Paradigms of receptor kinase signaling in plants

Plant receptor kinases (RKs) function as key plasma-membrane localized receptors in the perception of molecular ligands regulating development and environmental response. Through the perception of diverse ligands, RKs regulate various aspects throughout the plant life cycle from fertilization to seed set. Thirty years of research on plant RKs has generated a wealth of knowledge on how RKs perceive ligands and activate downstream signaling. In the present review, we synthesize this body of knowledge into five central paradigms of plant RK signaling: (1) RKs are encoded by expanded gene families, largely conserved throughout land plant evolution; (2) RKs perceive many different kinds of ligands through a range of ectodomain architectures; (3) RK complexes are typically activated by co-receptor recruitment; (4) post-translational modifications fulfill central roles in both the activation and attenuation of RK-mediated signaling; and, (5) RKs activate a common set of downstream signaling processes through receptor-like cytoplasmic kinases (RLCKs). For each of these paradigms, we discuss key illustrative examples and also highlight known exceptions. We conclude by presenting five critical gaps in our understanding of RK function

Importance of tyrosine phosphorylation for transmembrane signaling in plants

Reversible protein phosphorylation is a widespread post-translational modification fundamental for signaling across all domains of life. Tyrosine (Tyr) phosphorylation has recently emerged as being important for plant receptor kinase (RK)-mediated signaling, particularly during plant immunity. How Tyr phosphorylation regulates RK function is however largely unknown. Notably, the expansion of protein Tyr phosphatase and SH2 domain-containing protein families, which are the core of regulatory phospho-Tyr (pTyr) networks in choanozoans, did not occur in plants. Here, we summarize the current understanding of plant RK Tyr phosphorylation focusing on the critical role of a pTyr site (‘VIa-Tyr’) conserved in several plant RKs. Furthermore, we discuss the possibility of metazoan-like pTyr signaling modules in plants based on atypical components with convergent biochemical functions

A symbiotic footprint in the plant root microbiome

BACKGROUND: A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure. RESULTS: We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts. CONCLUSION: Our results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome - which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant

SDSS-HET Survey of Kepler Eclipsing Binaries. Description of the Survey and First Results

The Kepler mission has provided a treasure trove of eclipsing binaries (EBs), observed at extremely high photometric precision, nearly continuously for several years. We are carrying out a survey of ~100 of these EBs to derive dynamical masses and radii with precisions of 3% or better. We use multiplexed near-infrared H-band spectroscopy from the Sloan Digital Sky Survey-III and -IV APOGEE instrument and optical spectroscopy from the Hobby–Eberly Telescope High-resolution Spectrograph to derive double-lined spectroscopic orbits and dynamical mass ratios (q) for the EB sample, two of which we showcase in this paper. This orbital information is combined with Kepler photometry to derive orbital inclination, dynamical masses of the system components, radii, and temperatures. These measurements are directly applicable for benchmarking stellar models that are integrating the next generation of improvements, such as the magnetic suppression of convection efficiency, updated opacity tables, and fine-tuned equations of state. We selected our EB sample to include systems with low-mass (M ≾ 0.8 M⊙) primary or secondary components, as well as many EBs expected to populate the relatively sparse parameter space below ~0.5 M⊙. In this paper, we describe our EB sample and the analytical techniques we are utilizing, and also present masses and radii for two systems that inhabit particularly underpopulated regions of mass–radius–period space: KIC 2445134 and KIC 3003991. Our joint spectroscopic and photometric analysis of KIC 2445134 (q = 0.411 ± 0.001) yields masses and radii of M_A = 1.29 ± 0.03 M⊙, M_B = 0.53 ± 0.01 M⊙, R_A = 1.42 ± 0.01 R⊙, R_B = 0.510 ± 0.004 R⊙, and a temperature ratio of T_B/T_A = 0.635 ± 0.001; our analysis of KIC 3003991 (q = 0.298 ± 0.006) yields M_A = 0.74 ± 0.04 M⊙, M_B = 0.222 ± 0.007 M⊙, R_A = 0.84 ± 0.01 R⊙, R_B = 0.250 ± 0.004 R⊙, and a temperature ratio of T_B/T_A = 0.662 ± 0.001

Impact of crosshatch patterns in H2RGs on high-precision radial velocity measurements: exploration of measurement and mitigation paths with the Habitable-Zone Planet Finder

Teledyne’s H2RG detector images suffer from crosshatch like patterns, which arise from subpixel quantum efficiency (QE) variation. We present our measurements of this subpixel QE variation in the Habitable-Zone Planet Finder’s H2RG detector. We present a simple model to estimate the impact of subpixel QE variations on the radial velocity and how a first-order correction can be implemented to correct for the artifact in the spectrum. We also present how the HPF’s future upgraded laser frequency comb will enable us to implement this correction

Solar Contamination in Extreme-precision Radial-velocity Measurements: Deleterious Effects and Prospects for Mitigation

Solar contamination, due to moonlight and atmospheric scattering of sunlight, can cause systematic errors in stellar radial velocity (RV) measurements that significantly detract from the ~10 cm s−1 sensitivity required for the detection and characterization of terrestrial exoplanets in or near habitable zones of Sun-like stars. The addition of low-level spectral contamination at variable effective velocity offsets introduces systematic noise when measuring velocities using classical mask-based or template-based cross-correlation techniques. Here we present simulations estimating the range of RV measurement error induced by uncorrected scattered sunlight contamination. We explore potential correction techniques, using both simultaneous spectrometer sky fibers and broadband imaging via coherent fiber imaging bundles, that could reliably reduce this source of error to below the photon-noise limit of typical stellar observations. We discuss the limitations of these simulations, the underlying assumptions, and mitigation mechanisms. We also present and discuss the components designed and built into the NEID (NN-EXPLORE Exoplanet Investigations with Doppler spectroscopy) precision RV instrument for the WIYN 3.5 m telescope, to serve as an ongoing resource for the community to explore and evaluate correction techniques. We emphasize that while "bright time" has been traditionally adequate for RV science, the goal of 10 cm s−1 precision on the most interesting exoplanetary systems may necessitate access to darker skies for these next-generation instruments

Impact of crosshatch patterns in H2RGs on high-precision radial velocity measurements: exploration of measurement and mitigation paths with the Habitable-Zone Planet Finder

Teledyne’s H2RG detector images suffer from crosshatch like patterns, which arise from subpixel quantum efficiency (QE) variation. We present our measurements of this subpixel QE variation in the Habitable-Zone Planet Finder’s H2RG detector. We present a simple model to estimate the impact of subpixel QE variations on the radial velocity and how a first-order correction can be implemented to correct for the artifact in the spectrum. We also present how the HPF’s future upgraded laser frequency comb will enable us to implement this correction

Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyr-based motif

Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants

The DiskMass Survey. II. Error Budget

We present a performance analysis of the DiskMass Survey. The survey uses collisionless tracers in the form of disk stars to measure the surface-density of spiral disks, to provide an absolute calibration of the stellar mass-to-light ratio, and to yield robust estimates of the dark-matter halo density profile in the inner regions of galaxies. We find a disk inclination range of 25-35 degrees is optimal for our measurements, consistent with our survey design to select nearly face-on galaxies. Uncertainties in disk scale-heights are significant, but can be estimated from radial scale-lengths to 25% now, and more precisely in the future. We detail the spectroscopic analysis used to derive line-of-sight velocity dispersions, precise at low surface-brightness, and accurate in the presence of composite stellar populations. Our methods take full advantage of large-grasp integral-field spectroscopy and an extensive library of observed stars. We show that the baryon-to-total mass fraction (F_b) is not a well-defined observational quantity because it is coupled to the halo mass model. This remains true even when the disk mass is known and spatially-extended rotation curves are available. In contrast, the fraction of the rotation speed supplied by the disk at 2.2 scale lengths (disk maximality) is a robust observational indicator of the baryonic disk contribution to the potential. We construct the error-budget for the key quantities: dynamical disk mass surface-density, disk stellar mass-to-light ratio, and disk maximality (V_disk / V_circular). Random and systematic errors in these quantities for individual galaxies will be ~25%, while survey precision for sample quartiles are reduced to 10%, largely devoid of systematic errors outside of distance uncertainties.Comment: To appear in ApJ; 88 pages, 4 tables, 18 figures. High-resolution version available at http://www.astro.wisc.edu/~mab/publications/DMS_II_preprint.pd

Autophosphorylation-based calcium (Ca2+) sensitivity priming and Ca2+/Calmodulin inhibition of Arabidopsis thaliana Ca2+-dependent protein kinase 28 (CPK28)

Plant calcium (Ca2+) dependent protein kinases (CPKs) are composed of a dual specificity (Ser/Thr and Tyr) kinase domain tethered to a Calmodulin-like domain (CLD) via an autoinhibitory junction (J) and represent the primary Ca2+-dependent protein kinase activities in plant systems. While regulation of CPKs by Ca2+ has been extensively studied, the contribution of autophosphorylation in the control of CPK activity is less well understood. Furthermore, whether Calmodulin (CaM) contributes to CPK regulation, as is the case for Ca2+/CaM-dependent protein kinases (CaMKs) outside the plant lineage, remains an open question. We screened a subset of plant CPKs for CaM-binding and found that CPK28 is a high-affinity Ca2+/CaM-binding protein. Using synthetic peptides and native gel electrophoresis, we coarsely mapped the CaM-binding domain to a site within the CPK28 J domain that overlaps with the known site of intramolecular interaction between the J domain and CLD. Peptide kinase activity of fully dephosphorylated CPK28 was Ca2+-responsive and inhibited by Ca2+/CaM. Using in situ autophosphorylated protein, we expand on the known set of CPK28 autophosphorylation sites, and demonstrate that, unexpectedly, autophosphorylated CPK28 had enhanced activity at physiological concentrations of Ca2+ compared to dephosphorylated protein, suggesting that autophosphorylation functions to prime CPK28 for Ca2+-activation. Furthermore, CPK28 autophosphorylation substantially reduced sensitivity of the kinase to Ca2+/CaM inhibition. Overall, our analyses uncover new complexities in the control of CPK28 and provide mechanistic support for Ca2+ signaling specificity through Ca2+ sensor priming