Table of Contents
IN BRIEF
LARGE-SCALE BIOLOGY ARTICLES
- Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Data Sets
This study presents a novel computational methodology to predict functional associations between genes based on microarray data. The methodology termed “coprediction” uses a machine learning algorithm and is used to generate a gene network that is validated by identifying four novel regulators of seed germination and several of their functional relationships.
- Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes
Plant genomes contain a large number of short interspersed nuclear elements, which so far have been detected only randomly. A software tool was created integrating weakly conserved structural motifs for the analysis of genome sequences. Thousands of sequences from many plant taxa were identified, giving insights into their variability, localization along chromosomes, and evolution.
RESEARCH ARTICLES
- Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy
This work examines the changes that have occurred in 12 homoeologous genomic regions from three rounds of polyploidy that contributed to the current soybean genome. It finds that genes in networks with a high level of connectivity are more strongly conserved than those with low connectivity.
- Nonessential Plastid-Encoded Ribosomal Proteins in Tobacco: A Developmental Role for Plastid Translation and Implications for Reductive Genome Evolution
Of seven plastid genome-encoded ribosomal proteins analyzed by reverse genetics in tobacco (Nicotiana tabacum), two were found to be nonessential: S15 and L36. Elimination of ribosomal protein S15 produced normal plants, but elimination of L36 resulted in mutants with reduced apical dominance and strikingly altered leaf morphology, uncovering a role for plastid translational activity in plant development.
- Genetics, Evolution, and Adaptive Significance of the Selfing Syndrome in the Genus Capsella
This work analyzes the evolution of the selfing syndrome in Capsella. Several genetic changes underlie the smaller, less open flowers of the selfing C. rubella compared to its outbreeding ancestor C. grandiflora, and these appear to have been fixed before the geographical expansion of the C. rubella lineage. Also, the smaller flowers appear to be better adapted for efficient self-pollination.
- Arabidopsis TERMINAL FLOWER1 Is Involved in the Regulation of Flowering Time and Inflorescence Development through Transcriptional Repression
This work examines the function of TERMINAL FLOWER1 (TFL1) in transcription by fusing TFL1 to either a transcriptional activator or repressor domain, finding that the TFL1-repressor fusion replicates TFL1 function, but the TFL1-activator fusion produces a dominant-negative flowering phenotype, indicating that TFL1 acts as part of a transcriptional repression complex.
- Function and Evolution of a MicroRNA That Regulates a Ca2+-ATPase and Triggers the Formation of Phased Small Interfering RNAs in Tomato Reproductive Growth
MicroRNAs (miRNAs) regulate gene expression underpinning a wide variety of biological processes in most eukaryotes. This work provides insight into the evolution and function of a 22-nucleotide miRNA in tomato that regulates the expression of an autoinhibited Ca2+-ATPase, ACA10, and triggers formation of phased small interfering RNAs, which may play a role in reproductive growth.
- Tissue-Specific Expression of FLOWERING LOCUS T in Arabidopsis Is Maintained Independently of Polycomb Group Protein Repression
This study shows that the role of Polycomb Group (PcG) proteins in the regulatory network determining tissue-specific expression is not identical for all PcG-target genes. The data suggest that a positive regulatory factor produced in differentiated phloem companion cells sets a prerequisite for FT expression.
- A Wheat Homolog of MOTHER OF FT AND TFL1 Acts in the Regulation of Germination
Among the environmental signals affecting seed development, temperature is the most influential in the formation of seed dormancy in wheat. In this study, transcriptional profiling of the effects of temperature on seed dormancy formation identified MFT as a candidate gene for seed dormancy regulation.
- A Reduced-Function Allele Reveals That EARLY FLOWERING3 Repressive Action on the Circadian Clock Is Modulated by Phytochrome Signals in Arabidopsis
This work characterizes a hypomorphic allele of ELF3, delineating a functional domain needed to inhibit phytochrome action at ELF3. These findings are consistent with ELF3 being a multifunctional protein that integrates light signals to the circadian clock as a core repressive component of the oscillator.
- WOX4 Imparts Auxin Responsiveness to Cambium Cells in Arabidopsis
Extensive lateral growth of shoot and root axes is mediated mostly by the cambium, a meristematic tissue whose activity depends on the plant hormone auxin. This study reveals that the presence of the transcription factor WOX4 in cambium cells is essential for translating the accumulation of long distance–derived auxin into cell proliferation.
- Molecular Profiling of Stomatal Meristemoids Reveals New Component of Asymmetric Cell Division and Commonalities among Stem Cell Populations in Arabidopsis
This work presents the transcriptome profile of the meristemoid, a transient and low-density proliferating stomatal precursor cell with stem cell–like properties. The work identifies a new protein exhibiting polar localization during asymmetric division of stomatal cell lineages, reveals molecular characteristics of the meristemoid, and illuminates common themes in gene expression among plant stem cells.
- LAX PANICLE2 of Rice Encodes a Novel Nuclear Protein and Regulates the Formation of Axillary Meristems
This study reports the identification of a novel regulator of axillary meristem formation in rice, showing that LAX PANICLE2 (LAX2) likely acts in the maintenance of the axillary meristem. In addition, it reveals that LAX2 localizes to the nucleus and appears to form a dimer with LAX1, which is a basic helix-loop-helix transcriptional factor.
- POD1 Regulates Pollen Tube Guidance in Response to Micropylar Female Signaling and Acts in Early Embryo Patterning in Arabidopsis
This work examines the pollen defective in guidance1 (pod1) mutant and finds that it is defective in pollen tube guidance to the micropyle. Homozygous pod1 embryos also show lethality. POD1 is an endoplasmic reticulum (ER) luminal protein involved in ER protein retention.
- Biosynthesis and Defensive Function of Nδ-Acetylornithine, a Jasmonate-Induced Arabidopsis Metabolite
This work identifies the nonprotein amino acid Nδ-acetylornithine and an acetyltransferase that synthesizes it in Arabidopsis thaliana, thus revealing a new methyl jasmonate–inducible defense response. It demonstrates that the genomic resources available for Arabidopsis make it relatively easy to move from a identifying a plant metabolite to the discovery of a previously unknown enzymatic activity.
- The Transcription Factor ABI4 Is Required for the Ascorbic Acid–Dependent Regulation of Growth and Regulation of Jasmonate-Dependent Defense Signaling Pathways in Arabidopsis
This work demonstrates that low ascorbate triggers abscisic acid-, salicylic acid-, and jasmonate-dependent signaling pathways in leaves that together regulate plant growth and defense responses. It provides insights into how cellular redox state regulates the expression of transcription factors and controls plant growth.
- The Basic Helix-Loop-Helix Transcription Factor MYC2 Directly Represses PLETHORA Expression during Jasmonate-Mediated Modulation of the Root Stem Cell Niche in Arabidopsis
This study investigates the mechanisms underlying jasmonate-induced inhibition of primary root growth. Jasmonate inhibits the expression of two AP2-domain transcription factors, PLETHORA1 and 2, in a MYC2-dependent fashion. MYC2 is suggested to integrate the jasmonate and auxin pathways during the maintenance of the root stem cell niche.
- A Plasmodesmata-Localized Protein Mediates Crosstalk between Cell-to-Cell Communication and Innate Immunity in Arabidopsis
This study investigates how plants adopted a cellular strategy for defense against microbial pathogens by recruiting a plasmodesmata-localized protein to regulate cell-to-cell communication and augment innate immune responses.
- Arabidopsis RTNLB1 and RTNLB2 Reticulon-Like Proteins Regulate Intracellular Trafficking and Activity of the FLS2 Immune Receptor
This study finds that two reticulon proteins modulate the transport of an immune receptor to the cell membrane. The results highlight the role of receptor secretion in determining the receptor’s forward signaling efficacy and the cell’s response.
- CFL1, a WW Domain Protein, Regulates Cuticle Development by Modulating the Function of HDG1, a Class IV Homeodomain Transcription Factor, in Rice and Arabidopsis
This study identifies CFL1 as a negative regulator of cuticle development in rice and Arabidopsis. CFL1 interacts with a class IV homeodomain-leucine zipper transcription factor to modulate the expression of two genes known to be involved in cuticle development.
- Salt Stress–Induced Disassembly of Arabidopsis Cortical Microtubule Arrays Involves 26S Proteasome–Dependent Degradation of SPIRAL1
This study examines the relationship between salt stress tolerance and dynamic instability of microtubules, revealing an important role for proteasome-dependent regulation of SPR1 in the survival of plants challenged by high salinity.
- MutS HOMOLOG1 Is a Nucleoid Protein That Alters Mitochondrial and Plastid Properties and Plant Response to High Light
This work provides evidence, using genetic perturbation of the MSH1 nuclear gene in five plant species, that MSH1 functions within the mitochondrion and plastid to influence organellar genome behavior and plant growth patterns.
- Identification of the 7-Hydroxymethyl Chlorophyll a Reductase of the Chlorophyll Cycle in Arabidopsis
This study identifies the last remaining unknown enzyme responsible for the chlorophyll cycle. It shows that 7-HYDROXYMETHYL CHLOROPHYLL A REDUCTASE is a flavoprotein capable of carrying out a difficult reaction involving the substitution of an OH group with an H.
- Tetrapyrrole Synthesis of Photosynthetic Chromerids Is Likely Homologous to the Unusual Pathway of Apicomplexan Parasites
Chromera velia is the only known eukaryotic phototroph that uses the C4 pathway to synthesize chlorophyll. The tetrapyrrole synthetic pathway of this alga is an evolutionary mosaic of the pathways of both heterotrophic and photosynthetic eukaryotes and is similar to the unusual heme biosynthetic pathway of the related apicomplexan parasites.
- Multivesicular Bodies Mature from the Trans-Golgi Network/Early Endosome in Arabidopsis
This work examines the origin and fate of multivesicular bodies (MVBs)/late endosomes, tracing their formation back to the trans-Golgi network (TGN)/early endosome and showing that their maturation into MVBs requires V-ATPase activity and ESCRT for the formation of the intraluminal vesicles and annexins for the release of MVBs from the TGN as transport carriers that fuse with the vacuole.
- The Arabidopsis Na+/H+ Antiporters NHX1 and NHX2 Control Vacuolar pH and K+ Homeostasis to Regulate Growth, Flower Development, and Reproduction
This work examined the functions of NHX1 and NHX2, two members of the Arabidopsis thaliana Na+/H+ antiporter family, in cell growth and flower development, demonstrating that NHX1 and NHX2 regulate intravacuolar potassium and pH to control cell expansion. Plants lacking NHX1 and NHX2 displayed flower defects, lack siliques, have short hypocotyls and are sensitive to extracellular potassium but not sodium.
- The Xanthomonas Type III Effector XopD Targets the Arabidopsis Transcription Factor MYB30 to Suppress Plant Defense
This work identifies the Arabidopsis transcription factor MYB30, a positive regulator of plant defense, as a plant target of the type III effector XopD from the phytopathogenic bacterium Xanthomonas campestris. The XopD/MYB30 physical interaction results in inhibition of MYB30 transcriptional activation as part of a bacterial strategy that leads to promotion of disease development.
- Nicotiana attenuata LECTIN RECEPTOR KINASE1 Suppresses the Insect-Mediated Inhibition of Induced Defense Responses during Manduca sexta Herbivory
This work demonstrates that the oral secretion–inducible LECTIN RECEPTOR KINASE1 is indispensable during Manduca sexta herbivory to suppress the insect-mediated inhibition of defense responses and thereby to stimulate the unfettered jasmonic acid–mediated induction of defense metabolites.
- Condensin II Alleviates DNA Damage and Is Essential for Tolerance of Boron Overload Stress in Arabidopsis
This work presents insight into how boron (B) toxicity develops at the molecular level in plants and suggests a role of condenisn II genes in tolerance to B toxicity. Experiments show that excess B induces DNA damage, and condensin II is involved in the amelioration of this damage.
- Boron-Dependent Degradation of NIP5;1 mRNA for Acclimation to Excess Boron Conditions in Arabidopsis
NIP5;1 encodes a boron channel; this work shows that the 5′ untranslated region of NIP5;1 is required for mRNA accumulation in response to boron deficiency and mRNA degradation in response to high-boron conditions.
