RNA granule-clustered mitochondrial aminoacyl-tRNA synthetases form multiple complexes with the potential to fine-tune tRNA aminoacylation.

Mitochondrial RNA metabolism is suggested to occur in identified compartmentalized foci, i.e. mitochondrial RNA granules (MRGs). Mitochondrial aminoacyl-tRNA synthetases (mito aaRSs) catalyze tRNA charging and are key components in mitochondrial gene expression. Mutations of mito aaRSs are associated with various human disorders. However, the suborganelle distribution, interaction network and regulatory mechanism of mito aaRSs remain largely unknown. Here, we found that all mito aaRSs partly colocalize with MRG, and this colocalization is likely facilitated by tRNA-binding capacity. A fraction of human mitochondrial AlaRS (hmtAlaRS) and hmtSerRS formed a direct complex via interaction between catalytic domains in vivo. Aminoacylation activities of both hmtAlaRS and hmtSerRS were fine-tuned upon complex formation in vitro. We further established a full spectrum of interaction networks via immunoprecipitation and mass spectrometry for all mito aaRSs and discovered interactions between hmtSerRS and hmtAsnRS, between hmtSerRS and hmtTyrRS and between hmtThrRS and hmtArgRS. The activity of hmtTyrRS was also influenced by the presence of hmtSerRS. Notably, hmtSerRS utilized the same catalytic domain in mediating several interactions. Altogether, our results systematically analyzed the suborganelle localization and interaction network of mito aaRSs and discovered several mito aaRS-containing complexes, deepening our understanding of the functional and regulatory mechanisms of mito aaRSs.

Repeat-Enhancing Featured Ion-Guided Stoichiometry for Identification and Quantification of Direct Infusion Proteome.

The direct infusion-shotgun proteome analysis (DI-SPA) alongside data-independent acquisition mass spectrometry achieved fast proteome identification and quantification without chromatographic separation. However, robust peptide identification and quantification (label and label-free) for the DI-SPA data is still insufficient. We find that in the absence of chromatography, the identification of DI-SPA can be boosted by extending acquisition cycles repeatedly and maximizing the utilization of the featured repetition characteristics, combined with the machine learning-based automatic peptide scoring strategy. Here, we present the repeat-enhancing featured ion-guided stoichiometry (RE-FIGS), a complete and compact solution to (repeated) DI-SPA data. Using our strategy, the peptide identification can be improved above 30% with high reproducibility (70.0%). Notably, the label-free quantification of repeated DI-SPA can be successfully obtained with high accuracy (mean median error, 0.108) and high reproducibility (median error, 0.001). We believe our RE-FIGS method could boost the broad application of the (repeated) DI-SPA method and offer a new choice for proteomic analysis.

The human tRNA taurine modification enzyme GTPBP3 is an active GTPase linked to mitochondrial diseases.

GTPBP3 and MTO1 cooperatively catalyze 5-taurinomethyluridine (τm5U) biosynthesis at the 34th wobble position of mitochondrial tRNAs. Mutations in tRNAs, GTPBP3 or MTO1, causing τm5U hypomodification, lead to various diseases. However, efficient in vitro reconstitution and mechanistic study of τm5U modification have been challenging, in part due to the lack of pure and active enzymes. A previous study reported that purified human GTPBP3 (hGTPBP3) is inactive in GTP hydrolysis. Here, we identified the mature form of hGTPBP3 and showed that hGTPBP3 is an active GTPase in vitro that is critical for tRNA modification in vivo. Unexpectedly, the isolated G domain and a mutant with the N-terminal domain truncated catalyzed GTP hydrolysis to only a limited extent, exhibiting high Km values compared with that of the mature enzyme. We further described several important pathogenic mutations of hGTPBP3, associated with alterations in hGTPBP3 localization, structure and/or function in vitro and in vivo. Moreover, we discovered a novel cytoplasm-localized isoform of hGTPBP3, indicating an unknown potential noncanonical function of hGTPBP3. Together, our findings established, for the first time, the GTP hydrolysis mechanism of hGTPBP3 and laid a solid foundation for clarifying the τm5U modification mechanism and etiology of τm5U deficiency-related diseases.

Mutually exclusive substrate selection strategy by human m3C RNA transferases METTL2A and METTL6.

tRNAs harbor the most diverse posttranscriptional modifications. The 3-methylcytidine (m3C) is widely distributed at position C32 (m3C32) of eukaryotic tRNAThr and tRNASer species. m3C32 is decorated by the single methyltransferase Trm140 in budding yeasts; however, two (Trm140 and Trm141 in fission yeasts) or three enzymes (METTL2A, METTL2B and METTL6 in mammals) are involved in its biogenesis. The rationale for the existence of multiple m3C32 methyltransferases and their substrate discrimination mechanism is hitherto unknown. Here, we revealed that both METTL2A and METTL2B are expressed in vivo. We purified human METTL2A, METTL2B, and METTL6 to high homogeneity. We successfully reconstituted m3C32 modification activity for tRNAThr by METT2A and for tRNASer(GCU) by METTL6, assisted by seryl-tRNA synthetase (SerRS) in vitro. Compared with METTL2A, METTL2B exhibited dramatically lower activity in vitro. Both G35 and t6A at position 37 (t6A37) are necessary but insufficient prerequisites for tRNAThr m3C32 formation, while the anticodon loop and the long variable arm, but not t6A37, are key determinants for tRNASer(GCU) m3C32 biogenesis, likely being recognized synergistically by METTL6 and SerRS, respectively. Finally, we proposed a mutually exclusive substrate selection model to ensure correct discrimination among multiple tRNAs by multiple m3C32 methyltransferases.

MKRN3-mediated ubiquitination of Poly(A)-binding proteins modulates the stability and translation of GNRH1 mRNA in mammalian puberty.

The family of Poly(A)-binding proteins (PABPs) regulates the stability and translation of messenger RNAs (mRNAs). Here we reported that the three members of PABPs, including PABPC1, PABPC3 and PABPC4, were identified as novel substrates for MKRN3, whose deletion or loss-of-function mutations were genetically associated with human central precocious puberty (CPP). MKRN3-mediated ubiquitination was found to attenuate the binding of PABPs to the poly(A) tails of mRNA, which led to shortened poly(A) tail-length of GNRH1 mRNA and compromised the formation of translation initiation complex (TIC). Recently, we have shown that MKRN3 epigenetically regulates the transcription of GNRH1 through conjugating poly-Ub chains onto methyl-DNA bind protein 3 (MBD3). Therefore, MKRN3-mediated ubiquitin signalling could control both transcriptional and post-transcriptional switches of mammalian puberty initiation. While identifying MKRN3 as a novel tissue-specific translational regulator, our work also provided new mechanistic insights into the etiology of MKRN3 dysfunction-associated human CPP.

TreeQNet: a webserver for Treatment evaluation with Quantified Network.

BACKGROUND: Personalized therapy has been at the forefront of cancer care, making cancer treatment more effective. Since cancer patients respond individually to drug therapy, predicting the sensitivity of each patient to specific drugs is very helpful to apply therapeutic agents. Traditional methods focus on node (molecular) information but ignore relevant interactions among different nodes, which has very limited application in complex situations, such as cancer drug responses in real clinical practice. RESULTS: Treatment evaluation with Quantified Network (TreeQNet) is a webserver which could predict sensitivity to drugs for patients through the innovative use of proteomic and phosphoproteomic network from tumor tissues. CONCLUSION: TreeQNet service: http://bioinfo.ustc.edu.cn/ . TreeQNet source code: https://github.com/Really00/treeqnet-web-front/ .

Correction: CCNYL1, but Not CCNY, Cooperates with CDK16 to Regulate Spermatogenesis in Mouse.

[This corrects the article DOI: 10.1371/journal.pgen.1005485.].

FIGS: Featured Ion-Guided Stoichiometry for Data-Independent Proteomics through Dynamic Deconvolution.

Data-independent acquisition (DIA) has significant advantages for mass spectrometry (MS)-based peptide quantification, while mixed spectra remain challenging for precise stoichiometry. We here choose to analyze the library spectra in specific sets preferentially and locally. Accordingly, the featured ions are defined as the fragment ions uniquely assigned to corresponding precursors in a given spectrum set, which are generated by dynamic deconvolution of the mixed mass spectra. Then, we present featured ion-guided stoichiometry (FIGS), a universal method for accurate and robust peptide quantification for the DIA-MS data. We validate the high performance on the quantification sensitivity, accuracy, and efficiency of FIGS. Notably, our FIGS dramatically improves the quantification accuracy for the full dynamic range, especially for low-abundance peptides.

DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma.

BACKGROUND: Early recurrence is a major obstacle to prolonged postoperative survival in squamous cell lung carcinoma (SqCLC). The molecular mechanisms underlying early SqCLC recurrence remain unclear, and effective prognostic biomarkers for predicting early recurrence are needed. METHODS: We analyzed primary tumor samples of 20 SqCLC patients using quantitative proteomics to identify differentially-expressed proteins in patients who experienced early versus late disease recurrence. The expression and prognostic significance of DDX56 was evaluated using a SqCLC tumor tissue microarray and further verified using different online databases. We performed in vitro and in vivo experiments to obtain detailed molecular insight into the functional role of DDX56 in SqCLC. RESULTS: We found that DDX56 exhibited increased expression in tumors of patients who experienced early versus late disease recurrence. Increased DDX56 expression in SqCLC tumors was subsequently confirmed as an independent prognostic factor of poor recurrence-free survival in independent SqCLC cohorts. Functionally, DDX56 promotes SqCLC cell growth and migration in vitro, and xenograft tumor progression in vivo. Mechanistically, DDX56 post-transcriptionally promotes expression of multiple Wnt signaling pathway-related genes, including CTNNB1, WNT2B, and represses a subset of miRNAs, including miR-378a-3p, a known suppressor of Wnt signaling. Detailed analysis revealed that DDX56 facilitated degradation of primary miR-378a, leading to down-regulation of mature miR-378a-3p and thus derepression of the target gene WNT2B. CONCLUSION: We identified DDX56 as a novel independent prognostic biomarker that exerts its oncogenic effects through miRNA-mediated post-transcriptional regulation of Wnt signaling genes to promote early SqCLC recurrence. DDX56 may assist in identifying SqCLC patients at increased risk of early recurrence and who could benefit from Wnt signaling-targeted therapies.

CDK11 safeguards the identity of human embryonic stem cells via fine-tuning signaling pathways.

Signaling pathways transmit extracellular cues into cells and regulate transcriptome and epigenome to maintain or change the cell identity. Protein kinases and phosphatases are critical for signaling transduction and regulation. Here, we report that CDK11, a member of the CDK family, is required for the maintenance of human embryonic stem cell (hESC) self-renewal. Our results show that, among the three main isoforms of CDK11, CDK11p46 is the main isoform safeguarding the hESC identity. Mechanistically, CDK11 constrains two important mitogen-activated protein kinase (MAPK) signaling pathways (JNK and p38 signaling) through modulating the activity of protein phosphatase 1. Furthermore, CDK11 knockdown activates transforming growth factor ß (TGF-ß)/SMAD2/3 signaling and upregulates certain nonneural differentiation-associated genes. Taken together, this study uncovers a kinase required for hESC self-renewal through fine-tuning MAPK and TGF-ß signaling at appropriate levels. The kinase-phosphatase axis reported here may shed new light on the molecular mechanism sustaining the identity of hESCs.

Multi-in-One: Multiple-Proteases, One-Hour-Shot Strategy for Fast and High-Coverage Phosphoproteomic Investigation.

Although a multiple-protease based shotgun proteomics method was shown to improve coverage for phosphosite identification, this traditional pipeline is time-consuming and can be of low reproducibility. Here, we demonstrated a multi-in-one strategy to saturate the phosphosite coverage by combining the multiple-proteases based digestion, one-step enrichment, and one-shot data-independent acquisition (DIA) as short as 1 h. In the "three-in-one" workflow, more than 19,700 and 13,500 phosphosites could be identified in the trypsin-like and nontrypsin-like mixture, respectively. By combining and applying our "three-in-one" strategy, nearly 30,000 phosphosites could be successfully quantified with high reproducibility across samples. Meanwhile, we developed a faster and more robust method, in which over a single 66 min chromatographic method by "six-in-one" strategy, 19,445 phosphosites could be successfully localized, drastically reducing the database search time required in the traditional method. Inspiringly, this strategy further enabled us to discover 2,675 phosphorylation events on the low abundant transcription factors (TFs) in living cells with high coverage. More broadly, the multi-in-one strategy makes the multiple-protease digestion in large-scale analysis applicable, with low time-consuming, high sensitivity, improved coverage, and high reproducibility.

Luminescent Vesicles Self-assembled Directly from an Amphiphilic Europium Complex in an Ionic Liquid.

Novel luminescent vesicles with enhanced emission were successfully achieved for the first time by an amphiphilic europium complex through its spontaneously self-assembly in an ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim]PF6). The complex was prepared by europium ions coordinated with terpyridine ligands, which were modified with the hydrophilic ethoxy chains. The enhanced absolute quantum yield and prolonged fluorescence lifetime of complex in vesicles were observed because of the effective shielding of the quench effects caused by both solvent and complex concentration. Compared to the aggregates formed in other solvents, the vesicles obtained in [Bmim]PF6 showed the best luminescence intensity with the quantum efficiency (37.74%) and luminescent emission lifetime (1.915 ms) both increased about 10 times more. Furthermore, this europium complex was designed to show unsaturated coordination, which made the vesicle luminescence easily quenched when contacting with water. The fluorescence sensing of water with this vesicle as probe was therefore possible, where several unique properties like high sensitivity, low detection limit (0.05 vol %), visible color change, and fast response had been observed. Such designed systems are expected to provide strategies to develop novel supramolecular aggregates in ionic liquids and offer guidance for luminescence detection with facile and wide applications.

A luminescent lyotropic liquid crystal with UV irradiation induced photochromism.

Multicolored photoluminescence induced by UV irradiation in soft materials has invaluable potential in display and detection applications. Here, an ionic liquid (ethylammonium nitrate, EAN)-mediated luminescent lyotropic liquid crystal (LLC) has been fabricated, where an europium complex with two ligands (Eu(DBM)3BQ, DBM = dibenzoylmethane and BQ = 2,2'-biquinoline) was doped. The obtained LLC exhibited enhanced fluorescence intensity and lifetime compared to those of Eu(DBM)3BQ in EAN solution. Interestingly, the luminescent LLC color from the initial red emission of the complex was changed gradually to green when the UV exposure was extended. Though the DBM ligand displayed the typical photo-degradation, the emission intensity of BQ increased drastically. A mechanism based on an UV-induced trans-to-cis isomerization of BQ was proposed to explain such an unusual luminescence phenomenon. Both the experimental and computational results indicated an intra ligand charge transfer (ILCT) accompanied with the BQ isomerization under continuous UV irradiation, which resulted in the enhanced green light emission. The results obtained here are referable for better understanding the interplay between weak interactions and modulation of novel lanthanide-based photochromism systems under UV exposure.

Bacterial effector NleL promotes enterohemorrhagic E. coli-induced attaching and effacing lesions by ubiquitylating and inactivating JNK.

As a major diarrheagenic human pathogen, enterohemorrhagic Escherichia coli (EHEC) produce attaching and effacing (A/E) lesions, characterized by the formation of actin pedestals, on mammalian cells. A bacterial T3SS effector NleL from EHEC O157:H7 was recently shown to be a HECT-like E3 ligase in vitro, but its biological functions and host targets remain elusive. Here, we report that NleL is required to effectively promote EHEC-induced A/E lesions and bacterial infection. Furthermore, human c-Jun NH2-terminal kinases (JNKs) were identified as primary substrates of NleL. NleL-induced JNK ubiquitylation, particularly mono-ubiquitylation at the Lys 68 residue of JNK, impairs JNK's interaction with an upstream kinase MKK7, thus disrupting JNK phosphorylation and activation. This subsequently suppresses the transcriptional activity of activator protein-1 (AP-1), which modulates the formation of the EHEC-induced actin pedestals. Moreover, JNK knockdown or inhibition in host cells complements NleL deficiency in EHEC infection. Thus, we demonstrate that the effector protein NleL enhances the ability of EHEC to infect host cells by targeting host JNK, and elucidate an inhibitory role of ubiquitylation in regulating JNK phosphorylation.

CCNYL1, but Not CCNY, Cooperates with CDK16 to Regulate Spermatogenesis in Mouse.

Cyclin Y-like 1 (Ccnyl1) is a newly-identified member of the cyclin family and is highly similar in protein sequences to Cyclin Y (Ccny). However, the function of Ccnyl1 is poorly characterized in any organism. Here we found that Ccnyl1 was most abundantly expressed in the testis of mice and was about seven times higher than the level of Ccny. Male Ccnyl1-/- mice were infertile, whereas both male and female Ccny-/- mice displayed normal fertility. These results suggest that Ccnyl1, but not Ccny, is indispensable for male fertility. Spermatozoa obtained from Ccnyl1-/- mice displayed significantly impaired motility, and represented a thinned annulus region and/or a bent head. We found that the protein, but not the mRNA, level of cyclin-dependent kinase 16 (CDK16) was decreased in the testis of Ccnyl1-/- mice. Further study demonstrated that CCNYL1 interacted with CDK16 and this interaction mutually increased the stability of these two proteins. Moreover, the interaction increased the kinase activity of CDK16. In addition, we observed an alteration of phosphorylation levels of CDK16 in the presence of CCNYL1. We identified the phosphorylation sites of CDK16 by mass spectrometry and revealed that several phosphorylation modifications on the N-terminal region of CDK16 were indispensable for the CCNYL1 binding and the modulation of CDK16 kinase activity. Our results therefore reveal a previously unrecognized role of CCNYL1 in regulating spermatogenesis through the interaction and modulation of CDK16.

Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data.

Isobaric labeling techniques coupled with high-resolution mass spectrometry have been widely employed in proteomic workflows requiring relative quantification. For each high-resolution tandem mass spectrum (MS/MS), isobaric labeling techniques can be used not only to quantify the peptide from different samples by reporter ions, but also to identify the peptide it is derived from. Because the ions related to isobaric labeling may act as noise in database searching, the MS/MS spectrum should be preprocessed before peptide or protein identification. In this article, we demonstrate that there are a lot of high-frequency, high-abundance isobaric related ions in the MS/MS spectrum, and removing isobaric related ions combined with deisotoping and deconvolution in MS/MS preprocessing procedures significantly improves the peptide/protein identification sensitivity. The user-friendly software package TurboRaw2MGF (v2.0) has been implemented for converting raw TIC data files to mascot generic format files and can be downloaded for free from https://github.com/shengqh/RCPA.Tools/releases as part of the software suite ProteomicsTools. The data have been deposited to the ProteomeXchange with identifier PXD000994.

Quantitative Phosphoproteomics Revealed Glucose-Stimulated Responses of Islet Associated with Insulin Secretion.

As central tissue of glucose homeostasis, islet has been an important focus of diabetes research. Phosphorylation plays pivotal roles in islet function, especially in islet glucose-stimulated insulin secretion. A systematic view on how phosphorylation networks were coordinately regulated in this process remains lacking, partially due to the limited amount of islets from an individual for a phosphoproteomic analysis. Here we optimized the in-tip and best-ratio phosphopeptide enrichment strategy and a SILAC-based workflow for processing rat islet samples. With limited islet lysates from each individual rat (20-47 µg), we identified 8539 phosphosites on 2487 proteins. Subsequent quantitative analyses uncovered that short-term (30 min) high glucose stimulation induced coordinate responses of islet phosphoproteome on multiple biological levels, including insulin secretion related pathways, cytoskeleton dynamics, protein processing in ER and Golgi, transcription and translation, and so on. Furthermore, three glucose-responsive phosphosites (Prkar1a pT75pS77 and Tagln2 pS163) from the data set were proved to be correlated with insulin secretion. Overall, we initially gave an in-depth map of islet phosphoproteome regulated by glucose on individual rat level. This was a significant addition to our knowledge about how phosphorylation networks responded in insulin secretion. Also, the list of changed phosphosites was a valuable resource for molecular researchers in diabetes field.

CT-based radiomics models predict spontaneous intracerebral hemorrhage expansion and are comparable with CT angiography spot sign.

Background and purpose: This study aimed to investigate the efficacy of radiomics, based on non-contrast computed tomography (NCCT) and computed tomography angiography (CTA) images, in predicting early hematoma expansion (HE) in patients with spontaneous intracerebral hemorrhage (SICH). Additionally, the predictive performance of these models was compared with that of the established CTA spot sign. Materials and methods: A retrospective analysis was conducted using CT images from 182 patients with SICH. Data from the patients were divided into a training set (145 cases) and a testing set (37 cases) using random stratified sampling. Two radiomics models were constructed by combining quantitative features extracted from NCCT images (the NCCT model) and CTA images (the CTA model) using a logistic regression (LR) classifier. Additionally, a univariate LR model based on the CTA spot sign (the spot sign model) was established. The predictive performance of the two radiomics models and the spot sign model was compared according to the area under the receiver operating characteristic (ROC) curve (AUC). Results: For the training set, the AUCs of the NCCT, CTA, and spot sign models were 0.938, 0.904, and 0.726, respectively. Both the NCCT and CTA models demonstrated superior predictive performance compared to the spot sign model (all P < 0.001), with the performance of the two radiomics models being comparable (P = 0.068). For the testing set, the AUCs of the NCCT, CTA, and spot sign models were 0.925, 0.873, and 0.720, respectively, with only the NCCT model exhibiting significantly greater predictive value than the spot sign model (P = 0.041). Conclusion: Radiomics models based on NCCT and CTA images effectively predicted HE in patients with SICH. The predictive performances of the NCCT and CTA models were similar, with the NCCT model outperforming the spot sign model. These findings suggest that this approach has the potential to reduce the need for CTA examinations, thereby reducing radiation exposure and the use of contrast agents in future practice for the purpose of predicting hematoma expansion.

Plasma proteome profiling reveals the therapeutic effects of the PPAR pan-agonist chiglitazar on insulin sensitivity, lipid metabolism, and inflammation in type 2 diabetes.

Chiglitazar is a novel peroxisome proliferator-activated receptor (PPAR) pan-agonist, which passed phase III clinical trials and was newly approved in China for use as an adjunct to diet and exercise in glycemic control in adult patients with Type 2 Diabetes (T2D). To explore the circulating protein signatures associated with the administration of chiglitazar in T2D patients, we conducted a comparative longitudinal study using plasma proteome profiling. Of the 157 T2D patients included in the study, we administered chiglitazar to a specific group, while the controls were given either placebo or sitagliptin. The plasma proteomes were profiled at baseline and 12 and 24 weeks post-treatment using data-independent acquisition mass spectrometry (DIA-MS). Our study indicated that 13 proteins were associated with chiglitazar treatment in T2D patients, including 10 up-regulated proteins (SHBG, TF, APOA2, APOD, GSN, MBL2, CFD, PGLYRP2, A2M, and APOA1) and 3 down-regulated proteins (PRG4, FETUB, and C2) after treatment, which were implicated in the regulation of insulin sensitivity, lipid metabolism, and inflammation response. Our study provides insight into the response of chiglitazar treatment from a proteome perspective and demonstrates the multi-faceted effects of chiglitazar in T2D patients, which will help the clinical application of chiglitazar and further study of its action mechanism.

Identification of complex relationship between protein kinases and substrates during the cell cycle of HeLa cells by phosphoproteomic analysis.

Each phase of eukaryotic cell cycle is tightly controlled by multicomponent regulatory networks based on complex relationships of protein phosphorylation. In order to better understand the relationships between kinases and their substrate proteins during the progression of cell cycle, we analyzed phosphoproteome of HeLa cells during G1, S, and G2/M phases of cell cycle using our developed quantitative phosphoproteomic approaches. A total of 4776 high-confidence phosphorylation sites (phosphosites) in 1177 proteins were identified. Bioinformatics analysis for predicting kinase groups revealed that 46 kinase groups could be assigned to 4321 phosphosites. The majority of phosphoproteins harboring two or more phosphosites could be phosphorylated by different kinase groups, in which nine major kinase groups accounted for more than 90% phosphosites. Further analyses showed that approximately half of the examined two phosphosite combinations were correlatively regulated, regardless of whether the kinase groups were same or not. In general, the majority of proteins containing correlated phosphosites had solely co-regulated or counter-regulated phosphosites, and co-regulation was significantly more frequent than counter-regulation, suggesting that the former may be more important for regulating the cell cycle. In conclusion, our findings provide new insights into the complex regulatory mechanisms of protein phosphorylation networks during eukaryotic cell cycle.