Table of Contents
IN BRIEF
LARGE-SCALE BIOLOGY ARTICLE
- Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis
This article reports high-resolution mapping of the genomic locations that are hypersensitive to DNase I digestion (DH sites) in Arabidopsis thaliana. The DH site data sets in combination with known or putative protein binding motifs and gene expression data sets can be used to reveal protein binding footprints within a specific genomic region.
RESEARCH ARTICLES
- Pod Corn Is Caused by Rearrangement at the Tunicate1 Locus
Pod corn (Zea mays), once considered as ancestral to cultivated maize, has a striking phenotype in which each kernel is enclosed with chaff. This phenotype is explained by a chromosomal rearrangement at the Tunicate1 (Tu1) locus that alters the expression pattern of the Tu1 MADS box gene involved in determining floral organ identity.
- A Genome-Wide Regulatory Framework Identifies Maize Pericarp Color1 Controlled Genes
This study combines high-throughput RNA sequencing and chromatin immunoprecipitation and sequencing to examine the effect of Pericarp Color1 (P1) on global gene expression in maize pericarps and silks, finding that, in addition to regulating flavonoid biosynthesis genes, P1 modulates the expression of a much larger gene set involved in primary metabolism and production of other specialized compounds.
- Cyclic Peptides Arising by Evolutionary Parallelism via Asparaginyl-Endopeptidase–Mediated Biosynthesis
To produce highly stable peptides, we show that plant evolution has favored the involvement of a specific protease as well as a similar type of biosynthesis to cut and process peptides to be cyclic from many different precursor proteins. Using Momordica cochinchinensis, we describe the biosynthesis of knotted peptides with cyclic and noncyclic topologies from precursors encoding up to eight peptides.
- Evidence for a Role of Arabidopsis CDT1 Proteins in Gametophyte Development and Maintenance of Genome Integrity
Loss of function analysis reveals that the replication licensing factors CDT1a and CDT1b act redundantly during gametophyte development. In addition, reduced expression of these genes causes endogenous DNA stress in plants and results in spontaneous mutations, demonstrating that these two proteins are crucial to the maintenance of genome integrity both in vegetative and in reproductive cells.
- Downregulation of the δ-Subunit Reduces Mitochondrial ATP Synthase Levels, Alters Respiration, and Restricts Growth and Gametophyte Development in Arabidopsis
The mitochondrial ATP synthase is central to the cell’s energy metabolism. By disturbing the functionality of the ATP synthase, this work identified major short- and long-term changes to metabolite, transcript, and protein levels that led to delayed growth and reduced fertility. It provides new evidence that primary metabolism and gametophyte development seem to be linked by redox and biotic stress signaling.
- A Light-Regulated Genetic Module Was Recruited to Carpel Development in Arabidopsis following a Structural Change to SPATULA
This study provides insight into the evolution of flowering plants by demonstrating that a mechanism that modulates carpel margin development in Arabidopsis was recruited from light-regulated processes.
- The Time Required for Dormancy Release in Arabidopsis Is Determined by DELAY OF GERMINATION1 Protein Levels in Freshly Harvested Seeds
Seed dormancy prevents germination of freshly harvested seeds and is slowly released during seed storage by an unknown mechanism. This work shows that posttranslational modifications of the Arabidopsis thaliana protein DELAY OF GERMINATION1 occurring during seed storage can explain dormancy release.
- Nuclear Ribosome Biogenesis Mediated by the DIM1A rRNA Dimethylase Is Required for Organized Root Growth and Epidermal Patterning in Arabidopsis
Analysis of a root epidermal patterning mutant suggests a link between the regulation of translation and cell differentiation. The inability of this mutant to properly methylate its 18S rRNA leads to several developmental defects, including a failure to establish appropriate cell type–specific gene expression programs.
- Convergent Starvation Signals and Hormone Crosstalk in Regulating Nutrient Mobilization upon Germination in Cereals
This work shows that not only sugar but also nitrogen and phosphate starvation signals converge with GA signaling to promote the co-nuclear import of MYBS1 and MYBGA and expression of a large set of GA-inducible but functionally distinct hydrolases, transporters, and regulators active in nutrient mobilization required for seedling growth in rice and barley.
- AUX/LAX Genes Encode a Family of Auxin Influx Transporters That Perform Distinct Functions during Arabidopsis Development
This article describes the role of AUX/LAX auxin influx carriers in plant development, revealing that the auxin influx carrier LAX2 regulates vascular patterning in cotyledons. Although the AUX1/LAX family members share auxin transport characteristics, these transport activities seem to be dependent on their unique cell- or tissue-type expression patterns.
- The Transcription Factors BEL1 and SPL Are Required for Cytokinin and Auxin Signaling During Ovule Development in Arabidopsis
This article examines the role of cytokinin in ovule patterning, finding that cytokinin acts through the auxin efflux facilitator PIN1 and requires the transcription factors BEL1 and SPL/NZZ for proper patterning of the ovule.
- The Arabidopsis Mediator Subunit MED25 Differentially Regulates Jasmonate and Abscisic Acid Signaling through Interacting with the MYC2 and ABI5 Transcription Factors
This work describes that the MED25 subunit of the Arabidopsis thaliana Mediator complex positively regulates JA-mediated gene expression through interacting with the transcription factor MYC2. It also describes that MED25 negatively regulates ABA-mediated gene expression through interacting with the transcription factor ABI5.
- Arabidopsis JAGGED LATERAL ORGANS Acts with ASYMMETRIC LEAVES2 to Coordinate KNOX and PIN Expression in Shoot and Root Meristems
This study analyzes the genetic and protein interactions between the two LOB domain proteins JLO and AS2. Both proteins physically interact with each other but are also able to build homomeric complexes. Genetically, functions were identified that are seemingly common to JLO and AS2 in the regulation of KNOX and PIN expression. JLO depends for some of these functions on AS2.
- PROTON GRADIENT REGULATION5 Is Essential for Proper Acclimation of Arabidopsis Photosystem I to Naturally and Artificially Fluctuating Light Conditions
This work demonstrates that photosystem I, not photosystem II, is susceptible to photodamage under natural fluctuations in light intensity in Arabidopsis thaliana. PGR5 is an indispensable protein for protection of photosystem I, particularly in young plants. PGR5-mediated protection takes place via regulation of linear electron transfer, rather than via cyclic electron transfer.
- Arabidopsis Phytochrome A Is Modularly Structured to Integrate the Multiple Features That Are Required for a Highly Sensitized Phytochrome
This study analyzes a variety of chimeric phytochromes to identify distinct structural modules within the phytochrome A photoreceptor that confer specific properties.
- Functional Analyses of the Plant Photosystem I–Light-Harvesting Complex II Supercomplex Reveal That Light-Harvesting Complex II Loosely Bound to Photosystem II Is a Very Efficient Antenna for Photosystem I in State II
State transitions are a photosynthetic response that allows energy distribution balancing between photosystems. Here, a stable PSI-LHCII supercomplex is purified, and it is demonstrated that LHCIIs loosely bound to PSII in State I are the trimers mainly involved in state transitions. Mobile trimers become strongly bound to PSI in State II, and excitation energy transfer to PSI is fast and efficient.
- N-Terminal Structure of Maize Ferredoxin:NADP+ Reductase Determines Recruitment into Different Thylakoid Membrane Complexes
Maize chloroplasts conducting either cyclic or linear electron flow vary in their ferredoxin:NADP+ reductase (FNR) composition. By comparing FNR crystal structures and introducing modified FNRs back into plants, we show that N-terminal structure determines recruitment to different thylakoid complexes. Furthermore, electron flow is analyzed in plants enriched in FNR at alternative locations.
- A Flavin Binding Cryptochrome Photoreceptor Responds to Both Blue and Red Light in Chlamydomonas reinhardtii
An animal-like cryptochrome (aCRY) functions as a sensory blue light receptor in the green alga Chlamydomonas; in addition, this flavoprotein unexpectedly acts as a sensory red light receptor. For plant cryptochromes, the dark form is proposed to contain an oxidized flavin, whereas for aCRY, the broad spectral responses point to the neutral radical state in the dark.
- The CRYPTOCHROME1-Dependent Response to Excess Light Is Mediated through the Transcriptional Activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis
This work identifies ZML2 and its homolog ZML1 as key regulators of gene expression in the cry1-dependent response to excess light. ZML1/2 bind to the CryR1 cis-element in vitro and in vivo, and T-DNA insertion lines for ZML2 and ZML1 were sensitive to excess light, demonstrating misregulation of several cry1-dependent genes in response to excess light.
- Chloroplasts of Arabidopsis Are the Source and a Primary Target of a Plant-Specific Programmed Cell Death Signaling Pathway
Under mild light stress, plants enhance the production of singlet oxygen that acts as a signal. Singlet oxygen–mediated signaling forms an integral part of photosynthesis that translates environmental variability affecting photosynthetic electron transport into signals that regulate the readjustment of the plant to environmental changes.
- Differential Transit Peptide Recognition during Preprotein Binding and Translocation into Flowering Plant Plastids
Despite their identification >30 years ago, the mechanism of how chloroplast transit peptides direct precursor import remains enigmatic. This is more confounding in light of emerging genomic data that indicate ∼20% of plant genomes encode chloroplast-targeted proteins. This article develops a heuristic approach that may provide universal criteria for what makes a functional transit peptide.
- The Core of Chloroplast Nucleoids Contains Architectural SWIB Domain Proteins
The transcriptionally active chromosome from spinach chloroplasts was analyzed by two-dimensional gel electrophoresis and mass spectrometry to identify proteins involved in structuring of the nucleoid core. SWI/SNF complex B domain–containing proteins were identified that might be functional equivalents of the bacterial nucleoid-associated proteins involved in shaping of nucleoid architecture.
- BEX5/RabA1b Regulates trans-Golgi Network-to-Plasma Membrane Protein Trafficking in Arabidopsis
A fluorescence imaging-based forward genetic screen that detects components of endocytic recycling is used to identify BEX5/RabA1b as a regulator of protein trafficking to the plasma membrane.
- An Essential Pentatricopeptide Repeat Protein Facilitates 5′ Maturation and Translation Initiation of rps3 mRNA in Maize Mitochondria
This work finds that a maize PPR protein (MPPR6) localized to the mitochondria is directly involved in 5′ maturation and translation initiation of rps3 mRNA. This dual role supports a general principle of action for PPR proteins in RNA processing and translation.
- Reconstitution of Plant Alkane Biosynthesis in Yeast Demonstrates That Arabidopsis ECERIFERUM1 and ECERIFERUM3 Are Core Components of a Very-Long-Chain Alkane Synthesis Complex
Very-long-chain alkanes are major components of cuticular waxes, a protective layer covering aerial surfaces of plants. This article shows that the Arabidopsis thaliana CER1 protein interacts with the wax-associated CER3 protein and with the cytochrome b5 isoforms found in the endoplasmic reticulum, and that these proteins constitute the enzymatic complex catalyzing the redox-dependent plant alkane synthesis.
- Tomato GDSL1 Is Required for Cutin Deposition in the Fruit Cuticle
This study analyzes the mechanism by which cutin is deposited. GDSL1, which belongs to the GDSL esterase/acylhydrolase family of plant proteins, is found to play a key role in cutin deposition during fruit cuticle development.
- An Engineered Monolignol 4-O-Methyltransferase Depresses Lignin Biosynthesis and Confers Novel Metabolic Capability in Arabidopsis
Monolignol oxidative coupling is the primary process in lignin biosynthesis, which requires free phenol of a monolignol to generate active radicals. A 4-O-methyltransferase was created via protein engineering that masks the 4-hydroxyls of monolignols. Expressing this enzyme in Arabidopsis led to a substantial reduction of lignin content and concomitant production of novel phenolic esters.
- Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism
The authors demonstrate that parasite gene-specific silencing signals originating from a transgenic host are transferred into the invading parasite, leading to reduced parasite yield, stature, and infectivity. This article also refreshes the debate on the origin of haustoria as the authors use morphological and molecular evidence to show that haustoria have both stem and root characteristics.
