Effects of growth rate and promoter activity on single-cell protein expression

AbstractUnderstanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.

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Faculty Opinions recommendation of Stress-Induced Changes in Bone Marrow Stromal Cell Populations Revealed through Single-Cell Protein Expression Mapping.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.736146209.793575322 ◽

2020 ◽

Author(s):

Simón Méndez-Ferrer

Keyword(s):

Bone Marrow ◽

Protein Expression ◽

Single Cell ◽

Stromal Cell ◽

Bone Marrow Stromal Cell ◽

Single Cell Protein ◽

Cell Protein ◽

Cell Populations ◽

Marrow Stromal Cell ◽

Induced Changes

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Faculty Opinions recommendation of Stress-Induced Changes in Bone Marrow Stromal Cell Populations Revealed through Single-Cell Protein Expression Mapping.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.736146209.793568500 ◽

2019 ◽

Author(s):

John F DiPersio

Keyword(s):

Bone Marrow ◽

Protein Expression ◽

Single Cell ◽

Stromal Cell ◽

Bone Marrow Stromal Cell ◽

Single Cell Protein ◽

Cell Protein ◽

Cell Populations ◽

Marrow Stromal Cell ◽

Induced Changes

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The relationship of substrate, growth rate, and maintenance coefficient to single cell protein production

Biotechnology and Bioengineering ◽

10.1002/bit.260150109 ◽

1973 ◽

Vol 15 (1) ◽

pp. 117-127 ◽

Cited By ~ 53

Author(s):

Bernard J. Abbott ◽

Allen Clamen

Keyword(s):

Growth Rate ◽

Single Cell ◽

Protein Production ◽

Single Cell Protein ◽

Cell Protein ◽

Maintenance Coefficient ◽

Relationship Of ◽

The Relationship ◽

Single Cell Protein Production

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Multiplexed single cell protein expression analysis in solid tumours using a miniaturised microfluidic assay

Convergent Science Physical Oncology ◽

10.1088/2057-1739/aa6aae ◽

2017 ◽

Vol 3 (2) ◽

pp. 024003 ◽

Cited By ~ 8

Author(s):

Alastair J Magness ◽

James A Squires ◽

Beatrice Griffiths ◽

Khurum Khan ◽

Amanda Swain ◽

...

Keyword(s):

Protein Expression ◽

Single Cell ◽

Expression Analysis ◽

Single Cell Protein ◽

Solid Tumours ◽

Cell Protein

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Effect of Land Agricultural Fertilizer on Growth of Marine Single Cell Protein, Spirulina platensis, Chlorella vulgaris and Nannochloropsis

Omni-Akuatika ◽

10.20884/1.oa.2019.15.2.764 ◽

2019 ◽

Vol 15 (2) ◽

pp. 69

Author(s):

Purnama Sukardi ◽

Ferisa Wahyunika ◽

Tjahyo Winanto ◽

Norman Arie Prayogo ◽

Taufan Harisam ◽

...

Keyword(s):

Growth Rate ◽

Single Cell ◽

Protein Content ◽

Chlorella Vulgaris ◽

Spirulina Platensis ◽

Single Cell Protein ◽

Nannochloropsis Oculata ◽

Cell Protein ◽

C 30 ◽

Agricultural Fertilizer

This study aimed to determine the growth rate and protein content in Nannochloropsis oculata, Chlorella vulgaris, Spirulina platensis were cultured using agricultural fertilizers. The agricultural fertilizers used were Urea, ZA and TSP. Each single cell protein was cultured using the three types of fertilizers with a ratio of Urea: ZA and TSP as follows (A) 1: 2: 1 [(10:20:10 g / L)], (B) 2: 2: 1 [(20:20:10 g / L)] and (C) 3: 2: 1 [(30:20:10 g / L)], respectively. The results showed that the best ratio of Urea, ZA and TSP fertilizers to growth of Spirulina, Nannochloropsis oculata and Chlorella vulgaris was C [30:20:10 (g / L)] treatment. However, phyto-protein content in Nannochlorophsis differed significantly between fertilization treatments, C fertilization yielded the highest protein content (28.75±0.05%), when compared with A (25.13±0.01%) and B (25.14±0.02%), respectively. In Chlorella vulgaris, all fertilization treatments showed very significant differences, B fertilization (28.24%±00.006) yielded the highest phyto-protein content, if compared to A (23.63% ± 0.003) and C (19.74% ±0.006 ), respectively. All fertilization treatments showed very significant differences (P <0.05) on Spirulina platensis. The highest content of phyto-protein (62.68 + 0.05%) was present in treatment C, when compared to A (52.18 + 0.05%) and B (62.37 + 0.01%) treatments, respectively.

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Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARC

10.1101/749473 ◽

2019 ◽

Cited By ~ 1

Author(s):

Johan Reimegård ◽

Marcus Danielsson ◽

Marcel Tarbier ◽

Jens Schuster ◽

Sathishkumar Baskaran ◽

...

Keyword(s):

Protein Expression ◽

Mrna Expression ◽

Single Cell ◽

Single Cell Analysis ◽

Single Cells ◽

Embryonic Stem ◽

Single Cell Protein ◽

Cell Protein ◽

Depth Analysis ◽

Mrna And Protein Expression

ABSTRACTCombined measurements of mRNA and protein expression in single cells enables in-depth analysis of cellular states. We present single-cell protein and RNA co-profiling (SPARC), an approach to simultaneously measure global mRNA and large sets of intracellular protein in individual cells. Using SPARC, we show that mRNA expression fails to accurately reflect protein abundance at the time of measurement in human embryonic stem cells, although the direction of changes of mRNA and protein expression are in agreement during cellular differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do the corresponding transcripts. We further show that changes of the balance between protein and mRNA expression levels can be applied to infer expression kinetic trajectories, revealing future states of individual cells. Finally, we highlight that mRNA expression may be more varied among cells than levels of the corresponding proteins. Overall, our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. Accordingly, SPARC can offer valuable insights in gene expression programs of single cells.

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