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Stachniuk A, Trzpil A, Czeczko R, Nowicki Ł, Ziomkowska M, Fornal E. Absolute quantification of targeted rabbit liver- and meat tissue-specific peptide markers in highly processed food products. Food Chem 2024; 438:138069. [PMID: 38007955 DOI: 10.1016/j.foodchem.2023.138069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
A highly sensitive and selective method for the simultaneous absolute quantification of peptides unique to rabbit meat- and liver-specific tissue was developed using liquid chromatography - triple quadrupole mass spectrometry. Two rabbit skeletal muscle-specific peptides (SSVFVADPK and PHSHPALTPEQK), three rabbit liver tissue-specific peptides (FNLEALVTHTLPFEK, AILNYVANK, and TELAEPTSTR) and one peptide specific to both rabbit offal and skeletal muscle tissue (AFFGHYLYEVAR) were monitored. Analyses were performed using peptides labelled with stable isotopes (13C and 15N) as internal standards. Fifteen food samples containing rabbit meat and/or liver were analysed to verify compliance of the rabbit meat and liver composition with product labelling. One sample was adulterated with undeclared rabbit liver. The limit of detection and limit of quantification for the selected peptides of interest were in the range of 0.17 to 0.35 ng/mg and 0.57 to 1.17 ng/mg, respectively. The method may be useful for the determination of rabbit meat and liver tissue in highly processed food samples.
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Affiliation(s)
- Anna Stachniuk
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland.
| | - Alicja Trzpil
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Renata Czeczko
- Department of Chemistry, University of Live Sciences in Lublin, ul. Akademicka 15, 20-950 Lublin, Poland
| | - Łukasz Nowicki
- Altium International Sp. z o.o, ul. Puławska 303, 02-785 Warszawa, Poland
| | | | - Emilia Fornal
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland
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2
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Chen S, Zou Y, Song C, Cao K, Cai K, Wu Y, Zhang Z, Geng D, Sun W, Ouyang N, Zhang N, Li Z, Sun G, Zhang Y, Sun Y, Zhang Y. The role of glycolytic metabolic pathways in cardiovascular disease and potential therapeutic approaches. Basic Res Cardiol 2023; 118:48. [PMID: 37938421 PMCID: PMC10632287 DOI: 10.1007/s00395-023-01018-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
Cardiovascular disease (CVD) is a major threat to human health, accounting for 46% of non-communicable disease deaths. Glycolysis is a conserved and rigorous biological process that breaks down glucose into pyruvate, and its primary function is to provide the body with the energy and intermediate products needed for life activities. The non-glycolytic actions of enzymes associated with the glycolytic pathway have long been found to be associated with the development of CVD, typically exemplified by metabolic remodeling in heart failure, which is a condition in which the heart exhibits a rapid adaptive response to hypoxic and hypoxic conditions, occurring early in the course of heart failure. It is mainly characterized by a decrease in oxidative phosphorylation and a rise in the glycolytic pathway, and the rise in glycolysis is considered a hallmark of metabolic remodeling. In addition to this, the glycolytic metabolic pathway is the main source of energy for cardiomyocytes during ischemia-reperfusion. Not only that, the auxiliary pathways of glycolysis, such as the polyol pathway, hexosamine pathway, and pentose phosphate pathway, are also closely related to CVD. Therefore, targeting glycolysis is very attractive for therapeutic intervention in CVD. However, the relationship between glycolytic pathway and CVD is very complex, and some preclinical studies have confirmed that targeting glycolysis does have a certain degree of efficacy, but its specific role in the development of CVD has yet to be explored. This article aims to summarize the current knowledge regarding the glycolytic pathway and its key enzymes (including hexokinase (HK), phosphoglucose isomerase (PGI), phosphofructokinase-1 (PFK1), aldolase (Aldolase), phosphoglycerate metatase (PGAM), enolase (ENO) pyruvate kinase (PKM) lactate dehydrogenase (LDH)) for their role in cardiovascular diseases (e.g., heart failure, myocardial infarction, atherosclerosis) and possible emerging therapeutic targets.
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Affiliation(s)
- Shuxian Chen
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Yuanming Zou
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Chunyu Song
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Kexin Cao
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Kexin Cai
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Yanjiao Wu
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Zhaobo Zhang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Danxi Geng
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
| | - Nanxiang Ouyang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
| | - Naijin Zhang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
- Institute of Health Sciences, China Medical University, 77 Puhe Road, Shenbei New District, Shenyang, 110122, Liaoning Province, People's Republic of China.
- Key Laboratory of Reproductive and Genetic Medicine, China Medical University, National Health Commission, 77 Puhe Road, Shenbei New District, Shenyang, 110122, Liaoning Province, People's Republic of China.
| | - Zhao Li
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
| | - Guozhe Sun
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
| | - Yixiao Zhang
- Department of Urology Surgery, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning Province, People's Republic of China.
| | - Yingxian Sun
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
- Institute of Health Sciences, China Medical University, 77 Puhe Road, Shenbei New District, Shenyang, 110122, Liaoning Province, People's Republic of China.
| | - Ying Zhang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
- Institute of Health Sciences, China Medical University, 77 Puhe Road, Shenbei New District, Shenyang, 110122, Liaoning Province, People's Republic of China.
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3
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Olegovna LA, Alexandrovna VE, Sergeevna KA, Vasilievich MY, Alexandrovich SA. Aldolase of Mytilus galloprovincialis, Lamarck, 1819: Gene structure, tissue specificity of expression level and activity. Comp Biochem Physiol B Biochem Mol Biol 2023; 267:110862. [PMID: 37146868 DOI: 10.1016/j.cbpb.2023.110862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/07/2023]
Abstract
In the present study, the structure of the fructose-1,6-bisphosphataldolase (FBA) gene in Mytilus galloprovincialis (Lamarck, 1819) was analyzed and its tissue specificity of expression level and activity was determined. A 1092 base pairs (bps) complete coding sequence of the FBA gene was assembled from M. galloprovincialis transcriptome. Only one gene encoding FBA (MgFBA) was identified in the M. galloprovincialis genome. The length of MgFBA was 363 amino acids with a molecular mass of 39.7 kDa. According to the amino acid residues, the detected MgFBA gene is a type I aldolase. The FBA gene in M. galloprovincialis had 7 exons; the maximum intron length was about 2.5 kbps. Intraspecific nucleotide diversity (15 mutations) between MgFBAs from the Mediterranean mussels and the Black Sea mussels (present study) was detected. All mutations were synonymous. Tissue specificity in FBA expression level and activity was established. No direct correlation between these functions was found. The highest level of FBA gene expression is found in muscle tissue. According to the phylogenetic analyses, FBA gene in invertebrates could be considered the ancestral gene of muscle type aldolase, which may explain the character of tissue-specific expression.
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Affiliation(s)
| | - Vodiasova Ekaterina Alexandrovna
- Federal Research Center «Institute of Biology of Southern Seas RAS», Department Animal Physiology and Biochemistry, Moscow office: 38 Leninsky Ave., Moscow 119991, Russia; Sevastopol State University, Physic Department, 33 Universitetskaya Str., Sevastopol 299053, Russia
| | - Kokhan Alena Sergeevna
- Federal Research Center «Institute of Biology of Southern Seas RAS», Department Animal Physiology and Biochemistry, Moscow office: 38 Leninsky Ave., Moscow 119991, Russia
| | - Meger Yakov Vasilievich
- Sevastopol State University, Physic Department, 33 Universitetskaya Str., Sevastopol 299053, Russia
| | - Soldatov Alexander Alexandrovich
- Federal Research Center «Institute of Biology of Southern Seas RAS», Department Animal Physiology and Biochemistry, Moscow office: 38 Leninsky Ave., Moscow 119991, Russia; Sevastopol State University, Physic Department, 33 Universitetskaya Str., Sevastopol 299053, Russia
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Gorina YV, Salmina AB, Erofeev AI, Gerasimov EI, Bolshakova AV, Balaban PM, Bezprozvanny IB, Vlasova OL. Astrocyte Activation Markers. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:851-870. [PMID: 36180985 DOI: 10.1134/s0006297922090012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/16/2023]
Abstract
Astrocytes are the most common type of glial cells that provide homeostasis and protection of the central nervous system. Important specific characteristic of astrocytes is manifestation of morphological heterogeneity, which is directly dependent on localization in a particular area of the brain. Astrocytes can integrate into neural networks and keep neurons active in various areas of the brain. Moreover, astrocytes express a variety of receptors, channels, and membrane transporters, which underlie their peculiar metabolic activity, and, hence, determine plasticity of the central nervous system during development and aging. Such complex structural and functional organization of astrocytes requires the use of modern methods for their identification and analysis. Considering the important fact that determining the most appropriate marker for polymorphic and multiple subgroups of astrocytes is of decisive importance for studying their multifunctionality, this review presents markers, modern imaging techniques, and identification of astrocytes, which comprise a valuable resource for studying structural and functional properties of astrocytes, as well as facilitate better understanding of the extent to which astrocytes contribute to neuronal activity.
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Affiliation(s)
- Yana V Gorina
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia.
- Research Institute of Molecular Medicine and Pathobiochemistry, Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia
| | - Alla B Salmina
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
- Research Institute of Molecular Medicine and Pathobiochemistry, Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia
- Laboratory of Neurobiology and Tissue Engineering, Brain Institute, Research Center of Neurology, Moscow, 105064, Russia
| | - Alexander I Erofeev
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
| | - Evgeniy I Gerasimov
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
| | - Anastasia V Bolshakova
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
| | - Pavel M Balaban
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity, Moscow, 117485, Russia
| | - Ilya B Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Olga L Vlasova
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
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5
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Chou PC, Liu CM, Weng CH, Yang KC, Cheng ML, Lin YC, Yang RB, Shyu BC, Shyue SK, Liu JD, Chen SP, Hsiao M, Hu YF. Fibroblasts Drive Metabolic Reprogramming in Pacemaker Cardiomyocytes. Circ Res 2022; 131:6-20. [PMID: 35611699 DOI: 10.1161/circresaha.121.320301] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The sinoatrial node (SAN) is characterized by the microenvironment of pacemaker cardiomyocytes (PCs) encased with fibroblasts. An altered microenvironment leads to rhythm failure. Operable cell or tissue models are either generally lacking or difficult to handle. The biological process behind the milieu of SANs to evoke pacemaker rhythm is unknown. We explored how fibroblasts interact with PCs and regulate metabolic reprogramming and rhythmic activity in the SAN. METHODS Tbx18 (T-box transcription factor 18)-induced PCs and fibroblasts were used for cocultures and engineered tissues, which were used as the in vitro models to explore how fibroblasts regulate the functional integrity of SANs. RNA-sequencing, metabolomics, and cellular and molecular techniques were applied to characterize the molecular signals underlying metabolic reprogramming and identify its critical regulators. These pathways were further validated in vivo in rodents and induced human pluripotent stem cell-derived cardiomyocytes. RESULTS We observed that rhythmicity in Tbx18-induced PCs was regulated by aerobic glycolysis. Fibroblasts critically activated metabolic reprogramming and aerobic glycolysis within PCs, and, therefore, regulated pacemaker activity in PCs. The metabolic reprogramming was attributed to the exclusive induction of Aldoc (aldolase c) within PCs after fibroblast-PC integration. Fibroblasts activated the integrin-dependent mitogen-activated protein kinase-E2F1 signal through cell-cell contact and turned on Aldoc expression in PCs. Interruption of fibroblast-PC interaction or Aldoc knockdown nullified electrical activity. Engineered Tbx18-PC tissue sheets were generated to recapitulate the microenvironment within SANs. Aldoc-driven rhythmic machinery could be replicated within tissue sheets. Similar machinery was faithfully validated in de novo PCs of adult mice and rats, and in human PCs derived from induced pluripotent stem cells. CONCLUSIONS Fibroblasts drive Aldoc-mediated metabolic reprogramming and rhythmic regulation in SANs. This work details the cellular machinery behind the complex milieu of vertebrate SANs and opens a new direction for future therapy.
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Affiliation(s)
- Pei-Chun Chou
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taiwan. (P.-C.C., C.-M.L., C.-H.W., J.-D.L., Y.-F.H.).,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.)
| | - Chih-Min Liu
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taiwan. (P.-C.C., C.-M.L., C.-H.W., J.-D.L., Y.-F.H.).,Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan (C.-M.L., Y.-F.H.)
| | - Ching-Hui Weng
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taiwan. (P.-C.C., C.-M.L., C.-H.W., J.-D.L., Y.-F.H.).,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.)
| | - Kai-Chien Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.).,Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei (K.-C.Y.)
| | - Mei-Ling Cheng
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan City, Taiwan (M.-L.C.)
| | - Yuh-Charn Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.).,Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taiwan (Y.-C.L.)
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.)
| | - Bai-Chuang Shyu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.)
| | - Song-Kun Shyue
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.)
| | - Jin-Dian Liu
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taiwan. (P.-C.C., C.-M.L., C.-H.W., J.-D.L., Y.-F.H.).,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.)
| | - Shih-Pin Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taiwan. (S.-P.C.)
| | - Michael Hsiao
- The Genomics Research Center, Academia Sinica, Taipei, Taiwan (M.H.)
| | - Yu-Feng Hu
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taiwan. (P.-C.C., C.-M.L., C.-H.W., J.-D.L., Y.-F.H.).,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (P.-C.C., C.-H.W., K.-C.Y., Y.-C.L., R.-B.Y., B.-C.S., S.-K.S., J.-D.L., Y.-F.H.).,Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan (C.-M.L., Y.-F.H.)
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6
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Shaul YD, Yuan B, Thiru P, Nutter-Upham A, McCallum S, Lanzkron C, Bell GW, Sabatini DM. MERAV: a tool for comparing gene expression across human tissues and cell types. Nucleic Acids Res 2016; 44:D560-6. [PMID: 26626150 PMCID: PMC4702927 DOI: 10.1093/nar/gkv1337] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/16/2015] [Accepted: 11/16/2015] [Indexed: 12/25/2022] Open
Abstract
The oncogenic transformation of normal cells into malignant, rapidly proliferating cells requires major alterations in cell physiology. For example, the transformed cells remodel their metabolic processes to supply the additional demand for cellular building blocks. We have recently demonstrated essential metabolic processes in tumor progression through the development of a methodological analysis of gene expression. Here, we present the Metabolic gEne RApid Visualizer (MERAV, http://merav.wi.mit.edu), a web-based tool that can query a database comprising ∼4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors. MERAV has been designed as a powerful tool for whole genome analysis which offers multiple advantages: one can search many genes in parallel; compare gene expression among different tissue types as well as between normal and cancer cells; download raw data; and generate heatmaps; and finally, use its internal statistical tool. Most importantly, MERAV has been designed as a unique tool for analyzing metabolic processes as it includes matrixes specifically focused on metabolic genes and is linked to the Kyoto Encyclopedia of Genes and Genomes pathway search.
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Affiliation(s)
- Yoav D Shaul
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Broad Institute, Cambridge, MA 02142, USA
| | - Bingbing Yuan
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Andy Nutter-Upham
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Scott McCallum
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Carolyn Lanzkron
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Broad Institute, Cambridge, MA 02142, USA
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7
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Molecular and biochemical characterizations of three fructose-1,6-bisphosphate aldolases from Clonorchis sinensis. Mol Biochem Parasitol 2014; 194:36-43. [DOI: 10.1016/j.molbiopara.2014.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 04/13/2014] [Accepted: 04/15/2014] [Indexed: 11/20/2022]
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8
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Langellotti S, Romano M, Guarnaccia C, Granata V, Orrù S, Zagari A, Baralle FE, Salvatore F. A novel anti-aldolase C antibody specifically interacts with residues 85-102 of the protein. MAbs 2014; 6:708-17. [PMID: 24525694 PMCID: PMC4011915 DOI: 10.4161/mabs.28191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aldolase C is a brain-specific glycolytic isozyme whose complete repertoire of functions are obscure. This lack of knowledge can be addressed using molecular tools that discriminate the protein from the homologous, ubiquitous paralog aldolase A. The anti-aldolase C antibodies currently available are polyclonal and not highly specific. We obtained the novel monoclonal antibody 9F against human aldolase C, characterized its isoform specificity and tested its performance. First, we investigated the specificity of 9F for aldolase C. Then, using bioinformatic tools coupled to molecular cloning and chemical synthesis approaches, we produced truncated human aldolase C fragments, and assessed 9F binding to these fragments by western blot and ELISA assays. This strategy revealed that residues 85–102 harbor the epitope-containing region recognized by 9F. The efficiency of 9F was demonstrated also for immunoprecipitation assays. Finally, surface plasmon resonance revealed that the protein has a high affinity toward the epitope-containing peptide. Taken together, our findings show that epitope recognition is sequence-driven and is independent of the three-dimensional structure. In conclusion, given its specific molecular interaction, 9F is a novel and powerful tool to investigate aldolase C’s functions in the brain.
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Affiliation(s)
- Simona Langellotti
- CEINGE-Biotecnologie Avanzate; Naples, Italy; International Centre for Genetic Engineering and Biotechnology; Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences; University of Trieste; Trieste, Italy
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology; Trieste, Italy
| | | | - Stefania Orrù
- Department of Sports Science and Wellness; University of Naples "Parthenope"; Naples, Italy; IRCCS SDN-Foundation; Naples, Italy
| | | | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology; Trieste, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate; Naples, Italy; IRCCS SDN-Foundation; Naples, Italy
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9
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Lorenzatto KR, Monteiro KM, Paredes R, Paludo GP, da Fonsêca MM, Galanti N, Zaha A, Ferreira HB. Fructose-bisphosphate aldolase and enolase from Echinococcus granulosus: genes, expression patterns and protein interactions of two potential moonlighting proteins. Gene 2012; 506:76-84. [PMID: 22750316 DOI: 10.1016/j.gene.2012.06.046] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/26/2012] [Accepted: 06/17/2012] [Indexed: 01/16/2023]
Abstract
Glycolytic enzymes, such as fructose-bisphosphate aldolase (FBA) and enolase, have been described as complex multifunctional proteins that may perform non-glycolytic moonlighting functions, but little is known about such functions, especially in parasites. We have carried out in silico genomic searches in order to identify FBA and enolase coding sequences in Echinococcus granulosus, the causative agent of cystic hydatid disease. Four FBA genes and 3 enolase genes were found, and their sequences and exon-intron structures were characterized and compared to those of their orthologs in Echinococcus multilocularis, the causative agent of alveolar hydatid disease. To gather evidence of possible non-glycolytic functions, the expression profile of FBA and enolase isoforms detected in the E. granulosus pathogenic larval form (hydatid cyst) (EgFBA1 and EgEno1) was assessed. Using specific antibodies, EgFBA1 and EgEno1 were detected in protoscolex and germinal layer cells, as expected, but they were also found in the hydatid fluid, which contains parasite's excretory-secretory (ES) products. Besides, both proteins were found in protoscolex tegument and in vitro ES products, further suggesting possible non-glycolytic functions in the host-parasite interface. EgFBA1 modeled 3D structure predicted a F-actin binding site, and the ability of EgFBA1 to bind actin was confirmed experimentally, which was taken as an additional evidence of FBA multifunctionality in E. granulosus. Overall, our results represent the first experimental evidences of alternative functions performed by glycolytic enzymes in E. granulosus and provide relevant information for the understanding of their roles in host-parasite interplay.
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Affiliation(s)
- Karina Rodrigues Lorenzatto
- Laboratório de Genômica Estrutural e Funcional and Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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10
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Wang C, Wang H, Li Y, Liu B. Identification of a fructose-1,6-bisphosphate aldolase gene and association of the single nucleotide polymorphisms with growth traits in the clam Meretrix meretrix. Mol Biol Rep 2011; 39:5017-24. [PMID: 22160517 DOI: 10.1007/s11033-011-1298-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 11/30/2011] [Indexed: 11/28/2022]
Abstract
This study investigated whether there were single nucleotide polymorphisms (SNPs) in fructose-1,6-bisphosphate aldolase (FBA) gene associated with growth traits of the clam Meretrix meretrix. A FBA gene was identified in M. meretrix and its deduced amino acid residues shared high identity with type I aldolase. The FBA (MmeFBA) mRNA expression profile was examined by real-time PCR in different tissues and the significantly high expression level in foot and adduct muscle suggests that MmeFBA is a muscle type aldolase which functions in glycolytic pathway. In the MmeFBA gene, we identified four intron SNPs and three exon SNPs including a nonsynonymous SNP (mmfbae-2). These SNPs were genotyped in 205 clams from two clam populations with significantly different growth performance. Results showed that allele frequencies of three SNPs (mmfbai-1, mmfbai-3 and mmfbae-2) and the genotype frequency of mmfbai-1 were all significantly different between the two populations. The haplotype analysis further supported the three SNPs distributed differently between the two populations. This study successively characterized three growth-related SNPs in a gene involved in energy metabolism of M. meretrix. These findings could contribute the development of phenotype-selective breeding program in M. meretrix.
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Affiliation(s)
- Chao Wang
- Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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11
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ExprAlign--the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles. BMC Genomics 2009; 10:560. [PMID: 19939286 PMCID: PMC2790474 DOI: 10.1186/1471-2164-10-560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 11/26/2009] [Indexed: 12/05/2022] Open
Abstract
Background Sequence identification of ESTs from non-model species offers distinct challenges particularly when these species have duplicated genomes and when they are phylogenetically distant from sequenced model organisms. For the common carp, an environmental model of aquacultural interest, large numbers of ESTs remained unidentified using BLAST sequence alignment. We have used the expression profiles from large-scale microarray experiments to suggest gene identities. Results Expression profiles from ~700 cDNA microarrays describing responses of 7 major tissues to multiple environmental stressors were used to define a co-expression landscape. This was based on the Pearsons correlation coefficient relating each gene with all other genes, from which a network description provided clusters of highly correlated genes as 'mountains'. We show that these contain genes with known identities and genes with unknown identities, and that the correlation constitutes evidence of identity in the latter. This procedure has suggested identities to 522 of 2701 unknown carp ESTs sequences. We also discriminate several common carp genes and gene isoforms that were not discriminated by BLAST sequence alignment alone. Precision in identification was substantially improved by use of data from multiple tissues and treatments. Conclusion The detailed analysis of co-expression landscapes is a sensitive technique for suggesting an identity for the large number of BLAST unidentified cDNAs generated in EST projects. It is capable of detecting even subtle changes in expression profiles, and thereby of distinguishing genes with a common BLAST identity into different identities. It benefits from the use of multiple treatments or contrasts, and from the large-scale microarray data.
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Helbing CC, Ji L, Bailey CM, Veldhoen N, Zhang F, Holcombe GW, Kosian PA, Tietge J, Korte JJ, Degitz SJ. Identification of gene expression indicators for thyroid axis disruption in a Xenopus laevis metamorphosis screening assay. Part 2. Effects on the tail and hindlimb. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2007; 82:215-26. [PMID: 17399805 DOI: 10.1016/j.aquatox.2007.02.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 02/01/2007] [Accepted: 02/03/2007] [Indexed: 05/14/2023]
Abstract
Thyroid hormones (TH), thyroxine (T(4)) and 3,5,3'-triiodothyronine (T(3)), play crucial roles in regulation of growth, development and metabolism in vertebrates and are targets for endocrine disruptive agents. Perturbations in TH action can contribute to the development of disease states and the US Environmental Protection Agency is developing a high throughput screen using TH-dependent metamorphosis of the Xenopus laevis tadpole as an assay platform. Currently this methodology relies on external morphological endpoints and changes in central thyroid axis parameters. However, exposure-related changes in gene expression in TH-sensitive tissue types that occur over shorter time frames have the potential to augment this screen. Using a combination of cDNA array and real time quantitative polymerase chain reaction (QPCR) analyses, this study identifies molecular markers in tissues peripheral to the central thyroid axis. We examine the hindlimb and tail of tadpoles up to 96 h of continuous exposure to T(3), T(4), methimazole, propylthiouracil, or perchlorate. Several novel biomarker candidates are indicated that include transcripts encoding importin, RNA helicase II/Gu, and defender against death protein, DAD1. In combination with previously-identified biomarker candidates, these transcripts will greatly augment the predictive and diagnostic power of the Xenopus metamorphosis assay for perturbation of TH action.
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Affiliation(s)
- Caren C Helbing
- Department of Biochemistry and Microbiology, PO Box 3055, Stn. CSC, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.
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Cho PY, Lee MJ, Kim TI, Kang SY, Hong SJ. Expressed sequence tag analysis of adult Clonorchis sinensis, the Chinese liver fluke. Parasitol Res 2006; 99:602-8. [PMID: 16705464 DOI: 10.1007/s00436-006-0204-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
Abstract
Expressed sequence tag (EST) pools represent partial profiles of the gene expressions of organisms. In an effort to construct a Clonorchis sinensis EST pool, 2,387 ESTs were collected from an adult C. sinensis cDNA library and assembled into 1,573 clusters. Of these clusters, 1,225 ESTs (51%) were singletons and 348 clusters consisted of more than two ESTs. There were 848 clusters (54%) that shared significant identity with previously reported proteins, and of these, 401 clusters were categorized into 11 major functional protein classes. Three cDNA clones of fructose-1,6-bisphosphate (FBP) aldolase were selected from the C. sinensis EST pool and analyzed for phylogenic clustering. FBP clones encoded a complete polypeptide, which shared significant identity to those of vertebrate and invertebrate animals and clustered with those of trematodes. We believe that the EST pool described can be confidently used as a platform in multigene researches on C. sinensis gene expression.
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Affiliation(s)
- Pyo Yun Cho
- Department of Parasitology, Chung-Ang University College of Medicine, Tongjak-gu, Seoul 156-756, South Korea
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Johansen KA, Overturf K. Alterations in expression of genes associated with muscle metabolism and growth during nutritional restriction and refeeding in rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 2006; 144:119-27. [PMID: 16545592 DOI: 10.1016/j.cbpb.2006.02.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 01/25/2006] [Accepted: 02/04/2006] [Indexed: 11/26/2022]
Abstract
Rainbow trout, as well as many other species of fish, demonstrate the ability to survive starvation for long periods of time. During starvation, growth rate is decreased and muscle exhibits signs of wasting. However, upon resumption of feeding, accelerated growth is often observed. Alterations in muscle metabolism occur during feed restriction and refeeding, although the ways in which these alterations affect the molecular pathways that control muscle growth have not been fully determined. To analyze changes in muscle metabolism and growth during starvation and refeeding, real-time PCR was used to test the expression of six metabolic-related genes and eight muscle-specific genes in rainbow trout white muscle prior to and after 30 days of starvation, and after 4 and 14 days of refeeding. The six metabolic-related genes chosen are indicative of specific metabolic pathways: glycolysis, glycogenesis, gluconeogenesis, the pentose phosphate pathway, and fatty acid formation. The eight muscle specific genes chosen are key components in muscle growth and structural integrity, i.e., MRFs, MEFs, myostatins, and myosin. Alterations in expression of the tested metabolic-related genes and muscle-specific genes suggest that during both starvation and refeeding, changes in specific metabolic pathways initiate shifts in muscle that result mainly in the modification of myotube hypertrophy. The expression levels of many of the metabolic-related genes were altered during the refeeding period compared to those observed before the starvation period began. However, the accelerated growth often observed during refeeding is likely driven by changes in normal muscle metabolism, and the altered expression observed here may be a demonstration of those changes.
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Affiliation(s)
- Katherine A Johansen
- USDA-ARS, Hagerman Fish Culture Experiment Station, 3059F National Fish Hatchery Rd., Hagerman, ID 83332, USA
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Cañete-Soler R, Reddy KS, Tolan DR, Zhai J. Aldolases a and C are ribonucleolytic components of a neuronal complex that regulates the stability of the light-neurofilament mRNA. J Neurosci 2005; 25:4353-64. [PMID: 15858061 PMCID: PMC6725117 DOI: 10.1523/jneurosci.0885-05.2005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 03/16/2005] [Accepted: 03/22/2005] [Indexed: 01/26/2023] Open
Abstract
A 68 nucleotide segment of the light neurofilament (NF-L) mRNA, spanning the translation termination signal, participates in regulating the stability of the transcript in vivo. Aldolases A and C, but not B, interact specifically with this segment of the transcript in vitro. Aldolases A and C are glycolytic enzymes expressed in neural cells, and their mRNA binding activity represents a novel function of these isozymes. This unsuspected new activity was first uncovered by Northwestern blotting of a brainstem/spinal cord cDNA library. It was confirmed by two-dimensional fractionation of mouse brain cytosol followed by Northwestern hybridization and protein sequencing. Both neuronal aldolases interact specifically with the NF-L but not the heavy neurofilament mRNA, and their binding to the transcript excludes the poly(A)-binding protein (PABP) from the complex. Constitutive ectopic expression of aldolases A and C accelerates the decay of a neurofilament transgene (NF-L) driven by a tetracycline inducible system. In contrast, mutant transgenes lacking mRNA sequence for aldolase binding are stabilized. Our findings strongly suggest that aldolases A and C are regulatory components of a light neurofilament mRNA complex that modulates the stability of NF-L mRNA. This modulation likely involves endonucleolytic cleavage and a competing interaction with the PABP. Interactions of aldolases A and C in NF-L expression may be linked to regulatory pathways that maintain the highly asymmetrical form and function of large neurons.
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Affiliation(s)
- Rafaela Cañete-Soler
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19103, USA.
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