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Systematic analysis of protein turnover in primary cells.

ABSTRACT: A better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000?h. We identified 4000-6000 proteins in several non-dividing cell types, corresponding to 9699 unique protein identifications over the entire data set. We observed similar protein half-lives in B-cells, natural killer cells and monocytes, whereas hepatocytes and mouse embryonic neurons show substantial differences. Our data set extends and statistically validates the previous observation that subunits of protein complexes tend to have coherent turnover. Moreover, analysis of different proteasome and nuclear pore complex assemblies suggests that their turnover rate is architecture dependent. These results illustrate that our approach allows investigating protein turnover and its implications in various cell types.

SUBMITTER: Mathieson T

PROVIDER: S-EPMC5814408 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Systematic analysis of protein turnover in primary cells.

Mathieson Toby T Franken Holger H Kosinski Jan J Kurzawa Nils N Zinn Nico N Sweetman Gavain G Poeckel Daniel D Ratnu Vikram S VS Schramm Maike M Becher Isabelle I Steidel Michael M Noh Kyung-Min KM Bergamini Giovanna G Beck Martin M Bantscheff Marcus M Savitski Mikhail M MM

Nature communications 20180215 1

A better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000 h. We identified 4000-6000 proteins in several non-dividing cell types, corresponding to 9699 ...[more]

PMID: 29449567

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Project description:ObjectivesTo analyse the prevalence and determinants of turnover intention (TI) among primary health workers (PHWs) in China to provide evidence for improving retention measures.DesignSystemic review and meta-analysis.Data sourcesFour English-language databases (PubMed, EMBASE, Cochrane Library, PsycINFO) and three Chinese databases (CNKI, CSPD, CBM) were searched up to October 2019.Eligibility criteriaEligible studies were observational or descriptive studies conducted in mainland China. The prevalence of TI among health workers and related factors had to be explicitly reported in each included study.Data extraction and synthesisData were extracted by one author and reviewed independently by two other authors. For each factor analysed by a meta-analysis, the factor was required to be the same across different studies, and at least three studies had to include it. The quality of studies was assessed using the Newcastle-Ottawa Scale and heterogeneity was evaluated using the I2 statistic.ResultsWe identified 16 cross-sectional studies investigating a total of 37 672 PHWs. The prevalence of TI was 30.4%. Subgroup analysis revealed that the highest prevalence was observed in the community primary healthcare institutions and the eastern provinces of China. Meta-analyses indicated that 21 factors were significantly associated with TI, including demographic factors (gender, age, education, marital status), job characteristic factors (title, work seniority, remuneration, social status, organisational affiliation, work stress) and job satisfaction factors (learning and training opportunity, interpersonal relationship, work condition and environment, and so on).ConclusionThis study highlights the problem of TI among PHWs in China. Efforts should be made to improve conditions in both work-related areas and areas outside of work. Policymakers should continue to improve reward systems, the construction of infrastructure and promotion systems, and pay more attention to PHWs' lives outside of work and meet their living needs.

Project description:In higher eukaryotes many genes encode protein isoforms whose properties and biological roles are often poorly characterized. Here we describe systematic approaches for detection of either distinct isoforms, or separate pools of the same isoform, with differential biological properties. Using information from ion intensities we have estimated protein abundance levels and using rates of change in stable isotope labeling with amino acids in cell culture isotope ratios we measured turnover rates and subcellular distribution for the HeLa cell proteome. Protein isoforms were detected using three data analysis strategies that evaluate differences between stable isotope labeling with amino acids in cell culture isotope ratios for specific groups of peptides within the total set of peptides assigned to a protein. The candidate approach compares stable isotope labeling with amino acids in cell culture isotope ratios for predicted isoform-specific peptides, with ratio values for peptides shared by all the isoforms. The rule of thirds approach compares the mean isotope ratio values for all peptides in each of three equal segments along the linear length of the protein, assessing differences between segment values. The three in a row approach compares mean isotope ratio values for each sequential group of three adjacent peptides, assessing differences with the mean value for all peptides assigned to the protein. Protein isoforms were also detected and their properties evaluated by fractionating cell extracts on one-dimensional SDS-PAGE prior to trypsin digestion and MS analysis and independently evaluating isotope ratio values for the same peptides isolated from different gel slices. The effect of protein phosphorylation on turnover rates was analyzed by comparing mean turnover values calculated for all peptides assigned to a protein, either including, or excluding, values for cognate phosphopeptides. Collectively, these experimental and analytical approaches provide a framework for expanding the functional annotation of the genome.

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Systematic analysis of protein turnover in primary cells.

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Systematic analysis of protein turnover in primary cells.

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