Table of Contents
IN BRIEF
LARGE-SCALE BIOLOGY ARTICLES
- CellSeT: Novel Software to Extract and Analyze Structured Networks of Plant Cells from Confocal Images
This article presents a tool to aid researchers in the analysis of confocal images. Tissue-scale structure is used to aid the segmentation of any number of cells. Additional techniques are described that can quantify the fluorescence of nuclear reporters, determine membrane protein polarity, and take many additional biologically relevant measurements.
- Gene-Sharing Networks Reveal Organizing Principles of Transcriptomes in Arabidopsis and Other Multicellular Organisms
A novel computational pipeline was designed to study the distribution of gene expression levels across cell types, tissues, and organs in Arabidopsis, rice, human, and mouse. Thousands of cross-tissue gene-sharing events were identified and predicted gene functions were validated in Arabidopsis.
RESEARCH ARTICLES
- Patterns and Evolution of Nucleotide Landscapes in Seed Plants
Analysis of EST sequence data in more than 200 species reveals unexpected continuous variations in GC content in seed plant genomes, with several independent enrichment episodes from GC-poor and homogeneous genomes to more derived GC-rich and highly heterogeneous ones. It reveals the possible role of GC-biased gene conversion, a recombination-associated process favoring G and C bases.
- Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis
Genome-wide expression profiling identifies core elements of a transcriptional network that is regulated rapidly and reciprocally by light and vegetational shade signals, via a phytochrome transcription factor transduction interface. This signaling hub functions continuously to control early seedling and juvenile plant growth and development in response to the prevailing light environment.
- Disruption of OPR7 and OPR8 Reveals the Versatile Functions of Jasmonic Acid in Maize Development and Defense
Maize OPR7 and OPR8 are redundant paralogs responsible for JA biosynthesis. Double mutation in both genes revealed diverse roles of JA in developmental and defense processes, including regulation of sex determination and female organ outgrowth, anthocyanin pigmentation, leaf senescence, and immunity against insects and pathogens.
- NAP1 Family Histone Chaperones Are Required for Somatic Homologous Recombination in Arabidopsis
This work examines two types of histone chaperones and shows that depletion of NAP1 leads to decreased somatic homologous recombination (HR), but depletion of CAF-1 leads to increased HR and telomere shortening, which are NAP1 dependent and NAP1 independent, respectively. These results highlight distinct nucleosome assembly/disassembly pathways in regulation of genome stability and variability.
- The Fanconi Anemia Ortholog FANCM Ensures Ordered Homologous Recombination in Both Somatic and Meiotic Cells in Arabidopsis
Arabidopsis FANCM, a homolog of human FANCM, is involved in the suppression of somatic homologous recombination. Here, it is shown that At-FANCM also plays a key role in meiosis, as it ensures the controlled formation of genetic exchange by suppressing erroneous interactions between parental genomes and by controlling meiotic crossover formation between homologs.
- Differential Coloring Reveals That Plastids Do Not Form Networks for Exchanging Macromolecules
This work uses a photoconvertible protein for reappraising long-held views on interplastid connectivity via stroma-filled extensions. The findings contradict present thinking by demonstrating that each plastid is unique and does not fuse or exchange fluorescent proteins with other plastids. A strong basis for investigating plastid interactions with other cytoplasmic components is provided.
- An Inducible RNA Interference System in Physcomitrella patens Reveals a Dominant Role of Augmin in Phragmoplast Microtubule Generation
This study describes a conditional RNA interference system that enabled the knockdown of essential mitotic genes along with high-resolution live microscopy. Loss-of-function analyses of augmin and γ-TuRC constitute a proof of principle and provide insight into acentrosomal microtubule formation during plant mitosis.
- Characterization of the Arabidopsis Augmin Complex Uncovers Its Critical Function in the Assembly of the Acentrosomal Spindle and Phragmoplast Microtubule Arrays
This study reports the discovery of the Arabidopsis thaliana augmin complex composed of at least eight subunits, two of which are plant specific, that regulate the function of the γ-tubulin complex during mitosis and cytokinesis.
- Fern and Lycophyte Guard Cells Do Not Respond to Endogenous Abscisic Acid
Abscisic acid (ABA) is widely known to regulate stomatal movement. This study shows that despite the augmentation of ABA in fern and lycophyte tissues during drought, their guard cells respond passively to plant water content and not ABA levels. Stomatal insensitivity in these basal plant lineages supports the concept that the link between ABA and stomatal control is derived in seed plants.
- Arabidopsis Annexin1 Mediates the Radical-Activated Plasma Membrane Ca2+- and K+-Permeable Conductance in Root Cells
The Arabidopsis thaliana root cell plasma membrane contains a calcium channel that is activated by oxidizing conditions and operates in cell growth. It was identified here as the most abundant member of the Arabidopsis annexins. These are soluble proteins that can undergo conditional attachment to or insertion into membranes.
- NADPH Thioredoxin Reductase C Is Localized in Plastids of Photosynthetic and Nonphotosynthetic Tissues and Is Involved in Lateral Root Formation in Arabidopsis
NTRC functions in maintaining redox homeostasis of chloroplasts and heterotrophic plastids of Arabidopsis. Leaf-specific expression of NTRC was sufficient to restore leaf and root growth, but root-specific expression of NTRC was not. The results emphasize the function of chloroplasts not only as source of carbon and energy but also of signaling molecules for development of heterotrophic organs.
- De Novo Pyrimidine Nucleotide Synthesis Mainly Occurs outside of Plastids, but a Previously Undiscovered Nucleobase Importer Provides Substrates for the Essential Salvage Pathway in Arabidopsis
This work shows that the Nucleobase:Cation-Symporter1 family member PLUTO imports uracil, adenine, and guanine into plastids with high apparent affinity in a substrate-proton symport mode. It finds that PLUTO’s main function is to supply the essential plastidic pyrimidine salvage pathway with substrates for the formation of UMP.
- A Transit Peptide–Like Sorting Signal at the C Terminus Directs the Bienertia sinuspersici Preprotein Receptor Toc159 to the Chloroplast Outer Membrane
This study shows that the C-terminal tail of the preprotein receptor Toc159 possesses the physicochemical and structural properties of chloroplast transit peptides. A number of fluorescent protein fusion constructs consistently demonstrated that this sorting signal is essential for the targeting of the Toc159 receptor to the chloroplast outer membrane.
- Alternative Oxidases (AOX1a and AOX2) Can Functionally Substitute for Plastid Terminal Oxidase in Arabidopsis Chloroplasts
Plastid terminal oxidase (PTOX) is distantly similar to alternative oxidases (AOXs). Both reengineering of AOX1a into the plastid and overexpression of AOX2 are able to rescue the variegation phenotype of the Arabidopsis immutans mutant, which lacks PTOX. We propose that AOXs function in chloroplasts to supplement PTOX activity during early events in chloroplast biogenesis.
- Emergent Decarboxylase Activity and Attenuation of α/β-Hydrolase Activity during the Evolution of Methylketone Biosynthesis in Tomato
Methylketones are insecticidal compounds that accumulate in certain plants as defense against herbivorous pests. Methylketone biosynthesis is a two-step process within the plant, with the second step, decarboxylation of 3-keto acids, catalyzed by Methylketone Synthase1 (MKS1). This study focuses on understanding the enzymatic mechanism of MKS1, which differs from proteins of the same structural class.
- Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase–Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis
This article presents biochemical, kinetic, and structural characterizations of a bifunctional enzyme that catalyzes both the antepenultimate and the penultimate steps of biotin (vitamin B8) synthesis in Arabidopsis. This work shows that the intermediate substrate of the overall reaction is channeled between both distant active sites, probably through a polar trench at the surface of the enzyme.
- CDKF;1 and CDKD Protein Kinases Regulate Phosphorylation of Serine Residues in the C-Terminal Domain of Arabidopsis RNA Polymerase II
This work identifies the roles of Arabidopsis CDKF;1 and CDKD protein kinases in the regulation of position-specific Ser phosphorylation of RNA polymerase II C-terminal domain (RNAPII CTD) and demonstrates that changes in the deposition of RNAPII CTD phosphoserine marks alter cotranscriptional processing and stability of a set of small RNAs and transcripts involved in their biogenesis.
- Root-Derived Oxylipins Promote Green Peach Aphid Performance on Arabidopsis Foliage
Genetic and biochemical evidence provided here indicates that roots of Arabidopsis thaliana are the source of one or more oxylipins synthesized by the LOX5-encoded lipoxygenase. This oxylipin(s) facilitates colonization of the foliage by the phloem-feeding green peach aphid (Myzus persicae Sülzer) and promotes both insect feeding from sieve elements and water consumption from the xylem.
- Oleic Acid–Dependent Modulation of NITRIC OXIDE ASSOCIATED1 Protein Levels Regulates Nitric Oxide–Mediated Defense Signaling in Arabidopsis
This work shows that NITRIC OXIDE ASSOCIATED1 (NOA1) controlling nitric oxide (NO) biosynthesis is negatively regulated by oleic acid (18:1) via direct binding, leading to protease-dependent NOA1 degradation. Conversely, reductions in 18:1 lead to increased levels of NOA1, inducing NO synthesis and triggering upregulation of NO-responsive nuclear genes, thereby activating disease resistance.
- Requirement of the Cytosolic Interaction between PATHOGENESIS-RELATED PROTEIN10 and LEUCINE-RICH REPEAT PROTEIN1 for Cell Death and Defense Signaling in Pepper
This work identifies the pathogenesis-related protein10 (PR10) as an interacting partner of the leucine-rich repeat protein1 (LRR1). It shows that LRR1 expression enhances PR10-mediated cell death that is dependent on the cytoplasmic localization of the PR10-LRR1 complex.
- Lotus japonicus E3 Ligase SEVEN IN ABSENTIA4 Destabilizes the Symbiosis Receptor-Like Kinase SYMRK and Negatively Regulates Rhizobial Infection
This work shows that an E3 ubiquitin ligase interacts with, relocalizes, and negatively impacts the abundance of the symbiosis receptor kinase SYMRK. Our results implicate SINA E3 ligases in the turnover of SYMRK and suggest a clearance mechanism involving uptake from the plasma membrane.
COMMENTARY