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.

     

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.

     

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.

     

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.

     

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.

     

Global Lysine Crotonylation and 2-Hydroxyisobutyrylation in Phenotypically Different Toxoplasma gondii Parasites

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Highlights

• •Quantitative proteomes and epigenetic regulation of T. gondii.
• •Protein crotonylation and 2-hydroxyisobutylation in phenotypically different T. gondii parasites.
• •Regulation of invasion regulation of T. gondii by protein modification.
• •Lysine crotonylation and 2-hydroxyisobutylation regulated in multiple biological processes in phenotypically different T. gondii parasites.

     

Mapping Spatiotemporal Microproteomics Landscape in Experimental Model of Traumatic Brain Injury Unveils a link to Parkinson's Disease,

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Highlights

• •Spatiotemporal microproteomics analysis of TBI.
• •Injury site microproteomics reveal distinct phases in 10-day frame post TBI.
• •Uninjured proteomic profile is restored in TBI at 10 days post injury.
• •Substantia nigra protein post 3 days suggest link to Parkinson's disease.

     

Investigating Lactococcus lactis MG1363 Response to Phage p2 Infection at the Proteome Level

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Highlights

• •The proteomes of L. lactis MG1363 and phage p2 at different stages of infection were characterized.
• •16% (226/1412) of the bacterial proteins detected were unique to infected cultures.
• •A targeted approach using synthetic peptides improved the coverage of phage p2 proteome.
• •By means of proteogenomics, we uncovered a conserved phage protein coded by a previously unannotated gene.
• •Deletion of the bacterial gene llmg_0219 (unknown function) impedes phage p2 infection.

     

Pest sequences in nuclear proteins

• 1.1. Most of proteins which are rapidly degraded inside eukaryotic cells have been found to contain amino acid sequences (PEST sequences) enriched in proline, acidic residues (glutamic acid and/or aspartic acid) and hydrophilic residues (serine and threonine) (Rogers et al. (1986) Science234, 364–368).
• 2.2. This correlation was tested on nuclear proteins and a close relationship was found between nuclear protein stability and the presence of PEST regions.
• 3.3. Nuclear proteins with structural functions which can be considered as stable components of cell nuclei generally lack PEST sequences.
• 4.4. In contrast, regulatory nuclear factors which have specific and transient functions generally possess at least one PEST sequence.

     

Critical Role of a Sheath Phosphorylation Site On the Assembly and Function of an Atypical Type VI Secretion System

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Highlights

• •Phosphorylation on Y139 of the sheath protein IglB of Francisella.
• •IglB substitutions Y139A, Y139D or Y139E prevent T6SS formation.
• •Y139F substitution delays but does not abolish phagosomal escape in macrophages.
• •Insight into the role of sheath phosphorylation in T6SS biogenesis.

     

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.

     

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.

     

The quaternary structure of the lobster carapace carotenoprotein,crustacyanin: Studies using cross-linking agents

• 1.1. Three bis(imidoesters) of different span (ca 9–11 Å) have been used to form intermolecular cross-links between the apoproteins of the lobster carapace carotenoprotein, α-crustacyanin.
• 2.2. Dimethylpimelimidate(DMP) is the most effective of the three reagents in cross-linking the oligomeric α-crustacyanin, giving predominantly dimers between apoproteins from each of the two apoprotein classes. The native dimers, β-crustacyanins, are effectively cross-linked with this reagent.
• 3.3. The stability of DMP cross-linked α-crustacyanin and of the native carotenoprotein to urea treatment and to heating have been compared.
• 4.4. Reagents of longer (sulpho-N-hydroxy-succinimide ester; 18 Å) or shorter (1,5-difluoro-2,4-dinitrobenzene; 5 Å) spans than the bis(imidoesters) are similarly able to form cross-linked dimers with the crustacyanins, but less effectively under the conditions of the reactions.
• 5.5. The results are discussed in relation to the previously presented putative structure of β-crustacyanin (Keen et al. 1990b. Eur. J. Biochem. (submitted); Zagalsky et al., 1990. Comp. Biochem. Physiol.97B, 1–18) and to an alternative subunit interface arrangement of the apoproteins for the dimer.

     

Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry

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Highlights

• •Targeted mass spectrometry assay to quantify prion protein (PrP) in spinal fluid.
• •Precise measurement of PrP peptide concentration across protein domains.
• •Peptides are uniformly decreased in symptomatic prion disease patients.
• •Assay applicable to humans and preclinical species for drug development.

     

Probing H2O2-mediated Structural Dynamics of the Human 26S Proteasome Using Quantitative Cross-linking Mass Spectrometry (QXL-MS)

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Highlights

• •Two-step cross-linking coupled with affinity purification to facilitate structural analysis of protein complexes.
• •Integrated QXL-MS workflow for studying condition-dependent structural changes of protein complexes.
• •Mechanistic insights on in vivo H₂O₂-induced conformational dynamics of proteasome complexes.

     

Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus

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Highlights

• •BioID and IP-MS were conducted to generate a global ZIKV-host protein interactome
• •Interactome consists of >3000 high confidence ZIKV-host protein interactions
• •Data mining indicates that ZIKV proteins interact with multiple host cell organelles
• •An important role for peroxisomes in ZIKV infection is uncovered