles in both membrane function and cellular signaling. By identifying an Arabidopsis thaliana mutant lacking 3-ketodihydrosphinganine reductase, a critical enzyme in sphingolipid biosynthesis, this work uncovers a connection between sphingolipid metabolism in roots and whole-plant mineral ion homeostasis.

Protein–protein interactions are important mechanisms for genes and gene networks to function. This study demonstrates that, although the PAIR database has limited coverage, representing ~24% of the entire interactome with ~40% precision, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes.

A plant-specific molecular motor (KP1) specifically interacts with a channel protein (VDAC3) of the mitochondrial outer membrane and is targeted to mitochondria via its tail domain. In seedlings germinated at 4°C, either mutant of the two genes exhibited increased oxygen consumption, respiration imbalance, and reduced ATP levels.

Plants synthesize the growth hormone indole-3-acetic acid using a variety of incompletely understood pathways. This work demonstrates that the conversion of indole-3-butyric acid to indole-3-acetic acid contributes to wide-ranging auxin-regulated processes in Arabidopsis seedlings and that shutting off this auxin supply renders seedlings less able to respond to exogenous auxin.

The transition from vegetative to reproductive development is regulated by the activity of graft-transmissible flowering hormone, florigen, which is encoded by the FLOWERING LOCUS T (FT) family of mobile proteins. This work identified, among many maize FT-like genes, a single gene, ZCN8, which has all required characteristics to function as florigen.

This work presents a high-resolution time-course analysis of gene expression during development of a leaf from expansion through senescence. Enrichment in ontologies, sequence motifs, and transcription factor families within genes showing altered expression over time identified both metabolic pathways and potential regulators active at different stages of leaf development and senescence.

We report that the chromatin remodeling factor PICKLE and Polycomb group proteins antagonistically determine cell identity. Our study highlights an important role of PICKLE and Polycomb group proteins in regulating root meristem activity by regulating the expression of root stem cell and meristem marker genes.

Sphingolipids are a diverse group of essential membrane lipids thought to play important roles in both membrane function and cellular signaling. By identifying an Arabidopsis thaliana mutant lacking 3-ketodihydrosphinganine reductase, a critical enzyme in sphingolipid biosynthesis, this work uncovers a connection between sphingolipid metabolism in roots and whole-plant mineral ion homeostasis.

This study demonstrates that the tomato APETALA2a (AP2a) transcription factor modulates fruit ripening by negatively regulating ethylene biosynthesis and signaling. Various ripening regulators are shown to act upstream of AP2a. Gene expression analysis reveals that AP2a is involved in chloroplast to chromoplast transition.

Genes that are similarly expressed, or coexpressed, are often involved in related biological processes. Such coexpressed relationships also appear to be conserved across species. The PlaNet platform enables comparative analysis of genome-wide coexpression networks across seven plant species, thus enabling prediction of gene function and elucidation of the identity of functional homologs.

Based on their evolutionary origin, MADS box transcription factor genes have been divided into two classes, namely, type I and II. The plant-specific type II MIKC MADS box genes have been most intensively studied and shown to be key regulators of developmental processes, such as meristem identity, flowering time, and fruit and seed development. By contrast, very little is known about type I MADS domain transcription factors, and they have not attracted interest for a long time. A number of recent studies have now indicated a key regulatory role for type I MADS box factors in plant reproduction, in particular in specifying female gametophyte, embryo, and endosperm development. These analyses have also suggested that type I MADS box factors are decisive for setting reproductive boundaries between species.

Patatin-related phospholipase pPLAIIIβ lacks the canonical esterase catalytic center but possesses acyl-hydrolyzing and acyl-CoA thioesterase activities. Knockout and overexpression of pPLAIIIβ have opposite effects on the levels of membrane lipids, cellulose content, mechanical strength, and cell length. Thus, membrane lipid metabolism may be linked to cellulose production in Arabidopsis.

Sphingolipids are a diverse group of essential membrane lipids thought to play important roles in both membrane function and cellular signaling. By identifying an Arabidopsis thaliana mutant lacking 3-ketodihydrosphinganine reductase, a critical enzyme in sphingolipid biosynthesis, this work uncovers a connection between sphingolipid metabolism in roots and whole-plant mineral ion homeostasis.

This work shows that the Arabidopsis transcription factor BROTHER OF LUX ARRHYTHMO (BOA) is an activator in regulating the expression of CIRCADIAN CLOCK ASSOCIATED1 (CCA1). BOA forms a transcriptional feedback loop with CCA1 and regulates circadian rhythms in Arabidopsis.

This work presents a high-resolution time-course analysis of gene expression during development of a leaf from expansion through senescence. Enrichment in ontologies, sequence motifs, and transcription factor families within genes showing altered expression over time identified both metabolic pathways and potential regulators active at different stages of leaf development and senescence.

Sphingolipids are a diverse group of essential membrane lipids thought to play important roles in both membrane function and cellular signaling. By identifying an Arabidopsis thaliana mutant lacking 3-ketodihydrosphinganine reductase, a critical enzyme in sphingolipid biosynthesis, this work uncovers a connection between sphingolipid metabolism in roots and whole-plant mineral ion homeostasis.

This work presents a high-resolution time-course analysis of gene expression during development of a leaf from expansion through senescence. Enrichment in ontologies, sequence motifs, and transcription factor families within genes showing altered expression over time identified both metabolic pathways and potential regulators active at different stages of leaf development and senescence.

Based on their evolutionary origin, MADS box transcription factor genes have been divided into two classes, namely, type I and II. The plant-specific type II MIKC MADS box genes have been most intensively studied and shown to be key regulators of developmental processes, such as meristem identity, flowering time, and fruit and seed development. By contrast, very little is known about type I MADS domain transcription factors, and they have not attracted interest for a long time. A number of recent studies have now indicated a key regulatory role for type I MADS box factors in plant reproduction, in particular in specifying female gametophyte, embryo, and endosperm development. These analyses have also suggested that type I MADS box factors are decisive for setting reproductive boundaries between species.

This work presents a high-resolution time-course analysis of gene expression during development of a leaf from expansion through senescence. Enrichment in ontologies, sequence motifs, and transcription factor families within genes showing altered expression over time identified both metabolic pathways and potential regulators active at different stages of leaf development and senescence.

Genes that are similarly expressed, or coexpressed, are often involved in related biological processes. Such coexpressed relationships also appear to be conserved across species. The PlaNet platform enables comparative analysis of genome-wide coexpression networks across seven plant species, thus enabling prediction of gene function and elucidation of the identity of functional homologs.

This study provides evidence that two laccases, LAC4 and LAC17, participate in the polymerization of lignins in Arabidopsis stems. These findings suggest that the genetic engineering of lignin-specific laccases is a potentially innovative and promising tool for the fine-tuning of lignin content and structure.

This work provides evidence that deposition of cuticular waxes is intimately associated with plant responses to drought. The Arabidopsis MYB96 transcription factor functions as a regulator of ABA-mediated cuticular wax biosynthesis under drought conditions by binding directly to the promoters of genes encoding very-long-chain fatty acid–condensing enzymes involved in cuticular wax biosynthesis.

This study defines a previously unknown combinatorial interaction between transcription factors in plants and provides a better understanding of how plants integrate signals to regulate petal development. It also highlights the role of a motif in the bHLH transcription factor that resembles a motif that was previously shown to be important in auxin signaling.

Protein–protein interactions are important mechanisms for genes and gene networks to function. This study demonstrates that, although the PAIR database has limited coverage, representing ~24% of the entire interactome with ~40% precision, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes.

This work shows that the Arabidopsis transcription factor BROTHER OF LUX ARRHYTHMO (BOA) is an activator in regulating the expression of CIRCADIAN CLOCK ASSOCIATED1 (CCA1). BOA forms a transcriptional feedback loop with CCA1 and regulates circadian rhythms in Arabidopsis.

This study shows that geminivirus C2/L2 protein interferes with the derubylation of CUL1. Responses regulated by the CUL1-based SCF ubiquitin ligases, and particularly the response to jasmonates, are altered in transgenic Arabidopsis thaliana expressing C2/L2. The capability to selectively interfere with SCF complexes may define a novel and powerful strategy in viral infections.

Protein–protein interactions are important mechanisms for genes and gene networks to function. This study demonstrates that, although the PAIR database has limited coverage, representing ~24% of the entire interactome with ~40% precision, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes.

Based on their evolutionary origin, MADS box transcription factor genes have been divided into two classes, namely, type I and II. The plant-specific type II MIKC MADS box genes have been most intensively studied and shown to be key regulators of developmental processes, such as meristem identity, flowering time, and fruit and seed development. By contrast, very little is known about type I MADS domain transcription factors, and they have not attracted interest for a long time. A number of recent studies have now indicated a key regulatory role for type I MADS box factors in plant reproduction, in particular in specifying female gametophyte, embryo, and endosperm development. These analyses have also suggested that type I MADS box factors are decisive for setting reproductive boundaries between species.

This work presents a high-resolution time-course analysis of gene expression during development of a leaf from expansion through senescence. Enrichment in ontologies, sequence motifs, and transcription factor families within genes showing altered expression over time identified both metabolic pathways and potential regulators active at different stages of leaf development and senescence.

The transition from vegetative to reproductive development is regulated by the activity of graft-transmissible flowering hormone, florigen, which is encoded by the FLOWERING LOCUS T (FT) family of mobile proteins. This work identified, among many maize FT-like genes, a single gene, ZCN8, which has all required characteristics to function as florigen.

This work presents a high-resolution time-course analysis of gene expression during development of a leaf from expansion through senescence. Enrichment in ontologies, sequence motifs, and transcription factor families within genes showing altered expression over time identified both metabolic pathways and potential regulators active at different stages of leaf development and senescence.

Patatin-related phospholipase pPLAIIIβ lacks the canonical esterase catalytic center but possesses acyl-hydrolyzing and acyl-CoA thioesterase activities. Knockout and overexpression of pPLAIIIβ have opposite effects on the levels of membrane lipids, cellulose content, mechanical strength, and cell length. Thus, membrane lipid metabolism may be linked to cellulose production in Arabidopsis.

Genes that are similarly expressed, or coexpressed, are often involved in related biological processes. Such coexpressed relationships also appear to be conserved across species. The PlaNet platform enables comparative analysis of genome-wide coexpression networks across seven plant species, thus enabling prediction of gene function and elucidation of the identity of functional homologs.