Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis

Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the previously identified interactome of the Transport Protein Particle II (TRAPPII) complex required for TGN structure and function. We identified physical and genetic interactions between AtTRAPPII and shaggy-like kinases (GSK3/AtSKs) and provided in vitro and in vivo evidence that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the AtTRAPPII interactome is vast and considerably enriched in signaling components. An AtSK-TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.

Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis

Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi Network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the interactome of the Transport Protein Particle II (TRAPPII) complex, required for TGN structure and function. We identified physical and genetic interactions between TRAPPII and shaggy-like kinases (GSK3/AtSKs). Kinase assays and pharmacological inhibition provided in vitro and in vivo evidence that AtSKs target the TRAPPII-specific subunit AtTRS120/TRAPPC9. GSK3/AtSK phosphorylation sites in AtTRS120/TRAPPC9 were mutated, and the resulting AtTRS120 phosphovariants subjected to a variety of single and multiple stress conditions in planta . The non-phosphorylatable TRS120 mutant exhibited enhanced adaptation to multiple stress conditions and to osmotic stress whereas the phosphomimetic version was less resilient. Higher order inducible trappii atsk mutants had a synthetically enhanced defect in root gravitropism. Our results suggest that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the TRAPPII interactome is vast and considerably enriched in signaling components. An AtSK-TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.

Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion

Plants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.

A proteome-scale map of the SARS-CoV-2-human contactome

Understanding the mechanisms of coronavirus disease 2019 (COVID-19) disease severity to efficiently design therapies for emerging virus variants remains an urgent challenge of the ongoing pandemic. Infection and immune reactions are mediated by direct contacts between viral molecules and the host proteome, and the vast majority of these virus-host contacts (the 'contactome') have not been identified. Here, we present a systematic contactome map of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with the human host encompassing more than 200 binary virus-host and intraviral protein-protein interactions. We find that host proteins genetically associated with comorbidities of severe illness and long COVID are enriched in SARS-CoV-2 targeted network communities. Evaluating contactome-derived hypotheses, we demonstrate that viral NSP14 activates nuclear factor κB (NF-κB)-dependent transcription, even in the presence of cytokine signaling. Moreover, for several tested host proteins, genetic knock-down substantially reduces viral replication. Additionally, we show for USP25 that this effect is phenocopied by the small-molecule inhibitor AZ1. Our results connect viral proteins to human genetic architecture for COVID-19 severity and offer potential therapeutic targets.

Chemokine-like MDL proteins modulate flowering time and innate immunity in plants

Human macrophage migration inhibitory factor (MIF) is an atypical chemokine implicated in intercellular signaling and innate immunity. MIF orthologs (MIF/D-DT-like proteins, MDLs) are present throughout the plant kingdom, but remain experimentally unexplored in these organisms. Here, we provide an in planta characterization and functional analysis of the three-member gene/protein MDL family in Arabidopsis thaliana. Subcellular localization experiments indicated a nucleo-cytoplasmic distribution of MDL1 and MDL2, while MDL3 is localized to peroxisomes. Protein–protein interaction assays revealed the in vivo formation of MDL1, MDL2, and MDL3 homo-oligomers, as well as the formation of MDL1-MDL2 hetero-oligomers. Functionally, Arabidopsismdl mutants exhibited a delayed transition from vegetative to reproductive growth (flowering) under long-day conditions, but not in a short-day environment. In addition, mdl mutants were more resistant to colonization by the bacterial pathogen Pseudomonas syringae pv. maculicola. The latter phenotype was compromised by the additional mutation of SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2), a gene implicated in the defense-induced biosynthesis of the key signaling molecule salicylic acid. However, the enhanced antibacterial immunity was not associated with any constitutive or pathogen-induced alterations in the levels of characteristic phytohormones or defense-associated metabolites. Interestingly, bacterial infection triggered relocalization and accumulation of MDL1 and MDL2 at the peripheral lobes of leaf epidermal cells. Collectively, our data indicate redundant functionality and a complex interplay between the three chemokine-like Arabidopsis MDL proteins in the regulation of both developmental and immune-related processes. These insights expand the comparative cross-kingdom analysis of MIF/MDL signaling in human and plant systems.

[Unilateral retinal hemorrhage in infants-two cases of shaken baby syndrome?]

Ein 2,5 Monate alter Junge und ein 2 Monate altes Mädchen wurden wegen schwerer Bewusstseinstrübung pädiatrisch behandelt. Bei beiden Kindern fanden sich Subduralhämatome. Bei Verdacht auf nichtakzidentelles Schädel-Hirn-Trauma (NAHI) erfolgte eine Untersuchung des Augenhintergrundes, bei der sich bei beiden Säuglingen unilaterale Netzhautblutungen zeigten. Nach intensiver Differenzialdiagnostik wurde in beiden Fällen der Verdacht auf ein NAHI gestellt und eine rechtsmedizinische Begutachtung initiiert. Wichtig an dieser Fallserie ist, dass die Einseitigkeit von Netzhautblutungen ein NAHI nicht ausschließt.

Publisher Correction: Extensive signal integration by the phytohormone protein network

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

TRIPP Is a Plant-Specific Component of the Arabidopsis TRAPPII Membrane Trafficking Complex with Important Roles in Plant Development

How the membrane trafficking system spatially organizes intracellular activities and intercellular signaling networks in plants is not well understood. Transport Protein Particle (TRAPP) complexes play key roles in the selective delivery of membrane vesicles to various subcellular compartments in yeast and animals but remain to be fully characterized in plants. Here, we investigated TRAPP complexes in Arabidopsis (Arabidopsis thaliana) using immunoprecipitation followed by quantitative mass spectrometry analysis of AtTRS33, a conserved core component of all TRAPP complexes. We identified 14 AtTRS33-interacting proteins, including homologs of all 13 TRAPP components in mammals and a protein that has homologs only in multicellular photosynthetic organisms and is thus named TRAPP-Interacting Plant Protein (TRIPP). TRIPP specifically associates with the TRAPPII complex through binary interactions with two TRAPPII-specific subunits. TRIPP colocalized with a subset of TRS33 compartments and trans-Golgi network markers in a TRS33-dependent manner. Loss-of-function tripp mutants exhibited dwarfism, sterility, partial photomorphogenesis in the dark, reduced polarity of the auxin transporter PIN2, incomplete cross wall formation, and altered localization of a TRAPPII-specific component. Therefore, TRIPP is a plant-specific component of the TRAPPII complex with important functions in trafficking, plant growth, and development.

Interactions between Transport Protein Particle (TRAPP) complexes and Rab GTPases in Arabidopsis

Transport Protein Particle II (TRAPPII) is essential for exocytosis, endocytosis, protein sorting and cytokinesis. In spite of a considerable understanding of its biological role, little information is known about Arabidopsis TRAPPII complex topology and molecular function. In this study, independent proteomic approaches initiated with TRAPP components or Rab-A GTPase variants converge on the TRAPPII complex. We show that the Arabidopsis genome encodes the full complement of 13 TRAPPC subunits, including four previously unidentified components. A dimerization model is proposed to account for binary interactions between TRAPPII subunits. Preferential binding to dominant negative (GDP-bound) versus wild-type or constitutively active (GTP-bound) RAB-A2a variants discriminates between TRAPPII and TRAPPIII subunits and shows that Arabidopsis complexes differ from yeast but resemble metazoan TRAPP complexes. Analyzes of Rab-A mutant variants in trappii backgrounds provide genetic evidence that TRAPPII functions upstream of RAB-A2a, allowing us to propose that TRAPPII is likely to behave as a guanine nucleotide exchange factor (GEF) for the RAB-A2a GTPase. GEFs catalyze exchange of GDP for GTP; the GTP-bound, activated, Rab then recruits a diverse local network of Rab effectors to specify membrane identity in subsequent vesicle fusion events. Understanding GEF-Rab interactions will be crucial to unravel the co-ordination of plant membrane traffic.

Independent yet overlapping pathways ensure the robustness and responsiveness of trans-Golgi network functions in Arabidopsis

The trans-Golgi-network (TGN) has essential housekeeping functions in secretion, endocytosis and protein sorting, but also more specialized functions in plant development. How the robustness of basal TGN function is ensured while specialized functions are differentially regulated is poorly understood. Here, we investigate two key regulators of TGN structure and function, ECHIDNA and the Transport Protein Particle II (TRAPPII) tethering complex. An analysis of physical, network and genetic interactions suggests that two network communities are implicated in TGN function and that ECHIDNA and TRAPPII belong to distinct yet overlapping pathways. Whereas ECHIDNA and TRAPPII colocalized at the TGN in interphase cells, their localization diverged in dividing cells. Moreover, ECHIDNA and TRAPPII localization patterns were mutually independent. TGN structure, endocytosis and sorting decisions were differentially impacted in echidna and trappii mutants. Our analyses point to a partitioning of specialized TGN functions, with ECHIDNA being required for cell elongation and TRAPPII for cytokinesis. Two independent pathways able to compensate for each other might contribute to the robustness of TGN housekeeping functions and to the responsiveness and fine tuning of its specialized functions.

High-Quality Yeast-2-Hybrid Interaction Network Mapping

In this article, we describe a Y2H interaction mapping protocol for systematically screening medium-to-large collections of open reading frames (ORFs) against each other. The protocol is well suited for analysis of focused networks, for modules of interest, assembling genome-scale interactome maps, and investigating host-microbe interactions. The four-step high-throughput protocol has a demonstrated low false-discovery rate that is essential for producing meaningful network maps. Following the assembly of yeast expression clones from an existing ORFeome collection, we describe in detail the four-step procedure that begins with the primary screen using minipools, followed by secondary verification of primary positives, identification of candidate interaction pairs by sequencing, and a final verification step using fresh inoculants. In addition to this core protocol, aspects of network mapping and quality control will be discussed briefly. © 2018 by John Wiley & Sons, Inc.

Improved Automatic Segmentation of White Matter Hyperintensities in MRI Based on Multilevel Lesion Features

Brain white matter hyperintensities (WMHs) are linked to increased risk of cerebrovascular and neurodegenerative diseases among the elderly. Consequently, detection and characterization of WMHs are of significant clinical importance. We propose a novel approach for WMH segmentation from multi-contrast MRI where both voxel-based and lesion-based information are used to improve overall performance in both volume-oriented and object-oriented metrics. Our segmentation method (AMOS-2D) consists of four stages following a "generate-and-test" approach: pre-processing, Gaussian white matter (WM) modelling, hierarchical multi-threshold WMH segmentation and object-based WMH filtering using support vector machines. Data from 28 subjects was used in this study covering a wide range of lesion loads. Volumetric T1-weighted images and 2D fluid attenuated inversion recovery (FLAIR) images were used as basis for the WM model and lesion masks defined manually in each subject by experts were used for training and evaluating the proposed method. The method obtained an average agreement (in terms of the Dice similarity coefficient, DSC) with experts equivalent to inter-expert agreement both in terms of WMH number (DSC = 0.637 vs. 0.651) and volume (DSC = 0.743 vs. 0.781). It allowed higher accuracy in detecting WMH compared to alternative methods tested and was further found to be insensitive to WMH lesion burden. Good agreement with expert annotations combined with stable performance largely independent of lesion burden suggests that AMOS-2D will be a valuable tool for fully automated WMH segmentation in patients with cerebrovascular and neurodegenerative pathologies.

LSU network hubs integrate abiotic and biotic stress responses via interaction with the superoxide dismutase FSD2

In natural environments, plants often experience different stresses simultaneously, and adverse abiotic conditions can weaken the plant immune system. Interactome mapping revealed that the LOW SULPHUR UPREGULATED (LSU) proteins are hubs in an Arabidopsis protein interaction network that are targeted by virulence effectors from evolutionarily diverse pathogens. Here we show that LSU proteins are up-regulated in several abiotic and biotic stress conditions, such as nutrient depletion or salt stress, by both transcriptional and post-translational mechanisms. Interference with LSU expression prevents chloroplastic reactive oxygen species (ROS) production and proper stomatal closure during sulphur stress. We demonstrate that LSU1 interacts with the chloroplastic superoxide dismutase FSD2 and stimulates its enzymatic activity in vivo and in vitro. Pseudomonas syringae virulence effectors interfere with this interaction and preclude re-localization of LSU1 to chloroplasts. We demonstrate that reduced LSU levels cause a moderately enhanced disease susceptibility in plants exposed to abiotic stresses such as nutrient deficiency, high salinity, or heavy metal toxicity, whereas LSU1 overexpression confers significant disease resistance in several of these conditions. Our data suggest that the network hub LSU1 plays an important role in co-ordinating plant immune responses across a spectrum of abiotic stress conditions.

Cell cycle-regulated PLEIADE/AtMAP65-3 links membrane and microtubule dynamics during plant cytokinesis

Cytokinesis, the partitioning of the cytoplasm following nuclear division, requires extensive coordination between cell cycle cues, membrane trafficking and microtubule dynamics. Plant cytokinesis occurs within a transient membrane compartment known as the cell plate, to which vesicles are delivered by a plant-specific microtubule array, the phragmoplast. While membrane proteins required for cytokinesis are known, how these are coordinated with microtubule dynamics and regulated by cell cycle cues remains unclear. Here, we document physical and genetic interactions between Transport Protein Particle II (TRAPPII) tethering factors and microtubule-associated proteins of the PLEIADE/AtMAP65 family. These interactions do not specifically affect the recruitment of either TRAPPII or MAP65 proteins to the cell plate or midzone. Rather, and based on single versus double mutant phenotypes, it appears that they are required to coordinate cytokinesis with the nuclear division cycle. As MAP65 family members are known to be targets of cell cycle-regulated kinases, our results provide a conceptual framework for how membrane and microtubule dynamics may be coordinated with each other and with the nuclear cycle during plant cytokinesis.

Ocular color-coded sonography - a promising tool for neurologists and intensive care physicians

Ocular color-coded duplex sonography (OCCS), when performed within the safety limits of diagnostic ultrasonography, is an easy noninvasive technique with high potential for diagnosis and therapy in diseases with raised intracranial pressure and vascular diseases affecting the eye. Despite the capabilities of modern ultrasound systems and its scientific validation, OCCS has not gained widespread use in neurological practice. In this review, the authors describe the technique and main parameter settings of OCCS systems to reduce potential risks as thermal or cavitational effects for sensitive orbital structures. Applications of OCCS are the determination of intracranial pressure in emergency medicine, and follow-up evaluations of idiopathic intracranial hypertension and ventricular shunting by measuring the optic nerve sheath diameter. A diameter of 5.7 - 6.0 mm corresponds well with symptomatically increased intracranial pressure (> 20 cmH2O). OCCS also helps to discriminate between different etiologies of central retinal artery occlusion - by visualization of a "spot sign" and Doppler flow analysis of the central retinal artery - and aids the differential diagnosis of papilledema. At the end perspectives are illustrated that combine established ultrasound methods such as transcranial color-coded sonography with OCCS.

The retrobulbar "spot sign" as a discriminator between vasculitic and thrombo-embolic affections of the retinal blood supply

PURPOSE

Sudden retinal blindness is a common complication of temporal arteritis (TA). Another common cause is embolic occlusion of the central retinal artery (CRA). The aim of this prospective study was to examine the diagnostic value of hyperechoic material in the CRA for the exclusion of vasculitis as a cause. The authors used orbital color-coded sonography (OCCS) for the detection of hyperechoic material.

MATERIALS AND METHODS

24 patients with sudden vision loss were included in the study after the exclusion of other causes (e. g. vitreous bleeding, retinal detachment). Parallel to routine diagnostic workup, OCCS was performed in all patients.

RESULTS

7 patients with a diagnosis of TA presented with different degrees of hypoperfusion in the CRA without hyperechoic material (referred to as "spot sign") detected by OCCS. Diagnostic workup in the remaining 17 patients revealed other causes of sudden vision loss, such as central retinal artery occlusion (CRAO) (12), anterior ischemic optic neuropathy (AION) (2), upstream vascular stenosis or occlusion (2) and delayed reperfusion of the CRA (1). The hyperechoic "spot sign" was visible in 10 of 12 patients (83 %) with embolic CRAO. The detection of embolic CRAO using the "spot sign" had a sensitivity of 83 % and a specificity of 100 %. The missing "spot sign" in patients with TA was a highly specific finding (p-value 0.01).

CONCLUSION

The detection of the "spot sign" specifically minimizes the probability of TA as a reason for sudden blindness.

Preliminary case report of fatal anthrax in an injecting drug user in North-Rhine-Westphalia, Germany, December 2009

A fatal case of anthrax occurred in an injecting drug user in Germany, in December 2009. A potential link to similar cases in Scotland in the same time period is currently under investigation.

The relationships between leptin concentrations and body fat reserves in lambs are reduced by short-term fasting

Feed deprivation decreases plasma leptin concentrations depending on the amount of body fat reserves. While a greater response was observed in lean than in fat humans and rats, a few results for ruminants are inconsistent. The objective of this study was to determine the influence of feed deprivation on plasma leptin concentration in growing lambs with different body fat reserves and on the relationship between leptin and fatness. In addition, we included other hormones (growth hormone, GH; insulin-like growth factor-I, IGF-I and insulin) involved in tissue development. Thirty male lambs of 40 kg live weight were used. Blood was sampled before and after a fasting period of 24 h. The lambs were slaughtered and dissected into several fat and lean tissues. Feed deprivation reduced plasma leptin by an average of 34.6% (p < 0.001). Obese lambs exhibited a greater decline of leptin than lean lambs (2.50 vs. 1.36 ng/ml, p < 0.05). The correlations between leptin and several fat tissues were lower in those lambs than that were fasted. This indicates that leptin concentrations after short-term fasting scarcely reflect the extent of body fat reserves but reflect more the actual metabolic situation. Body fat did not significantly influence the response of GH, IGF-I and insulin to fasting in most cases.

Relationship between plasma leptin concentrations and carcass composition in fattening mutton: a comparison with ultrasound results

Positive relationships between circulating leptin concentrations and body fat content have been established in sheep when covering a rather broad range of age and/or body weight. The usefulness of leptin measurements for predicting carcass fat has yet to be evaluated specifically in fattening lambs. We therefore measured plasma leptin concentrations in 56 male lambs half and half Merino Mutton and Blackheaded Mutton. Subcutaneous fat thickness was measured by ultrasound 1 day before the lambs were slaughtered at 35 or 45 kg live weight. Carcass composition was determined by tissue dissection. The coefficients of correlations between leptin and the different amounts in fat depots ranged from 0.40 to 0.56 within the two live weight groups, and from 0.53 to 0.64 when taking the two groups together. Carcass fat percentage was estimated by leptin concentrations with the same accuracy (R2 = 0.34) as with ultrasound fat thickness. The accuracy was higher for leptin in the 35 kg-group whereas the accuracy was higher for ultrasound fat thickness in the 45 kg-group (R2 = 0.26 vs. 0.31). A combination of leptin and ultrasound fat thickness clearly enhanced the precision of estimation in all groups. Further investigations on the influence of factors such as breed, gender, duration of feed withdrawal or photoperiod on the association between leptin and carcass composition are necessary before the suitability of plasma leptin concentration for practical application can be evaluated.

Prediction of lamb carcass composition by impedance spectroscopy

The objective of this study was to compare impedance spectroscopy with resistance measurements at a single frequency (50 kHz) for the prediction of lamb carcass composition. The impedance spectrum is usually recorded by measuring the complex impedance at various frequencies (frequency domain); however, in this study, we also applied the faster and simpler measurement in the time domain (application of a current step and measurement of the voltage response). The study was carried out on 24 male, German Black-headed Mutton lambs with an average BW of 45 kg. Frequency- and time domain-based impedance measurements were collected at 20 min and 24 h postmortem with different electrode placements. Real and imaginary parts at various frequencies were calculated from the locus diagram. Left sides were dissected into lean, fat, and bone, and right sides were ground to determine actual carcass composition. Crude fat, crude protein, and moisture were chemically analyzed on ground samples. Frequency- and time domain-based measurements did not provide the same absolute impedance values; however, the high correlations (P < 0.001) between these methods for the "real parts" showed that they ranked individuals in the same order. Most of the time domain data correlated higher to carcass composition than did the frequency domain data. The real parts of impedance showed correlations between -0.37 (P > 0.05) and -0.74 (P < 0.001) to water, crude fat, lean, and fatty tissue, whereas the relations to CP were much lower (from 0.00 to -0.47, P < 0.05). Electrode placements at different locations did not substantially improve the correlations with carcass composition. The "imaginary parts" of impedance were not suitable for the prediction of carcass composition. The highest accuracy (R2 = 0.66) was reached for the estimation of crude fat percentage by a regression equation with the time domain-based impedance measured at 24 h postmortem. Furthermore, there was not a clear superiority of measurements in a wide frequency range over a single frequency measurement at 50 kHz for the prediction of carcass composition. Even though we calculated the impedance at 50 kHz based on the locus diagram, which allowed for a high precision for predicting this impedance trait, single-frequency impedance devices typically used in practice cannot record the locus diagram and, therefore, exhibit a greater amount of uncertainty.

P(y)-a parameter for meat quality

The P(y) is a parameter which assesses the integrity of the cell membranes. It is a direct indicator for the volume fraction of cells surrounded by insulating cell membranes. The P(y) has been shown to correlate well with meat quality parameters like the drip loss or pH. It is a useful parameter for the discrimination between normal suited meat and PSE meat. The measurement is instantaneous and nondestructive. Due to aging of meat, P(y) depends on the time post mortem. It shows the highest significance between 4 and 24 h p.m.

Evidence for import of a lysyl-tRNA into marsupial mitochondria

The mitochondrial tRNA gene for lysine was analyzed in 11 different marsupial mammals. Whereas its location is conserved when compared with other vertebrate mitochondrial genomes, its primary sequence and inferred secondary structure are highly unusual and variable. For example, eight species lack the expected anticodon. Because the corresponding transcripts are not altered by any RNA-editing mechanism, the lysyl-tRNA gene seems to represent a mitochondrial pseudogene. Purification of marsupial mitochondria and in vitro aminoacylation of isolated tRNAs with lysine, followed by analysis of aminoacylated tRNAs, show that a nuclear-encoded tRNA(Lys) is associated with marsupial mitochondria. We conclude that a functional tRNA(Lys) encoded in the nuclear genome is imported into mitochondria in marsupials. Thus, tRNA import is not restricted to plant, yeast, and protozoan mitochondria but also occurs also in mammals.

Structural and functional similarities between the central eukaryotic initiation factor (eIF)4A-binding domain of mammalian eIF4G and the eIF4A-binding domain of yeast eIF4G

The translation eukaryotic initiation factor (eIF)4G of the yeast Saccharomyces cerevisiae interacts with the RNA helicase eIF4A (a member of the DEAD-box protein family; where DEAD corresponds to Asp-Glu-Ala-Asp) through a C-terminal domain in eIF4G (amino acids 542-883). Mammalian eIF4G has two interaction domains for eIF4A, a central domain and a domain close to the C-terminus. This raises the question of whether eIF4A binding to eIF4G is conserved between yeast and mammalian cells or whether it is different. We isolated eIF4G1 mutants defective in eIF4A binding and showed that these mutants are strongly impaired in translation and growth. Extracts from mutants displaying a temperature-sensitive phenotype for growth have low in vitro translation activity, which can be restored by addition of the purified eIF4G1-eIF4E complex, but not by eIF4E alone. Analysis of mutant eIF4G(542-883) proteins defective in eIF4A binding shows that the interaction of yeast eIF4A with eIF4G1 depends on amino acid motifs that are conserved between the yeast eIF4A-binding site and the central eIF4A-binding domain of mammalian eIF4G. We show that mammalian eIF4A binds tightly to yeast eIF4G1 and, furthermore, that mutant yeast eIF4G(542-883) proteins, which do not bind yeast eIF4A, do not interact with mammalian eIF4A. Despite the conservation of the eIF4A-binding site in eIF4G and the strong sequence conservation between yeast and mammalian eIF4A (66% identity; 82% similarity at the amino acid level) mammalian eIF4A does not substitute for the yeast factor in vivo and is not functional in a yeast in vitro translation system.

Conjugated organometallic polymers containing Vollhardt's cyclobutadiene complex: aggregation and morphologies

Organometallic polymers were prepared by acyclic diyne metathesis (ADIMET) or by Pd-catalyzed coupling of 1,3-diethynylcyclobutadiene(cyclopentadienyl)cobalt with a suitably substituted diiodobenzene. The polymers obtained by Heck coupling show a degree of polymerization (Pn) of 20-60. The monomers for ADIMET were made by the Pd-catalyzed coupling of [1,3-bis(trimethylsilylethynyl)-2,4-bis(trimethylsilyl)cyclobutadiene](cyclopentadienyl)cobalt to 1-bromo-2,5-dialkyl-4-propynylbenzenes in the presence of KOH in yields of 40-48%. The monomers carry hexyl, ethylhexyl, and (S)-3,7-dimethyloctyl side chains. Polymerization of the propynylated monomers furnishes organometallic polymers with a Pn of up to 230 arylene-ethynylene units. The polymers were fully characterized by polarizing microscopy, transmission electron microscopy, circular dichroism, differential scanning calorimetry, and X-ray diffraction (XRD). They show nematic, lyotropic liquid crystalline phases as well as chiroptical properties from which aggregation in poor solvents and in the solid state can be concluded. Lamellar or irregular honeycomb-shaped morphologies in these organometallic polymers can be detected by electron microscopy.

Environmental factors can confound identification of a major gene effect: results from a segregation analysis of a simulated population of lung cancer families

Proper control of environmental factors can be crucial to the identification of genes that influence susceptibility to a complex trait, especially for a trait such as lung cancer, for which the environmental factor (smoking) accounts for a significant etiologic fraction of the disease. An earlier segregation analysis of 337 Louisiana families, which incorporated direct measure of tobacco consumption, provided evidence for autosomal codominant inheritance of a major gene that influenced age at onset of lung cancer. Subsequent analyses were performed in which the families were stratified into two subsets based on birth cohort of the proband; results suggested the presence of heterogeneity that were postulated to reflect the influence of cohort trends in tobacco consumption. To evaluate this hypothesis further, we simulated a population of three-generation pedigrees in which an autosomal dominant mode of susceptibility to lung cancer was transmitted, but tobacco use varied across generations corresponding to published trends in smoking. A total of 200,000 individuals in families of various sizes, ages, and cigarette smoking habits were simulated from 1900 to 1980. From this population, 324 families (2,405 individuals) with 380 cases of lung cancer were ascertained through 328 lung cancer probands. Complex segregation analysis was performed using the REGTL program of S.A.G.E. in which pack-years of tobacco exposure were incorporated directly into the likelihood calculations. Although the no major gene, environmental, and Mendelian recessive hypotheses were rejected, both dominant and codominant transmission provided a good fit to the data. Thus in a population of simulated families with autosomal dominant susceptibility to lung cancer, intergenerational differences in tobacco consumption led to the detection of autosomal codominant transmission as an acceptable hypothesis. These results underscore the potential danger of segregation analysis of complex traits in which exposure to known environmental influences may differ across generations.

Genomic cloning, chromosomal mapping, and expression analysis of msal-2

Mutations of SALL1 related to spalt of Drosophila have been found to cause Townes-Brocks syndrome, suggesting a function of SALL1 for the development of anus, limbs, ears, and kidneys. No function is yet known for SALL2, another human spalt-like gene. The structure of SALL2 is different from SALL1 and all other vertebrate spalt-like genes described in mouse, Xenopus, and Medaka, suggesting that SALL2-like genes might also exist in other vertebrates. Consistent with this hypothesis, we isolated and characterized a SALL2 homologous mouse gene, Msal-2. In contrast to other vertebrate spalt-like genes both SALL2 and Msal-2 encode only three double zinc finger domains, the most carboxyterminal of which only distantly resembles spalt-like zinc fingers. The evolutionary conservation of SALL2/Msal-2 suggests that two lines of sal-like genes with presumably different functions arose from an early evolutionary duplication of a common ancestor gene. Msal-2 is expressed throughout embryonic development but also in adult tissues, predominantly in brain. However, the function of SALL2/Msal-2 still needs to be determined.

SALL3, a new member of the human spalt-like gene family, maps to 18q23

spalt (sal) of Drosophila melanogaster is an important developmental regulator gene and encodes a zinc finger protein of unusual but characteristic structure. Two human sal-like genes have been isolated so far, SALL1 on chromosome 16q12.1 and SALL2 on chromosome 14q11.1-q12.1. Truncating mutations of SALL1 have been shown to cause Townes-Brocks syndrome and are thought to result in SALL1 haploinsufficiency. Sequence comparison of SALL1 to the related genes Msal in mouse and Xsal-1 in Xenopus laevis suggested that SALL1 was not the human orthologue of Msal and Xsal-1. By database searching and genomic cloning, we isolated an EST and a corresponding human cosmid clone, which contain coding sequence of a human gene highly similar to mouse Msal. This gene, named SALL3, was found to be expressed in different regions of human fetal brain and in different adult human tissues. The chromosomal localization of SALL3 at 18q23 suggests that haploinsufficiency of this gene might contribute to the phenotype of patients with 18q deletion syndrome.

Interaction of translation initiation factor eIF4G with eIF4A in the yeast Saccharomyces cerevisiae

Eukaryotic initiation factor (eIF) 4A is an essential protein that, in conjunction with eIF4B, catalyzes the ATP-dependent melting of RNA secondary structure in the 5'-untranslated region of mRNA during translation initiation. In higher eukaryotes, eIF4A is assumed to be recruited to the mRNA through its interaction with eIF4G. However, the failure to detect this interaction in yeast brought into question the generality of this model. The work presented here demonstrates that yeast eIF4G interacts with eIF4A both in vivo and in vitro. The eIF4A-binding site was mapped to amino acids 542-883 of yeast eIF4G1. Expression in yeast cells of the eIF4G1 domain that binds eIF4A results in cell growth inhibition, and addition of this domain to an eIF4A-dependent in vitro system inhibits translation in a dose-dependent manner. Both in vitro translation and cell growth can be specifically restored by increasing the eIF4A concentration. These data demonstrate that yeast eIF4A and eIF4G interact and suggest that this interaction is required for translation and cell growth.

CLN3 expression is sufficient to restore G1-to-S-phase progression in Saccharomyces cerevisiae mutants defective in translation initiation factor eIF4E

The essential cap-binding protein (eIF4E) of Saccharomyces cerevisiae is encoded by the CDC33 (wild-type) gene, originally isolated as a mutant, cdc33-1, which arrests growth in the G1 phase of the cell cycle at 37 degrees C. We show that other cdc33 mutants also arrest in G1. One of the first events required for G1-to-S-phase progression is the increased expression of cyclin 3. Constructs carrying the 5'-untranslated region of CLN3 fused to lacZ exhibit weak reporter activity, which is significantly decreased in a cdc33-1 mutant, implying that CLN3 mRNA is an inefficiently translated mRNA that is sensitive to perturbations in the translation machinery. A cdc33-1 strain expressing either stable Cln3p (Cln3-1p) or a hybrid UBI4 5'-CLN3 mRNA, whose translation displays decreased dependence on eIF4E, arrested randomly in the cell cycle. In these cells CLN2 mRNA levels remained high, indicating that Cln3p activity is maintained. Induction of a hybrid UBI4 5'-CLN3 message in a cdc33-1 mutant previously arrested in G1 also caused entry into a new cell cycle. We conclude that eIF4E activity in the G1-phase is critical in allowing sufficient Cln3p activity to enable yeast cells to enter a new cell cycle.

Agonist and antagonists induce homodimerization and mixed ligand heterodimerization of human progesterone receptors in vivo by a mammalian two-hybrid assay

This study utilizes the mammalian two-hybrid system to examine the role of ligand in the dimerization of human progesterone receptor (hPR). The GAL4 DNA-binding domain and the herpes simplex virus VP16 transactivation domain were fused to the amino terminus of full-length hPR (both the A and B isoforms) to produce chimeric proteins. PR dimerization was detected by the ability of cotransfected GAL4/PR and VP16/PR chimeras in COS cells to induce expression of a reporter gene under the control of GAL4-binding sites (pG5CAT). Hormone agonist-dependent interactions were observed between the two like isoforms of PR (A-A and B-B) and between PR-A and PR-B (A-B), indicating that hormone can stimulate the formation of the three possible dimeric forms of PR within cells. In contrast, neither type I (ZK98299) nor type II (RU486, ZK112993) progestin antagonists stimulated interaction between these same hybrid PR proteins. However, activation of the VP16/PR chimera by antagonists on a progesterone response element-controlled reporter gene (DHRE-E1b-CAT) was only a fraction (4-13%) of that stimulated by agonist R5020. One possibility for the failure to detect an induction in the two-hybrid assay is antagonist-induced repression of the activity of the VP16/PR fusion protein rather than a failure of antagonists to stimulate interaction between the hybrid proteins. To test this idea, an UP-1 carboxyl-terminal truncation mutant of PR was used to construct the two-hybrid proteins. PR-UP-1 selectively binds antagonists, but not agonists, and is fully activated in response to antagonists. Both types of progestin antagonists stimulated interactions between GAL4/PR(UP-1) and VP16/PR(UP-1) hybrid proteins, indicating that antagonists are capable of stimulating PR dimerization in cells and do not function by disrupting or preventing dimerization. To determine whether PR bound to an antagonist can dimerize in whole cells with PR bound to agonist, GAL4/PR(UP-1) was paired in the two-hybrid assay with a VP16/PR fusion protein harboring a point mutation in PR at amino acid 722 (Gly-Cys) that specifically binds progestin agonist but not antagonist. Neither R5020 nor RU486 alone stimulated interaction between these ligand-specific PR hybrid proteins. However, strong interaction was detected by addition of both agonist and antagonists, indicating the formation of mixed ligand heterodimers and that both PR partners require ligand for dimerization to occur. Based on electrophoretic gel mobility shift assays (EMSAs), these heterodimers appear to have substantially reduced DNA binding activity. Progestin antagonists inhibit agonist activation of PR at concentrations that are too low to be accounted for by a simple competition mechanism for binding to PR. We propose that antiprogestin inactivation of PR in trans by heterodimerization contributes to the biological potency of these compounds.

The RNA recognition motif of yeast translation initiation factor Tif3/eIF4B is required but not sufficient for RNA strand-exchange and translational activity

The Saccharomyces cerevisiae TIF3 gene encodes a 436-amino acid (aa) protein that is the yeast homologue of mammalian translation Initiation factor eIF4B. Tif3p can be divided into three parts, the N-terminal region with an RNA recognition motif (RRM) (aa 1-182), followed in the middle part by a sevenfold repeat of 26 amino acids rich in basic and acidic residues (as 183-350), and a C-terminal region without homology to any known sequence (aa 351-436). We have analyzed several Tif3 proteins with deletions at their N and C termini for their ability (1) to complement a tif3delta strain in vivo, (2) to stimulate Tif3-dependent translation extracts, (3) to bind to single-stranded RNA, and (4) to catalyze RNA strand-exchange in vitro. Here we report that yeast Tif3/eIF4B contains at least two RNA binding domains able to bind to single-stranded RNA. One is located in the N-terminal region of the protein carrying the RRM, the other in the C-terminal two-thirds region of Tif3p. The RRM-containing domain and three of the seven repeat motifs are essential for RNA strand-exchange activity of Tif3p and translation in vitro and for complementation of a tif3delta strain, suggesting an important role for RNA strand-exchange activity in translation.

High-mobility group chromatin proteins 1 and 2 functionally interact with steroid hormone receptors to enhance their DNA binding in vitro and transcriptional activity in mammalian cells

We previously reported that the chromatin high-mobility group protein 1 (HMG-1) enhances the sequence-specific DNA binding activity of progesterone receptor (PR) in vitro, thus providing the first evidence that HMG-1 may have a coregulatory role in steroid receptor-mediated gene transcription. Here we show that HMG-1 and the highly related HMG-2 stimulate DNA binding by other steroid receptors, including estrogen, androgen, and glucocorticoid receptors, but have no effect on DNA binding by several nonsteroid nuclear receptors, including retinoid acid receptor (RAR), retinoic X receptor (RXR), and vitamin D receptor (VDR). As highly purified recombinant full-length proteins, all steroid receptors tested exhibited weak binding affinity for their optimal palindromic hormone response elements (HREs), and the addition of purified HMG-1 or -2 substantially increased their affinity for HREs. Purified RAR, RXR, and VDR also exhibited little to no detectable binding to their cognate direct repeat HREs but, in contrast to results with steroid receptors, the addition of HMG-1 or HMG-2 had no stimulatory effect. Instead, the addition of purified RXR enhanced RAR and VDR DNA binding through a heterodimerization mechanism and HMG-1 or HMG-2 had no further effect on DNA binding by RXR-RAR or RXR-VDR heterodimers. HMG-1 and HMG-2 (HMG-1/-2) themselves do not bind to progesterone response elements, but in the presence of PR they were detected as part of an HMG-PR-DNA ternary complex. HMG-1/-2 can also interact transiently in vitro with PR in the absence of DNA; however, no direct protein interaction was detected with VDR. These results, taken together with the fact that PR can bend its target DNA and that HMG-1/-2 are non-sequence-specific DNA binding proteins that recognize DNA structure, suggest that HMG-1/-2 are recruited to the PR-DNA complex by the combined effect of transient protein interaction and DNA bending. In transient-transfection assays, coexpression of HMG-1 or HMG-2 increased PR-mediated transcription in mammalian cells by as much as 7- to 10-fold without altering the basal promoter activity of target reporter genes. This increase in PR-mediated gene activation by coexpression of HMG-1/-2 was observed in different cell types and with different target promoters, suggesting a generality to the functional interaction between HMG-1/-2 and PR in vivo. Cotransfection of HMG-1 also increased reporter gene activation mediated by other steroid receptors, including glucocorticoid and androgen receptors, but it had a minimal influence on VDR-dependent transcription in vivo. These results support the conclusion that HMG-1/-2 are coregulatory proteins that increase the DNA binding and transcriptional activity of the steroid hormone class of receptors but that do not functionally interact with certain nonsteroid classes of nuclear receptors.

The deterministic limit of infectious disease models with dynamic partners

This paper analyzes the large population dynamics of an infectious disease model with contacts that occur during partnerships. The model allows for concurrent partnerships following a very broad class of dynamic laws. Previous work, with a stochastic version of the model, computed the reproductive number, the initial growth rate, and the final size. In the present paper, the deterministic system that is the limit for large populations is constructed. The construction is unusual in requiring two different scaling factors. Next, the approximation used by Watts and May for a related model is compared with the exact solution. This approximation is most accurate at the beginning of the epidemic and when partnerships are short. Lastly, the model is generalized to allow dependencies among partnerships. This generalization permits proportional mixing with an arbitrary distribution on the number of partners.

The TOR (target of rapamycin) signal transduction pathway regulates the stability of translation initiation factor eIF4G in the yeast Saccharomyces cerevisiae

Initiation factor eIF4G is an essential protein required for initiation of mRNA translation via the 5' cap-dependent pathway. It interacts with eIF4E (the mRNA 5' cap-binding protein) and serves as an anchor for the assembly of further initiation factors. With treatment of Saccharomyces cerevisiae with rapamycin or with entry of cells into the diauxic phase, eIF4G is rapidly degraded, whereas initiation factors eIF4E and eIF4A remain stable. We propose that nutritional deprivation or interruption of the TOR signal transduction pathway induces eIF4G degradation.

Translation initiation factor-dependent extracts from yeast Saccharomyces cerevisiae

Translation initiation factor-dependent extracts are prepared from Saccharomyces cerevisiae strains that have no or reduced activity of a translation initiation factor. Elimination of factor activity can be achieved by deletion of the gene encoding the factor if it is not essential for the survival of the strain. If the gene is essential it is placed under the control of the regulatable GAL1 promoter and its expression is shut off in vivo. Alternatively, a temperature-sensitive mutation can be introduced into the gene and the activity of the gene product eliminated in vitro by preincubation of the extract at the nonpermissive temperature. Factor-dependent extracts can be complemented in vitro with purified initiation factor preparations isolated from S. cerevisiae or from Escherichia coli cells expressing them from plasmid-encoded constructs. To simplify the purification of the factors they may be expressed as fusion proteins with N- or C-terminal tags. Initiation factor-dependent extracts can be used to study initiation factor structure-function relationships and initiation factor requirements for specific mRNA translation.

A novel inhibitor of cap-dependent translation initiation in yeast: p20 competes with eIF4G for binding to eIF4E

In the yeast Saccharomyces cerevisiae a small protein named p20 is found associated with translation initiation factor eIF4E, the mRNA cap-binding protein. We demonstrate here that p20 is a repressor of cap-dependent translation initiation. p20 shows amino acid sequence homology to a region of eIF4G, the large subunit of the cap-binding protein complex eIF4F, which carries the binding site for eIF4E. Both, eIF4G and p20 bind to eIF4E and compete with each other for binding to eIF4E. The eIF4E-p20 complex can bind to the cap structure and inhibit cap-dependent but not cap-independent translation initiation: the translation of a mRNA with the 67 nucleotide omega sequence of tobacco mosaic virus in its 5' untranslated region (which was previously shown to render translation cap-independent) is not inhibited by p20. Whereas the translation of the same mRNA lacking the omega sequence is strongly inhibited by p20. Disruption of CAF20, the gene encoding p20, stimulates the growth of yeast cells, overexpression of p20 causes slower growth of yeast cells. These results show that p20 is a regulator of eIF4E activity which represses cap-dependent initiation of translation by interfering with the interaction of eIF4E with eIF4G, e.g. the formation of the eIF4F-complex.

Decreasing disability in the 21st century: the future effects of controlling six fatal and nonfatal conditions

OBJECTIVES

This study assessed the effects of reducing fatal and nonfatal health conditions on the number of functionally limited older Americans in the coming decades.

METHODS

Data from the 1990 census and the Longitudinal Study of Aging were used to project the number of functionally limited older Americans from 2001 to 2049, assuming 1% biennial reductions in five conditions that shorten life expectancy (coronary artery disease, stroke, cancer, diabetes, and confusion) and one condition that decreases functional ability (arthritis).

RESULTS

Decreasing the prevalence of arthritis by 1% every 2 years would lead to a much greater reduction in functional limitation between 2001 and 2049 (4 million person-years) than would decreasing any of the other conditions by the same amount. Decreases in two fatal conditions (cancer and coronary artery disease) would lead to increases in functional limitation (0.9 and 0.1 million person-years, respectively).

CONCLUSIONS

Advances against common nonfatal disabling conditions would be more effective than advances against fatal conditions in blunting the large increase in the functionally limited older population anticipated in the 21st century.

Stoichiometry and site-specific phosphorylation of human progesterone receptor in native target cells and in the baculovirus expression system

Human progesterone receptor (PR) in T47D breast cancer cells is phosphorylated on nine different serine residues; three are hormone-inducible (Ser102, Ser294, and Ser345), while others are basal but hormone-stimulated. In the present study, we have compared the phosphorylation state of native and recombinant PR expressed in a baculovirus insect cell system. Stoichiometric measurements showed that unliganded native PR in T47D cells was approximately 50% phosphorylated ( approximately 4 phosphates/PR) and became essentially 100% phosphorylated ( approximately 9 phosphates/PR) when bound to hormone. Unliganded PR expressed in Sf9 insect cells was phosphorylated with a similar stoichiometry ( approximately 3 phosphates/PR), but the phosphate content did not change with hormone addition. Site-specific phosphorylation analyzed by tryptic phosphopeptide mapping and manual peptide sequencing revealed that expressed PR bound to hormone in the Sf9 insect cells was phosphorylated on all the same sites as hormone-treated PR in T47D cells. Only minor differences were detected in the relative proportion of three sites (two basal sites and Ser345) and phosphorylation did not occur on alternate sites. Interestingly, unliganded baculovirus-expressed PR was constitutively phosphorylated on hormone inducible sites and was phosphorylated on basal sites to the same extent as hormone treated PR. Thus, in the absence of hormone, the phosphorylation state of baculovirus-expressed PR resembled that of the hyperphosphorylated native PR. In contrast to native PR, the expressed receptor in cytosols of Sf9 cells did not form a large oligomeric complex suggesting that hyperphosphorylation may be due to dissociation of the complex in the absence of hormone. This study demonstrating phosphorylation on correct sites with a stoichiometry similar to that of native PR indicates that overexpressed PR in the baculovirus system is suitable for in vitro structure/function studies.

Displacement correction and surface reconstruction of the retina using scanning laser ophthalmoscopic images

A method for a three-dimensional surface reconstruction of the retina in the area of the papilla is presented. The surface reconstruction is based on a sequence of discrete gray-level images of the retina recorded by a scanning laser ophthalmoscope (SLO). The underlying assumption of the surface reconstruction algorithm developed here is that the depth information is also encoded in the brightness values of the single pixels in addition to the ordinary spatial 2D information. The brightness of an image position depends on the degree of reflection of a confocal laser beam. Only those surface structures located directly in the focus plane of the confocal laser beam produce a high response to the laser light. The displacements between the single images of a sequence are considered to be approximately linear and are corrected by applying the cepstrum technique. The depth is estimated from the volumetric representation of the image sequence by searching for the maximal value of the brightness within a computed depth profile, at every image position. In the resulting images, disturbances occurring during the recording cause incorrect local estimations of the depth. These local disturbances are corrected by applying specially developed surface improvement processes. The work is concluded with a comparison of several different approaches to reduce the noise and disturbances in SLO image data.