ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor,

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Highlights

• •Identification of the first evolutionary divergent sirtuin ScCobB2 in bacteria.
• •Implementing a global quantitative succinylome between ΔScCobB2 and WT cells.
• •ScCobB2 regulates S. coelicolor protein biosynthesis and carbon metabolism pathways.
• •The divergent sirtuin enzymes are prevalent in other groups of Actinobacteria.

     

Phytoplasma-induced Changes in the Acetylome and Succinylome of Paulownia tomentosa Provide Evidence for Involvement of Acetylated Proteins in Witches' Broom Disease

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Highlights

• •Quantitative global proteome, acetylome and succinylome of phytoplasma-infected Paulownia tomentosa seedlings.
• •Acetylation may be more important than succinylation in response to phytoplasma infection.
• •Acetylation modified the activities of POR and RuBisCO.
• •Possible model to elucidate the molecular mechanism responses to PaWB from proteome and PTMs.

     

Proteomic Profiling of Human Prostate Cancer-associated Fibroblasts (CAF) Reveals LOXL2-dependent Regulation of the Tumor Microenvironment

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Highlights

• •Quantitative (phoshpo)proteome of primary cell cultures of patient-matched prostate CAF and NPF.
• •Key CAF-associated proteins validated using orthogonal methodologies.
• •LOXL2 inhibitors D-penicillamine and PXS-S2A impaired CAF migration and ECM alignment.
• •Pre-treatment with LOXL2 inhibitors impaired migratory capacity of RWPE-2 cells in co-culture.

     

Identification of Novel Natural Substrates of Fibroblast Activation Protein-alpha by Differential Degradomics and Proteomics

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Highlights

• •Natural substrates of FAP were identified using degradomic and proteomic techniques and FAP gene knockout mouse derived embryonic fibroblasts stably transduced with enzymatically active or inactive FAP.
• •Terminal amine isotopic labelling of substrates (TAILS) based degradomics identified cleavage sites in collagens, and many other extracellular matrix (ECM) and associated proteins.
• •Cleavages of lysyl oxidase-like-1, CXCL-5, CSF-1 and C1qT6 by FAP were confirmed in vitro.
• •Differential metabolic labelling coupled with quantitative proteomic analysis implicated FAP in regulating proteins that are associated with ECM, ECM-cell interactions, coagulation, metabolism and wound healing.

     

psims - A Declarative Writer for mzML and mzIdentML for Python

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Highlights

• •Incrementally build mzML 1.1, and mzIdentML 1.2 files in Python over a file stream.
• •Traverse controlled vocabularies using common mapping patterns.
• •Generate byte offset index as the document streams.
• •Manage referential integrity on-the-fly.

     

High-density Peptide Arrays Help to Identify Linear Immunogenic B-cell Epitopes in Individuals Naturally Exposed to Malaria Infection

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Highlights

• •Profiling antibody responses of patients with naturally acquired malaria immunity.
• •High-density peptide arrays featuring linear epitopes.
• •Epitope mapping of known and potential novel vaccine candidates.
• •Novel immunogenic epitopes discovered, and known antibody target motifs confirmed.

     

Intact Transition Epitope Mapping – Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE),

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Highlights

• •Multiplex epitope mapping/antigenic determinant identification in the gas phase.
• •Intact transition and controlled dissociation of immune complexes by MS.
• •Simultaneous identification and amino acid sequence determination of epitopes.
• •Simplified in-solution sample handling because of ion manipulation and filtering by MS.

     

Proteomics,Glycomics, and Glycoproteomics of Matrisome Molecules

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Highlights

• •Highly glycosylated matrisome proteins and their binding partners comprise extracellular networks that mediate tissue-specific cellular microenvironments.
• •Elucidation of roles of matrisome molecules in disease mechanisms requires detailed mapping of matrisome glycosylation and other post-translational modifications.
• •We review tissue workup methods for matrisome proteomics, glycomics and glycoproteomics.
• •The combination of proteomics, glycomics and glycoproteomics profiles matrisome protein modifications distinct from those studied by immunohistochemistry.

     

The Proteome of Pig Spermatozoa Is Remodeled During Ejaculation

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Highlights

• •Proteome of mature boar spermatozoa from cauda epididymal and ejaculated sources were analyzed by iTRAQ-based LC-MS/MS.
• •1,723 sperm proteins identified (974 of Sus scrofa taxonomy).
• •1,602 sperm proteins quantified (960 of Sus scrofa taxonomy).
• •32 Sus scrofa sperm proteins were differentially expressed among sperm sources.
• •The proteome of boar spermatozoa is remodelled during ejaculation.

     

Whole Proteome Profiling of N-Myristoyltransferase Activity and Inhibition Using Sortase A

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Highlights

• •Application of Sortase A to label protein N-termini across the whole proteome.
• •Novel gel, proteomic and ELISA-based methods to determine N-myristoylation of proteins in cells, without metabolic labelling.
• •Side by side mass spectrometric quantification of changes in protein N-myristoylation by two complementary methods.
• •Improved Biotin-Neutravidin affinity enrichment protocol.

     

Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicus,

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Highlights

• •Protein acetylation at Lys residues and the N terminus occurs widely in Sulfolobus.
• •SisPat preferentially acetylates a group of acyl-CoA synthetases.
• •SisArd1 acetylates the majority of the acetylated N termini identified in the cell.
• •SisArd1, but not SisPat, is required for the optimal growth of the organism.

     

Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal Axes,

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Highlights

• •Quantitative proteomics of mitotic chromosome scaffold isolated from chicken DT40 cells.
• •BAZ1B identified in the isolated mitotic chromosome scaffold localizes to mitotic chromosome axes.
• •BAZ1B knockout caused prophase delay because of altered chromosome condensation timing and impaired mitosis progression.
• •BAZ1B knockout did not affect prometaphase chromosome structure.

     

Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics

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Highlights

• •The developed Ac-LysargiNase showed higher stability and activity than before.
• •The merged spectra of the mirror peptides achieved nearly complete ion coverage.
• •pNovoM obviously increased the efficiency and accuracy of peptide sequencing.
• •The mirror enzymatic strategy achieved precision de novo sequencing on proteome scales.

     

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability,

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Highlights

• •Our search identifies 2,134 kinase-substrate phosphosite pairs in breast cancer.
• •CDKs and MAPKs are dominant regulators of trans substrate-phosphorylation.
• •Druggability, outcomes, and immune signatures related to kinase-substrates.
• •Experimentally validated activated phosphosites of ERBB2, EIF4EBP1, and EGFR.

     

Integrated Proteomics Reveals Apoptosis-related Mechanisms Associated with Placental Malaria*

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Highlights

• •An integrated proteome, phosphoproteome and glycoproteome analysis was applied to past P. falciparum-infected placentas.
• •A total of 2946 proteins, 1733 N-linked glycosites and 4100 phosphosites were identified and quantified in the human placentas.
• •AKT and ERK signaling pathways are associated to an increased apoptosis in past P. falciparum-infected placentas.

     

Comparative Secretome Analyses of Primary Murine White and Brown Adipocytes Reveal Novel Adipokines

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Highlights

• •First comparative proteomic analysis of white and brown adipocyte secretomes.
• •100 novel adipokines differentially secreted from white versus brown adipocytes.
• •Functionally enriched protein class changes in white and brown adipocytes.
• •200 novel, NE-responsive adipokines from brown adipocytes.

     

A Robust and Versatile Automated Glycoanalytical Technology for Serum Antibodies and Acute Phase Proteins: Ovarian Cancer Case Study

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Highlights

• •Quantitative high-throughput glycoanalytical technology as a diagnostic tool for ovarian cancer detection.
• •Multiplexed approach harnessing N-glycan data for six glycoproteins from a single biological sample.
• •Detailed characterization of human serum N-glycans from antibodies IgG, IgM and IgA and acute phase proteins transferrin, haptoglobin and alpha-1-antitrypsin.
• •Structural differences in antibody and acute phase protein glycosylation for mechanistic insights.