Table of Contents
IN BRIEF
REVIEWS
LARGE-SCALE BIOLOGY ARTICLES
- A Guideline to Family-Wide Comparative State-of-the-Art Quantitative RT-PCR Analysis Exemplified with a Brassicaceae Cross-Species Seed Germination Case Study
Developmental processes like seed germination are characterized by massive transcriptome changes. This study compares seed transcriptome data sets of different Brassicaceae to identify stable expressed reference genes for cross-species quantitative RT-PCR normalization. A workflow is presented for improving RNA quality, quantitative RT-PCR performance, and normalization when analyzing expression changes across species.
- Transcriptional Programming and Functional Interactions within the Phytophthora sojae RXLR Effector Repertoire
This study presents a broad functional survey of a large sample of candidate RXLR effectors in the oomycete pathogen of soybean (Phytophthora sojae). Suppression of plant defense, transcription patterns, and polymorphisms were assayed. Essential effectors and effector subsets with distinct expression patterns and defense suppression activities were identified.
RESEARCH ARTICLES
- Evolution of C4 Photosynthesis in the Genus Flaveria: How Many and Which Genes Does It Take to Make C4?
We carried out a comparative transcriptome analysis in leaves of five closely related C3, C4, and C3-C4 intermediate Flaveria species to gain insight into the extent to which gene expression patterns were altered in the evolutionary progression from C3 to C4. The comparative analysis indicates that C4 evolution affected far more biological functions than only photosynthesis.
- Developmental Analysis of a Medicago truncatula smooth leaf margin1 Mutant Reveals Context-Dependent Effects on Compound Leaf Development
This work shows that a mutation of the PIN1 ortholog in Medicago truncatula, SLM1, caused multiple terminal leaflets and a reduction of lateral leaflets. Characterization of the mutant reveals that the terminal leaflet primordium in M. truncatula has a unique developmental mechanism and the elaboration of compound leaves is context dependent and tightly correlated with the auxin/SLM1 module.
- STENOFOLIA Regulates Blade Outgrowth and Leaf Vascular Patterning in Medicago truncatula and Nicotiana sylvestris
This study shows that a WUSCHEL-like gene, STENOFOLIA (STF), is required for blade outgrowth, and its deletion accounts for the classical bladeless lam1 phenotype of tobacco (Nicotiana sylvestris). STF confers morphogenetic competence to leaf primordial margins and coordinates auxin/cytokinin homeostasis and hormone crosstalk with sugar metabolism, integrating metabolic and developmental signals.
- The COP1 Ortholog PPS Regulates the Juvenile–Adult and Vegetative–Reproductive Phase Changes in Rice
Rice pps is a heterochronic mutant that shows a prolonged juvenile phase by repressing GA biosynthetic genes and altering expression patterns of microRNA genes but is early flowering. Positional cloning revealed that PPS is the ortholog of Arabidopsis COP1. Although PPS has a role in photomorphogenesis as COP1 does, PPS has additional roles in vegetative phase change and flowering time regulation.
- The Arabidopsis NAC Transcription Factor VNI2 Integrates Abscisic Acid Signals into Leaf Senescence via the COR/RD Genes
This work demonstrates that plant responses to environmental stress are intimately associated with leaf longevity. The Arabidopsis VNI2 transcription factor functions as a regulator of abscisic acid–mediated leaf longevity by binding directly to the promoters of COR and RD genes involved in abiotic stress resistance.
- Analysis of Cytokinin Mutants and Regulation of Cytokinin Metabolic Genes Reveals Important Regulatory Roles of Cytokinins in Drought, Salt and Abscisic Acid Responses, and Abscisic Acid Biosynthesis
Functional analyses of cytokinin (CK)-deficient plants provide direct evidence that CKs negatively regulate plant response to drought and salt stresses. CK-deficient plants exhibited a strong stress-tolerant phenotype associated with abscisic acid (ABA) hypersensitivity. This study suggests that mutual regulation mechanisms between CK and ABA affect the plant’s adaptation to stressors and plant growth and development.
- Gibberellin Regulates PIN-FORMED Abundance and Is Required for Auxin Transport–Dependent Growth and Development in Arabidopsis thaliana
This work presents physiological, cell biological, and developmental data that establish that gibberellins (GA) is required for proper polar auxin transport in Arabidopsis thaliana. It shows that the GA pathway interacts with PIN protein-dependent auxin transport and development, suggesting that at least some of the growth defects of GA biosynthesis and signaling mutants are a result of altered auxin transport.
- Targeted mRNA Oxidation Regulates Sunflower Seed Dormancy Alleviation during Dry After-Ripening
This works shows that sunflower seed dormancy alleviation during dry after-ripening is associated with oxidation of a specific subset of 24 seed stored mRNAs. Oxidized transcripts are not translated into their corresponding proteins during subsequent seed imbibition, which may govern cell signaling leading to germination.
- The MYB80 Transcription Factor Is Required for Pollen Development and the Regulation of Tapetal Programmed Cell Death in Arabidopsis thaliana
This work examines downstream targets of MYB80 and shows that an aspartic protease regulated by MYB80 is involved in the timing of programmed cell death of the tapetum in the Arabidopsis anther.
- Defective Pollen Wall Is Required for Anther and Microspore Development in Rice and Encodes a Fatty Acyl Carrier Protein Reductase
A rice male-sterile mutant, defective pollen wall (dpw), which has defective anthers and pollen grains, is isolated and characterized. DPW is found to encode a fatty acyl carrier protein reductase that is active during the synthesis of the anther cuticle and pollen sporopollenin.
- Malonyl-CoA Synthetase, Encoded by ACYL ACTIVATING ENZYME13, Is Essential for Growth and Development of Arabidopsis
Malonic acid inhibits succinate dehydrogenase and is toxic to Arabidopsis seedlings. Biochemical assays demonstrate that ACYL ACTIVATING ENZYME13 (AAE13) of Arabidopsis is a malonyl-CoA synthetase. Characterization of an aae13 mutant indicates that the malonyl-CoA synthetase encoded by AAE13 is required for detoxification of endogenous malonate and for healthy growth and development of plants.
- Parameters Affecting Telomere-Mediated Chromosomal Truncation in Arabidopsis
This work describes the development of a robust and quantitative system for elucidating the sequences and trans-acting factors required for de novo telomere formation in Arabidopsis thaliana. We determine that genetic redundancy and the nonhomologous end-joining factors Ku and Lig4 facilitate higher levels of de novo telomere formation.
- ROP GTPases Act with the Receptor-Like Protein PAN1 to Polarize Asymmetric Cell Division in Maize
This study demonstrates a role for Rho family GTPases (ROPs) in asymmetric cell division in maize. Functional and localization studies together with analysis of physical interactions demonstrate that ROPs function cooperatively with the receptor-like protein PAN1 to promote the premitotic polarization of subsidiary mother cells during stomatal complex development.
- Transcription Factor–Dependent Chromatin Remodeling at Heat Shock and Copper-Responsive Promoters in Chlamydomonas reinhardtii
Transcription factors mediating acclimation to abiotic stress in Chlamydomonas reinhardtii regulate the expression of their target genes via histone acetylation, histone methylation, nucleosome eviction, and polymerase loading/activation. At each target promoter, these means are employed quite individually to establish a characteristic chromatin state allowing for a fine-tuning of gene expression.
- Live Cell Imaging Reveals Structural Associations between the Actin and Microtubule Cytoskeleton in Arabidopsis
This work investigates coordinated actin filament and microtubule activities. It shows that actin filaments and microtubules interact dynamically and that actin filaments depend on microtubules to recover following drug-induced depolymerization events.
- The Plant-Specific Actin Binding Protein SCAB1 Stabilizes Actin Filaments and Regulates Stomatal Movement in Arabidopsis
This study shows the identification of a plant-specific actin binding protein, STOMATAL CLOSURE-RELATED ACTIN BINDING PROTEIN1, which associates with and stabilizes microfilaments, and regulates microfilament reorganization during stomatal closure in response to drought stress.
- Maize opaque5 Encodes Monogalactosyldiacylglycerol Synthase and Specifically Affects Galactolipids Necessary for Amyloplast and Chloroplast Function
The maize gene opaque5 encodes a monogalactosyldiacylglycerol synthase. Mutant analysis reveals that galactolipids with five double bonds are needed for thylakoid membrane function and cannot be substituted by the prevalent species with six double bonds. Galactolipid reduction results in altered starch granules, indicating a connection between amyloplast membranes and starch biosynthesis.
- Subunit Stoichiometry, Evolution, and Functional Implications of an Asymmetric Plant Plastid ClpP/R Protease Complex in Arabidopsis
This study determines the subunit stoichiometry of the tetradecameric caseinolytic protease (Clp) protease, the most abundant soluble protease in plant plastids. Using tagged Clp subunits and stable isotope-labeled peptides for mass spectrometry-based quantification, this analysis provides information that is critical for understanding the interaction of Clp protease with Clp chaperones and substrate delivery systems.
- Sphingolipids Containing Very-Long-Chain Fatty Acids Define a Secretory Pathway for Specific Polar Plasma Membrane Protein Targeting in Arabidopsis
This study shows that Arabidopsis has two classes of ceramide synthases discriminating acyl chain length and also that very-long-acyl-chain sphingolipids are required for polar auxin transport in particular during lateral root emergence. These lipids define a secretory pathway with specific endomembrane compartments and polar auxin transport protein cargoes.
- The Plasma Membrane of the Cyanobacterium Gloeobacter violaceus Contains Segregated Bioenergetic Domains
Gloeobacter violaceus, the most primordial of known organisms performing oxygenic photosynthesis, evolved before the evolutionary appearance of thylakoid membranes. This study demonstrates the presence of bioenergetic domains in its cytoplasmic membrane. The formation of these membrane domains might constitute evolutionary precursors of the thylakoid membrane.
- Tunable Membrane Binding of the Intrinsically Disordered Dehydrin Lti30, a Cold-Induced Plant Stress Protein
The dehydrin family of proteins is upregulated in response to desiccation and cold stress and is thought to protect the plant by stabilizing the plasma membrane. This study characterizes the interaction between a typical dehydrin (Lti30) and lipid membranes.
- Botrytis cinerea Manipulates the Antagonistic Effects between Immune Pathways to Promote Disease Development in Tomato
Botrytis cinerea is a necrotrophic pathogen that causes grey mould disease in a broad host range, including tomato, grapes, potato, and strawberry. Here, we report that B. cinerea secretes a virulence factor that hijacks the plant’s own crosstalk network to promote disease development.
- A Barley ROP GTPase ACTIVATING PROTEIN Associates with Microtubules and Regulates Entry of the Barley Powdery Mildew Fungus into Leaf Epidermal Cells
Little is known about the role the cytoskeleton plays in signaling with regard to the outcome of plant–microbe interactions. This work describes a regulator of cytoskeleton organization and of disease susceptibility shuttling between microtubules and the monomeric G-protein RACB at the cell periphery.
- The Arabidopsis Leucine-Rich Repeat Receptor–Like Kinases BAK1/SERK3 and BKK1/SERK4 Are Required for Innate Immunity to Hemibiotrophic and Biotrophic Pathogens
This work demonstrates that the leucine-rich receptor kinases (LRR-RKs) EFR and FLS2 form a ligand-induced complex with several LRR-RKs that belong to the SERK subfamily. Among these, BAK1 and BKK1 play an important role in responses to EF-Tu, flagellin, and other elicitors of plant defense and are required for full immunity to hemibiotrophic and biotrophic pathogens.
- Cytosolic γ-Glutamyl Peptidases Process Glutathione Conjugates in the Biosynthesis of Glucosinolates and Camalexin in Arabidopsis
This work demonstrates that glutathione is the sulfur donor for the biosynthesis of glucosinolates, plant compounds that play important roles in agriculture, ecology, and human health. Furthermore, it identifies the enzymes that act immediately downstream of the sulfur donation step (γ-glutamylpeptidases), thereby assigning a previously unknown in planta function to this family of enzymes.
