Table of Contents
IN THIS ISSUE
IN BRIEF
CURRENT PERSPECTIVE ESSAY: SPECIAL SERIES ON LARGE-SCALE BIOLOGY
RESEARCH ARTICLES
- Dothideomycete–Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum
Dothideomycetes is a large class of filamentous fungi containing many necrotrophic fungal pathogens. This work describes the genome sequence and extensive EST data of the wheat pathogen Stagonospora nodorum. Gene prediction analyses suggest a minimum of 10,762 nuclear genes contained in 38 Mbp and reveal gene families and enzymatic functions likely to be important in the host–parasite interaction.
- Compound Leaf Development and Evolution in the Legumes
Expression of KNOX1 genes in leaves is commonly associated with compound leaf development. The expression of KNOX1 genes was lost in the inverted repeat–lacking clade of legumes. In this clade, the FLORICAULA/LEAFY gene likely adopted a prominent role in establishing leaf complexity.
- A Feedback Regulatory Module Formed by LITTLE ZIPPER and HD-ZIPIII Genes
Transcription of a family of small leucine zipper proteins, the LITTLE ZIPPERs (ZPRs), is induced by the REVOLUTA (REV) transcription factor. A model in which the ZPR protein feedback inhibits REV activity, thus promoting abaxial leaf development, is presented and experimentally supported.
- Evolution and Function of a cis-Regulatory Module for Mesophyll-Specific Gene Expression in the C4 Dicot Flaveria trinervia
C4 plants evolved several times independently from C3 plants. C4 photosynthesis requires cell-specific expression of the genes encoding the enzymes involved in this photosynthetic pathway. This work shows how a cis-regulatory motif, responsible for cell-specific expression of a C4 ppc gene, evolved at the molecular level.
- Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype
Homoeologous chromosome rearrangements are a major mechanism contributing to changes in gene expression and phenotypic variation in newly resynthesized Brassica napus allopolyploids. These data suggest that homoeologous rearrangements are an important early evolutionary force in B. napus leading to rapid genetic and phenotypic divergence.
- Genome-Wide Analysis of mRNA Decay Rates and Their Determinants in Arabidopsis thaliana
The decay rates of transcripts in Arabidopsis cells were found to be affected by several features of the transcript, revealing multilevel regulation of transcript stability. Similar changes in transcript abundance by transcriptional inhibition and various abiotic stresses revealed that inhibition of transcription could be a determinant of changes in transcript abundance during environmental stress.
- Riboswitch Control of Gene Expression in Plants by Splicing and Alternative 3′ End Processing of mRNAs
This work reveals that a thiamin pyrophosphate–sensing riboswitch is present in the 3′ untranslated region of the thiamin biosynthetic gene THIC of many plant species and demonstrates that riboswitch-mediated regulation of alternative 3′ end processing is critical for metabolite-dependent feedback control of THIC expression.
- Arabidopsis FIERY1, XRN2, and XRN3 Are Endogenous RNA Silencing Suppressors
Posttranscriptional gene silencing (PTGS) is a eukaryotic defense mechanism against foreign invaders of the genome. This study identifies three proteins, XRN2, XRN3, and FRY1, as PTGS suppressors. FRY1 likely suppresses PTGS by regulating the XRNs, which in turn regulate the accumulation of RNAs that trigger PTGS. This work also points to the essential role of XRN3 during development.
- PRR3 Is a Vascular Regulator of TOC1 Stability in the Arabidopsis Circadian Clock
An oscillator that resonates with the diurnal cycle is crucial for optimal plant growth. Here, it is shown that the Arabidopsis regulator PRR3 protects the core clock component TOC1 from degradation. PRR3 expression and function appear more prominent in the vasculature, suggesting a mechanism that fine-tunes the plant clock in this tissue, a parallel to the well-known tissue-specific clocks of animals.
- Distinct Light and Clock Modulation of Cytosolic Free Ca2+ Oscillations and Rhythmic CHLOROPHYLL A/B BINDING PROTEIN2 Promoter Activity in Arabidopsis
This study reports that the circadian regulation of cytosolic-free Ca2+ requires both light and a circadian oscillator. Genetic differences between the oscillator regulating Ca2+ and that regulating CAB2 promoter activity suggest the presence of multiple circadian oscillators in Arabidopsis, possibly with different molecular architectures and cellular locations.
- Nitrate Signaling by the Regulatory Gene NIT2 in Chlamydomonas
Chlamydomonas mutants incapable of growth on nitrate and lacking the ability to activate nitrate reductase (NIA1) gene expression were found to harbor mutations in the nitrate assimilation-specific regulatory gene NIT2. NIT2 was found to encode a putative transcription factor that is a central regulator required for nitrate-induced activation of NIA1 promoter activity.
- VPS9a, the Common Activator for Two Distinct Types of Rab5 GTPases, Is Essential for the Development of Arabidopsis thaliana
The activation of Rab GTPases must be regulated spatiotemporally, which is critical to fulfill their functions correctly. This study has identified an activating factor for Rab GTPases in Arabidopsis, named VPS9a, which equally activates all three Rab5 members of Arabidopsis. VPS9a was found to be essential for various plant functions, including embryogenesis, organ formation, and cytokinesis.
- The Homeotic Protein AGAMOUS Controls Late Stamen Development by Regulating a Jasmonate Biosynthetic Gene in Arabidopsis
Timed activation of the floral homeotic gene AGAMOUS (AG) shows that AG has stage-specific functions throughout stamen development, including anther maturation and filament elongation in late stamen organogenesis. It is further shown that AG coordinates late stamen development through the direct transcriptional regulation of a catalytic enzyme of the lipid-derived phytohormone jasmonic acid.
- MALE STERILITY1 Is Required for Tapetal Development and Pollen Wall Biosynthesis
Expression of MALE STERILITY1 is tightly regulated, involving a self-regulatory feedback mechanism and transient MS1 protein expression, suggesting that its removal is required for pollen development. Genes associated with pollen wall and coat formation show altered expression in ms1, and a number of transcription factors and Cys proteases were identified as putative regulatory targets.
- Arabidopsis MALE STERILITY1 Encodes a PHD-Type Transcription Factor and Regulates Pollen and Tapetum Development
MS1 encodes a nuclear factor required for pollen development. Through the use of fusion with a transcriptional repression domain, it is shown that MS1 is a transcriptional activator. Putative direct target genes of MS1 are identified using a dexamethasone induction system. It is proposed that MS1 is involved in transcriptional regulation crucial for postmeiotic tapetum and pollen development.
- The Central Cell Plays a Critical Role in Pollen Tube Guidance in Arabidopsis
CENTRAL CELL GUIDANCE (CCG) is identified as a putative transcriptional regulator essential for pollen tube guidance. CCG encodes a nuclear protein with an N-terminal conserved zinc β-ribbon domain that is expressed in the central cell of the female gametophyte and plays a critical role in pollen tube guidance.
- Cell-Fate Switch of Synergid to Egg Cell in Arabidopsis eostre Mutant Embryo Sacs Arises from Misexpression of the BEL1-Like Homeodomain Gene BLH1
The female gametophyte mutant eostre is defective in the establishment of cell fates in the embryo sac, so that a synergid cell can acquire egg cell identity. This study indicates that these defects arise from ectopic activity of BELL-KNOX TALE complexes and that normal development of the Arabidopsis embryo sac requires suppression of their activity that might be mediated by OVATE family proteins.
- Comparison of Petunia inflata S-Locus F-Box Protein (Pi SLF) with Pi SLF–Like Proteins Reveals Its Unique Function in S-RNase–Based Self-Incompatibility
Biochemical and in vivo studies of Pi SLF and Pi SLF–like proteins demonstrate that, among F-box proteins, Pi SLF has a unique function in controlling pollen behavior in self-incompatibility. These studies also identify a domain of Pi SLF responsible for strong interactions with non-self S-RNases and a potential allele-specific domain negatively regulating the interactions with self S-RNase.
- A Viroid RNA with a Specific Structural Motif Inhibits Chloroplast Development
A non-protein-coding viroid RNA with a specific structural motif interferes with an early step of chloroplast development, ultimately leading to an albino-variegated phenotype resembling that of certain variegated plant mutants in which plastid rRNA maturation is also impaired. These results highlight the potential of viroids for further dissection of RNA trafficking and pathogenesis in plants.
- Synthesis of the D2 Protein of Photosystem II in Chlamydomonas Is Controlled by a High Molecular Mass Complex Containing the RNA Stabilization Factor Nac2 and the Translational Activator RBP40
Chloroplast gene expression is regulated mainly at the posttranscriptional level. This work identifies a translational activator for the chloroplast psbD mRNA and demonstrates its functional and physical association with a factor required for psbD mRNA stabilization.
- Photosystem II Assembly and Repair Are Differentially Localized in Chlamydomonas
In situ evidence reveals that photosystem II subunits encoded by chloroplast mRNAs are synthesized and assembled in a novel compartment in the chloroplast of Chlamydomonas. Synthesis of the D1 subunit for the repair of photodamaged photosystem II complexes was detected generally at thylakoid membranes, consistent with the current model.
- BIN4, a Novel Component of the Plant DNA Topoisomerase VI Complex, Is Required for Endoreduplication in Arabidopsis
BIN4 encodes a plant-specific, DNA binding protein that acts as a component of the plant DNA topoisomerase VI complex. Loss of BIN4 triggers an ATM- and ATR-dependent DNA damage response in postmitotic cells, and this leads to an early arrest of endoreduplication in Arabidopsis.
- Downregulation of Cinnamoyl-Coenzyme A Reductase in Poplar: Multiple-Level Phenotyping Reveals Effects on Cell Wall Polymer Metabolism and Structure
Transgenic poplar, downregulated for a gene involved in lignin biosynthesis, was phenotyped at multiple levels. The data show that in addition to the anticipated lower lignin levels, the xylem unexpectedly had lower levels of hemicelluloses, and the residual lignin incorporated ferulic acid, now to be considered as a new lignin monomer. Chemical pulping of field-grown wood was facilitated.
- Saturated Very-Long-Chain Fatty Acids Promote Cotton Fiber and Arabidopsis Cell Elongation by Activating Ethylene Biosynthesis
It is shown that fatty acids with chain lengths >20, especially saturated C24, stimulate significant elongation growth in both cotton fiber and Arabidopsis root and stem cells. This growth-promoting effect is brought about by an enhanced ethylene biosynthesis and signaling, suggesting that the current paradigm for the mechanism of cell elongation may be reassessed.
- Profilin Is Essential for Tip Growth in the Moss Physcomitrella patens
The small actin monomer binding protein, profilin, was shown to be essential for tip growth and for the proper organization of the actin cytoskeleton. Using a complementation assay, the actin and polyproline binding sites on profilin were shown to be required for profilin function in vivo.
- Glycolytic Enzymes Associate Dynamically with Mitochondria in Response to Respiratory Demand and Support Substrate Channeling
Glycolytic enzymes have been shown to partition between the cytosol and the outer surface of the mitochondrion, but the functional significance of this partitioning is not known. Here, it is shown that glycolytic enzymes associate with mitochondria dynamically in response to respiratory demand and that the mitochondrially associated enzymes support substrate channeling.
- Functional Definition of Outer Membrane Proteins Involved in Preprotein Import into Mitochondria
Proteins are imported through the mitochondrial membranes by complex machinery. In this study, three Arabidopsis mitochondrial outer membrane proteins, TOM20, METAXIN, and mtOM64, were demonstrated to interact directly with proteins targeted to mitochondria and to be involved in the process of protein import.
- Nitrate Efflux at the Root Plasma Membrane: Identification of an Arabidopsis Excretion Transporter
Upon various stresses, plant roots may paradoxically undergo a net excretion of NO3−, the molecular basis and biological role of which are unknown. This report presents the characterization of a plasma membrane transporter responsible for the root NO3− excretion triggered by acidification stresses. It belongs to a subclass of seven members of the large NRT1/PTR family to which it introduces a novel function.
- ARGONAUTE4 Is Required for Resistance to Pseudomonas syringae in Arabidopsis
ARGONAUTE4, a component of the pathway that mediates the transcriptional gene silencing associated with siRNA in plants, is shown to play a pivotal role in disease resistance and susceptibility to microbial pathogens in Arabidopsis. These results suggest that gene methylation may mediate critical aspects of plant susceptibility to pathogens.
- Structural and Functional Analysis of SGT1 Reveals That Its Interaction with HSP90 Is Required for the Accumulation of Rx, an R Protein Involved in Plant Immunity
Mutational analyses, NMR-based interaction surface mapping, and biochemical reconstitution experiments reveal fundamental properties of SGT1, which determine interactions with HSP90 and RAR1 related to disease resistance.
- SAD2, an Importin β-Like Protein, Is Required for UV-B Response in Arabidopsis by Mediating MYB4 Nuclear Trafficking
Accurate nuclear translocation of signal molecules is essential for plant growth and development. SAD2 is required to transport MYB4 into the nucleus in Arabidopsis, and studying this nuclear translocation process has allowed us to show that the MYB4 transcript and protein are involved in a negative autoregulatory feedback loop and that they are important for UV-B tolerance in plants.
- Lysigenous Aerenchyma Formation in Arabidopsis Is Controlled by LESION SIMULATING DISEASE1
Each year, flooding greatly reduces global crop yields. In this work, we describe the formation of lysigenous aerenchyma in Arabidopsis in response to root hypoxia caused by flooding and propose the genetic system essential for this process. This work shows that Arabidopsis is a novel and valid experimental system for the development of flooding-tolerant crops.
