Virulence Factors Produced by Staphylococcus aureus Biofilms Have a Moonlighting Function Contributing to Biofilm Integrity

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Highlights

• •Establishment of a flow system allowing multi-omics analysis of S. aureus biofilms.
• •Biofilm proteome profiling (intracellular and ECM) plus metabolic footprint analysis.
• •Virulence factors and ribosomal proteins stabilize the ECM as moonlighting proteins.
• •They act as electrostatic bridges between anionic cell surfaces, eDNA and metabolites.

     

Metabolic Cross-talk Between Human Bronchial Epithelial Cells and Internalized Staphylococcus aureus as a Driver for Infection*

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Highlights

• •Interplay of epithelial cells and internalized S. aureus was dissected over 96 h.
• •Surviving host cells contain nonreplicating bacteria that persists in the cytoplasm.
• •Competition over resources triggers temporal metabolic changes.
• •Metabolic adaptation of host and bacteria determines the outcome of infection.

     

Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase,as a Novel Regulator of Root Meristem Maintenance

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Highlights

• •Auxin responsive proteins in Arabidopsis roots were identified from 3,514 detected proteins.
• •All six auxin receptors are stable in response to hormone via novel MRM assays.
• •The >100 differentially expressed proteins exhibit dynamic and transient responses to auxin.
• •Phenotypic screening of the top responsive proteins uncovered several novel root mutants.

     

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.

     

Effects of Size and Geographical Origin on Atlantic salmon,Salmo salar,Mucin O-Glycan Repertoire

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Highlights

• •Atlantic salmon O-glycome expanded to 169 structures in three epithelia.
• •Low interindividual variation amongst all populations and geographical regions.
• •Small variations in glycosylation between geographical locations and fish size.
• •Prominent fucosylation in gastrointestinal mucins from Tasmanian fish.

     

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level

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Highlights

• •Rapamycin and zinc induce moderate but significant mitochondrial proteome changes.
• •The mitochondrial proteins processing system is robust under subtoxic conditions.
• •Rapamycin and zinc perturb the mitochondrial proteins processing system.
• •Rapamycin and zinc perturb the mitochondrial proteins homeostasis.

     

Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling,Glycan-array Data,and Mass Spectrometry

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Highlights

• •Method to probe the isomeric variants of the glycans attached to purified proteins.
• •Uses multiple rounds of glycosidase cleavage and lectin profiling.
• •Computation integration of lectin-binding, glycan-array, and mass spectrometry data.
• •Applied to microspots for compatibility with analyzing low-abundance proteins.

     

Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila,

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Highlights

• •A global lysine succinylome was investigated in A. hydrophila.
• •The lysine succinylation modifications play crucial role on various metabolic pathways.
• •Reversible succinylation on Lys23 and Lys30 regulates the activity of S-ribosylhomocysteine lyase LuxS.
• •Lysine succinylation modifications of LuxS affect quorum sensing and metabolism.

     

DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

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Highlights

• •Open source software for comprehensive HDX-MS data analysis.
• •Automatic back-exchange correction options.
• •Rigorous statistical analysis of the significance of uptake differences.
• •High quality visualization tools.

     

Decreased Antibiotic Susceptibility Driven by Global Remodeling of the Klebsiella pneumoniae Proteome

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Highlights

• •Global proteomic remodeling alters antibiotic susceptibility in K. pneumoniae.
• •Drug specific transport, sugar utilization, central metabolism, capsule synthesis.
• •Common pathways of reactive oxygen scavenging, turnover of misfolded proteins.
• •Integrated adjustments and unique drug-specific features for drug combinations.

     

Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila,

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Highlights

• •Proteomic landscapes of Drosophila somatic and reproductive tissues during aging.
• •Pulsed metabolic labeling determines a decline in protein synthesis with age.
• •Drosophila model of human Parkinson's disease signifies an early-onset decline in protein synthesis.
• •Collapse of proteostasis and mitochondria are early signals for normal aging.

     

A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance

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Highlights

• •Quantitative (phospho)proteome analysis of antibiotic treatment in E. coli.
• •Largest bacterial phosphorylation catalogue.
• •Specific phosphorylation motifs changes during resistance development.
• •Phosphorylation mediated signaling could be a potential target for drug design.

     

Metabolic,Anti-apoptotic and Immune Evasion Strategies of Primary Human Myeloma Cells Indicate Adaptations to Hypoxia*

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Highlights

• •In-depth proteome profiling of primary human myeloma cells
• •Characteristics of myeloma cells are related to hypoxic bone marrow conditions
• •Myeloma cells show specific immune evasion strategies
• •Metabolic adaptations involve tumor and stroma cells

     

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.

     

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.

     

BioID Performed on Golgi Enriched Fractions Identify C10orf76 as a GBF1 Binding Protein Essential for Golgi Maintenance and Secretion

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Highlights

• •BioID with Golgi fractions identified C10orf76 as proximal to GBF1.
• •Tagged C10orf76 overlaps with Golgi markers.
• •C10orf76 binds GBF1 and exchanges rapidly between free and bound forms.
• •C10orf76 is essential for maintenance of the Golgi and for secretion.

     

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.

     

Integrated Analysis of Transcriptomic,miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis

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Highlights

• •mRNA-seq, miRNA-seq, proteomes of P. fulvidraco, P. vachelli, hybrid Huangyou-1.
• •Predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM.
• •Immune, metabolism, digestion, absorption, proliferation, development generate heterosis.
• •High parental gene/protein with low parental miRNAs inherit from the mother or father.