The role of a class III gibberellin 2-oxidase in tomato internode elongation

[EN] A network of environmental inputs and internal signaling controls plant growth, development and organ elongation. In particular, the growth-promoting hormone gibberellin (GA) has been shown to play a significant role in organ elongation. The use of tomato as a model organism to study elongation presents an opportunity to study the genetic control of internode-specific elongation in a eudicot species with a sympodial growth habit and substantial internodes that can and do respond to external stimuli. To investigate internode elongation, a mutant with an elongated hypocotyl and internodes but wild-type petioles was identified through a forward genetic screen. In addition to stem-specific elongation, this mutant, named tomato internode elongated -1 (tie-1) is more sensitive to the GA biosynthetic inhibitor paclobutrazol and has altered levels of intermediate and bioactive GAs compared with wild-type plants. The mutation responsible for the internode elongation phenotype was mapped to GA2oxidase 7, a class III GA 2-oxidase in the GA biosynthetic pathway, through a bulked segregant analysis and bioinformatic pipeline, and confirmed by transgenic complementation. Furthermore, bacterially expressed recombinant TIE protein was shown to have bona fide GA 2-oxidase activity. These results define a critical role for this gene in internode elongation and are significant because they further the understanding of the role of GA biosynthetic genes in organ-specific elongation.This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303. We thank the Tomato Genetics Resource Center for providing seed of the M82 and Heinz cultivars. The material was developed by and/or obtained from the UC Davis/C M Rick Tomato Genetics Resource Center and maintained by the Department of Plant Sciences, University of California, Davis, CA 95616, USA. We thank Anthony Bolger, Alisdair Fernie and Bjorn Usadel for providing us with access to pre-publication genomic reads of the S. lycopersicum cultivar M82, and Cristina Urbez and Noel Blanco-Tourinan (IBMCP, Spain) for technical help with in vitro production of TIE1. This work was supported in part by the Elsie Taylor Stocking Memorial Fellowship awarded to ASL in 2013, by NSF grant IOS-0820854, by USDA National Institute of Food and Agriculture project CA-D-PLB-2465-H, by internal UC Davis funds, and by Spanish Ministry of Economy and Competitiveness grant BFU2016-80621-P.Lavelle, A.; Gath, N.; Devisetty, U.; Carrera Bergua, E.; Lopez Diaz, I.; Blazquez Rodriguez, MA.; Maloof, J. (2018). The role of a class III gibberellin 2-oxidase in tomato internode elongation. 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Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth.

In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana PIFs initiate transcriptional reprogramming in both organs within 15 min, comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. We show that cotyledon-derived auxin is both necessary and sufficient to initiate hypocotyl growth, but we also provide evidence for the functional importance of the local PIF-induced response. With time, the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between different developmentally regulated growth processes and responses to the environment in different organs

Stratigraphy and geochronology of the Tambien Group, Ethiopia: evidence for globally synchronous carbon isotope change in the Neoproterozoic

The Neoproterozoic Era was an interval characterized by profound environmental and biological transitions. Existing age models for Neoproterozoic nonglacial intervals largely have been based on correlation of carbonate carbon isotope values, but there are few tests of the assumed synchroneity of these records between basins. In contrast to the ash-poor successions typically targeted for Neoproterozoic chemostratigraphy, the Tonian to Cryogenian Tambien Group (Tigray region, Ethiopia) was deposited in an arc-proximal basin where volcanic tuffs suitable for U-Pb geochronology are preserved within the mixed carbonate-siliciclastic sedimentary succession. The Tambien Group culminates in a diamictite interpreted to correlate to the ca. 717–662 Ma Sturtian snowball Earth glaciation. New physical stratigraphic data and high-precision U-Pb dates from intercalated tuffs lead to a new stratigraphic framework for the Tambien Group that confirms identification of negative δ13C values from Assem Formation limestones with the ca. 800 Ma Bitter Springs carbon isotope stage. Integration with data from the Fifteenmile Group of northwestern Canada constitutes a positive test for the global synchroneity of the Bitter Spring Stage and constrains the stage to have started after 811.51 ± 0.25 Ma and to have ended before 788.72 ± 0.24 Ma. These new temporal constraints strengthen the case for interpreting Neoproterozoic carbon isotope variation as a record of large-scale changes to the carbon cycle and provide a framework for age models of paleogeographic change, geochemical cycling, and environmental evolution during the radiation of early eukaryotes

Time series modeling of cell cycle exit identifies Brd4 dependent regulation of cerebellar neurogenesis

Cerebellar neuronal progenitors undergo a series of divisions before irreversibly exiting the cell cycle and differentiating into neurons. Dysfunction of this process underlies many neurological diseases including ataxia and the most common pediatric brain tumor, medulloblastoma. To better define the pathways controlling the most abundant neuronal cells in the mammalian cerebellum, cerebellar granule cell progenitors (GCPs), we performed RNA-sequencing of GCPs exiting the cell cycle. Time-series modeling of GCP cell cycle exit identified downregulation of activity of the epigenetic reader protein Brd4. Brd4 binding to the Gli1 locus is controlled by Casein Kinase 1δ (CK1 δ)-dependent phosphorylation during GCP proliferation, and decreases during GCP cell cycle exit. Importantly, conditional deletion of Brd4 in vivo in the developing cerebellum induces cerebellar morphological deficits and ataxia. These studies define an essential role for Brd4 in cerebellar granule cell neurogenesis and are critical for designing clinical trials utilizing Brd4 inhibitors in neurological indications

The Ca and Mg isotope record of the Cryogenian Trezona carbon isotope excursion

This work was supported by a grant from the Simons Foundation (SCOL 611878, ASCA) and the Carlsberg Foundation to ASCA. ASCA and CJB also acknowledge support from the Danish National Research Foundation (Grant No. DNRF53). ACM and CVR acknowledge support from NSF (EAR-0842946) for funding fieldwork on the Trezona Formation in South Australia. JAH acknowledges support from NSF (IES-1410317) and from NSF OCE CAREER Grant (1654571).The Trezona carbon isotope excursion is recorded on five different continents in platform carbonates deposited prior to the end-Cryogenian Marinoan glaciation (>635 Ma) and represents a change in carbon isotope values of 16–18‰. Based on the spatial and temporal reproducibility, the excursion previously has been interpreted as tracking the carbon isotopic composition of dissolved inorganic carbon in the global ocean before the descent into a snowball Earth. However, in modern restricted shallow marine and freshwater settings, carbon isotope values have a similarly large range, which is mostly independent from open ocean chemistry and instead reflects local processes. In this study, we combine calcium, magnesium, and strontium isotope geochemistry with a numerical model of carbonate diagenesis to disentangle the degree to which the Trezona excursion reflects changes in global seawater chemistry versus local shallow-water platform environments. Our analysis demonstrates that the most extreme carbon isotope values (∼-10‰ versus +10‰) are preserved in former platform aragonite that was neomorphosed to calcite during sediment-buffered conditions and record the primary carbon isotope composition of platform-top surface waters. In contrast, the downturn and recovery of the Trezona excursion are recorded in carbonates that were altered during early fluid-buffered diagenesis and commonly are dolomitized. We also find that the nadir of the Trezona excursion is associated with a fractional increase in siliciclastic sediments, whereas the recovery from the excursion correlates with a relative increase in carbonate. This relationship suggests that the extreme negative isotopic shift in platform aragonite occurred in concert with periods of increased input of siliciclastic sediments, changes in water depth, and possibly nutrients to platform environments. Although the process for generating extremely negative carbon isotope values in Neoproterozoic platform carbonates remains enigmatic, we speculate that these excursions reflect kinetic isotope effects associated with CO2 invasion in platform waters during periods of intense primary productivity.Publisher PDFPeer reviewe

Long-term Earth-Moon evolution with high-level orbit and ocean tide models

Tides and Earth‐Moon system evolution are coupled over geological time. Tidal energy dissipation on Earth slows [Formula: see text] rotation rate, increases obliquity, lunar orbit semi‐major axis and eccentricity, and decreases lunar inclination. Tidal and core‐mantle boundary dissipation within the Moon decrease inclination, eccentricity and semi‐major axis. Here we integrate the Earth‐Moon system backwards for 4.5 Ga with orbital dynamics and explicit ocean tide models that are “high‐level” (i.e., not idealized). To account for uncertain plate tectonic histories, we employ Monte Carlo simulations, with tidal energy dissipation rates (normalized relative to astronomical forcing parameters) randomly selected from ocean tide simulations with modern ocean basin geometry and with 55, 116, and 252 Ma reconstructed basin paleogeometries. The normalized dissipation rates depend upon basin geometry and [Formula: see text] rotation rate. Faster Earth rotation generally yields lower normalized dissipation rates. The Monte Carlo results provide a spread of possible early values for the Earth‐Moon system parameters. Of consequence for ocean circulation and climate, absolute (un‐normalized) ocean tidal energy dissipation rates on the early Earth may have exceeded [Formula: see text] rate due to a closer Moon. Prior to [Formula: see text] , evolution of inclination and eccentricity is dominated by tidal and core‐mantle boundary dissipation within the Moon, which yield high lunar orbit inclinations in the early Earth‐Moon system. A drawback for our results is that the semi‐major axis does not collapse to near‐zero values at 4.5 Ga, as indicated by most lunar formation models. Additional processes, missing from our current efforts, are discussed as topics for future investigation