Table of Contents
Research
Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal AxesOur quantitative proteomics study determined the protein composition of the mitotic chromosome scaffold. MS results revealed a novel component of the chromosome scaffold, BAZ1B, which was localized to the mitotic chromosome axis. Our results using BAZ1A/B double-KO cells suggest that BAZ1 proteins are essential for timely chromosome condensation at mitosis entry.
Integrated Proteomics Reveals Apoptosis-related Mechanisms Associated with Placental Malaria*This paper investigated the molecular pathways modulated in past P. falciparum-infected placentas. The proteome, phosphoproteome and glycoproteome analysis of P. falciparum-infected placentas that had developed placental malaria during pregnancy but had the parasites cleared by pharmacological treatment, revealed the activation of AKT and ERK signaling pathways and apoptosis. These molecular features open new perspectives towards novel therapeutic solutions.
Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophilaThe affinity antibody purification combined with LC MS/MS was used to investigate the lysine succinylome profile of A. hydrophila ATCC7966. A total of 666 lysine succinylation proteins were identified and analyzed in depth to better understand its regulatory roles. Lysine succinylation modifications on S-ribosylhomocysteine lyase were further studied and shown to regulate its cellular physiology and affect bacterial quorum sensing behavior of A. hydrophila.
Integrative Proteomic and Phosphoproteomic Profiling of Testis from Wip1 Phosphatase-Knockout Mice: Insights into Mechanisms of Reduced Fertility*Wei et al. apply multi-layer proteomic profiling and systems biology approaches to define Wip1-deficient testis proteome and phosphoproteome landscapes, and they identify cell adhesion/tight junction, sperm motility, and inflammatory response pathways. These data establish the mechanism that proinflammatory cytokines may impair the blood-testis barrier dynamics by decreasing the expression of junction-associated proteins in Wip1 null testes, leading to subfertility and spermatogenesis defects.
Common Metabolic Pathways Implicated in Resistance to Chemotherapy Point to a Key Mitochondrial Role in Breast CancerQuantitative MS-based proteomics enabled to distinguish metabolic differences of triple negative breast cancer cells and corresponding chemoresistant and cancer stem cells (CSC). This puts mitochondria in a spotlight for cancer therapy and places bactericidal antibiotics; – particularly linezolid- as effective agents for eliminating CSC and resistant cells.
Identification of a Specific Translational Machinery via TCTP–EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA)Translationally controlled tumor protein (TCTP) is a novel biological target for neurofibromatosis type 1 (NF1)-associated tumors. Here, we identified specific TCTP-interacting proteins by affinity purification and data-independent mass spectrometry acquisition (AP-DIA/SWATH). TCTP mainly interacts with elongation factors in NF1-tumor cells. Interestingly, TCTP directly binds to EF1A2 and activates EF1A2-dependent translation machinery. Inhibiting the TCTP–EF1A2 interaction significantly caused dramatic suppression of growth in NF1-tumor cells. Our findings demonstrate that a translation machinery via TCTP–EF1A2 could represent a therapeutic target of NF1-tumors.
Characterization of Proteome Variation During Modern Maize BreedingThe integrated multi-omics analysis provides insights into variation at different gene expression levels during the adaption of modern maize from tropical to temperate regions. Population-specific proteome variation mirrors genetic variation better than mRNA levels, and a class of cis-QTLs were identified that regulate protein abundance with little or no effect on mRNA levels. Thus, the discordance between protein and mRNA levels indicates far greater evolutionary stability of proteome during modern maize breeding.
Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of HeterodimerizationThis study characterized the β4-integrin interacting proteome using BioID proximity-dependent biotinylation in epithelial MDCK cells. The analysis identified several novel type II hemidesmosome (HD)-associated proteins and revealed potential connecting protein modules that could orchestrate the observed coordinated coassembly of HDs and focal adhesions (FAs). Curiously, unlike the formation of HDs, the assembly of β4-interactome did not depend on α6β4-heterodimerization.
Proteomic Analysis of Baboon Cerebral Artery Reveals Potential Pathways of Damage by Prenatal Alcohol ExposureProteome analysis was performed to determine whether fetal alcohol exposure during mid-pregnancy would evoke changes in protein profile of fetal cerebral artery in baboons. We detected that levels of 238 proteins differed significantly between control and alcohol-exposed fetuses. Proteins of metabolic pathways represented one of the major targets of alcohol. The differences were detected near term, long after alcohol exposure took place. Our findings point at novel targets of alcohol within developing brain vessels.
Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant Arabidopsis thalianaThermal profiles and melting temperatures have been modeled for over 1700 proteins from the model plant Arabidopsis thaliana using six biological replicates, providing a solid groundwork for future thermal shift studies in the species. Highly significant global correlations were found between melting temperature and several protein characteristics, including molecular weight, secondary structure content, and hydrophobic and charged accessible surface areas.
Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone BindingThe oligomerization (and particularly dimerization) of Hsp70 proteins plays an important role in their chaperoning activities. Here, we report that human stress-inducible Hsp70 possesses the highest propensity among analyzed Hsp70 homologs to form dimers in the presence of ATP. ATP-bound Hsp70 assembles in solution as an antiparallel dimer closely resembling the dimeric structures captured in DnaK and BiP crystals. ATP-dependent Hsp70 dimerization is necessary for efficient Hsp40 interaction and is differentially affected by TPR cochaperone binding.
Identification of TEX101-associated Proteins Through Proteomic Measurement of Human Spermatozoa Homozygous for the Missense Variant rs35033974TEX101 protein is a validated biomarker of male infertility and a potential germ cell-surface chaperone. Near-complete degradation of variant G99V TEX101 protein was discovered in men homozygous and heterozygous for the missense variant rs35033974. Differential proteomic profiling revealed TEX101-associated proteins down-regulated in rs35033974hh spermatozoa, including LY6K protein.
Carcinogenic Helicobacter pylori Strains Selectively Dysregulate the In Vivo Gastric Proteome, Which May Be Associated with Stomach Cancer ProgressionHelicobacter pylori is the strongest risk factor for gastric cancer. Initial interactions between H. pylori and its host occur at the epithelial cell surface, and this activates signaling pathways that drive oncogenesis. This manuscript defines strain-specific gastric epithelial proteomic changes induced by H. pylori in vivo that are critical for initiation of the gastric carcinogenesis. Protein targets were validated in human gastric epithelial cells in vitro, primary human gastric epithelial monolayers, and H. pylori-infected gerbil and human tissue in vivo.
Surface Loops in a Single SH2 Domain Are Capable of Encoding the Spectrum of Specificity of the SH2 FamilyThe role of surface loops in encoding SH2 domain specificity has been systematically investigated by characterizing a group of loop variants obtained from screening phage-displayed SH2 domain libraries. The reported results support a general role for the EF loop (which connects the β-strands E and F) and the BG loop (which connects the α-helix B and β-strand G) in encoding SH2 specificity, add to our understanding of the mechanism of target sequence recognition by an SH2 domain in cells, and have general implications for the evolution of binding specificity of protein interaction modules.
Technological Innovation and Resources
FlashPack: Fast and Simple Preparation of Ultrahigh-performance Capillary Columns for LC-MS*FlashPack is a fast and simple protocol for capillary column packing. It is developed for the classical 100 bars pressure bomb setup and ultrahigh sorbent concentrations. It provides a 100-fold increase in packing rate and reduces packing time with sub-2 μm sorbents to a few minutes for HPLC columns and to less than an hour for 50 cm UHPLC columns. Custom-produced columns offer performance on par with commercially available capillary columns.
PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human ProteomePTMiner post-processes the coarse and error-prone results of an open search of MS/MS spectra. It confidently filters and localizes the modifications (mass shifts) using the transfer FDR and an empirical Bayesian method. Evaluated on simulated and synthetic peptide data, PTMiner showed much higher accuracy than two open search engines and the Ascore algorithm. PTMiner was used to comprehensively characterize the PTMs in a draft map of human proteome, resulting in over 1.7 million modifications confidently identified and localized.
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