A modification-centric assessment tool for the performance of chemoproteomic probes.

Chemoproteomics has emerged as a key technology to expand the functional space in complex proteomes for probing fundamental biology and for discovering new small-molecule-based therapies. Here we report a modification-centric computational tool termed pChem to provide a streamlined pipeline for unbiased performance assessment of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized by pChem, with masses accurately calculated and sites precisely localized. pChem exports on-demand reports by scoring the profiling efficiency, modification homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to eighteen bioorthogonal probes. These analyses reveal that the formation of unexpected probe-derived modifications can be driven by endogenous reactive metabolites (for example, bioactive aldehydes and glutathione). pChem is a powerful and user-friendly tool that aims to facilitate the development of probes for the ever-growing field of chemoproteomics.

Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins.

Human embryonic stem cells (hESCs) have the capacity for self-renewal and multilineage differentiation, which are of clinical importance for regeneration medicine. Despite the significant progress of hESC study, the complete hESC proteome atlas, especially the surface protein composition, awaits delineation. According to the latest release of neXtProt database (January 17, 2018; 19 658 PE1, 2, 3, and 4 human proteins), membrane proteins present the major category (1047; 48%) among all 2186 missing proteins (MPs). We conducted a deep subcellular proteomics analysis of hESCs to identify the nuclear, cytoplasmic, and membrane proteins in hESCs and to mine missing membrane proteins in the very early cell status. To our knowledge, our study achieved the largest data set with confident identification of 11 970 unique proteins (1% false discovery rate at peptide, protein, and PSM levels), including the most-comprehensive description of 6 138 annotated membrane proteins in hESCs. Following the HPP guideline, we identified 26 gold (neXtProt PE2, 3, and 4 MPs) and 87 silver (potential MP candidates with a single unique peptide detected) MPs, of which 69 were membrane proteins, and the expression of 21 gold MPs was further verified either by multiple reaction monitoring mass spectrometry or by matching synthetic peptides in the Peptide Atlas database. Functional analysis of the MPs revealed their potential roles in the pluripotency-related pathways and the lineage- and tissue-specific differentiation processes. Our proteome map of hESCs may provide a rich resource not only for the identification of MPs in the human proteome but also for the investigation on self-renewal and differentiation of hESC. All mass spectrometry data were deposited in ProteomeXchange via jPOST with identifier PXD009840.

The roles of signaling pathways in regulating kidney development.

The development of mammalian kidney is a complex process. The reciprocal inductive interactions between epithelial cells and metanephric mesenchymal cells determine cell fates including proliferation, growth, apoptosis, and eventually contribute to the formation of an intact kidney. Multiple signaling pathways, including the GDNF/Ret, Wnt and BMP signaling pathways, have been shown to regulate the development of kidney. A myriad of signaling pathways and their cross-talks form a precise spatiotemporal regulatory network, which ensures the kidney to be properly organized. In this review, we summarize the physiological process of kidney development as well as the involved signaling pathways and their interplay.

[Bioinformatics advances in protein ubiquitination].

Ubiquitin-proteasome system (UPS) mediates 80% to 85% of the protein degradation in eukaryotic cells. The characteristics of UPS pathway are dependent on ATP, efficient and highly selective. Ubiquitination not only participates in protein degradation, but also directly affects protein activity and localization. Ubiquitination can regulate multiple cellular processes including cell cycle progression, apoptosis, transcriptional regulation, DNA damage repair and immune response. More and more datasets about UPS are published, and it is necessary to organize and analyze these data efficiently. We re-view the related bioinformatics studies in UPS datasets, such as collection of UPS related proteins, construction and analysis of ubiquitination networks, prediction of ubiquitination sites and motifs. Some potential perspectives are also discussed.

Repopulating Kupffer cells originate directly from hematopoietic stem cells.

BACKGROUND: Kupffer cells (KCs) originate from yolk-sac progenitors before birth. Throughout adulthood, they self-maintain independently from the input of circulating monocytes (MOs) at a steady state and are replenished within 2 weeks after having been depleted, but the origin of repopulating KCs in adults remains unclear. The current paradigm dictates that repopulating KCs originate from preexisting KCs or monocytes, but there remains a lack of fate-mapping evidence. METHODS: We first traced the fate of preexisting KCs and that of monocytic cells with tissue-resident macrophage-specific and monocytic cell-specific fate-mapping mouse models, respectively. Secondly, we performed genetic lineage tracing to determine the type of progenitor cells involved in response to KC-depletion in mice. Finally, we traced the fate of hematopoietic stem cells (HSCs) in an HSC-specific fate-mapping mouse model, in the context of chronic liver inflammation induced by repeated carbon tetrachloride treatment. RESULTS: By using fate-mapping mouse models, we found no evidence that repopulating KCs originate from preexisting KCs or MOs and found that in response to KC-depletion, HSCs proliferated in the bone marrow, mobilized into the blood, adoptively transferred into the liver and differentiated into KCs. Then, in the chronic liver inflammation context, we confirmed that repopulating KCs originated directly from HSCs. CONCLUSION: Taken together, these findings provided in vivo fate-mapping evidence that repopulating KCs originate directly from HSCs, which presents a completely novel understanding of the cellular origin of repopulating KCs and shedding light on the divergent roles of KCs in liver homeostasis and diseases.

Cellular differentiation into hyphae and spores in halophilic archaea.

Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.

In vivo termini amino acid labeling for quantitative proteomics.

Quantitative proteomics is one of the research hotspots in the proteomics field and presently maturing rapidly into an important branch. The two most typical quantitative methods, stable isotope labeling with amino acids in cell culture (SILAC) and isobaric tags for relative and absolute quantification (iTRAQ), have been widely and effectively applied in solving various biological and medical problems. Here, we describe a novel quantitative strategy, termed "IVTAL", for in vivo termini amino acid labeling, which combines some advantages of the two methods above. The core of this strategy is a set of heavy amino acid (13)C(6)-arginine and (13)C(6)-lysine and specific endoproteinase Lys-N and Arg-C that yield some labeled isobaric peptides by cell culture and enzymatic digestion, which are indistinguishable in the MS scan but exhibit multiple MS/MS reporter b, y ion pairs in a full mass range that support quantitation. Relative quantification of cell states can be achieved by calculating the intensity ratio of the corresponding reporter b, y ions in the MS/MS scan. The experimental analysis for various proportions of mixed HeLa cell samples indicated that the novel strategy showed an abundance of reliable quantitative information, a high sensitivity, and a good dynamic range of nearly 2 orders of magnitude. IVTAL, as a highly accurate and reliable quantitative proteomic approach, is expected to be compatible with any cell culture system and to be especially effective for the analysis of multiple post-translational modificational sites in one peptide.

[Identification, modeling and simulation of key pathways underlying certain cancers].

Cancer is a complex disease which greatly affects the human health. It has been widely reported that certain biological pathways play important roles in the process of tumorigenesis, tumor progression and metastasis. Identification and simulation of these pathways can help to understand the underlying mechanisms. With the deposition of huge amount of microarray data, many groups have developed a series of algorithms and models to analyze the microarray datasets for the identification and simulation of tumor related pathways. In this paper, firstly we review the recent development of these algorithms and models; then list the related software and data sources; and finally discuss the existence problems and perspectives in this field.

[Association of human microRNA related genetic variations with cancer].

microRNAs (miRNAs) are a highly conserved class of small noncoding RNAs that regulate gene expression by post-transcriptional degradation or translational repression. miRNAs are involved in the regulation of cell apoptosis, proliferation, differentiation and other physiological processes, and are closely related with the development of cancer. More recently, it has been proposed that the presence of genetic variations (e.g., single nucleotide polymorphism and copy number variation) in microRNA genes, their biogenesis pathway and target binding sites affect the miRNA processing machinery and targeting, and have a significant genetic effect. In this review, we focus on the miRNA-related genetic variations and cancer susceptibility and progression.

[Review for the regulatory functions of KRAB zinc finger proteins in embryonic development and tumorgenesis of higher vertebrates].

KRAB-containing zinc-finger proteins (KRAB-ZFPs) first arose in the tetrapod vertebrates, and evolved quickly. Till Homo sapiens, they have become the largest family of transcription factors. Despite the molecular mechanism of transcription regulation by KRAB-ZFPs has been clarified in some degree, the higher-vertebrate-specific biological functions of the KRAB-ZFP family are still largely unknown. This review focused on the important regulatory functions of the KRAB-ZFP in embryonic development and tumorgenesis, which will benefit to the comprehensive understanding of biological roles of KRAB-ZFP in different physiological and pathological states. All of the systematic information will facilitate the further theoretical and applied studies of KRAB-ZFPs.

[Recent development of metabonomics and its applications in clinical research].

In the post-genomic era, systems biology is central to the biological sciences. Functional genomics such as transcriptomics and proteomics can simultaneous determine massive gene or protein expression changes following drug treatment or other intervention. However, these changes can't be coupled directly to changes in biological function. As a result, metabonomics and its many pseudonyms (metabolomics, metabolic profiling, etc.) have exploded onto the scientific scene in the past several years. Metabonomics is a rapidly growing research area and a system approach for comprehensive and quantitative analysis of the global metabolites in a biological matrix. Analytical chemistry approach is necessary for the development of comprehensive metabonomics investigations. Fundamentally, there are two types of metabonomics approaches: mass-spectrometry (MS) based and nuclear magnetic resonance (NMR) methodologies. Metabonomics measurements provide a wealth of data information and interpretation of these data relies mainly on chemometrics approaches to perform large-scale data analysis and data visualization, such as principal and independent component analysis, multidimensional scaling, a variety of clustering techniques, and discriminant function analysis, among many others. In this review, the recent development of analytical and statistical techniques used in metabonomics is summarized. Major applications of metabonomics relevant to clinical and preclinical study are then reviewed. The applications of metabonomics in study of liver diseases, cancers and other diseases have proved useful both as an experimental tool for pathogenesis mechanism re-search and ultimately a tool for diagnosis and monitoring treatment response of these diseases. Next, the applications of metabonomics in preclinical toxicology are discussed and the role that metabonomics might do in pharmaceutical research and development is explained with special reference to the aims and achievements of the Consortium for Metabonomic Toxicology (COMET), and the concept of pharmacometabonomics as a way of predicting an individual's response to treatment is highlighted. Finally, the role of metabonomics in elucidating the function of the unknown or novel enzyme is mentioned.

[Advances on mutant p53 research].

Inactivation of tumor suppressor gene is a key event in carcinogenesis. p53 is one of the most important tumor suppressor genes in the genome, and its mutations are found in approximately 50% of human cancers. p53 mutation is also the main cause for human Li-Fraumeni syndrome. The vast majority of p53 mutations are missense mutations, and the corresponding mutant p53 proteins not only lose wild-type p53 tumor suppressor activities, but also gain new oncogenic properties favoring cancer development. Here, we mainly discussed the structural and functional alterations of mutant p53, the molecular mechanisms underlying gain of oncogenic functions, and the strategies and explorations of suppressing mutant p53 activities.

Theophylline attenuates microwave-induced impairment of memory acquisition.

Numerous studies have shown that acute microwave exposure causes cognitive deficits in animals, possibly via hyperthermia, but the biological effect of microwave exposure on memory processing is still unknown. The release of adenosine is demonstrated to be a general way for the cells to respond to metabolically stressful conditions such as hypoxia and ischemia. The present study aimed to examine whether adenosine mediates biological effects of microwave exposure on memory processing using a continuous multiple-trial inhibitory avoidance task. Results demonstrated that microwave exposure for 20 min before training impaired memory acquisition and retention performance in mice, assessed by the number of training trials and by latency to enter the dark compartment. The mice exposed to microwave radiation showed a dose-dependent hyperthermia. Moreover, the cell numbers of hippocampus were decreased in the mice receiving microwave exposure at an average power density of 50 mW/cm(2), indicating the anatomical correlation to hippocampal-amygdaloid structures corresponding with the memory disrupt of the mice. Administration of theophylline, a nonspecific adenosine receptor antagonist, 30 min before microwave exposure, completely antagonized the impairment of inhibitory avoidance acquisition but not retention. These results suggest that the adenosine regulation pathway was partially involved in microwave-induced impairment of inhibitory avoidance memory.

[KAP-1, a scaffold protein in transcription regulation].

KAP-1 (Alternative names: TIF1beta or TRIM28) is one member of transcriptional intermediary factors, which acts as a scaffold in many transcription regulation complexes. The N-terminal RBCC domain of KAP-1 can interact with KRAB-ZFPs, MDM2, MM1, C/EBPbeta, etc. KAP-1's C-terminal PHD and Bromodomain is two integrated transcriptional repression domains, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity. In addition, KAP-1 can interact with HP1s (heterochromatin protein 1) and then bind to histones via its HP1BD which is a small segment in the central region of KAP-1. It is indicated by many researches that KAP-1, a scaffold protein in transcription regulation, mainly acts as a corepressor in many repression complexes. Meanwhile, it also acts as a coactivator sometimes. It is reported that KAP-1 related transcription regulation complexes exert functions essential for spermiogenesis and early embryo development. This regulation is one pattern of epigenetic regulations.

[Technique progress in the study of protein/peptide phosphorylation].

Phosphorylation is an important protein chemical modification which plays vital roles in completion and change of protein function. There are lots of technique difficulties in this field which become the challenges of the research. In recent years, phosphorylation research has made many novel achievements profit from the breakthroughs of cross-correlation techniques. In this article, we introduce the technique development of this research field from many aspects such as detection of phosphorylated proteins, enrichment of phosphorylated proteins and peptides, improvement of biological mass spectrometry-based techniques, quantification and comparison of phosphorylated proteins and peptides.

[Detection and controlling for population stratification in association studies of human complex disease].

Case-control studies, which serve as standard design for genetic association analysis, can be the most practical and powerful approach to detect genetic polymorphisms contributing to susceptibility to complex human diseases. However, considerable concern has been expressed that this approach is prone to population stratification, which can lead to biased or spurious results. We review several methods to detect and account for population stratification; these methods include nuclear family-based transmission/disequilibrium test (TDT), and genomic control (GC) and structured association (SA) based on unlinked genetic markers.

[Chemical probe in the proteomics].

With the proteomics concept introduction and effective projects implement as Human Plasma Project, the proteomics research is being developed rapidly, which is based on the analytical chemistry and physical chemistry. More and more biologists paid attention to this field, and got some important results in cell biology and biochemistry. The variation of protein quantity and various modifications in the cell reflects the environment stress and the function requirement. To investigate these variations, proteomic technology provided powerful tools. In this article, chemical probe in quantitative and modification study is discussed in details.

[Constructing gene regulatory network from microarray data].

With the rapid deposition of the microarray data in recent years, microarray data has increasingly become an important data source for bioinformatics research. Based on microarray date, constructing gene regulatory networks has also become a hotspot. By constructing the gene regulatory network, we can identify the complicated regulatory relationships, uncover the regulatory patterns in the cell, and gain the systematic view for biological process. Recently, many algorithms have also been introduced in this field to determine gene regulatory networks based on such high-throughput microarray data. In this paper, we review the development of these algorithms, with a particular emphasis on their improvement of theory and method. At last, we present the available software and platform and discuss the development trends in this field.

[Progress in the study of histone methyltransferases].

Site- and state-specific lysine methylation of histones is catalyzed by a family of proteins including those contain the evolutionarily conserved SET domain. Research on histone methyltransferases is a part of epigenetics, which plays a fundamental role in heterochromatin formation, X-chromosome inactivation and transcription regulation. Aberrant histone methylation was linked to a number of developmental disorders and human disease including several carcinomas. Histone lysine methylation is a functionally complex process, as it can either activate or repress transcription, depending on sequence-specific lysine methylation site in histones. Non-histone proteins were found to be methylated by SET domain-containing histone methyltransferases whose primary targets were presumed to be histones. The researches on histone methyltransferases will make a completely new space for transcriptional activity, embryonic development, cell differentiation, and signal transduction.