A cryptic natural variant allele of BYPASS2 suppresses the bypass1 mutant phenotype.

The Arabidopsis (Arabidopsis thaliana) BYPASS1 (BPS1) gene encodes a protein with no functionally characterized domains, and loss-of-function mutants (e.g. bps1-2 in Col-0) present a severe growth arrest phenotype that is evoked by a root-derived graft-transmissible small molecule that we call dalekin.

Overcoming the field-of-view to diameter trade-off in microendoscopy via computational optrode-array microscopy.

High-resolution microscopy of deep tissue with large field-of-view (FOV) is critical for elucidating organization of cellular structures in plant biology. Microscopy with an implanted probe offers an effective solution. However, there exists a fundamental trade-off between the FOV and probe diameter arising from aberrations inherent in conventional imaging optics (typically, FOV < 30% of diameter).

Beyond transcription: compelling open questions in plant RNA biology.

The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article.

DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs.

Gene transcription is counterbalanced by messenger RNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA hellicases of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs. These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics.

Beyond transcription factors: roles of mRNA decay in regulating gene expression in plants.

Gene expression is typically quantified as RNA abundance, which is influenced by both synthesis (transcription) and decay. Cytoplasmic decay typically initiates by deadenylation, after which decay can occur through any of three cytoplasmic decay pathways. Recent advances reveal several mechanisms by which RNA decay is regulated to control RNA abundance.

mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy.

The decay of mRNA plays a vital role in modulating mRNA abundance, which, in turn, influences cellular and organismal processes. In plants and metazoans, three distinct pathways carry out the decay of most cytoplasmic mRNAs: The mRNA decapping complex, which requires the scaffold protein VARICOSE (VCS), removes a protective 5' cap, allowing for 5' to 3' decay via EXORIBONUCLEASE4 (XRN4, XRN1 in metazoans and yeast), and both the exosome and SUPPRESSOR OF VCS (SOV)/DIS3L2 degrade RNAs in the 3' to 5' direction. However, the unique biological contributions of these three pathways, and whether they degrade specialized sets of transcripts, are unknown.

The Mobile bypass Signal Arrests Shoot Growth by Disrupting Shoot Apical Meristem Maintenance, Cytokinin Signaling, and WUS Transcription Factor Expression.

The bypass1 (bps1) mutant of Arabidopsis (Arabidopsis thaliana) produces a root-sourced compound (the bps signal) that moves to the shoot and is sufficient to arrest growth of a wild-type shoot; however, the mechanism of growth arrest is not understood. Here, we show that the earliest shoot defect arises during germination and is a failure of bps1 mutants to maintain their shoot apical meristem (SAM). This finding suggested that the bps signal might affect expression or function of SAM regulatory genes, and we found WUSCHEL (WUS) expression to be repressed in bps1 mutants.

The LSM1-7 Complex Differentially Regulates Arabidopsis Tolerance to Abiotic Stress Conditions by Promoting Selective mRNA Decapping.

In eukaryotes, the decapping machinery is highly conserved and plays an essential role in controlling mRNA stability, a key step in the regulation of gene expression. Yet, the role of mRNA decapping in shaping gene expression profiles in response to environmental cues and the operating molecular mechanisms are poorly understood. Here, we provide genetic and molecular evidence that a component of the decapping machinery, the LSM1-7 complex, plays a critical role in plant tolerance to abiotic stresses.

The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2.

Multi-layered defense responses are activated in plants upon recognition of invading pathogens. Transmembrane receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and activate MAP kinase cascades, which regulate changes in gene expression to produce appropriate immune responses. For example, Arabidopsis MAP kinase 4 (MPK4) regulates the expression of a subset of defense genes via at least one WRKY transcription factor.

Long-distance signaling in bypass1 mutants: bioassay development reveals the bps signal to be a metabolite.

Root-to-shoot signaling is used by plants to coordinate shoot development with the conditions experienced by the roots. A mobile and biologically active compound, the bps signal, is over-produced in roots of an Arabidopsis thaliana mutant called bypass1 (bps1), and might also be a normally produced signaling molecule in wild-type plants. Our goal is to identify the bps signal chemically, which will then allow us to assess its production in normal plants.

The bps signal: embryonic arrest from an auxin-independent mechanism in bypass triple mutants.

Long-distance signaling is essential for coordination of plant development and environmental responses. We originally isolated a tiny mutant named bypass1 (bps1), which has defects in shoot and root development. The bps1 roots overproduce a mobile signal (bps signal) that arrests both root and shoot development.

In the absence of BYPASS1-related gene function, the bps signal disrupts embryogenesis by an auxin-independent mechanism.

Development is often coordinated by biologically active mobile compounds that move between cells or organs. Arabidopsis mutants with defects in the BYPASS1 (BPS1) gene overproduce an active mobile compound that moves from the root to the shoot and inhibits growth. Here, we describe two related Arabidopsis genes, BPS2 and BPS3.

BYPASS1: synthesis of the mobile root-derived signal requires active root growth and arrests early leaf development.

Background: The Arabidopsis bypass1 (bps1) mutant root produces a biologically active mobile compound that induces shoot growth arrest. However it is unknown whether the root retains the capacity to synthesize the mobile compound, or if only shoots of young seedlings are sensitive. It is also unknown how this compound induces arrest of shoot growth.

Conserved RNaseII domain protein functions in cytoplasmic mRNA decay and suppresses Arabidopsis decapping mutant phenotypes.

Both transcription and RNA decay are critical for normal gene regulation. Arabidopsis mutants with defects in VARICOSE (VCS), a decapping complex scaffold protein, lack mRNA decapping and 5'-to-3' decay. These mutants show either severe or suppressed phenotypes, depending on the Arabidopsis accession.

Plasmodesmata formation: poking holes in walls with ise.

Secondary plasmodesmata are cytoplasmic channels connecting adjacent plant cells that arise after cell division. How membrane-delimited channels penetrate cell walls is unknown, but now two genes, ISE1 and ISE2, are shown to be required for pathways that limit their formation.

BYPASS1: how a tiny mutant tells a big story about root-to-shoot signaling.

Plants coordinate their development using long-distance signaling. The vascular system provides a route for long-distance movement, and specifically the xylem for root-to-shoot signaling. Root-to-shoot signals play roles communicating soil conditions, and these signals are important for agricultural water conservation.

Kill the messenger: mRNA decay and plant development.

A pervasive theme in development is that dynamic changes in gene expression drive developmental progression; yet in studies of gene expression, the general RNA decay pathways have historically played second fiddle to transcription. However, recent advances in this field have revealed a surprising degree of mRNA specificity for particular branches of these RNA decay pathways. General cytoplasmic mRNA decay typically initiates with deadenylation, following which the deadenylated mRNA can continue decay from the 3'-end through the action of the exosome, or it can undergo 5'-to-3' decay.

Widespread translational inhibition by plant miRNAs and siRNAs.

High complementarity between plant microRNAs (miRNAs) and their messenger RNA targets is thought to cause silencing, prevalently by endonucleolytic cleavage. We have isolated Arabidopsis mutants defective in miRNA action. Their analysis provides evidence that plant miRNA-guided silencing has a widespread translational inhibitory component that is genetically separable from endonucleolytic cleavage.

Plant development: PXY and polar cell division in the procambium.

The vascular stem-cell tissue known as procambium generates phloem cells on one side and xylem cells on the other. The Arabidopsis PXY gene encodes a leucine-rich repeat receptor-like kinase that is required for polar divisions of procambial cells.

Components of the Arabidopsis mRNA decapping complex are required for early seedling development.

To understand the mechanisms controlling vein patterning in Arabidopsis thaliana, we analyzed two phenotypically similar mutants, varicose (vcs) and trident (tdt). We had previously identified VCS, and recently, human VCS was shown to function in mRNA decapping. Here, we report that TDT encodes the mRNA-decapping enzyme.

Dissecting the biosynthetic pathway for the bypass1 root-derived signal.

The Arabidopsis BYPASS1 (BPS1) gene is required for normal root and shoot development. In bps1 mutants, grafting and root excision experiments have shown that mutant roots produce a transmissible signal that is capable of arresting shoot development. In addition, we previously showed that growth of bps1 mutants on the carotenoid biosynthesis inhibitor fluridone resulted in partial rescue of both leaf and root defects.

SCARFACE encodes an ARF-GAP that is required for normal auxin efflux and vein patterning in Arabidopsis.

To identify molecular mechanisms controlling vein patterns, we analyzed scarface (sfc) mutants. sfc cotyledon and leaf veins are largely fragmented, unlike the interconnected networks in wild-type plants. SFC encodes an ADP ribosylation factor GTPase activating protein (ARF-GAP), a class with well-established roles in vesicle trafficking regulation.

Vascular development: the long and winding road.

Vascular development involves the specification of distinct meristematic cells that proliferate and then differentiate into two separate multicellular tissues: xylem and phloem. Organ-specific patterning, which requires the co-ordination of vascular development with organogenesis, introduces another layer of complexity to the development of vascular tissues. Because vascular tissues develop internally, analyses of their development are technically challenging.

BYPASS1 negatively regulates a root-derived signal that controls plant architecture.

Plant architecture is regulated by endogenous developmental programs, but it can also be strongly influenced by cues derived from the environment. For example, rhizosphere conditions such as water and nutrient availability affect shoot and root architecture; this implicates the root as a source of signals that can override endogenous developmental programs. Cytokinin, abscisic acid, and carotenoid derivatives have all been implicated as long-distance signals that can be derived from the root.

VARICOSE, a WD-domain protein, is required for leaf blade development.

To gain insight into the processes controlling leaf development, we characterized an Arabidopsis mutant, varicose (vcs), with leaf and shoot apical meristem defects. The vcs phenotype is temperature dependent; low temperature growth largely suppressed defects, whereas high growth temperatures resulted in severe leaf and meristem defects. VCS encodes a putative WD-domain containing protein, suggesting a function involving protein-protein interactions.