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Dickson ZW, Golding GB. Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions. J Mol Evol 2024; 92:153-168. [PMID: 38485789 DOI: 10.1007/s00239-024-10158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/24/2024] [Indexed: 04/02/2024]
Abstract
Protein Protein low complexity regions (LCRs) are compositionally biased amino acid sequences, many of which have significant evolutionary impacts on the proteins which contain them. They are mutationally unstable experiencing higher rates of indels and substitutions than higher complexity regions. LCRs also impact the expression of their proteins, likely through multiple effects along the path from gene transcription, through translation, and eventual protein degradation. It has been observed that proteins which contain LCRs are associated with elevated transcript abundance (TAb), despite having lower protein abundance. We have gathered and integrated human data to investigate the co-evolution of TAb and LCRs through ancestral reconstructions and model inference using an approximate Bayesian calculation based method. We observe that on short evolutionary timescales TAb evolution is significantly impacted by changes in LCR length, with insertions driving TAb down. But in contrast, the observed data is best explained by indel rates in LCRs which are unaffected by shifts in TAb. Our work demonstrates a coupling between LCR and TAb evolution, and the utility of incorporating multiple responses into evolutionary analyses.
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Affiliation(s)
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON, Canada
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2
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Pardede BP, Karja NWK, Said S, Kaiin EM, Agil M, Sumantri C, Purwantara B, Supriatna I. Bovine nucleoprotein transitions genes and protein abundance as valuable markers of sperm motility and the correlation with fertility. Theriogenology 2024; 215:86-94. [PMID: 38016305 DOI: 10.1016/j.theriogenology.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/29/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
Bovine nucleoprotein transitions (TNPs), specifically TNP1 and TNP2, are essential molecules in sperm nucleus rich in arginine and lysine. These molecules act in the phase between histone expulsion and before incorporation of protamine in the spermatid nucleus. Therefore, this study aimed to analyze genes and protein abundance of TNP1 and TNP2 in sperm to determine the potential as motility markers and correlation with fertility in the field. An objective evaluation method, CASA-Sperm Vision, was used to separate 22 bulls into two groups (mg-A and mg-B) based on their increasing motility. Sperm quality parameters were also examined including velocity, mitochondrial membrane potential (MMP) by the JC-1 method, head defects using William staining, and DNA fragmentation by Halomax. TNPs genes abundance was performed using the RT-qPCR method, and the protein abundance was examined with the EIA approach. The fertility rate was also analyzed based on the conception rate generated from each bull in the field, with the data obtained from iSIKHNAS. The results showed that TNPs genes and protein abundance were significantly higher (P < 0.05) in mg-A compared to mg-B, followed by various sperm quality parameters and fertility rates (P < 0.05). Positive correlations were found in TNPs genes and protein abundance with motility, velocity, MMP, and fertility (P < 0.01). Meanwhile, a negative correlation (P < 0.01) was found between head defects and DNA fragmentation. These results showed the potential of TNPs as sperm motility markers and bull fertility.
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Affiliation(s)
- Berlin Pandapotan Pardede
- Division of Reproduction and Obstetrics, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia; Research Center for Applied Zoology, National Research, and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
| | - Ni Wayan Kurniani Karja
- Division of Reproduction and Obstetrics, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Syahruddin Said
- Research Center for Applied Zoology, National Research, and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ekayanti Mulyawati Kaiin
- Research Center for Applied Zoology, National Research, and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Muhammad Agil
- Division of Reproduction and Obstetrics, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia.
| | - Cece Sumantri
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Indonesia
| | - Bambang Purwantara
- Division of Reproduction and Obstetrics, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - Iman Supriatna
- Division of Reproduction and Obstetrics, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
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de Almeida NM, de Almeida AAF, de Almeida Santos N, Mora-Ocampo IY, Pirovani CP. Leaf proteomic profiles in cacao scion-rootstock combinations tolerant and intolerant to cadmium toxicity. Plant Physiol Biochem 2023; 203:107987. [PMID: 37722279 DOI: 10.1016/j.plaphy.2023.107987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023]
Abstract
Cd contamination in cacao beans is one of the major problems faced by cocoa producing countries in Latin America. Cacao scion-rootstock combinations influence the Cd accumulation in the shoot of the plant. The objective of this work was to carry out a comparative analysis between cacao scion rootstock combinations (CCN 51/BN 34, CCN 51/PS 13.19, CCN 51/PH 16 and CCN 51/CCN 51), contrasting for tolerance to cadmium (Cd) toxicity, by means of leaf proteomic profiles, in order to elucidate molecular mechanisms involved in tolerance to Cd toxicity. Cacao scion-rootstock combinations were grown in soil with 150 mg Cd kg-1 soil, together with the control treatment. Leaf samples were collected 96 h after treatments were applied. There were alterations in the leaf proteome of the cacao scion-rootstock combinations, whose molecular responses to Cd toxicity varied depending on the combination. Leaf proteomic analyzes provided important information regarding the molecular mechanisms involved in the tolerance and intolerance of cacao scion-rootstock combinations to Cd toxicity. Enzymatic and non-enzymatic antioxidant systems, efficient for eliminating ROS, especially the expressions of APX and SOD, in addition to the increase in the abundance of metalloproteins, such as ferredoxins, rubredoxin, ALMT, Trx-1 and ABC-transporter were key mechanisms used in the Cd detoxification in cacao scion-rootstock combinations tolerant to Cd toxicity. Carboxylic acid metabolism, glucose activation and signal transduction were also important processes in the responses of cacao scion-rootstock combinations to Cd toxicity. The results confirmed CCN 51/BN 34 as a cacao scion-rootstock combination efficient in tolerance to Cd toxicity.
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Affiliation(s)
- Nicolle Moreira de Almeida
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Alex-Alan Furtado de Almeida
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Nayara de Almeida Santos
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Irma Yuliana Mora-Ocampo
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Carlos Priminho Pirovani
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
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Lapehn S, Colacino JA, Harris C. Spatiotemporal protein dynamics during early organogenesis in mouse conceptuses treated with valproic acid. Neurotoxicol Teratol 2023; 99:107286. [PMID: 37442398 PMCID: PMC10697214 DOI: 10.1016/j.ntt.2023.107286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Valproic acid (VPA) is an anti-epileptic medication that increases the risk of neural tube defect (NTD) outcomes in infants exposed during gestation. Previous studies into VPA's mechanism of action have focused on alterations in gene expression and metabolism but have failed to consider how exposure changes the abundance of critical developmental proteins over time. This study evaluates the effects of VPA on protein abundance in the developmentally distinct tissues of the mouse visceral yolk sac (VYS) and embryo proper (EMB) using mouse whole embryo culture. Embryos were exposed to 600 μM VPA at 2 h intervals over 10 h during early organogenesis with the aim of identifying protein pathways relevant to VPA's mechanism of action in failed NTC. Protein abundance was measured through tandem mass tag (TMT) labeling followed by liquid chromatography and mass spectrometry. Overall, there were over 1500 proteins with altered abundance after VPA exposure in the EMB or VYS with 428 of these proteins showing previous gene expression associations with VPA exposure. Limited overlap of significant proteins between tissues supported the conclusion of independent roles for the VYS and EMB in response to VPA. Pathway analysis of proteins with increased or decreased abundance identified multiple pathways with mechanistic relevance to NTC and embryonic development including convergent extension, Wnt Signaling/planar cell polarity, cellular migration, cellular proliferation, cell death, and cytoskeletal organization processes as targets of VPA. Clustering of co-regulated proteins to identify shared patterns of protein abundance over time highlighted 4 h and 6/10 h as periods of divergent protein abundance between control and VPA-treated samples in the VYS and EMB, respectively. Overall, this study demonstrated that VPA temporally alters protein content in critical developmental pathways in the VYS and the EMB during early organogenesis in mice.
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Affiliation(s)
- Samantha Lapehn
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Craig Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
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Adav SS, Leung CY, Ng KW. Profiling of hair proteome revealed individual demographics. Forensic Sci Int Genet 2023; 66:102914. [PMID: 37482024 DOI: 10.1016/j.fsigen.2023.102914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
Human hair is often found at crime scenes, persists for a long time, and is a valuable biological specimen in forensic investigations. Hair contains minimal intact nuclear DNA for the discrimination of individual identity. In such cases, proteomics evaluation of hair proteins could provide an attractive alternative for protein-based human identification. Therefore, this study adopted a proteomic approach to profile hair shafts from both males and females across different ethnic populations including Chinese, Indians, Malays, and Filipinos in their 20-80 s. First, hair proteins were extracted by different methods to adopt the most suitable protocol that produced the highest extraction efficiency based on most significant enrichment of keratins and keratin-associated proteins. Abundance of hair keratins including both types I and II, and keratin-associated proteins, estimated using label-free quantification, showed distinguishable profiles, and the possibilities of distinguishing individuals within each ethnic origin. Similarly, several protein candidates and their abundances could be used to distinguish sex and age of individuals. This study explored the possibility of utilizing hair proteomics phenotyping in forensic science to differentiate individuals across various ethnic groups, sex and age.
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Affiliation(s)
- Sunil S Adav
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Ching Yung Leung
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Kee Woei Ng
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141, Singapore.
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Ramazan S, Jan N, John R. Comparative protein analysis of two maize genotypes with contrasting tolerance to low temperature. BMC Plant Biol 2023; 23:183. [PMID: 37020183 PMCID: PMC10074880 DOI: 10.1186/s12870-023-04198-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Low temperature (LT) stress is one of the major environmental stress factors affecting the growth and yield of maize (Zea mays L.). Hence, it is important to unravel the molecular mechanisms behind LT stress tolerance to improve molecular breeding in LT tolerant genotypes. In the present study, two maize genotypes viz. Gurez local from Kashmir Himalaya and tropical grown GM6, were dissected for their LT stress response in terms of accumulation of differentially regulated proteins (DRPs). Leaf proteome analysis at three-leaf stage of maize seedlings subjected to LT stress of 6 °C for a total of 12 h duration was performed using two dimensional gel electrophoresis (2D-PAGE) followed by subsequent identification of the proteins involved. RESULTS After MALDI-TOF (Matrix-assisted laser desorption/ionization-time of flight) and bioinformatics analysis, 19 proteins were successfully identified in Gurez local, while as 10 proteins were found to get successful identification in GM6. The interesting observations from the present investigation is the identification of three novel proteins viz. threonine dehydratase biosynthetic chloroplastic, thylakoidal processing peptidase 1 chloroplastic, and nodulin-like protein, whose role in abiotic stress tolerance, in general, and LT stress, in particular, has not been reported so far. It is important to highlight here that most of LT responsive proteins including the three novel proteins were identified from Gurez local only, owing to its exceptional LT tolerance. From the protein profiles, obtained in both genotypes immediately after LT stress perception, it was inferred that stress responsive protein accumulation and their expression fashion help the Gurez local in seedling establishment and withstand unfavorable conditions as compared to GM6. This was inferred from the findings of pathway enrichment analysis like regulation of seed growth, timing of floral transition, lipid glycosylation, and aspartate family amino acid catabolic processes, besides other key stress defense mechanisms. However, in GM6, metabolic pathways enriched were found to be involved in more general processes including cell cycle DNA replication and regulation of phenylpropanoid metabolism. Furthermore, majority of the qRT-PCR results of the selected proteins demonstrated positive correlation between protein levels and transcript abundance, thereby strengthening our findings. CONCLUSIONS In conclusion, our findings reported majority of the identified proteins in Gurez local exhibiting up-regulated pattern under LT stress as compared to GM6. Furthermore, three novel proteins induced by LT stress were found in Gurez local, requiring further functional validation. Therefore, our results offer more insights for elucidating the molecular networks mediating LT stress tolerance in maize.
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Affiliation(s)
- Salika Ramazan
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India
| | - Nelofer Jan
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India
| | - Riffat John
- Plant Molecular Biology Lab, Department of Botany, University of Kashmir, Srinagar, Kashmir, 190 006, India.
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Lyons SP, Wilson RJ, Muoio DM, Grimsrud PA. Proteomics and phosphoproteomics datasets of a muscle-specific STIM1 loss-of-function mouse model. Data Brief 2022; 42:108051. [PMID: 35345842 PMCID: PMC8956960 DOI: 10.1016/j.dib.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 11/01/2022] Open
Abstract
STIM1 is an ER/SR transmembrane protein that interacts with ORAI1 to activate store operated Ca2+ entry (SOCE) upon ER/SR depletion of calcium. Normally highly expressed in skeletal muscle, STIM1 deficiency causes significant changes to mitochondrial ultrastructure that do not occur with loss of ORAI1 or other components of SOCE. The datasets in this article are from large-scale proteomics and phosphoproteomics experiments in an inducible mouse model of skeletal muscle-specific STIM1 knock out (KO). These data reveal statistically significant changes in the relative abundance of specific proteins and sites of protein phosphorylation in STIM1 KO gastrocnemius. Protein samples from five biological replicates of each condition (+/- STIM1) were enzymatically digested, the resulting peptides labeled with tandem mass tag (TMT) reagents, mixed, and fractionated. Phosphopeptides were enriched and a small amount of each input retained for protein abundance analysis. All phosphopeptide and input fractions were analyzed by nano LC-MS/MS on a Q Exactive Plus Orbitrap mass spectrometer, searched with Proteome Discoverer software, and processed with in-house R-scripts for data normalization and statistical analysis. Article published in Molecular Metabolism [1].
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Affiliation(s)
- Scott P. Lyons
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
| | - Rebecca J. Wilson
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
| | - Deborah M. Muoio
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
- Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University School of Medicine, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27701, USA
| | - Paul A. Grimsrud
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
- Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University School of Medicine, Durham, NC 27701, USA
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Palenchar PM. The Influence of Codon Usage, Protein Abundance, and Protein Stability on Protein Evolution Vary by Evolutionary Distance and the Type of Protein. Protein J 2022; 41:216-229. [PMID: 35147896 DOI: 10.1007/s10930-022-10045-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 12/01/2022]
Abstract
In general, the evolutionary rate of proteins is not primarily related to protein and amino acid functions, and factors such as protein abundance, codon usage, and the protein's TM are more important. To better understand the factors that affect protein evolution, E. coli MG1655 orthologs were compared to those in closely related bacteria and to more distantly related prokaryotes, eukaryotes, and archaea. Also, the evolution of different types of proteins was studied. The analyses indicate that the amino acid conservation of enzymes that do not use macromolecules (e.g. DNA, RNA, and proteins) as substrates and that carry out metabolic processes involving small molecules (i.e. small molecule enzymes) is different than other enzymes. For example, the small molecule enzymes have a lower percent identity than other enzymes when sequences from closely related bacteria are compared. Analyses indicate the lower percent identity is not a result of the amino acid or codon usage of the small molecule enzymes. The small molecule enzymes also don't have a significantly lower protein abundance indicating that is also not likely an important factor driving differences in amino acid conservation. Analyses indicate different methods to measure the TM of proteins have different relationships between amino acid conservation over different evolutionary distances. In totality, the results demonstrate that the relationship between the factors thought to affect protein evolution (protein abundance, codon usage, and proteins TMs) and protein evolution are complex and depend on the factor, the organisms, and the type of proteins being analyzed.
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Affiliation(s)
- Peter M Palenchar
- Department of Chemistry, Villanova University, 800 E. Lancaster Ave, Villanova, PA, 19805, USA.
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Deng D, Zi Z. Absolute Quantification of TGF-β Signaling Proteins Using Quantitative Western Blot. Methods Mol Biol 2022; 2488:1-12. [PMID: 35347678 DOI: 10.1007/978-1-0716-2277-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell signaling governs the basic functions of cells by molecular interactions that involve of many proteins. The abundance of signaling proteins can directly influence cellular responses to external signal, contributing to cellular heterogeneity. Absolute quantification of proteins is important for modeling and understanding the complex signaling network. Here, we introduce how to measure the amount of TGF-β signaling proteins using quantitative immunoblotting. In addition, we discuss how to convert the measurements of protein abundance to the quantities of absolute molecules per cell. This method is generally applicable to the absolute quantification of other proteins.
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Affiliation(s)
- Difan Deng
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, Berlin, Germany
| | - Zhike Zi
- Department of Experimental Toxicology and ZEBET, German Federal Institute for Risk Assessment, Berlin, Germany.
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Kurzawski M, Szeląg-Pieniek S, Łapczuk-Romańska J, Wrzesiński M, Oswald S, Droździk M. The reference liver-CYP450 and UGT enzymes in healthy donor and metastatic livers: the impact of genotype. Pharmacol Rep 2021. [PMID: 34741761 DOI: 10.1007/s43440-021-00337-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/17/2021] [Accepted: 10/27/2021] [Indexed: 11/10/2022]
Abstract
Background Hepatic enzymes involved in drug metabolism vary markedly in expression, abundance and activity, which affects individual susceptibility to drugs and toxicants. The present study aimed to compare mRNA expression and protein abundance of the most pharmacologically relevant drug-metabolizing enzymes in two main sources of the control liver samples that are used as the reference, i.e. organ donor livers and non-tumorous tissue from metastatic livers. An association analysis of the most common genetic variants with mRNA and protein levels was also performed. Methods The CYP450 and UGT enzymes (CYP1A2, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, CYP3A5, UGT1A1, UGT1A3, UGT2B7 and UGT2B15) were analyzed for mRNA (qPCR) and protein abundance (LC–MS/MS) in healthy donors (n = 11) and metastatic (n = 13) livers. Genotyping was performed by means of TaqMan assays and pyrosequencing. Results Significantly higher protein abundance in the metastatic livers was observed in case of CYP2C9, CYP2D6, and UGT2B7, and for UGT1A3 the difference was only significant at mRNA level. For all the enzymes except CYP2E1 some significant correlation between mRNA and protein content was observed, and for UGT1A1 an inverse correlation with age was noted. CYP2C19, CYP3A5 and CYP2D6 were significantly affected by genotype. Conclusion The selection of a control group for the study on drug-metabolizing enzymes (e.g. in pathological states) may possibly affect its conclusions on differences in mRNA and protein content. Genotyping for common functional variants of CYP450 enzymes should be performed in all studies on drug-metabolizing enzymes. Supplementary Information The online version contains supplementary material available at 10.1007/s43440-021-00337-w.
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Ramesh A, Wheeldon I. Western Blotting of Membrane-Bound Proteins in Yarrowia lipolytica. Methods Mol Biol 2021; 2307:233-47. [PMID: 33847994 DOI: 10.1007/978-1-0716-1414-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
With the discovery of Western blotting as first described by Towbin et al. in 1979, the transfer and visualization of electrophoretically separated proteins on membranes has become the de facto method for the qualitative and quantitative detection of proteins of interest. In this method, proteins are resolved by electrophoresis on a polyacrylamide gel, followed by a transfer of the separated proteins onto a nitrocellulose or polyvinyl difluoride (PVDF) membrane. Once immobilized on these membranes, the protein of interest can be detected and visualized by exploiting antigen-antibody interactions. However, not all proteins are amenable to easy detection by Western blotting. Integral membrane proteins are a class of proteins that are attached to a biological membrane through a series of transmembrane segments that span the width of the membrane. Due to the inherent hydrophobicity of these proteins and their tendency to aggregate, the characterization and detection of these proteins can be challenging. In this methods chapter, we present a protocol for the easy detection and quantification of these proteins in the industrially important oleaginous yeast Yarrowia lipolytica. The first protocol describes a Western blotting procedure to quantify soluble cytosolic proteins of interest in Yarrowia lipolytica from its total cell lysate. The second protocol describes modifications to the first that are done to enhance detection and quantification of membrane-bound proteins in Yarrowia lipolytica from its total cell lysate, without the need for isolating the membrane-bound proteins, for use in Western blotting. The immunoblotting strategies described here should serve as an efficient and simple guide to quantify both cytosolic and the intractable membrane-bound proteins in Yarrowia lipolytica.
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Abstract
Ras proteins and other small molecular weight GTPases are molecular switches controlling a wide range of cellular functions. High homology and functional redundancy between closely related family members are commonly observed. Antibody-based methods are commonly used to characterize their protein expression. However, these approaches are typically semi-quantitative, and the requirement to use different antibodies means that this strategy is not suited for comparative analysis of the relative expression of proteins expressed by different genes. We present a mass spectrometry-based method that precisely quantifies the protein copy number per cell of a protein of interest. We provide detailed protocols for the generation of isotopically labeled protein standards, cell/tissue processing, mass-spectrometry optimization, and subsequent utilization for the absolute quantitation of the abundance of a protein of interest. As examples, we provide instructions for the quantification of HRAS, KRAS4A, KRAS4B, NRAS, RALA, and RALB in cell line and tissue-derived samples.
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Affiliation(s)
- Fiona E Hood
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Yasmina M Sahraoui
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Rosalind E Jenkins
- Centre for Drug Safety Science Bioanalytical Facility, Division of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Ian Prior
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
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Szeląg-Pieniek S, Oswald S, Post M, Łapczuk-Romańska J, Droździk M, Kurzawski M. Hepatic drug-metabolizing enzymes and drug transporters in Wilson's disease patients with liver failure. Pharmacol Rep 2021. [PMID: 34117631 DOI: 10.1007/s43440-021-00290-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/22/2022]
Abstract
Background Wilson’s disease is a genetic disorder inherited in a recessive manner, caused by mutations in the copper-transporter ATP7B. Although it is a well-known disease, currently available treatments are far from satisfactory and their efficacy varies in individual patients. Due to the lack of information about drug-metabolizing enzymes and drug transporters profile in Wilson’s disease livers, we aimed to evaluate the mRNA expression and protein abundance of selected enzymes and drug transporters in this liver disorder. Methods We analyzed gene expression (qPCR) and protein abundance (LC–MS/MS) of 14 drug-metabolizing enzymes and 16 drug transporters in hepatic tissue from Wilson’s disease patients with liver failure (n = 7, Child–Pugh class B and C) and metastatic control livers (n = 20). Results In presented work, we demonstrated a downregulation of majority of CYP450 and UGT enzymes. Gene expression of analyzed enzymes ranged between 18 and 65% compared to control group and significantly lower protein content of CYP1A1, CYP1A2, CYP2C8, CYP2C9, CYP3A4 and CYP3A5 enzymes was observed in Wilson’s disease. Moreover, a general decrease in hepatocellular uptake carriers from SLC superfamily (significant at protein level for NTCP and OATP2B1) was observed. As for ABC transporters, the protein abundance of BSEP and MRP2 was significantly lower, while levels of P-gp and MRP4 transporters were significantly higher in Wilson’s disease. Conclusions Altered hepatic expression of drug‐metabolizing enzymes and drug transporters in Wilson’s disease patients with liver failure may result in changes of drug pharmacokinetics in that group of patients. Supplementary Information The online version contains supplementary material available at 10.1007/s43440-021-00290-8.
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Perdomo JA, Buchner P, Carmo-Silva E. The relative abundance of wheat Rubisco activase isoforms is post-transcriptionally regulated. Photosynth Res 2021; 148:47-56. [PMID: 33796933 PMCID: PMC8154801 DOI: 10.1007/s11120-021-00830-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/11/2021] [Indexed: 06/06/2023]
Abstract
Diurnal rhythms and light availability affect transcription-translation feedback loops that regulate the synthesis of photosynthetic proteins. The CO2-fixing enzyme Rubisco is the most abundant protein in the leaves of major crop species and its activity depends on interaction with the molecular chaperone Rubisco activase (Rca). In Triticum aestivum L. (wheat), three Rca isoforms are present that differ in their regulatory properties. Here, we tested the hypothesis that the relative abundance of the redox-sensitive and redox-insensitive Rca isoforms could be differentially regulated throughout light-dark diel cycle in wheat. While TaRca1-β expression was consistently negligible throughout the day, transcript levels of both TaRca2-β and TaRca2-α were higher and increased at the start of the day, with peak levels occurring at the middle of the photoperiod. Abundance of TaRca-β protein was maximal 1.5 h after the peak in TaRca2-β expression, but the abundance of TaRca-α remained constant during the entire photoperiod. The redox-sensitive TaRca-α isoform was less abundant, representing 85% of the redox-insensitive TaRca-β at the transcript level and 12.5% at the protein level. Expression of Rubisco large and small subunit genes did not show a consistent pattern throughout the diel cycle, but the abundance of Rubisco decreased by up to 20% during the dark period in fully expanded wheat leaves. These results, combined with a lack of correlation between transcript and protein abundance for both Rca isoforms and Rubisco throughout the entire diel cycle, suggest that the abundance of these photosynthetic enzymes is post-transcriptionally regulated.
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Affiliation(s)
| | - Peter Buchner
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
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15
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Abstract
BACKGROUND Cell-to-cell variation in gene expression strongly affects population behavior and is key to multiple biological processes. While codon usage is known to affect ensemble gene expression, how codon usage influences variation in gene expression between single cells is not well understood. RESULTS Here, we used a Sort-seq based massively parallel strategy to quantify gene expression variation from a green fluorescent protein (GFP) library containing synonymous codons in Escherichia coli. We found that sequences containing codons with higher tRNA Adaptation Index (TAI) scores, and higher codon adaptation index (CAI) scores, have higher GFP variance. This trend is not observed for codons with high Normalized Translation Efficiency Index (nTE) scores nor from the free energy of folding of the mRNA secondary structure. GFP noise, or squared coefficient of variance (CV2), scales with mean protein abundance for low-abundant proteins but does not change at high mean protein abundance. CONCLUSIONS Our results suggest that the main source of noise for high-abundance proteins is likely not originating at translation elongation. Additionally, the drastic change in mean protein abundance with small changes in protein noise seen from our library implies that codon optimization can be performed without concerning gene expression noise for biotechnology applications.
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Affiliation(s)
- Alexander Schmitz
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
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16
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Sun Y, Zhao J, Patil SB, Fang J, Liu J, Li X. Improved dual luciferase reporter (DLR) assay to determine the protein stability. Anal Biochem 2021; 612:114021. [PMID: 33189704 DOI: 10.1016/j.ab.2020.114021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022]
Abstract
We developed a binary vector co-expressing firefly luciferase (FF) and Renilla luciferase (REN) to detect protein stability in response to different stimuli, and verified the functionality of the vector. The StrigoQuant-like reporter expressing FF and REN in one transcript is a sensitive tool for detecting protein abundance in different genotypes. However, we found that significant differences in the relative FF/REN ratio of empty StrigoQuant vector in different genotypes. Therefore, to determine the actual protein abundance, the relative FF/REN ratio of the protein of interest should be normalized to that of the empty vector.
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Affiliation(s)
- Yinglu Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, ICS, CAAS, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, ICS, CAAS, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Suyash Bhimgonda Patil
- National Key Facility for Crop Gene Resources and Genetic Improvement, ICS, CAAS, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, ICS, CAAS, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, ICS, CAAS, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, ICS, CAAS, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
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17
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Li L, Meng H, Zhang J, Liu Y, Zou Q, Gao Y, Yang H, Lai L. A tunable, rapid, and precise drug control of protein expression by combining transcriptional and post-translational regulation systems. J Genet Genomics 2020; 47:705-712. [PMID: 33549479 DOI: 10.1016/j.jgg.2020.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/10/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Abstract
Rapid, precise, and tunable regulation of protein abundance would be significantly useful in a variety of biotechnologies and biomedical applications. Here, we describe a system that allows tunable and rapid drug control of gene expression for either gene activation or inactivation in mammalian cells. We construct the system by coupling Tet-on 3G and small molecule-assisted shutoff systems, which can respectively induce transcriptional activation and protein degradation in the presence of corresponding small molecules. This dual-input drug inducer regulation system facilitates a bidirectional control of gene expression. The gene of interest can be precisely controlled by dual small molecules in a broad dynamic range of expression from overexpression to complete silence, allowing gene function study in a comprehensive expression profile. Our results reveal that the bidirectional control system enables sensitive dosage- and time-dependent regulation for either turn-on or shutoff of gene expression. We also apply this system for inducible genome editing and gene activation mediated by clustered regularly interspaced short palindromic repeats. The system provides an integrated platform for studying multiple biological processes by manipulating gene expression in a more flexible way.
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Affiliation(s)
- Li Li
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Hongyi Meng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Jianmin Zhang
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Yang Liu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qingjian Zou
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Yi Gao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.
| | - Huaqiang Yang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Liangxue Lai
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
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18
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Ameling S, Bischof J, Dörr M, Könemann S, Empen K, Weitmann K, Klingel K, Beug D, Dhople VM, Völker U, Hammer E, Felix SB. Analysis of DCM associated protein alterations of human right and left ventricles. J Proteomics 2020; 231:104018. [PMID: 33075551 DOI: 10.1016/j.jprot.2020.104018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/30/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
Dilated cardiomyopathy (DCM) is characterized by ventricular chamber enlargement and impaired myocardial function. Endomyocardial biopsies (EMB) enable immunohistochemical and molecular characterization of this disease. However, knowledge about specific molecular patterns and their relation to cardiac function in both ventricles is rare. Therefore, we performed a mass spectrometric analysis of 28 paired EMBs of left (LV) and right ventricles (RV) of patients with DCM or suspected myocarditis allowing quantitative profiling of 743 proteins. We analysed associations between protein abundance of LV and RV as well as the echocardiographic parameters LVEF, TAPSE, LVEDDI, and RVEDDI by linear regression models. Overall, more LV than RV proteins were associated with LV parameters or with RVEDDI. Most LV and RV proteins increasing in level with impairing of LVEF were annotated to structural components of cardiac tissue. Additionally, a high proportion of LV proteins with metabolic functions decreased in level with decreasing LVEF. Results were validated with LV heart sections of a genetic murine heart failure model. The study shows, that remodelling and systolic dysfunction in DCM is mirrored by distinct alterations in protein composition of both ventricles. Loss of LV systolic function is reflected predominantly by alterations in proteins assigned to metabolic functions in the LV whereas structural remodelling was more obvious in the RV. Alterations related to intermediate filaments were seen in both ventricles and highlight such proteins as early indicators of LV loss of function. SIGNIFICANCE: The present study report protein sets in the RV and the LV being associated with ventricular function and remodelling in DCM. Protein abundances in the LV and the RV emphasize and expand current knowledge on pathophysiological changes in heart failure and DCM. While RV and LV EMBs do not differ concerning diagnostic assessment of inflammatory status and virus persistence, additional information reflecting disease severity associated protein alterations can be gained by EMB protein profiling. RV and LV protein data provided complementary information. The protein pattern of the LV reflects metabolic changes and an impaired energy production, which is associated with the degree of LV systolic dysfunction and remodelling and may yield important information about the disease status in DCM. On the other hand, at this disease stage of DCM with still preserved RV function, RV alterations in structural proteins may reflect myocardial compensatory protective mechanisms for maintenance of structure and cellular function. The study highlight particular proteins being of interest as heart failure biomarkers in both ventricles which seem to reflect the severity of the disease. Further comparative studies between different HF aetiologies have to evaluate those proteins as markers specific for DCM.
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Affiliation(s)
- Sabine Ameling
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Straße 8, D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Julia Bischof
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Straße 8, D-17475 Greifswald, Germany
| | - Marcus Dörr
- Department for Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Str., D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Stephanie Könemann
- Department for Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Str., D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Klaus Empen
- Department for Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Str., D-17475 Greifswald, Germany
| | - Kerstin Weitmann
- Institute for Community Medicine, University Medicine Greifswald, Ellernholzstr. 1, D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Karin Klingel
- Cardiopathology, Institute for Molecular Pathology and Neuropathology, University Hospital Tübingen, Liebermeisterstr. 8, D-72076 Tübingen, Germany
| | - Daniel Beug
- Department for Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Str., D-17475 Greifswald, Germany
| | - Vishnu Mukund Dhople
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Straße 8, D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Straße 8, D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Straße 8, D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.
| | - Stephan B Felix
- Department for Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Str., D-17475 Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.
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19
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Xu F, Wang S, Dai X, Mundra PA, Zheng J. Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data. Methods 2021; 189:65-73. [PMID: 33039573 DOI: 10.1016/j.ymeth.2020.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 08/20/2020] [Accepted: 10/03/2020] [Indexed: 11/23/2022] Open
Abstract
Single-cell protein abundance is a fundamental type of information to characterize cell states. Due to high cost and technical barriers, however, direct quantification of proteins is difficult. Single-cell RNA sequencing (scRNA-seq) data, serving as a cost-effective substitute of single-cell proteomics, may not accurately reflect protein expression levels due to measurement error, noise, post-transcriptional and translational regulation, etc. The recently emerging single-cell multimodal omics data, e.g. CITE-seq and REAP-seq, can simultaneously profile RNA and protein abundances in single cells, providing labeled data for predictive modeling in a supervised learning framework. Deep neural network-based transfer learning method has been applied to imputation of surface protein abundances from single-cell transcriptomic data. However, it is unclear if the artificial neural network is the best model, and it is desirable to improve the prediction performance (e.g. accuracy, interpretability) of machine learning models. In this paper, we compared several tree-based ensemble learning methods with neural network models, and found that ensemble learning often performed better than neural network, and Random Forest (RF) performed the best overall. Moreover, we used the feature importance scores from RF to interpret biological mechanisms underlying the prediction. Our study demonstrates the effectiveness of ensemble learning for reliable protein abundances prediction using single-cell multimodal omics data, and paves the way for knowledge discovery by mining single-cell multi-omics data in large scale.
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20
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Maurya VK, Gupta SK, Sharma M, Majumder B, Deeba F, Pandey N, Pandey V. Growth, physiological and proteomic responses in field grown wheat varieties exposed to elevated CO 2 under high ambient ozone. Physiol Mol Biol Plants 2020; 26:1437-1461. [PMID: 32647460 PMCID: PMC7326879 DOI: 10.1007/s12298-020-00828-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/09/2020] [Accepted: 05/08/2020] [Indexed: 05/25/2023]
Abstract
The present study investigated growth, biochemical, physiological, yield and proteomic changes in 3 wheat varieties exposed to elevated CO2 (515 ppm) in a background of high ambient ozone in field. Ethylenediurea (EDU) was used as antiozonant. Average ozone concentration was 59 ppb and was sufficient enough to exert phytotoxic effects. Elevated carbon dioxide (eCO2) and EDU application individually or in combination negated the adverse effects of ozone by modulating antioxidants and antioxidative enzymes. Differential leaf proteomics revealed that at vegetative stage major changes in protein abundance were due to EDU treatment (47, 52 and 41 proteins in PBW-343, LOK1 and HD-2967, respectively). Combined treatment of eCO2 and EDU was more responsible for changes in 37 proteins during flowering stage of PBW-343 and LOK1. Functional categorization revealed more than 60% differentially abundant protein collectively belonging to carbon metabolism, protein synthesis assembly and degradation and photosynthesis. At both the growth stages, LOK1 was more responsive to eCO2 and combined treatment (eCO2 + EDU). HD-2967 was more positively responsive to EDU and combined treatment. eCO2 in combination of EDU protected these varieties against high ambient O3.
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Affiliation(s)
- Vivek K. Maurya
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Department of Botany, University of Lucknow, Lucknow, 226001 India
| | - Sunil K. Gupta
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Marisha Sharma
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Baisakhi Majumder
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Farah Deeba
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Biotechnology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015 India
| | - Nalini Pandey
- Department of Botany, University of Lucknow, Lucknow, 226001 India
| | - Vivek Pandey
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, 226001 India
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21
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Victor MP, Acharya D, Chakraborty S, Ghosh TC. The combined influence of codon composition and tRNA copy number regulates translational efficiency by influencing synonymous nucleotide substitution. Gene 2020; 745:144640. [PMID: 32247037 DOI: 10.1016/j.gene.2020.144640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 01/26/2023]
Abstract
Codon usage bias is an important genomic phenomenon, where highly expressed genes use optimal codons for smoother translation with high yield, facilitated by the cognate tRNAs. Here, we presented the tRNA co-adaptation index (co-AI) by correlating tRNA gene copy number and codon composition in Saccharomyces cerevisiae. We observed that this co-AI is positively correlated with protein abundance and translation rate. Considering nucleotide substitutions, co-AI influences synonymous substitutions more than gene expression and protein abundance, the most important determinants of evolutionary rate. Co-AI correlates positively with mRNA secondary structure stability and mRNA half-life, which may lead to protein accumulation under high co-AI. However, the highly expressed proteins encoded by high co-AI genes are assisted by molecular chaperones to attain their proper functional conformation and prevent accumulation.
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Affiliation(s)
- Manish P Victor
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, India
| | - Debarun Acharya
- Department of Microbiology, Bose Institute, Kolkata, West Bengal, India.
| | | | - Tapash C Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, India; Department of Microbiology, Raiganj University, Raiganj, West Bengal, India.
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22
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Maurya VK, Gupta SK, Sharma M, Majumder B, Deeba F, Pandey N, Pandey V. Proteomic changes may lead to yield alteration in maize under carbon dioxide enriched condition. 3 Biotech 2020; 10:203. [PMID: 32328402 PMCID: PMC7160224 DOI: 10.1007/s13205-020-02189-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022] Open
Abstract
In the present study, the effect of elevated CO2 on growth, physiology, yield and proteome was studied on two maize (Zea mays L.) varieties grown under Free-air CO2 enrichment. Growth in high CO2 (530 ppm) did not affect either photosynthesis or pigment contents in both varieties. Reduced MDA content, antioxidant and antioxidative enzymes levels were observed in both varieties in response to high CO2. PEHM-5 accumulated more biomass than SMH-3031 under eCO2. PEHM-5 also had more seed starch and total soluble sugar than SMH-3031. However, SMH-3031 had increased number of seed per cob than PEHM-5. Interestingly, thousand seed weight was significantly increased in PEHM-5 only, while it was decreased in SMH-3031 under eCO2. We observed increased seed size in PEHM-5, while the size of the SMH-3031 seeds remained unaltered. Leaf proteomics revealed more abundance of proteins related to Calvin cycle, protein synthesis assembly and degradation, defense and redox homeostasis in PEHM-5 that contributed to better growth and yield in elevated CO2. While in SMH-3031 leaf, proteins related to Calvin cycle, defense and redox homeostasis were less abundant in elevated CO2 resulting in average growth and yield. The results showed a differential response of two maize varieties to eCO2.
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Affiliation(s)
- Vivek K. Maurya
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, 226001 India
| | - Sunil K. Gupta
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Marisha Sharma
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Baisakhi Majumder
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Farah Deeba
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Nalini Pandey
- Department of Botany, University of Lucknow, Lucknow, 226001 India
| | - Vivek Pandey
- Plant Ecology and Climate Change Science Division, CSIR-National Botanical Research Institute, Lucknow, India
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23
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Cattoglio C, Darzacq X, Tjian R, Hansen AS. Estimating Cellular Abundances of Halo-tagged Proteins in Live Mammalian Cells by Flow Cytometry. Bio Protoc 2020; 10:e3527. [PMID: 33654751 DOI: 10.21769/bioprotoc.3527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/24/2019] [Accepted: 01/29/2020] [Indexed: 11/02/2022] Open
Abstract
Accurate abundance measurements of cellular proteins are required to achieve a quantitative and predictive understanding of any biological process inside the cell. Existing methods to determine absolute protein abundances are labor-intensive and/or require sophisticated experimental and computational infrastructure (e.g., fluorescence correlation spectroscopy (FCS)-calibrated imaging and quantitative mass spectrometry). Here we detail a straightforward flow cytometry-based method to measure the absolute abundance of any Halo-tagged protein in live cells that uses a standard mammalian cell line with a known number of Halo-CTCF proteins recently characterized in our lab. The protocol only comprises a few steps. First, a cell line expressing the Halo-tagged protein of interest is grown and labeled side-by-side with our standard line. Then, average fluorescence intensities are measured by conventional flow cytometry analysis and finally a simple calculation is applied to estimate the absolute number of the Halo-tagged protein of interest per cell. Once the protein of interest has been endogenously tagged with HaloTag, which we routinely achieve by Cas9-mediated genome editing, the presented protocol is fast, convenient, reproducible, cost-effective and readily accessible.
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Affiliation(s)
- Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
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24
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Walsh JR, Woodhouse MR, Andorf CM, Sen TZ. Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. BMC Plant Biol 2020; 20:4. [PMID: 31900107 PMCID: PMC6942271 DOI: 10.1186/s12870-019-2218-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 12/24/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstructed by mapping syntenic regions to the sorghum chromosomes. During evolution, maize has had uneven gene loss between each ancient subgenome. Fractionation and divergence between these genomes continue today, constantly changing genetic make-up and phenotypes and influencing agronomic traits. RESULTS Here we regenerate the subgenome reconstructions for the most recent maize reference genome assembly. Based on both expression and abundance data for homeologous gene pairs across multiple tissues, we observed functional divergence of genes across subgenomes. Although the genes in the larger maize subgenome are often expressing more highly than their homeologs in the smaller subgenome, we observed cases where homeolog expression dominance switches in different tissues. We demonstrate for the first time that protein abundances are higher in the larger subgenome, but they also show tissue-specific dominance, a pattern similar to RNA expression dominance. We also find that pollen expression is uniquely decoupled from protein abundance. CONCLUSION Our study shows that the larger subgenome has a greater range of functional assignments and that there is a relative lack of overlap between the subgenomes in terms of gene functions than would be suggested by similar patterns of gene expression and protein abundance. Our study also revealed that some reactions are catalyzed uniquely by the larger and smaller subgenomes. The tissue-specific, nonequivalent expression-level dominance pattern observed here implies a change in regulatory control which favors differentiated selective pressure on the retained duplicates leading to eventual change in gene functions.
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Affiliation(s)
- Jesse R Walsh
- U.S. Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Margaret R Woodhouse
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, 94710, USA
| | - Carson M Andorf
- U.S. Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA
| | - Taner Z Sen
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, 94710, USA.
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
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25
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Kraus AJ, Cosentino RO. Ribosome Profiling in Trypanosomatids. Methods Mol Biol 2019; 1971:109-22. [PMID: 30980300 DOI: 10.1007/978-1-4939-9210-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Ribosomes are the machinery responsible for reading mRNAs and translating them into proteins. The ribosome profiling approach is based on high-throughput sequencing of ribosome-protected mRNAs. RNAs not harboring ribosomes are removed by nuclease digestion leaving the so-called ribosome "footprints." The purified "footprint" RNA molecules are processed into DNA libraries and their individual abundance is determined by deep sequencing. Ribosome profiling reveals the portion of transcripts which are actually protein-coding and can be used for differential gene expression analysis addressing rates of protein synthesis, and translational control and efficiency.
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Vasquez MC, Lippert MR, White C, Walter RK, Tomanek L. Proteomic changes across a natural temperature gradient in a marine gastropod. Mar Environ Res 2019; 149:137-147. [PMID: 31204014 DOI: 10.1016/j.marenvres.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/01/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Responses of marine ectotherms to variable environmental temperature often entails maintanence of cellular homeostasis and physiological function through temperature compensation and physiological changes. We investigated the physiological response to thermal stress by examining proteomic changes in the marine kelp forest gastropod and emerging fisheries species Kellet's whelk (Kelletia kelletii) across a naturally-existing thermal gradient that ranges from a warmer-water site inside the species' native range and extends to the northern, cold-water edge of the range. We hypothesized that abundance of cellular stress response and energy metabolism proteins would increase with decreasing temperature in support of cold-compensation. Our exploratory proteomic analysis of whelk gill tissue (N = 6 whelks) from each of the four California Channel Island sites revealed protein abundance changes related to the cytoskeleton, energy metabolism/oxidative stress, and cell signaling. The changes did not correlate consistently with temperature. Nonetheless, whelks from the coldest island site showed increased abundance of energy metabolism and oxidative stress proteins, possibly suggesting oxidative damage of lipid membranes that is ameliorated by antioxidants and may aid in their cold stress response. Similarly, our exploratory analysis revealed abundances of cell signaling proteins that were higher at the coldest site compared to the warmest site, possibly indicating an importance for cell signaling regulation in relatively cooler environments. This study provides protein targets for future studies related to thermal effects in marine animals and may contribute to understanding the physiological response of marine organisms to future ocean conditions.
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Affiliation(s)
- M Christina Vasquez
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA.
| | - Marilla R Lippert
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Crow White
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Ryan K Walter
- Physics Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Lars Tomanek
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
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27
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Kurzawski M, Szeląg-Pieniek S, Łapczuk-Romańska J, Wrzesiński M, Sieńko J, Oswald S, Droździk M. The reference liver - ABC and SLC drug transporters in healthy donor and metastatic livers. Pharmacol Rep 2019; 71:738-745. [PMID: 31207436 DOI: 10.1016/j.pharep.2019.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Analysis of results and conclusions in studies dedicated to pathology of the liver are usually based on comparison of pathological liver specimens and control/reference (considered as healthy) tissues. There are two main sources of the control liver samples used as the reference livers, i.e. deceased organ donor livers and non-tumorous tissue from metastatic livers, which are also applied for drug transporter investigations. However, no information has yet been published on drug transporters in these two major types of reference livers. METHODS We explored ABC (P-gp, MRP1, MRP2, MRP3, MRP4, BCRP, BSEP) and SLC (NTCP, MCT1, OCT1, OCT3, OAT2, OATP1B1, OATP1B3, OATP2B1) family transporters expression (qPCR) and protein abundance (LC-MS/MS) in healthy donors (n = 9) and metastatic (n = 13) livers. RESULTS The analysis of mRNA content revealed significant differences in ABCB11, ABCC1, ABCG2, SLC10A1, SLC16A1, SLCO1B1 and SLCO2B1 gene expression between livers from organ donors and patients who underwent surgical resection of metastatic tumors. The protein abundance of NTCP was significantly higher, whereas of P-gp significantly lower in non-tumorous tissues from metastatic livers. Greater inter-individual variability in protein abundance of all studied transporters in subjects with metastatic colon cancer was also observed. CONCLUSIONS The results suggest that final conclusions in liver pathology studies may depend on the reference liver tissue used, especially in gene expression studies.
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Affiliation(s)
- Mateusz Kurzawski
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland.
| | - Sylwia Szeląg-Pieniek
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland
| | - Joanna Łapczuk-Romańska
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland
| | - Maciej Wrzesiński
- Department of General and Transplantation Surgery, Marie Curie Regional Hospital, Szczecin, Poland
| | - Jerzy Sieńko
- Department of General and Transplantation Surgery, Pomeranian Medical University, Szczecin, Poland
| | - Stefan Oswald
- Department of Clinical Pharmacology, University Medicine of Greifswald, Greifswald, Germany
| | - Marek Droździk
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland
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28
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Mai Y, Dou L, Murdan S, Basit AW. An animal's sex influences the effects of the excipient PEG 400 on the intestinal P-gp protein and mRNA levels, which has implications for oral drug absorption. Eur J Pharm Sci 2018; 120:53-60. [PMID: 29678614 DOI: 10.1016/j.ejps.2018.04.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/18/2018] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
There is a growing body of evidence which suggests that formerly regarded "inert" pharmaceutical excipients have the potential to influence oral drug bioavailability. The solubilizing agent polyethylene glycol 400 (PEG 400), for instance, has a sex-specific effect on P-glycoprotein (P-gp)-mediated drug bioavailability. We hypothesized that such an effect could be via PEG-induced alteration of P-gp activity and/or expression to different extents in males and females. To test this hypothesis in vivo, we investigated the influence of orally administered PEG 400 on the protein content and mRNA expression of P-gp in different regions of the gastrointestinal tract in male and female rats. Fasted rats received an oral dose of PEG 400 and at different time intervals, rats were sacrificed and their intestines were collected. The P-gp protein and mRNA expression in different intestinal segments (duodenum, jejunum, ileum and colon) were measured by Western blotting and PCR, respectively. It was found that P-gp protein and mRNA levels increased along the gastrointestinal tract in control animals (i.e. without PEG administration), and was higher in males compared to the female rats. The oral administration of PEG 400 decreased the P-gp expression in the jejunum, ileum and colon of males but not in the corresponding segments in females. This sex-dependent influence of PEG 400 on P-gp levels reflects and explains the sex-related effect of PEG 400 on oral absorption of certain drugs. The data further adds to the growing literature on the importance of taking into consideration an individual's sex for optimal drug administration.
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Affiliation(s)
- Yang Mai
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Liu Dou
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Sudaxshina Murdan
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Abdul W Basit
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom.
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29
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Delius J, Trautmann S, Médard G, Kuster B, Hannig M, Hofmann T. Label-free quantitative proteome analysis of the surface-bound salivary pellicle. Colloids Surf B Biointerfaces 2017; 152:68-76. [PMID: 28086104 DOI: 10.1016/j.colsurfb.2017.01.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/17/2022]
Abstract
The salivary pellicle, covering natural as well as restored tooth surfaces in the oral cavity as an immobilized protein-rich layer, acts as an important physico-chemical and biological mediator at the tooth-saliva-interface. For the first time, the pellicle's proteome of individual volunteers were analyzed separately on three consecutive days and the relative protein abundance determined by a label-free quantitative nano-LC-MS/MS approach. A total of 72 major proteins were identified in the initial pellicles formed intraorally on dental ceramic specimens already after 3min with high inter-individual and inter-day consistency. In comparison, significant differences in protein abundance were evident between subjects, thus indicating unique individual pellicle profiles. Furthermore, the relative protein abundance in pellicles was compared to the proteome pattern in the corresponding saliva samples of the same individuals to provide first data on significantly enriched and depleted salivary proteins (p <0.05) within the surface-bound salivary pellicle. Our findings reveal the initial adsorption of salivary proteins at the solid-liquid interface to be a rapid, highly selective, and reproducible process leading to the immobilization of a broad range of protective proteins and enzymes on the substratum surface within a few minutes. This provides evidence that the pellicle layer might be physiologically functional even without further maturation.
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Affiliation(s)
- Judith Delius
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Simone Trautmann
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, University Hospital, Saarland University, Building 73, 66421 Homburg/Saar, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, University Hospital, Saarland University, Building 73, 66421 Homburg/Saar, Germany.
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany.
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Abstract
This protocol is used to assay the effect of protein over-expression on fitness of E. coli. It is based on a plasmid expression of a protein of interest from an arabinose-regulated pBAD promoter followed by the measurement of the intracellular protein abundance by Western blot along with the measurement of growth parameters of E. coli cell expressing this protein.
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Affiliation(s)
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, Israel
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA, USA
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31
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Choi MY, Park SH. Adjustable under-expression of yeast mating pathway proteins in Saccharomyces cerevisiae using a programmed ribosomal frameshift. Appl Microbiol Biotechnol 2016; 100:4997-5005. [PMID: 26837218 DOI: 10.1007/s00253-016-7335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/13/2016] [Accepted: 01/17/2016] [Indexed: 10/22/2022]
Abstract
Experimental research in molecular biology frequently relies on the promotion or suppression of gene expression, an important tool in the study of its functions. Although yeast is among the most studied model systems with the ease of maintenance and manipulation, current experimental methods are mostly limited to gene deletion, suppression or overexpression of genes. Therefore, the ability to reduce protein expressions and then observing the effects would promote a better understanding of the exact functions and their interactions. Reducing protein expression is mainly limited by the difficulties associated with controlling the reduction level, and in some cases, the initial endogenous abundance is too low. For the under-expression to be useful as an experimental tool, repeatability and stability of reduced expression is important. We found that cis-elements in programmed -1 ribosomal frameshifting (-1RFS) of beet western yellow virus (BWYV) could be utilized to reduced protein expression in Saccharomyces cerevisiae. The two main advantages of using -1RFS are adjustable reduction rates and ease of use. To demonstrate the utility of this under-expression system, examples of reduced protein abundance were shown using yeast mating pathway components. The abundance of MAP kinase Fus3 was reduced to approximately 28-75 % of the wild-type value. Other MAP kinase mating pathway components, including Ste5, Ste11, and Ste7, were also under-expressed to verify that the -1RFS system works with different proteins. Furthermore, reduced Fus3 abundance altered the overall signal transduction outcome of the mating pathway, demonstrating the potential for further studies of signal transduction adjustment via under-expression.
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Chen S, Luo Y, Ding G, Xu F. Comparative analysis of Brassica napus plasma membrane proteins under phosphorus deficiency using label-free and MaxQuant-based proteomics approaches. J Proteomics 2015; 133:144-152. [PMID: 26746009 DOI: 10.1016/j.jprot.2015.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/14/2015] [Accepted: 12/18/2015] [Indexed: 12/27/2022]
Abstract
UNLABELLED Phosphorus (P) deficiency is a primary constraint for plant growth in terrestrial ecosystems. To better understand the genotypic differences in the adaptation mechanism of Brassica napus to P deficiency, we purified the plasma membrane (PM) from the roots of two genotypes: P-efficient "Eyou Changjia" and P-inefficient "B104-2". Combining label-free quantitative proteomics with the MaxQuant approach, a total of 71 proteins that significantly changed in abundances were identified in the two genotypes in response to P-free starvation, including 31 in "Eyou Changjia" and 40 in "B104-2". Based on comparative genomics study, 28 proteins were mapped to the confidence intervals of quantitative trait loci (QTLs) for P efficiency related traits. Seven decreased proteins with transporter activity were found to be located in the PM by subcellular localization analyses. These proteins involved in intracellular protein transport and ATP hydrolysis coupled proton transport were mapped to the QTL for P content and dry weight. Compared with "B104-2", more decreased proteins referring to transporter activity were found in "Eyou Changjia", showing that substance exchange was decreased in response to short-term P-free starvation. Together with the finding, more decreased proteins functioning in signal transduction and protein synthesis/degradation suggested that "Eyou Changjia" could slow the progression of growth and save more P in response to short-term P-free starvation. BIOLOGICAL SIGNIFICANCE P deficiency seriously limits the production and quality of B. napus. Roots absorb water and nutrients and anchor the plant in the soil. Therefore, to study root PM proteome under P stress would be helpful to understand the adaptation mechanism for P deficiency. However, PM proteome analysis in B. napus has been seldom reported due to the high hydrophobicity and low abundance of PM. Thus, we herein investigated the PM proteome alteration of roots in two B. napus genotypes, with different P deficient tolerances, in response to P-free starvation. The present study offers new insights and novel information for better understanding the adaptative response to P deficiency in B. napus.
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Affiliation(s)
- Shuisen Chen
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ying Luo
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China.
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Li JJ, Bickel PJ, Biggin MD. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2014; 2:e270. [PMID: 24688849 PMCID: PMC3940484 DOI: 10.7717/peerj.270] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/22/2014] [Indexed: 12/17/2022] Open
Abstract
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 12% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R2 = 0.13). Based on this, our second strategy suggests that mRNA levels explain ∼81% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates only apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by Hebenstreit et al. (2012), we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ∼40% of genes that are non-expressed.
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Affiliation(s)
- Jingyi Jessica Li
- Department of Statistics, University of California , Berkeley, CA , USA ; Departments of Statistics and Human Genetics, University of California , Los Angeles, CA , USA
| | - Peter J Bickel
- Department of Statistics, University of California , Berkeley, CA , USA
| | - Mark D Biggin
- Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
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