scholarly journals How Do Cells Adapt? Stories Told in Landscapes

Author(s):  
Luca Agozzino ◽  
Gábor Balázsi ◽  
Jin Wang ◽  
Ken A. Dill

Cells adapt to changing environments. Perturb a cell and it returns to a point of homeostasis. Perturb a population and it evolves toward a fitness peak. We review quantitative models of the forces of adaptation and their visualizations on landscapes. While some adaptations result from single mutations or few-gene effects, others are more cooperative, more delocalized in the genome, and more universal and physical. For example, homeostasis and evolution depend on protein folding and aggregation, energy and protein production, protein diffusion, molecular motor speeds and efficiencies, and protein expression levels. Models provide a way to learn about the fitness of cells and cell populations by making and testing hypotheses.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3674-3674
Author(s):  
Amberly Moreno-Bost ◽  
Susann Szmania ◽  
Katie Stone ◽  
Jumei Shi ◽  
Tarun K. Garg ◽  
...  

Abstract Demethylating agents and histone deacetylase inhibitors (HDACi) are epigenetic modulators that can induce re-expression of tumor suppressor and cell cycle proteins that have been silenced through aberrant hypermethylation associated with tumoral transformation. Azacitidine (Aza) is a cytosine analogue that primarily affects RNA during transcription. However, DNA is also a target for demethylation during replication thereby increasing gene re-expression. Treatment with HDACi, such as MGCD0103 (MGC), can synergize with demethylating agents to boost the epigenetic effects of either drug used alone. Our gene expression profiling data shows that the cancer-testis antigen MAGE-A3 is expressed in 31% of myeloma patients at diagnosis and the frequency of expression is increased at relapse to 49% (n=51 paired samples, p<0.001, unpublished data). However, expression of MAGE-A3 is often heterogeneous. We hypothesized that the combination of Aza and MGC could induce MAGE-A3 expression, thus facilitating killing of myeloma cells by MAGE-A3 specific CTLs isolated from a HLA-A68 positive patient post MAGE-A3 protein vaccination (J Immunother2007; 30:847). The MAGE-A3 negative myeloma cell line LP1 was first transfected with HLA-A68. MAGE-A3 protein production was optimized by dose finding and time course experiments using Aza alone or Aza and MGC sequentially. Induction of MAGE-A3 RNA expression was assessed by real time PCR and protein expression by Western blotting. 51Cr-release assays were used to measure killing of Aza/MGC treated cell lines by MAGE-A3 specific CTLs. MAGE-A3 RNA expression was detected in LP1-A68 treated with 500nM Aza for 3 days and expression was enhanced by sequential treatment with 1mM MGC for 1 day when compared to Aza treatment alone. However, protein expression was low. In an effort to optimize protein production, we increased the time of treatment with 500nM Aza to 5 days and with 500nM MGC to 2 days. After this sequential treatment, protein was clearly expressed (Figure 1) and LP1-A68 cells were killed by MAGE-A3 specific CTLs (specific lysis: 70% ± 9% at E:T ratio of 5:1), whilst untreated controls only showed background killing (specific lysis: 12% ± 5%) (Figure 2). Repeat experiments are in progress to verify these results. 500nM Aza in vitro is comparable to a clinically achievable in vivo dose of 12.5mg/m2 (Leukemia2008; 22:965). 500nM MGC is comparable to a 280mg/m2in vivo dose (Blood2006; 108: 1954). Additional titration experiments with MGC will be tested to achieve clinically relevant concentrations in vivo that can induce MAGE-A3 expression. In conclusion, epigenetic modulation by Aza and MGC can enhance MAGE-A3 expression and result in increased killing by MAGE-A3 specific CTLs. Hypomethylating agents and HDACi may be useful to sensitize tumor cells to immune effectors. Figure 1. Treatment with 50nM Aza and/or sequential MGC at 500 nM induces de nono expression of MAGE-A3 protein in the myeloma a cell line transfectant LP1 A68. Figure 1. Treatment with 50nM Aza and/or sequential MGC at 500 nM induces de nono expression of MAGE-A3 protein in the myeloma a cell line transfectant LP1 A68. Figure 2. Lysis of LP-1 A68 Aza/MGC treated targets by MAGE-A3 specific CTL effective. Figure 2. Lysis of LP-1 A68 Aza/MGC treated targets by MAGE-A3 specific CTL effective.


2021 ◽  
Vol 17 ◽  
pp. 439-460
Author(s):  
Vladimir Kubyshkin ◽  
Rebecca Davis ◽  
Nediljko Budisa

Due to the heterocyclic structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades. We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide proline-to-fluoroproline substitutions could be possible. We suggest a hypothetical scenario for the use of laboratory evolutionary methods with fluoroprolines as a suitable vehicle to introduce fluorine into living cells. This approach may enable creation of synthetic cells endowed with artificial biodiversity, containing fluorine as a bioelement.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jennifer A. Schmidt ◽  
Lubna V. Richter ◽  
Lisa A. Condoluci ◽  
Beth A. Ahner

Abstract Background The global demand for functional proteins is extensive, diverse, and constantly increasing. Medicine, agriculture, and industrial manufacturing all rely on high-quality proteins as major active components or process additives. Historically, these demands have been met by microbial bioreactors that are expensive to operate and maintain, prone to contamination, and relatively inflexible to changing market demands. Well-established crop cultivation techniques coupled with new advancements in genetic engineering may offer a cheaper and more versatile protein production platform. Chloroplast-engineered plants, like tobacco, have the potential to produce large quantities of high-value proteins, but often result in engineered plants with mutant phenotypes. This technology needs to be fine-tuned for commercial applications to maximize target protein yield while maintaining robust plant growth. Results Here, we show that a previously developed Nicotiana tabacum line, TetC-cel6A, can produce an industrial cellulase at levels of up to 28% of total soluble protein (TSP) with a slight dwarf phenotype but no loss in biomass. In seedlings, the dwarf phenotype is recovered by exogenous application of gibberellic acid. We also demonstrate that accumulating foreign protein represents an added burden to the plants’ metabolism that can make them more sensitive to limiting growth conditions such as low nitrogen. The biomass of nitrogen-limited TetC-cel6A plants was found to be as much as 40% lower than wildtype (WT) tobacco, although heterologous cellulase production was not greatly reduced compared to well-fertilized TetC-cel6A plants. Furthermore, cultivation at elevated carbon dioxide (1600 ppm CO2) restored biomass accumulation in TetC-cel6A plants to that of WT, while also increasing total heterologous protein yield (mg Cel6A plant−1) by 50–70%. Conclusions The work reported here demonstrates that well-fertilized tobacco plants have a substantial degree of flexibility in protein metabolism and can accommodate considerable levels of some recombinant proteins without exhibiting deleterious mutant phenotypes. Furthermore, we show that the alterations to protein expression triggered by growth at elevated CO2 can help rebalance endogenous protein expression and/or increase foreign protein production in chloroplast-engineered tobacco.


Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 879
Author(s):  
Shunsuke Okada ◽  
Motonori Matsusaki ◽  
Masaki Okumura ◽  
Takahiro Muraoka

Oxidative protein folding is a biological process to obtain a native conformation of a protein through disulfide-bond formation between cysteine residues. In a cell, disulfide-catalysts such as protein disulfide isomerase promote the oxidative protein folding. Inspired by the active sites of the disulfide-catalysts, synthetic redox-active thiol compounds have been developed, which have shown significant promotion of the folding processes. In our previous study, coupling effects of a thiol group and guanidyl unit on the folding promotion were reported. Herein, we investigated the influences of a spacer between the thiol group and guanidyl unit. A conjugate between thiol and guanidyl units with a diethylene glycol spacer (GdnDEG-SH) showed lower folding promotion effect compared to the thiol–guanidyl conjugate without the spacer (GdnSH). Lower acidity and a more reductive property of the thiol group of GdnDEG-SH compared to those of GdnSH likely resulted in the reduced efficiency of the folding promotion. Thus, the spacer between the thiol and guanidyl groups is critical for the promotion of oxidative protein folding.


Author(s):  
Joana Figueiredo ◽  
Ana Sofia Ribeiro ◽  
Tânia Mestre ◽  
Sofia Esménio ◽  
Martina Fonseca ◽  
...  

Author(s):  
Mark Lorch

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.


2010 ◽  
Author(s):  
Elisabeth Kuhn ◽  
Elisabeth Naschberger ◽  
Andreas Konrad ◽  
Roland S. Croner ◽  
Helmut Münstedt ◽  
...  

mBio ◽  
2020 ◽  
Vol 11 (6) ◽  
Author(s):  
Qi Qi ◽  
Feiran Li ◽  
Rosemary Yu ◽  
Martin K. M. Engqvist ◽  
Verena Siewers ◽  
...  

ABSTRACT Protein folding is often considered the flux controlling process in protein synthesis and secretion. Here, two previously isolated Saccharomyces cerevisiae strains with increased α-amylase productivity were analyzed in chemostat cultures at different dilution rates using multi-omics data. Based on the analysis, we identified different routes of the protein folding pathway to improve protein production. In the first strain, the increased abundance of proteins working on the folding process, coordinated with upregulated glycogen metabolism and trehalose metabolism, helped increase α-amylase productivity 1.95-fold compared to the level in the original strain in chemostat culture at a dilution rate of 0.2/h. The second strain further strengthened the folding precision to improve protein production. More precise folding helps the cell improve protein production efficiency and reduce the expenditure of energy on the handling of misfolded proteins. As calculated using an enzyme-constrained genome-scale metabolic model, the second strain had an increased productivity of 2.36-fold with lower energy expenditure than that of the original under the same condition. Further study revealed that the regulation of N-glycans played an important role in the folding precision control and that overexpression of the glucosidase Cwh41p can significantly improve protein production, especially for the strains with improved folding capacity but lower folding precision. Our findings elucidated in detail the mechanisms in two strains having improved protein productivity and thereby provided novel insights for industrial recombinant protein production as well as demonstrating how multi-omics analysis can be used for identification of novel strain-engineering targets. IMPORTANCE Protein folding plays an important role in protein maturation and secretion. In recombinant protein production, many studies have focused on the folding pathway to improve productivity. Here, we identified two different routes for improving protein production by yeast. We found that improving folding precision is a better strategy. Dysfunction of this process is also associated with several aberrant protein-associated human diseases. Here, our findings about the role of glucosidase Cwh41p in the precision control system and the characterization of the strain with a more precise folding process could contribute to the development of novel therapeutic strategies.


1976 ◽  
Vol 144 (1) ◽  
pp. 113-122 ◽  
Author(s):  
L Chess ◽  
R Evans ◽  
R E Humphreys ◽  
J L Strominger ◽  
S F Schlossman

Rabbit antisera to the human B-cell-specific antigen complex, p23,30, was used to define further the functional heterogeneity of isolated human lymphocyte subpopulations. Specific depletion of p23,30-bearing cells from Ig-negative cell populations and Ig-negative, E rosette-negative (Null) populations by either complement-mediated lysis or by physical separation on goat antirabbit Fab immunoabsorbent columns, eliminates the antibody-dependent cellular cytotoxic (ADCC) function. Furthermore, binding of anti-p23,30 serum to the effector cell surface inhibits ADCC but does not interfere with EA rosette formation. Apparently p23,30 represents a cell surface site which is distinct from the Fc receptor but which is important in the triggering of ADCC. In addition, depletion of p23,30-bearing cells from unfractionated cell populations, Ig-positive B-cell populations and Ig-negative, E rosette-negative (Null) populations eliminates the capacity of these populations to secrete immunoglobulin during subsequent culturing. Thus both the Ig-secreting cells and the ADCC effector cells within the Ig-negative, E rosette-negative (Null) population reside in the same population of cells which bears the p23,30 antigen.


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