scholarly journals Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

2021 ◽  
Author(s):  
Ibrahim E. Elsemman ◽  
Angelica Rodrigues Prado ◽  
Pranas Grigaitis ◽  
Manuel Garcia Albornoz ◽  
Victoria Harman ◽  
...  
Keyword(s):  
Growth Rate ◽  
Protein Expression ◽  
Expression Profiles ◽  
Reaction Network ◽  
Cellular Growth ◽  
Metabolic Adaptation ◽  
Overflow Metabolism ◽  
Metabolic Reaction ◽  
Glucose Limitation ◽  
Metabolic Strategies

When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here we developed a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions (16304 reactions in total). The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data revealed that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation - known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimization, providing a framework to understand metabolic adaptation in eukaryal cells.

scholarly journals The effect of natural selection on the propagation of protein expression noise to bacterial growth

2021 ◽  
Vol 17 (7) ◽  
pp. e1009208
Author(s):  
Laurens H. J. Krah ◽  
Rutger Hermsen
Keyword(s):  
Growth Rate ◽  
Natural Selection ◽  
Protein Expression ◽  
Low Noise ◽  
Cellular Growth ◽  
Expression Level ◽  
Bacterial Cells ◽  
Data Set ◽  
Physiological Variables ◽  
Expression Noise

In bacterial cells, protein expression is a highly stochastic process. Gene expression noise moreover propagates through the cell and adds to fluctuations in the cellular growth rate. A common intuition is that, due to their relatively high noise amplitudes, proteins with a low mean expression level are the most important drivers of fluctuations in physiological variables. In this work, we challenge this intuition by considering the effect of natural selection on noise propagation. Mathematically, the contribution of each protein species to the noise in the growth rate depends on two factors: the noise amplitude of the protein’s expression level, and the sensitivity of the growth rate to fluctuations in that protein’s concentration. We argue that natural selection, while shaping mean abundances to increase the mean growth rate, also affects cellular sensitivities. In the limit in which cells grow optimally fast, the growth rate becomes most sensitive to fluctuations in highly abundant proteins. This causes abundant proteins to overall contribute strongly to the noise in the growth rate, despite their low noise levels. We further explore this result in an experimental data set of protein abundances, and test key assumptions in an evolving, stochastic toy model of cellular growth.

scholarly journals Honeysuckle Aqueous Extracts Induced let-7a Suppress EV71 Replication and Pathogenesis In Vitro and In Vivo and Is Predicted to Inhibit SARS-CoV-2

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 308
Author(s):  
Ying-Ray Lee ◽  
Chia-Ming Chang ◽  
Yuan-Chieh Yeh ◽  
Chi-Ying F. Huang ◽  
Feng-Mao Lin ◽  
...  
Keyword(s):  
Protein Expression ◽  
Western Blotting ◽  
Expression Profiles ◽  
Plaque Assay ◽  
Virus Titer ◽  
Enterovirus 71 ◽  
Luciferase Reporter ◽  
Pathogen Invasion

Honeysuckle (Lonicera japonica Thunb) is a traditional Chinese medicine (TCM) with an antipathogenic activity. MicroRNAs (miRNAs) are small non-coding RNA molecules that are ubiquitously expressed in cells. Endogenous miRNA may function as an innate response to block pathogen invasion. The miRNA expression profiles of both mice and humans after the ingestion of honeysuckle were obtained. Fifteen overexpressed miRNAs overlapped and were predicted to be capable of targeting three viruses: dengue virus (DENV), enterovirus 71 (EV71) and SARS-CoV-2. Among them, let-7a was examined to be capable of targeting the EV71 RNA genome by reporter assay and Western blotting. Moreover, honeysuckle-induced let-7a suppression of EV71 RNA and protein expression as well as viral replication were investigated both in vitro and in vivo. We demonstrated that let-7a targeted EV71 at the predicted sequences using luciferase reporter plasmids as well as two infectious replicons (pMP4-y-5 and pTOPO-4643). The suppression of EV71 replication and viral load was demonstrated in two cell lines by luciferase activity, RT-PCR, real-time PCR, Western blotting and plaque assay. Furthermore, EV71-infected suckling mice fed honeysuckle extract or inoculated with let-7a showed decreased clinical scores and a prolonged survival time accompanied with decreased viral RNA, protein expression and virus titer. The ingestion of honeysuckle attenuates EV71 replication and related pathogenesis partially through the upregulation of let-7a expression both in vitro and in vivo. Our previous report and the current findings imply that both honeysuckle and upregulated let-7a can execute a suppressive function against the replication of DENV and EV71. Taken together, this evidence indicates that honeysuckle can induce the expression of let-7a and that this miRNA as well as 11 other miRNAs have great potential to prevent and suppress EV71 replication.

scholarly journals SLC6A8-mediated intracellular creatine accumulation enhances hypoxic breast cancer cell survival via ameliorating oxidative stress

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Qiao Li ◽  
Manran Liu ◽  
Yan Sun ◽  
Ting Jin ◽  
Pengpeng Zhu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Overall Survival ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Histological Grade ◽  
Metabolic Adaptation ◽  
Mitochondrial Activity ◽  
Cell Viability Assay ◽  
Ki 67 ◽  
The Impact

Abstract Background Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, with poor prognosis and limited treatment options. Hypoxia is a key hallmark of TNBC. Metabolic adaptation promotes progression of TNBC cells that are located within the hypoxic tumor regions. However, it is not well understood regarding the precise molecular mechanisms underlying the regulation of metabolic adaptions by hypoxia. Methods RNA sequencing was performed to analyze the gene expression profiles in MDA-MB-231 cell line (20% O2 and 1% O2). Expressions of Slc6a8, which encodes the creatine transporter protein, were detected in breast cancer cells and tissues by quantitative real-time PCR. Immunohistochemistry was performed to detect SLC6A8 protein abundances in tumor tissues. Clinicopathologic correlation and overall survival were evaluated by chi-square test and Kaplan-Meier analysis, respectively. Cell viability assay and flow cytometry analysis with Annexin V/PI double staining were performed to investigate the impact of SLC6A8-mediated uptake of creatine on viability of hypoxic TNBC cells. TNBC orthotopic mouse model was used to evaluate the effects of creatine in vivo. Results SLC6A8 was aberrantly upregulated in TNBC cells in hypoxia. SLC6A8 was drastically overexpressed in TNBC tissues and its level was tightly associated with advanced TNM stage, higher histological grade and worse overall survival of TNBC patients. We found that SLC6A8 was transcriptionally upregulated by p65/NF-κB and mediated accumulation of intracellular creatine in hypoxia. SLC6A8-mediated accumulation of creatine promoted survival and suppressed apoptosis via maintaining redox homeostasis in hypoxic TNBC cells. Furthermore, creatine was required to facilitate tumor growth in xenograft mouse models. Mechanistically, intracellular creatine bolstered cell antioxidant defense by reducing mitochondrial activity and oxygen consumption rates to reduce accumulation of intracellular reactive oxygen species, ultimately activating AKT-ERK signaling, the activation of which protected the viability of hypoxic TNBC cells via mediating the upregulation of Ki-67 and Bcl-2, and the downregulation of Bax and cleaved Caspase-3. Conclusions Our study indicates that SLC6A8-mediated creatine accumulation plays an important role in promoting TNBC progression, and may provide a potential therapeutic strategy option for treatment of SLC6A8 high expressed TNBC.

P-652 Protein expression profiles in non-small cell lung cancer. A tissue microarray-based study of 142 cases

Lung Cancer ◽  
2005 ◽  
Vol 49 ◽  
pp. S290 ◽  
Author(s):  
E. Conde ◽  
R. García Luján ◽  
A. López Encuentra ◽  
L. Sánchez ◽  
M. Sánchez-Céspedes ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Protein Expression ◽  
Small Cell Lung Cancer ◽  
Tissue Microarray ◽  
Cell Lung Cancer ◽  
Expression Profiles ◽  
Small Cell ◽  
Small Cell Lung ◽  
Protein Expression Profiles

scholarly journals Brain death induces the alteration of liver protein expression profiles in rabbits

2014 ◽  
Vol 34 (2) ◽  
pp. 578-584 ◽  
Author(s):  
BING DU ◽  
LING LI ◽  
ZHIBIAO ZHONG ◽  
XIAOLI FAN ◽  
BINGBING QIAO ◽  
...  
Keyword(s):  
Protein Expression ◽  
Brain Death ◽  
Expression Profiles ◽  
Liver Protein ◽  
Protein Expression Profiles

Fluoride exposure inhibits protein expression and enzyme activity in the lung-stage larvae ofAscaris suum

Parasitology ◽  
2006 ◽  
Vol 133 (4) ◽  
pp. 497-508 ◽  
Author(s):  
M. K. ISLAM ◽  
T. MIYOSHI ◽  
M. YAMADA ◽  
M. A. ALIM ◽  
X. HUANG ◽  
...  
Keyword(s):  
Protein Expression ◽  
Expression Profiles ◽  
Immunoblot Analysis ◽  
Specific Protein ◽  
Inorganic Pyrophosphatase ◽  
2D Electrophoresis ◽  
Peptide Mass ◽  
Enzyme Families ◽  
Protein Expression Profiles ◽  
Peptide Mass Spectrometry

Sodium fluoride (NaF) is an anion that has been previously shown to block the moulting process ofAscaris suumlarvae. This study describes moulting and development-specific protein expression profiles ofA. suumlung-stage L3 (AsLL3) following NaF exposure. AsLL3s cultured in the presence or absence of NaF were prepared for protein analysis using two-dimensional (2D) electrophoresis. NaF exposure inhibited at least 22 proteins in AsLL3 compared with moulted larvae (i.e. AsLL4). A further comparison of AsLL4 with those of pre-cultured AsLL3 and NaF-exposed AsLL3 revealed 8 stage-specifically and 4 over-expressed proteins. Immunoblot analysis revealed an inhibition by NaF of 19 immunoreactive proteins. Enzyme assay and immunochemical data showed an inhibition of the moulting-specific inorganic pyrophosphatase activity by 41% and a decreased expression in NaF-treated larvae, indicating its significance in the moulting process. A protein spot associated with NaF inhibition was isolated and identified by peptide mass spectrometry and bioinformatics approaches to be a member of 3–hydroxyacyl–CoA dehydrogenase/short-chain dehydrogenase enzyme families. These results have implications for the identification of proteins specific to the moulting process as potential chemotherapeutic targets.

ProteinChip Technology Reveals Distinctive Protein Expression Profiles in the Urine of Bladder Cancer Patients

2005 ◽  
Vol 47 (6) ◽  
pp. 885-894 ◽  
Author(s):  
J. Mueller ◽  
F. von Eggeling ◽  
D. Driesch ◽  
J. Schubert ◽  
C. Melle ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Protein Expression ◽  
Cancer Patients ◽  
Expression Profiles ◽  
Protein Expression Profiles
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