Intron-mediated induction of phenotypic heterogeneity

AbstractIntrons are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns2–4. Despite recent findings on the role of RP introns under stress and starvation5–7, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling8 with single-cell protein measurements9, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B mediated by 5’UTR-intron retention in its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to resume growth sooner after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal intron retention as a new mechanism for inducing phenotypic heterogeneity in changing environments10,11 and suggest that duplicated RP genes in yeast serve to resolve the evolutionary conflict between precise expression control and environmental responsiveness12.

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Intron-mediated induction of phenotypic heterogeneity

10.21203/rs.3.rs-264697/v1 ◽

2021 ◽

Author(s):

Tobias Bollenbach ◽

Adriana Espinosa-Cantú ◽

Martin Lukačišin

Keyword(s):

Intron Retention ◽

Ribosomal Subunit ◽

Single Cell Protein ◽

Phenotypic Heterogeneity ◽

Cell Protein ◽

Natural Environments ◽

Protein Levels ◽

Fitness Advantage ◽

Evolutionary Conflict ◽

Environmental Responsiveness

Abstract Introns are universally present in the nuclear genomes of eukaryotes. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns. Despite recent findings on the role of RP introns under stress and starvation, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling with single-cell protein measurements, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B mediated by 5’UTR-intron retention in its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to resume growth sooner after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal intron retention as a new mechanism for inducing phenotypic heterogeneity in changing environments and suggest that duplicated RP genes in yeast serve to resolve the evolutionary conflict between precise expression control and environmental responsiveness.

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Single cell protein analysis for systems biology

Essays in Biochemistry ◽

10.1042/ebc20180014 ◽

2018 ◽

Vol 62 (4) ◽

pp. 595-605 ◽

Cited By ~ 18

Author(s):

Ezra Levy ◽

Nikolai Slavov

Keyword(s):

Systems Biology ◽

Single Cell ◽

Cell Fate ◽

Fluorescent Proteins ◽

Single Cells ◽

Protein Analysis ◽

Single Cell Protein ◽

Cell Protein ◽

Protein Levels ◽

Trade Offs

The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have regulatory roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review examples connecting protein levels and their dynamics in single cells to cellular functions. Such findings were made possible by the introduction of antibodies, and subsequently fluorescent proteins, for tracking protein levels in single cells. However, in heterogeneous cell populations, such as tumors or differentiating stem cells, cellular decisions are controlled by hundreds, even thousands of proteins acting in concert. Characterizing such complex systems demands measurements of thousands of proteins across thousands of single cells. This demand has inspired the development of new methods for single-cell protein analysis, and we discuss their trade-offs, with an emphasis on their specificity and coverage. We finish by highlighting the potential of emerging mass-spec methods to enable systems-level measurement of single-cell proteomes with unprecedented coverage and specificity. Combining such methods with methods for quantitating the transcriptomes and metabolomes of single cells will provide essential data for advancing quantitative systems biology.

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Single cell protein analysis for systems biology

10.7287/peerj.preprints.26965 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ezra Levy ◽

Nikolai Slavov

Keyword(s):

Systems Biology ◽

Single Cell ◽

Cell Fate ◽

Fluorescent Proteins ◽

Single Cells ◽

Protein Analysis ◽

Single Cell Protein ◽

Cell Protein ◽

Protein Levels ◽

Trade Offs

The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have functional roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review such examples of connecting protein levels and their dynamics in single cells to cellular functions. Such findings were made possible by the introduction of antibodies, and subsequently fluorescent proteins, for tracking protein levels in single cells. However, in heterogeneous cell populations, such as tumors or differentiating stem cells, cellular decisions are controlled by hundreds, even thousands of proteins acting in concert. Characterizing such complex systems demands measurements of thousands of proteins across thousands of single cells. This demand has inspired the development of new methods for single cell protein analysis, and we discuss their trade-offs, with emphasis on their specificity and coverage. We finish by highlighting the potential of emerging mass-spec methods to enable systems-level measurement of single-cell proteomes with unprecedented coverage and specificity. Combining such methods with methods for quantifying the trasncriptomes and metabolomes of single cells will provide essential data for advancing quantitative systems biology.

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Single cell protein analysis for systems biology

10.7287/peerj.preprints.26965v1 ◽

2018 ◽

Cited By ~ 2

Author(s):

Ezra Levy ◽

Nikolai Slavov

Keyword(s):

Systems Biology ◽

Single Cell ◽

Cell Fate ◽

Fluorescent Proteins ◽

Single Cells ◽

Protein Analysis ◽

Single Cell Protein ◽

Cell Protein ◽

Protein Levels ◽

Trade Offs

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Platelet Aggregation in Rats in Relation to Hyperuricaemia Induced by Dietary Single-Cell Protein and to Protein Deficiency

Thrombosis and Haemostasis ◽

10.1055/s-0038-1646695 ◽

1978 ◽

Vol 39 (02) ◽

pp. 346-359 ◽

Cited By ~ 3

Author(s):

P D Winocour ◽

M R Turner ◽

T G Taylor ◽

K A Munday

Keyword(s):

Uric Acid ◽

Platelet Count ◽

Platelet Aggregation ◽

Time Lag ◽

Blood Platelet ◽

Single Cell Protein ◽

Cell Protein ◽

Low Protein ◽

Blood Platelet Count ◽

Rat Platelets

SummaryA major limitation to single-cell protein (SCP) as a human food is its high nucleic acid content, the purine moiety of which is metabolised to uric acid. Rats given a Fusarium mould as a source of SCP in diets containing oxonate, a uricase inhibitor, showed elevated plasma and kidney uric acid concentrations after 21 d, which were related to the level of dietary mould. ADP-induced and thrombin-induced platelet aggregation was greater in the hyperuricaemic rats than in controls and a progressive increase in aggregation with increasing levels of dietary mould was observed. Furthermore a time-lag, exceeding the life-span of rat platelets, was observed between the development of hyperuricaemia and the increase in aggregation. A similar time-lag was observed between the lowering of the hyperuricaemia and the reduction of platelet aggregation when oxonate was removed from the diet.If human platelets react to uric acid in the same manner as rat platelets this might explain the link that has been suggested between hyperuricaemia and ischaemic heart disease. In that event diets high in nucleic acids might be contra-indicated in people at risk from ischaemic heart disease.In rats given a low protein diet (50 g casein/kg) for 21 d ADP-induced and thrombin-induced platelet aggregation and whole blood platelet count were reduced compared with control animals receiving 200 g casein/kg diet but not in rats given 90 or 130 g casein/kg diet. A study of the time course on this effect indicated that the reduction both in aggregation tendency and in whole blood platelet count occurred after 4 d of feeding the low protein diet. These values were further reduced with time.

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