Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

Protein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent acquisition (DIA) with regards to sensitivity in single run analysis and data completeness have not yet been explored. Here, we develop a sensitive workflow combining diGly antibody-based enrichment and optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identifies 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells – double the number and quantitative accuracy of data dependent acquisition. Applied to TNF signaling, the workflow comprehensively captures known sites while adding many novel ones. An in-depth, systems-wide investigation of ubiquitination across the circadian cycle uncovers hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting new connections between metabolism and circadian regulation.

Protein ubiquitylation is often studied by proteomics but how data independent acquisition (DIA) may advance these studies remains to be explored. Here, the authors show that DIA improves ubiquitylation site identification and quantification, enabling them to characterize the circadian ubiquitinome in human cells.

Phosphoproteome and Proteome Sample Preparation from Mouse Tissues for Circadian Analysis

Recent advances in mass spectrometry (MS)-based quantitative proteomics now allow the identification and quantification of deep proteomes and post-translational modifications (PTMs) in relatively short times. Therefore, in the last few years, this technology has proven successful in the circadian field to characterize temporal oscillations of the proteome and more recently PTMs in cellular systems and in tissues. In this chapter, we describe a robust and simple protocol, based on the EasyPhos workflow, to enable preparation of large number of proteomes and phosphoproteomes from mouse tissues for MS-based quantitative analysis. We additionally discuss computational methods to analyze proteome and phosphoproteome time series to determine circadian oscillations.

Sleep-wake cycles drive daily dynamics of synaptic phosphorylation

The circadian clock drives daily changes of physiology, including sleep-wake cycles, through regulation of transcription, protein abundance, and function. Circadian phosphorylation controls cellular processes in peripheral organs, but little is known about its role in brain function and synaptic activity. We applied advanced quantitative phosphoproteomics to mouse forebrain synaptoneurosomes isolated across 24 hours, accurately quantifying almost 8000 phosphopeptides. Half of the synaptic phosphoproteins, including numerous kinases, had large-amplitude rhythms peaking at rest-activity and activity-rest transitions. Bioinformatic analyses revealed global temporal control of synaptic function through phosphorylation, including synaptic transmission, cytoskeleton reorganization, and excitatory/inhibitory balance. Sleep deprivation abolished 98% of all phosphorylation cycles in synaptoneurosomes, indicating that sleep-wake cycles rather than circadian signals are main drivers of synaptic phosphorylation, responding to both sleep and wake pressures.

The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep

Neurons have adapted mechanisms to traffic RNA and protein into distant dendritic and axonal arbors. Taking a biochemical approach, we reveal that forebrain synaptic transcript accumulation shows overwhelmingly daily rhythms, with two-thirds of synaptic transcripts showing time-of-day–dependent abundance independent of oscillations in the soma. These transcripts formed two sharp temporal and functional clusters, with transcripts preceding dawn related to metabolism and translation and those anticipating dusk related to synaptic transmission. Characterization of the synaptic proteome around the clock demonstrates the functional relevance of temporal gating for synaptic processes and energy homeostasis. Unexpectedly, sleep deprivation completely abolished proteome but not transcript oscillations. Altogether, the emerging picture is one of a circadian anticipation of messenger RNA needs in the synapse followed by translation as demanded by sleep-wake cycles.

The non-classical nuclear import carrier Transportin 1 modulates circadian rhythms through its effect on PER1 nuclear localization

Circadian clocks are molecular timekeeping mechanisms that allow organisms to anticipate daily changes in their environment. The fundamental cellular basis of these clocks is delayed negative feedback gene regulation with PERIOD and CRYPTOCHROME containing protein complexes as main inhibitory elements. For a correct circadian period, it is essential that such clock protein complexes accumulate in the nucleus in a precisely timed manner, a mechanism that is poorly understood. We performed a systematic RNAi-mediated screen in human cells and identified 15 genes associated with the nucleo-cytoplasmic translocation machinery, whose expression is important for circadian clock dynamics. Among them was Transportin 1 (TNPO1), a non-classical nuclear import carrier, whose knockdown and knockout led to short circadian periods. TNPO1 was found in endogenous clock protein complexes and particularly binds to PER1 regulating its (but not PER2's) nuclear localization. While PER1 is also transported to the nucleus by the classical, Importin β-mediated pathway, TNPO1 depletion slowed down PER1 nuclear import rate as revealed by fluorescence recovery after photobleaching (FRAP) experiments. In addition, we found that TNPO1-mediated nuclear import may constitute a novel input pathway of how cellular redox state signals to the clock, since redox stress increases binding of TNPO1 to PER1 and decreases its nuclear localization. Together, our RNAi screen knocking down import carriers (but also export carriers) results in short and long circadian periods indicating that the regulatory pathways that control the timing of clock protein subcellular localization are far more complex than previously assumed. TNPO1 is one of the novel players essential for normal circadian periods and potentially for redox regulation of the clock.

Sheep and goats as indicator animals for the circulation of CCHFV in the environment

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus, which causes a serious illness with case-fatality rates of up to 80% in humans. CCHFV is endemic in many countries of Africa, Asia and Southeastern Europe. Next to the countries with endemic areas, the distribution of CCHFV is unknown in Southeastern Europe. As the antibody prevalence in animals is a good indicator for the presence or absence of the virus in a region, seroepidemiological studies can be used for the definition of risk areas for CCHFV. The aim of the present study was to reveal which ruminant species is best suited as indicator for the detection of a CCHFV circulation in an area. Therefore, the prevalence rates in sheep, goats and cattle in different regions of Albania and Former Yugoslav Republic of Macedonia were investigated. As there are no commercial tests available for the detection of CCHFV-specific antibodies in animals, two commercial tests for testing human sera were adapted for the investigation of sera from sheep and goats, and new in-house ELISAs were developed. The investigation of serum samples with these highly sensitive and specific assays (94-100%) resulted in an overall prevalence rate of 23% for Albania and of 49% for Former Yugoslav Republic of Macedonia. Significant lower seroprevalence rates for CCHFV were found in cattle than in small ruminants in given areas. These results indicate that small ruminants are more suitable indicator animals for CCHFV infections and should therefore be tested preferentially, when risk areas are to be identified.

Synthesis of quaternary α-perfluoroalkyl lactams via electrophilic perfluoroalkylation

The efficient one-pot perfluoroalkylation of lactams by hypervalent iodine reagents is catalysed by trimethylsilyl triflimide.

[How can young academics be recruited? Acceptance and effects of urological practice-oriented training]

BACKGROUND

There is an increasing lack of young doctors in German hospitals, including urology departments. The aim of this study was to evaluate the benefit of urology practice-oriented courses for German students in a skills laboratory with respect to acceptance, learning success and enthusiasm of the students for urology.

METHODS

Transurethral catheterization, digital rectal examination and kidney/bladder sonography were trained in the urology course. Using a 12-point questionnaire, acceptance and quality of the training were evaluated. Learning success was checked using a urological OSCE-station (Objective Structured Clinical Examination). Additionally, participants were questioned on interest in urology and the consideration of future work in the field (medical elective or practical year).

RESULTS

A total of 147 questionnaires from 190 participating students were suitable for analysis. Acceptance and quality of training were highly ranked accompanied by a very satisfying objective and subjective learning success. Interest for urology was stimulated in 98.4 % and future work in urology was imaginable for 60.4 % of the students.

DISCUSSION

Practice-oriented urology student courses show high acceptance, high learning success and increase of attractiveness of urology. The training of urological skills represents a sufficient tool to entice students for urology and is helpful in enhancing the future of urology.

Preliminary studies on the chemical properties of the toxic principle from Diamphidia nigroornata larvae, a source of Bushman arrow poison

The Bushmen of southern Africa use the expressed contents of beetle larvae (Diamphidia, Lebistina and Polyclada species) as arrow poison. an aqueous extract of Diamphidia nigroornata larvae was fractionated by gel filtration on Sephadex G-50. Two fractions were obtained: one (I) of high molecular weight which contains a protein of 60 000 daltons, and a low molecular weight fraction (II) of non-protein nature. Both fractions proved to be lethal to mice: an LD50 of 0.5 - 0.95 (I) and 3.2 - 3.5 (II) mg/kg (intraperitoneal injection), respectively, was determined. The toxic principle of fraction I could be partly separated from the protein by ammonium sulfate precipitation followed by gel filtration. That of fraction II was further resolved into several subfractions by gel filtration of Sephadex G-10; however, the lethal activity was completely lost during purification. In thin-layer chromatography the low molecular weight toxin(s) did not react with reagents for steroids, alkaloids, sugars or terpenes, but showed a positive ninhydrin reaction. It is concluded that the toxic principle of the Bushman arrow poison is a highly labile, low molecular weight compound which is closely attached or bound to a protein protecting it from inactivation.