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Transcriptome Profiling across Five Tissues of Giant Panda. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3852586. [PMID: 32851066 PMCID: PMC7436357 DOI: 10.1155/2020/3852586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/03/2020] [Accepted: 06/01/2020] [Indexed: 11/18/2022]
Abstract
Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
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Omics Approaches for Identifying Physiological Adaptations to Genome Instability in Aging. Int J Mol Sci 2017; 18:ijms18112329. [PMID: 29113067 PMCID: PMC5713298 DOI: 10.3390/ijms18112329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 10/29/2017] [Indexed: 12/25/2022] Open
Abstract
DNA damage causally contributes to aging and age-related diseases. The declining functioning of tissues and organs during aging can lead to the increased risk of succumbing to aging-associated diseases. Congenital syndromes that are caused by heritable mutations in DNA repair pathways lead to cancer susceptibility and accelerated aging, thus underlining the importance of genome maintenance for withstanding aging. High-throughput mass-spectrometry-based approaches have recently contributed to identifying signalling response networks and gaining a more comprehensive understanding of the physiological adaptations occurring upon unrepaired DNA damage. The insulin-like signalling pathway has been implicated in a DNA damage response (DDR) network that includes epidermal growth factor (EGF)-, AMP-activated protein kinases (AMPK)- and the target of rapamycin (TOR)-like signalling pathways, which are known regulators of growth, metabolism, and stress responses. The same pathways, together with the autophagy-mediated proteostatic response and the decline in energy metabolism have also been found to be similarly regulated during natural aging, suggesting striking parallels in the physiological adaptation upon persistent DNA damage due to DNA repair defects and long-term low-level DNA damage accumulation occurring during natural aging. These insights will be an important starting point to study the interplay between signalling networks involved in progeroid syndromes that are caused by DNA repair deficiencies and to gain new understanding of the consequences of DNA damage in the aging process.
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Abstract
The incidence and prevalence of cardiac diseases, which are the main cause of death worldwide, are likely to increase because of population ageing. Prevailing theories about the mechanisms of ageing feature the gradual derailment of cellular protein homeostasis (proteostasis) and loss of protein quality control as central factors. In the heart, loss of protein patency, owing to flaws in genetically-determined design or because of environmentally-induced 'wear and tear', can overwhelm protein quality control, thereby triggering derailment of proteostasis and contributing to cardiac ageing. Failure of protein quality control involves impairment of chaperones, ubiquitin-proteosomal systems, autophagy, and loss of sarcomeric and cytoskeletal proteins, all of which relate to induction of cardiomyocyte senescence. Targeting protein quality control to maintain cardiac proteostasis offers a novel therapeutic strategy to promote cardiac health and combat cardiac disease. Currently marketed drugs are available to explore this concept in the clinical setting.
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Affiliation(s)
- Robert H Henning
- Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Center, De Boelelaan 1117, 1081 HZ Amsterdam, The Netherlands
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Wang S, Lu Y, Sun X, Wu D, Fu B, Chen Y, Deng H, Chen X. Identification of common and differential mechanisms of glomerulus and tubule senescence in 24-month-old rats by quantitative LC-MS/MS. Proteomics 2016; 16:2706-2717. [PMID: 27452873 DOI: 10.1002/pmic.201600121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/05/2016] [Accepted: 07/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Shiyu Wang
- Department of Nephrology; Chinese PLA General Hospital; Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases; Beijing P.R. China
- Department of Nephrology; The Second Hospital of Jilin University; Changchun Jilin P.R. China
| | - Yang Lu
- Department of Nephrology; Chinese PLA General Hospital; Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases; Beijing P.R. China
| | - Xuefeng Sun
- Department of Nephrology; Chinese PLA General Hospital; Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases; Beijing P.R. China
| | - Di Wu
- Department of Nephrology; Chinese PLA General Hospital; Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases; Beijing P.R. China
| | - Bo Fu
- Department of Nephrology; Chinese PLA General Hospital; Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases; Beijing P.R. China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics; School of Life Sciences; Tsinghua University; Beijing P.R. China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics; School of Life Sciences; Tsinghua University; Beijing P.R. China
| | - Xiangmei Chen
- Department of Nephrology; Chinese PLA General Hospital; Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases; Beijing P.R. China
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Chakravarti B, Sherpa C, Bose D, Paul Chowdhury K, Khadar K, Zhang YC, Chakravarti DN. Pancreatic proteome profiling of type 1 diabetic mouse: Differential expression of proteins involved in exocrine function, stress response, growth, apoptosis and metabolism. Biochem Biophys Res Commun 2016; 487:930-936. [PMID: 27125462 DOI: 10.1016/j.bbrc.2016.04.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 04/22/2016] [Indexed: 11/29/2022]
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease in which the pancreatic β-cells fail to produce insulin. In addition to such change in the endocrine function, the exocrine function of the pancreas is altered as well. To understand the molecular basis of the changes in both endocrine and exocrine pancreatic functions due to T1D, the proteome profile of the pancreas of control and diabetic mouse was compared using two dimensional gel electrophoresis (2D-GE) and the differentially expressed proteins identified by electrospray ionization liquid chromatography-tandem mass spectrometry (ESI-LC-MS/MS). Among several hundred protein spots analyzed, the expression levels of 27 protein spots were found to be up-regulated while that of 16 protein spots were down-regulated due to T1D. We were able to identify 23 up-regulated and 9 down-regulated protein spots and classified them by bioinformatic analysis into different functional categories: (i) exocrine enzymes (or their precursors) involved in the metabolism of proteins, lipids, and carbohydrates; (ii) chaperone/stress response; and (iii) growth, apoptosis, amino acid metabolism or energy metabolism. Several proteins were found to be present in multiple forms, possibly resulting from proteolysis and/or post-translational modifications. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, which is the major catalytic subunit of succinate dehydrogenase (SDH), was found to be one of the proteins whose expression was increased in T1D mouse pancreata. Since altered expression of a protein can modify its functional activity, we tested and observed that the activity of SDH, a key metabolic enzyme, was increased in the T1D mouse pancreata as well. The potential role of the altered expression of different proteins in T1D associated pathology in mouse is discussed.
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Affiliation(s)
- Bulbul Chakravarti
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA; Department of Biology, York College, The City University of New York, Jamaica, NY, USA; Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Chheten Sherpa
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Devasrie Bose
- Department of Biology, York College, The City University of New York, Jamaica, NY, USA; Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Kakoli Paul Chowdhury
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Kavita Khadar
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Yuan Clare Zhang
- Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Deb N Chakravarti
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA; Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA.
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Wiersma M, Henning RH, Brundel BJJM. Derailed Proteostasis as a Determinant of Cardiac Aging. Can J Cardiol 2016; 32:1166.e11-20. [PMID: 27345610 DOI: 10.1016/j.cjca.2016.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/21/2016] [Accepted: 03/07/2016] [Indexed: 01/12/2023] Open
Abstract
Age comprises the single most important risk factor for cardiac disease development. The incidence and prevalence of cardiac diseases, which represents the main cause of death worldwide, will increase even more because of the aging population. A hallmark of aging is that it is accompanied by a gradual derailment of proteostasis (eg, the homeostasis of protein synthesis, folding, assembly, trafficking, function, and degradation). Loss of proteostasis is highly relevant to cardiomyocytes, because they are postmitotic cells and therefore not constantly replenished by proliferation. The derailment of proteostasis during aging is thus an important factor that preconditions for the development of age-related cardiac diseases, such as atrial fibrillation. In turn, frailty of proteostasis in aging cardiomyocytes is exemplified by its accelerated derailment in multiple cardiac diseases. Here, we review 2 major components of the proteostasis network, the stress-responsive and protein degradation pathways, in healthy and aged cardiomyocytes. Furthermore, we discuss the relation between derailment of proteostasis and age-related cardiac diseases, including atrial fibrillation. Finally, we introduce novel therapeutic targets that might possibly attenuate cardiac aging and thus limit cardiac disease progression.
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Affiliation(s)
- Marit Wiersma
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Robert H Henning
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bianca J J M Brundel
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands.
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Liu X, Fan Q, Yang G, Wang L. Proteomic profiling of aging in glomeruli of mice by using two-dimensional differential gel electrophoresis. Med Sci Monit 2015; 21:419-25. [PMID: 25659849 PMCID: PMC4548697 DOI: 10.12659/msm.892512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background Glomerular proteins were analyzed by proteomics to screen proteins participating in maturation of glomeruli before senescence and to find key proteins involved in the aging process. Material/Methods Glomeruli of C57BL/6 mice at 8 and 20 weeks were separated by kidney perfusion. Proteomic profiles of glomeruli were investigated by using two-dimensional differential gel electrophoresis and MALDI-TOF mass spectrometry. Results We identified 22 differentially expressed proteins. Among them, 3 proteins were significantly up-regulated and 19 proteins were significantly down-regulated in mature mice. Out of these 22 proteins, 18% take part in protein transport, protein targeting, and proteolysis; 5% in glycolysis; 14% in transcription; 9% in electron transport; 9% were chaperones; and 9% were hydrolases. Conclusions Our results provide insights into the glomerular differentially expressed proteins correlated with renal aging. In this study we found that aging altered the expression of ATP synthase subunit beta. Further studies on this protein might help to understand the mechanism of renal aging.
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Affiliation(s)
- Xiaodan Liu
- Department of Nephrology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Qiuling Fan
- Department of Nephrology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Gang Yang
- Department of Nephrology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Lining Wang
- Department of Nephrology, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China (mainland)
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Nkuipou-Kenfack E, Koeck T, Mischak H, Pich A, Schanstra JP, Zürbig P, Schumacher B. Proteome analysis in the assessment of ageing. Ageing Res Rev 2014; 18:74-85. [PMID: 25257180 DOI: 10.1016/j.arr.2014.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/05/2014] [Accepted: 09/15/2014] [Indexed: 12/14/2022]
Abstract
Based on demographic trends, the societies in many developed countries are facing an increasing number and proportion of people over the age of 65. The raise in elderly populations along with improved health-care will be concomitant with an increased prevalence of ageing-associated chronic conditions like cardiovascular, renal, and respiratory diseases, arthritis, dementia, and diabetes mellitus. This is expected to pose unprecedented challenges both for individuals and societies and their health care systems. An ultimate goal of ageing research is therefore the understanding of physiological ageing and the achievement of 'healthy' ageing by decreasing age-related pathologies. However, on a molecular level, ageing is a complex multi-mechanistic process whose contributing factors may vary individually, partly overlap with pathological alterations, and are often poorly understood. Proteome analysis potentially allows modelling of these multifactorial processes. This review summarises recent proteomic research on age-related changes identified in animal models and human studies. We combined this information with pathway analysis to identify molecular mechanisms associated with ageing. We identified some molecular pathways that are affected in most or even all organs and others that are organ-specific. However, appropriately powered studies are needed to confirm these findings based in in silico evaluation.
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Affiliation(s)
- Esther Nkuipou-Kenfack
- Mosaiques Diagnostics GmbH, Hannover, Germany; Hannover Medical School, Core Facility Proteomics, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
| | | | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany; BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Andreas Pich
- Hannover Medical School, Core Facility Proteomics, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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De Loor J, Gevaert K, Hoste E, Meyer E. How has urinary proteomics contributed to the discovery of early biomarkers of acute kidney injury? Expert Rev Proteomics 2014; 11:415-24. [PMID: 24961846 DOI: 10.1586/14789450.2014.932252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the past decade, analysis of the urinary proteome (urinary proteomics) has intensified in response to the need for novel biomarkers that support early diagnosis of kidney diseases. In particular, this also applies to acute kidney injury, which is a heterogeneous complex syndrome with a still-increasing incidence at the intensive care unit. Unfortunately, this major need remains largely unmet to date. The current report aims to explain why attempts to implement urinary proteomic-discovered acute kidney injury diagnostic candidates in the intensive care unit setting have not yet led to success. Subsequently, some key notes are provided that should enhance the chance of translating selected urinary proteomic candidates to valuable tools for the nephrologist and intensivist in the near future.
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Affiliation(s)
- Jorien De Loor
- Ghent University, Department of Pharmacology, Toxicology and Biochemistry, B-9820 Merelbeke, Belgium
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Selenium-binding protein 1: its physiological function, dependence on aryl hydrocarbon receptors, and role in wasting syndrome by 2,3,7,8-tetrachlorodibenzo-p-dioxin. Biochim Biophys Acta Gen Subj 2013; 1830:3616-24. [PMID: 23500078 DOI: 10.1016/j.bbagen.2013.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 02/15/2013] [Accepted: 03/06/2013] [Indexed: 01/31/2023]
Abstract
BACKGROUND Selenium-binding protein 1 (Selenbp1) is suggested to play a role in tumor suppression, and may be involved in the toxicity produced by dioxin, an activator of aryl hydrocarbon receptors (AhR). However, the mechanism or likelihood is largely unknown because of the limited information available about the physiological role of Selenbp1. METHODS To address this issue, we generated Selenbp1-null [Selenbp1 (-/-)] mice, and examined the toxic effect of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in this mouse model. RESULTS Selenbp1 (-/-) mice exhibited only a few differences from wild-type mice in their apparent phenotypes. However, a DNA microarray experiment showed that many genes including Notch1 and Cdk1, which are known to be enhanced in ovarian carcinoma, are also increased in the ovaries of Selenbp1 (-/-) mice. Based on the different responses to TCDD between C57BL/6J and DBA/2J strains of mice, the expression of Selenbp1 is suggested to be under the control of AhR. However, wasting syndrome by TCDD occurred equally in Selenbp1 (-/-) and (+/+) mice. CONCLUSIONS The above pieces of evidence suggest that 1) Selenbp1 suppresses the expression of tumor-promoting genes although a reduction in Selenbp1 alone is not very serious as far as the animals are concerned; and 2) Selenbp1 induction by TCDD is neither a pre-requisite for toxicity nor a protective response for combating TCDD toxicity. GENERAL SIGNIFICANCE Selenbp1 (-/-) mice exhibit little difference in their apparent phenotype and responsiveness to dioxin compared with the wild-type. This may be due to the compensation of Selenbp1 function by a closely-related protein, Selenbp2.
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Differential hepatic protein tyrosine nitration of mouse due to aging - effect on mitochondrial energy metabolism, quality control machinery of the endoplasmic reticulum and metabolism of drugs. Biochem Biophys Res Commun 2012; 430:231-5. [PMID: 23159622 DOI: 10.1016/j.bbrc.2012.10.142] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 10/28/2012] [Indexed: 11/22/2022]
Abstract
Aging is the inevitable fate of life which leads to the gradual loss of functions of different organs and organelles of all living organisms. The liver is no exception. Oxidative damage to proteins and other macromolecules is widely believed to be the primary cause of aging. One form of oxidative damage is tyrosine nitration of proteins, resulting in the potential loss of their functions. In this study, the effect of age on the nitration of tyrosine in mouse liver proteins was examined. Liver proteins from young (19-22 weeks) and old (24 months) C57/BL6 male mice were separated using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and electroblotted onto nitrocellulose membranes. Proteins undergoing tyrosine nitration were identified using anti-nitrotyrosine antibody. Three different protein bands were found to contain significantly increased levels of nitrotyrosine in old mice (Wilconxon rank-sum test, p<0.05). Electrospray ionization liquid chromatography tandem mass spectrometry (ESI-LC-MS/MS) was used to identify the proteins in these bands, which included aldehyde dehydrogenase 2, Aldehyde dehydrogenase family 1, subfamily A1, ATP synthase, H(+) transporting, mitochondrial F1 complex, β subunit, selenium-binding protein 2, and protein disulfide-isomerase precursor. The possible impairment of their functions can lead to altered hepatic activity and have been discussed.
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Abstract
Organs are complex structures that consist of multiple tissues with different levels of gene expression. To achieve comprehensive coverage and accurate quantitation data, organs ideally should be separated into morphologic and/or functional substructures before gene or protein expression analysis. However, because of complex morphology and elaborate isolation protocols, to date this often has been difficult to achieve. Kidneys are organs in which functional and morphologic subdivision is especially important. Each subunit of the kidney, the nephron, consists of more than 10 subsegments with distinct morphologic and functional characteristics. For a full understanding of kidney physiology, global gene and protein expression analyses have to be performed at the level of the nephron subsegments; however, such studies have been extremely rare to date. Here we describe the latest approaches in quantitative high-accuracy mass spectrometry-based proteomics and their application to quantitative proteomics studies of the whole kidney and nephron subsegments, both in human beings and in animal models. We compare these studies with similar studies performed on other organ substructures. We argue that the newest technologies used for preparation, processing, and measurement of small amounts of starting material are finally enabling global and subsegment-specific quantitative measurement of protein levels in the kidney and other organs. These new technologies and approaches are making a decisive impact on our understanding of the (patho)physiological processes at the molecular level.
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Noh JY, Oh SH, Lee JH, Kwon YS, Ryu DJ, Lee KH. Can blood components with age-related changes influence the ageing of endothelial cells? Exp Dermatol 2010; 19:339-46. [DOI: 10.1111/j.1600-0625.2009.01010.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Brégère C, Rebrin I, Gallaher TK, Sohal RS. Effects of age and calorie restriction on tryptophan nitration, protein content, and activity of succinyl-CoA:3-ketoacid CoA transferase in rat kidney mitochondria. Free Radic Biol Med 2010; 48:609-18. [PMID: 20025965 PMCID: PMC2818783 DOI: 10.1016/j.freeradbiomed.2009.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 12/07/2009] [Accepted: 12/10/2009] [Indexed: 01/16/2023]
Abstract
This study examined the protein targets of nitration and the consequent impact on protein function in rat kidney mitochondria at 4, 13, 19, and 24 months of age. Succinyl-CoA transferase (SCOT), a rate-limiting enzyme in the degradation of ketone bodies, was the most intensely reactive protein against anti-3-nitrotyrosine antibody in rat kidney mitochondria. However, subsequent mass spectrometric and amino acid analyses of purified SCOT indicated that tryptophan 372, rather than a tyrosine residue, was the actual site of simultaneous additions of nitro and hydroxy groups. This finding suggests that identification of nitrated tyrosine residues based solely on reactivity with anti-3-nitrotyrosine antibody can be potentially misleading. Between 4 and 24 months of age, the amounts of SCOT protein and catalytic activity, expressed per milligram of mitochondrial proteins, decreased by 55 and 45%, respectively. SCOT, and particularly its nitrated carboxy-terminal region, was relatively more susceptible to in vitro proteolysis than other randomly selected kidney mitochondrial proteins. The age-related decreases in SCOT protein amount and catalytic activity were prevented by a relatively long-term 40% reduction in the amount of food intake. Loss of SCOT protein in the aged rats may attenuate the capacity of kidney mitochondria to utilize ketone bodies for energy production.
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Affiliation(s)
- Catherine Brégère
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033
- Biology Division, California Institute of Technology, Pasadena, CA 91125
| | - Igor Rebrin
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033
| | - Timothy K. Gallaher
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033
| | - Rajindar S. Sohal
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033
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Chakravarti B, Fathy P, Sindicich M, Mallik B, Chakravarti DN. Comparison of SYPRO Ruby and Flamingo fluorescent stains for application in proteomic research. Anal Biochem 2009; 398:1-6. [PMID: 19917264 DOI: 10.1016/j.ab.2009.07.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 07/22/2009] [Accepted: 07/23/2009] [Indexed: 11/18/2022]
Abstract
Fluorescent dyes are widely used for the detection and quantitation of proteins separated by polyacrylamide gel electrophoresis. SYPRO Ruby is one such fluorescent dye widely used for this purpose. More recently, another fluorescent dye, Flamingo, is available for expression proteomic research. Using a standard ultraviolet (UV) transilluminator and a charge-coupled device (CCD)-based imaging system, the relative sensitivity of these two different fluorescent stains with regard to detection of protein spots separated by two-dimensional gel electrophoresis (2D-GE) and identification by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) were compared. Using mouse kidney and liver homogenates as well as Escherichia coli extract, we detected a greater number of protein spots using Flamingo compared with SYPRO Ruby. In addition, when we compared the number of matched peptides and the percentage of amino acid residues identified for 22 different protein spots of mouse kidney proteome, we observed a higher number of matched peptides and a higher percentage of amino acid residues for the majority of the proteins using Flamingo compared with SYPRO Ruby. Also, we were able to characterize a protein spot that can be detected by Flamingo only. Therefore, we recommend Flamingo over SYPRO Ruby to be used for studies on expression proteomics.
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Affiliation(s)
- Bulbul Chakravarti
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA 91711, USA.
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Amelina H, Cristobal S. Proteomic study on gender differences in aging kidney of mice. Proteome Sci 2009; 7:16. [PMID: 19358702 PMCID: PMC2673210 DOI: 10.1186/1477-5956-7-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 04/09/2009] [Indexed: 11/23/2022] Open
Abstract
Background This study aims to analyze sex differences in mice aging kidney. We applied a proteomic technique based on subfractionation, and liquid chromatography coupled with 2-DE. Samples from male and female CD1-Swiss outbred mice from 28 weeks, 52 weeks, and 76 weeks were analysed by 2-DE, and selected proteins were identified by matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Results This proteomic analysis detected age-related changes in protein expression in 55 protein-spots, corresponding to 22 spots in males and 33 spots in females. We found a protein expression signature (PES) of aging composed by 8 spots, common for both genders. The identified proteins indicated increases in oxidative and proteolytic proteins and decreases in glycolytic proteins, and antioxidant enzymes. Conclusion Our results provide insights into the gender differences associated to the decline of kidney function in aging. Thus, we show that proteomics can provide valuable information on age-related changes in expression levels of proteins and related modifications. This pilot study is still far from providing candidates for aging-biomarkers. However, we suggest that the analysis of these proteins could suggest mechanisms of cellular aging in kidney, and improve the kidney selection for transplantation.
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Affiliation(s)
- Hanna Amelina
- Department of Biochemistry and Biophysics, Stockholm University, Sweden.
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