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Smith LB, Anderson CV, Withangage MHH, Koch A, Roberts TJ, Liebl AL. Relationship between gene expression networks and muscle contractile physiology differences in Anolis lizards. J Comp Physiol B 2022; 192:489-499. [PMID: 35596083 DOI: 10.1007/s00360-022-01441-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022]
Abstract
Muscles facilitate most animal behavior, from eating to fleeing. However, to generate the variation in behavior necessary for survival, different muscles must perform differently; for instance, sprinting requires multiple rapid muscle contractions, whereas biting may require fewer contractions but greater force. Here, we use a transcriptomic approach to identify genes associated with variation in muscle contractile physiology among different muscles from the same individual. We measured differential gene expression between a leg and jaw muscle of Anolis lizards known to differ in muscle contractile physiology and performance. For each individual, one muscle was used to measure muscle contractile physiology, including contractile velocity (Vmax and V40), specific tension, power ratio, and twitch time, whereas the contralateral muscle was used to extract RNA for transcriptomic sequencing. Using the transcriptomic data, we found clear clustering of muscle type. Expression of genes clustered in gene ontology (GO) terms related to muscle contraction and extracellular matrix was, on average, negatively correlated with Vmax and slower twitch times but positively correlated to power ratio and V40. Conversely, genes related to the GO terms related to aerobic respiration were downregulated in muscles with higher power ratio and V40, and over-expressed as twitch time decreased. Determining the molecular mechanisms that underlie variation in muscle contractile physiology can begin to explain how organisms are able to optimize behavior under variable conditions. Future studies pursuing the effects of differential gene expression across muscle types in different environments might inform researchers about how differences develop across species, populations, and individuals varying in ecological history.
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Affiliation(s)
- Luke B Smith
- Department of Biology, University of South Dakota, Vermillion, SD, USA.,Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | | | - Miyuraj H Hikkaduwa Withangage
- Department of Biology, University of South Dakota, Vermillion, SD, USA.,College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA, USA
| | - Andrew Koch
- Department of Biology, University of South Dakota, Vermillion, SD, USA
| | - Thomas J Roberts
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Andrea L Liebl
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
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2
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Abstract
Knowledge accumulated in the field of energetics of muscle contraction has been reviewed in this article. Active muscle converts chemical energy into heat and work. Therefore, measurements of heat production and mechanical work provide the framework for understanding the process of energy conversion in contraction. In the 1970s, precise comparison between energy output and the associated chemical reactions was performed. It has been found that the two do not match in several situations, resulting in an energy balance discrepancy. More recently, efforts in resolving these discrepancies in the energy balance have been made involving chemical analysis, phosphorus nuclear magnetic resonance spectroscopy, and microcalorimetry. Through reviewing the evidence from these studies, the energy balance discrepancy developed early during isometric contraction has become well understood on a quantitative basis. In this situation energy balance is established when we take into account the binding of Ca to sarcoplasmic proteins such as troponin and parvalbumin, and also the shift of cross-bridge states. On the other hand, the energy balance discrepancy observed during rapid shortening still remains to be clarified. The problem may be related to the essential mechanism of cross-bridge action.
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Affiliation(s)
- Kazuhiro Yamada
- Department of Neurophysiology, University of Oita Faculty of Medicine, Yufu, Oita, 879-5593, Japan.
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3
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Stary CM, Hogan MC. Cytosolic calcium transients are a determinant of contraction-induced HSP72 transcription in single skeletal muscle fibers. J Appl Physiol (1985) 2016; 120:1260-6. [PMID: 26869714 DOI: 10.1152/japplphysiol.01060.2015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/04/2016] [Indexed: 11/22/2022] Open
Abstract
The intrinsic activating factors that induce transcription of heat shock protein 72 (HSP72) in skeletal muscle following exercise remain unclear. We hypothesized that the cytosolic Ca(2+) transient that occurs with depolarization is a determinant. We utilized intact, single skeletal muscle fibers from Xenopus laevis to test the role of the cytosolic Ca(2+) transient and several other exercise-related factors (fatigue, hypoxia, AMP kinase, and cross-bridge cycling) on the activation of HSP72 transcription. HSP72 and HSP60 mRNA levels were assessed with real-time quantitative PCR; cytosolic Ca(2+) concentration ([Ca(2+)]cyt) was assessed with fura-2. Both fatiguing and nonfatiguing contractions resulted in a significant increase in HSP72 mRNA. As expected, peak [Ca(2+)]cyt remained tightly coupled with peak developed tension in contracting fibers. Pretreatment with N-benzyl-p-toluene sulfonamide (BTS) resulted in depressed peak developed tension with stimulation, while peak [Ca(2+)]cyt remained largely unchanged from control values. Despite excitation-contraction uncoupling, BTS-treated fibers displayed a significant increase in HSP72 mRNA. Treatment of fibers with hypoxia (Po2: <3 mmHg) or AMP kinase activation had no effect on HSP72 mRNA levels. These results suggest that the intermittent cytosolic Ca(2+) transient that occurs with skeletal muscle depolarization provides a sufficient activating stimulus for HSP72 transcription. Metabolic or mechanical factors associated with fatigue development and cross-bridge cycling likely play a more limited role.
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Affiliation(s)
- Creed M Stary
- Department of Medicine, University of California, San Diego, La Jolla, California; and Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Michael C Hogan
- Department of Medicine, University of California, San Diego, La Jolla, California; and
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4
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Bellgard M, Taplin R, Chapman B, Livk A, Wellington C, Hunter A, Lipscombe R. Classification of fish samples via an integrated proteomics and bioinformatics approach. Proteomics 2013; 13:3124-30. [DOI: 10.1002/pmic.201200426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Matthew Bellgard
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
| | - Ross Taplin
- Curtin Business School; Curtin University; Western Australia Australia
| | - Brett Chapman
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
| | - Andreja Livk
- Proteomics International Pty Ltd; Western Australia Australia
| | - Crispin Wellington
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
| | - Adam Hunter
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
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5
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Wong ESW, Papenfuss AT, Heger A, Hsu AL, Ponting CP, Miller RD, Fenelon JC, Renfree MB, Gibbs RA, Belov K. Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby. BMC Genomics 2011; 12:420. [PMID: 21854594 PMCID: PMC3173455 DOI: 10.1186/1471-2164-12-420] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 08/19/2011] [Indexed: 02/08/2023] Open
Abstract
Background The thymus plays a critical role in the development and maturation of T-cells. Humans have a single thoracic thymus and presence of a second thymus is considered an anomaly. However, many vertebrates have multiple thymuses. The tammar wallaby has two thymuses: a thoracic thymus (typically found in all mammals) and a dominant cervical thymus. Researchers have known about the presence of the two wallaby thymuses since the 1800s, but no genome-wide research has been carried out into possible functional differences between the two thymic tissues. Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby. Results We show that both the tammar thoracic and the cervical thymuses displayed gene expression profiles consistent with roles in T-cell development. Both thymuses expressed genes that mediate distinct phases of T-cells differentiation, including the initial commitment of blood stem cells to the T-lineage, the generation of T-cell receptor diversity and development of thymic epithelial cells. Crucial immune genes, such as chemokines were also present. Comparable patterns of expression of non-coding RNAs were seen. 67 genes differentially expressed between the two thymuses were detected, and the possible significance of these results are discussed. Conclusion This is the first study comparing the transcriptomes of two thymuses from a single individual. Our finding supports that both thymuses are functionally equivalent and drive T-cell development. These results are an important first step in the understanding of the genetic processes that govern marsupial immunity, and also allow us to begin to trace the evolution of the mammalian immune system.
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Affiliation(s)
- Emily S W Wong
- Faculty of Veterinary Sciences, University of Sydney, Sydney, NSW 2006, Australia
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Bozinovic G, Sit TL, Hinton DE, Oleksiak MF. Gene expression throughout a vertebrate's embryogenesis. BMC Genomics 2011; 12:132. [PMID: 21356103 PMCID: PMC3062618 DOI: 10.1186/1471-2164-12-132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 02/28/2011] [Indexed: 12/25/2022] Open
Abstract
Background Describing the patterns of gene expression during embryonic development has broadened our understanding of the processes and patterns that define morphogenesis. Yet gene expression patterns have not been described throughout vertebrate embryogenesis. This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage. Results Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. Five adjacent stages have disproportionately more significant changes in gene expression (> 200 genes) relative to other stages: four to eight and eight to sixteen cell stages, onset of circulation, pre and post-hatch, and during complete yolk absorption. The fewest differences among adjacent stages occur during gastrulation. Yet, at stage 16, (pre-mid-gastrulation) the largest number of genes has peak expression. This stage has an over representation of genes in oxidative respiration and protein expression (ribosomes, translational genes and proteases). Unexpectedly, among all ribosomal genes, both strong positive and negative correlations occur. Similar correlated patterns of expression occur among all significant genes. Conclusions These data provide statistical support for the temporal dynamics of developmental gene expression during all stages of vertebrate development.
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Affiliation(s)
- Goran Bozinovic
- Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, 27695-7633, USA
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Influence of aging and long-term swimming exercise on parvalbumin distribution in rat hearts. Acta Histochem 2010; 112:72-80. [PMID: 19004479 DOI: 10.1016/j.acthis.2008.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/03/2008] [Accepted: 09/04/2008] [Indexed: 11/22/2022]
Abstract
Parvalbumin (PV), which is a small (12kDa) cytoplasmic calcium-binding protein, has been implicated in mediating relaxation in cardiac myocytes. The influence of aging and exercise on the distribution of PV in rat heart was investigated. Male Wistar rats aged 3, 6, 12 and 18-months were divided into sedentary and exercise groups. The exercise group underwent exercise in the form of regular swimming for 6 months. The hearts were processed for immunohistochemistry and Western blotting. The intensity of PV immunoreactivity was strong in the 9 and 12-month hearts and decreased in the 18-month hearts. The smallest amount was detected in the 24-month rat hearts when compared to those of the 9, 12 and 18-month rat hearts. Significantly less PV was detected in the 18 and 24-month hearts compared to the 12-month rat hearts (P<0.05). The intensity of PV immunoreactivity was considerably stronger in hearts of the 9, 12 and 18-months exercised rats than in hearts of age-matched sedentary rats. However, in the hearts of 24-month rats, immunoreactivity was only slightly stronger in the exercised rats in comparison with those of sedentary rats. A significant increase of PV detection in hearts was found in the exercised rats in comparison with sedentary rats in the 9 (P<0.05) and 18-month samples (P<0.01). Our data indicate that PV is down-regulated in the rat heart during aging. In addition, our data indicate that long-term swimming exercise could induce an increase of PV expression.
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Brownridge P, de Mello LV, Peters M, McLean L, Claydon A, Cossins AR, Whitfield PD, Young IS. Regional variation in parvalbumin isoform expression correlates with muscle performance in common carp (Cyprinus carpio). ACTA ACUST UNITED AC 2009; 212:184-93. [PMID: 19112137 DOI: 10.1242/jeb.021857] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mechanical properties of the axial muscles vary along the length of a fish's body. This variation in performance correlates with the expression of certain muscle proteins. Parvalbumin (PARV) is an important calcium binding protein that helps modulate intracellular calcium levels which set the size and shape of the muscle calcium transient. It therefore has a central role in determining the functional properties of the muscle. Transcript data revealed eight specific isoforms of PARV in common carp (Cyprinus carpio) skeletal muscle which we classified as alpha1 and beta1-7. This study is the first to show expression of all eight skeletal muscle PARV isoforms in carp at the protein level and relate regional differences in expression to performance. All of the PARV isoforms were characterised at the protein level using 2D-PAGE and tandem mass spectrometry. Comparison of carp muscle from different regions of the fish revealed a higher level of expression of PARV isoforms beta4 and beta5 in the anterior region, which was accompanied by an increase in the rate of relaxation. We postulate that changes in specific PARV isoform expression are an important part of the adaptive change in muscle mechanical properties in response to varying functional demands and environmental change.
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Affiliation(s)
- Philip Brownridge
- Faculty of Veterinary Science, University of Liverpool, Liverpool, UK
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9
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Stary CM, Walsh BJ, Knapp AE, Brafman D, Hogan MC. Elevation in heat shock protein 72 mRNA following contractions in isolated single skeletal muscle fibers. Am J Physiol Regul Integr Comp Physiol 2008; 295:R642-8. [PMID: 18525012 PMCID: PMC2519928 DOI: 10.1152/ajpregu.00852.2007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 06/02/2008] [Indexed: 11/22/2022]
Abstract
The purpose of the present study was 1) to develop a stable model for measuring contraction-induced elevations in mRNA in single skeletal muscle fibers and 2) to utilize this model to investigate the response of heat shock protein 72 (HSP72) mRNA following an acute bout of fatiguing contractions. Living, intact skeletal muscle fibers were microdissected from lumbrical muscle of Xenopus laevis and either electrically stimulated for 15 min of tetanic contractions (EX; n=26) or not stimulated to contract (REST; n=14). The relative mean developed tension of EX fibers decreased to 29+/-7% of initial peak tension at the stimulation end point. Following treatment, individual fibers were allowed to recover for 1 (n=9), 2 (n=8), or 4 h (n=9) prior to isolation of total cellular mRNA. HSP72, HSP60, and cardiac alpha-actin mRNA content were then assessed in individual fibers using quantitative PCR detection. Relative HSP72 mRNA content was significantly (P<0.05) elevated at the 2-h postcontraction time point relative to REST fibers when normalized to either HSP60 (18.5+/-7.5-fold) or cardiac alpha-actin (14.7+/-4.3-fold), although not at the 1- or 4-h time points. These data indicate that 1) extraction of RNA followed by relative quantification of mRNA of select genes in isolated single skeletal muscle fibers can be reliably performed, 2) HSP60 and cardiac alpha-actin are suitable endogenous normalizing genes in skeletal muscle following contractions, and 3) a significantly elevated content of HSP72 mRNA is detectable in skeletal muscle 2 h after a single bout of fatiguing contractions, despite minimal temperature changes and without influence from extracellular sources.
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Affiliation(s)
- Creed M Stary
- Division of Physiology, Department of Medicine, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0623, USA
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10
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Schiavone R, Zilli L, Storelli C, Vilella S. Identification by proteome analysis of muscle proteins in sea bream (Sparus aurata). Eur Food Res Technol 2008. [DOI: 10.1007/s00217-008-0859-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Chen L, Hefle SL, Taylor SL, Swoboda I, Goodman RE. Detecting fish parvalbumin with commercial mouse monoclonal anti-frog parvalbumin IgG. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:5577-82. [PMID: 16848548 DOI: 10.1021/jf060291g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Parvalbumin is a calcium-binding muscle protein that is highly conserved across fish species and amphibians. It is the major cross-reactive allergen associated with both fish and frog allergy. We used two-dimensional electrophoretic and immunoblotting techniques to investigate the utility of a commercial monoclonal anti-frog parvalbumin IgG for detecting parvalbumin present in some commonly consumed fish species. The 2D electrophoresis and immunoblots revealed species-specific differences in proteins that appear to represent various numbers of isoforms of parvalbumin in carp (5), catfish (3), cod (1) and tilapia (2). No parvalbumin was detected in yellowfin tuna. Based on minor differences in relative intensities of protein staining and immunodetection, parvalbumin isoforms may have slight differences in the epitope region recognized by the anti-frog parvalbumin antibody. These results suggest that the frog anti-parvalbumin antibody can be used as a valuable tool to detect parvalbumins from the fish tested in this study, except yellowfin tuna.
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Affiliation(s)
- Lingyun Chen
- Food Allergy Research and Resource Program, University of Nebraska, Lincoln, Nebraska 68583-0919, USA, and Department of Pathophysiology, General Hospital, Medical University of Vienna, Wahringer Gurtel 18-20, Vienna A-1090, Austria
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12
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Huq F, Lebeche D, Iyer V, Liao R, Hajjar RJ. Gene Transfer of Parvalbumin Improves Diastolic Dysfunction in Senescent Myocytes. Circulation 2004; 109:2780-5. [PMID: 15173024 DOI: 10.1161/01.cir.0000131764.62242.96] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Impaired relaxation is a cardinal feature of senescent myocardial dysfunction. Recently, adenoviral gene transfer of parvalbumin, a small calcium-buffering protein found exclusively in skeletal muscle and neurons, has been shown to improve cardiomyocyte relaxation in disease models of diastolic dysfunction. The goal of this study was to investigate whether parvalbumin gene transfer could reverse diastolic dysfunction in senescent cardiomyocytes. METHODS AND RESULTS Myocytes were isolated from senescent (26 months) and adult (6 months) F344/BN hybrid rats and were infected with Ad.Parv.GFP (where GFP is green fluorescent protein) or Ad.betagal.GFP at a multiplicity of infection of 250 for 48 hours. Uninfected senescent and adult myocytes served as controls. After stimulation at a frequency of 0.5 Hz, intracellular calcium transients and myocyte contractility were measured using dual excitation spectrofluorometry and video-edge detection system (Ionoptix). Parvalbumin significantly improved relaxation parameters in senescent myocytes: Both the rate of calcium transient decay and the rate of myocyte relengthening were dramatically increased in senescent cardiac myocytes transduced with parvalbumin compared with nontransduced and GFP-expressing controls, with no effect on myocyte shortening. CONCLUSIONS Parvalbumin expression corrects impaired relaxation in aging myocytes. Given that abnormalities of myocyte relaxation underlie diastolic dysfunction in a large proportion of elderly patients with heart failure, gene transfer of parvalbumin may thus be a novel approach to target diastolic dysfunction in senescent myocardium.
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Affiliation(s)
- Fawzia Huq
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Mass 02129, USA
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Lännergren J, Westerblad H, Bruton JD. Changes in mitochondrial Ca2+ detected with Rhod-2 in single frog and mouse skeletal muscle fibres during and after repeated tetanic contractions. J Muscle Res Cell Motil 2002; 22:265-75. [PMID: 11763199 DOI: 10.1023/a:1012227009544] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The present study investigated mitochondrial Ca2+ uptake and release in intact living skeletal muscle fibres subjected to bouts of repetitive activity. Confocal microscopy was used in conjunction with the Ca2+-sensitive dye Rhod-2 to monitor changes in mitochondrial Ca2+ in single Xenopus or mouse muscle fibres. A marked increase in the mitochondrial Ca2+ occurred in Xenopus fibres after 10 tetani applied at 4 s intervals. The mitochondrial Ca2+ continued to increase with increasing number of tetani. After the end of tetanic stimulation, mitochondrial Ca2+ declined to 50% of the maximal increase within 10 min and thereafter took up to 60 min to return to its original value. Depolarization of the mitochondria with FCCP greatly attenuated the rise in the mitochondrial Ca2+ evoked by repetitive tetanic stimulation. In addition, FCCP slowed the rate of decay of the tetanic Ca2+ transient which in turn led to an elevation of resting cytosolic Ca2+. Accumulation of Ca2+ in the mitochondria was accompanied by a modest mitochondrial depolarization. In contrast to the situation in Xenopus fibres, mitochondria in mouse toe muscle fibres did not show any change in the mitochondrial Ca2+ during repetitive stimulation and FCCP had no effect on the rate of decay of the tetanic Ca2+ transient. It is concluded that in Xenopus fibres, mitochondria play a role in the regulation of cytosolic Ca2+ and contribute to the relaxation of tetanic Ca2+ transients. In contrast to their important role in Xenopus fibres, mitochondria in mouse fast-twitch skeletal fibres play little role in Ca2+ homeostasis.
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Affiliation(s)
- J Lännergren
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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Truong K, Ikura M. Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach. BMC Bioinformatics 2002; 3:1. [PMID: 11818024 PMCID: PMC65048 DOI: 10.1186/1471-2105-3-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2001] [Accepted: 01/10/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include the development of classification systems capable of distinguishing between subfamilies within a structurally and functionally diverse superfamily. This would be helpful in elucidating sequence-structure-function relationships of proteins. RESULTS Here, we present a method to diagnose sequences into subfamilies by employing hidden Markov models (HMMs) to find windows of residues that are distinct among subfamilies (called signatures). The method starts with a multiple sequence alignment (MSA) of the subfamily. Then, we build a HMM database representing all sliding windows of the MSA of a fixed size. Finally, we construct a HMM histogram of the matches of each sliding window in the entire superfamily. To illustrate the efficacy of the method, we have applied the analysis to find subfamily signatures in two well-studied superfamilies: the cadherin and the EF-hand protein superfamilies. As a corollary, the HMM histograms of the analyzed subfamilies revealed information about their Ca2+ binding sites and loops. CONCLUSIONS The method is used to create HMM databases to diagnose subfamilies of protein superfamilies that complement broad profile and motif databases such as BLOCKS, PROSITE, Pfam, SMART, PRINTS and InterPro.
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Affiliation(s)
- Kevin Truong
- Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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15
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Wahr PA, Michele DE, Metzger JM. Parvalbumin gene transfer corrects diastolic dysfunction in diseased cardiac myocytes. Proc Natl Acad Sci U S A 1999; 96:11982-5. [PMID: 10518562 PMCID: PMC18398 DOI: 10.1073/pnas.96.21.11982] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heart failure frequently involves diastolic dysfunction that is characterized by a prolonged relaxation. This prolonged relaxation is typically the result of a decreased rate of intracellular Ca(2+) sequestration. No effective treatment for this decreased Ca(2+) sequestration rate currently exists. As an approach to possibly correct diastolic dysfunction, we hypothesized that expression of the Ca(2+) binding protein parvalbumin in cardiac myocytes would lead to increased rates of Ca(2+) sequestration and mechanical relaxation. Parvalbumin, which is normally absent in cardiac tissue, is known to act as a soluble relaxing factor in fast skeletal muscle fibers by acting as a delayed Ca(2+) sink. As a test of the hypothesis, gene transfer was used to express parvalbumin in isolated adult cardiac myocytes. We report here that expression of parvalbumin dramatically increases the rate of Ca(2+) sequestration and the relaxation rate in normal cardiac myocytes. Importantly, parvalbumin fully restored the relaxation rate in diseased cardiac myocytes isolated from an animal model of human diastolic dysfunction. These findings indicate that parvalbumin gene transfer offers unique potential as a possible direct treatment for diastolic dysfunction in failing hearts.
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Affiliation(s)
- P A Wahr
- Department of Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Savolainen J, Vornanen M. Parvalbumin content in striated muscles of the common shrew (Sorex araneus). CAN J ZOOL 1998. [DOI: 10.1139/z98-160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The parvalbumin content of mammalian muscles correlates positively with isometric relaxation rate and fiber type IIB frequency of the muscles but negatively with animal size. Since shrews are small-bodied animals with a relatively low number of type IIB fibers, it is of some interest to know how the parvalbumin content of shrew muscle correlates with the above factors. Parvalbumin content in heart, diaphragm, and gastrocnemius muscle of the common shrew, mouse, and rat was determined electrophoretically. Parvalbumin was not found in heart muscle of any species. Shrew diaphragm (0.29 ± 0.04 g/kg) had significantly less parvalbumin than mouse (0.63 ± 0.11 g/kg) or rat (0.54 ± 0.09 g/kg) diaphragm. Similarly, the parvalbumin content of shrew gastrocnemius muscle (0.28 ± 0.04 g/kg) was significantly lower than in that of mouse (2.88 ± 0.38 g/kg) or rat (0.96 ± 0.25 g/kg) gastrocnemius muscle. The isometric twitch of the gastrocnemius muscle was somewhat faster than the twitch of the diaphragm in all three species. The isometric contractions of shrew and mouse skeletal muscles were generally very similar in duration, with the exception of the relaxation time of the gastrocnemius muscle, which was shorter in the mouse. Diaphragm and gastrocnemius muscle of the rat were clearly slower than the respective muscles in the mouse or shrew with regard to both the contraction and relaxation phases. The half-relaxation time of isometric contractions correlated relatively weakly with parvalbumin content of the muscles (r = 0.40) but more strongly with their fiber IIB content (r = 0.81). The unexpectedly low parvalbumin content and relatively slow rate of contraction in shrew skeletal muscles are attributed to the exceptional fiber type composition, i.e., a high proportion of type IID fibers.
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17
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From Single Fibers to Whole Muscle. J Appl Biomech 1997. [DOI: 10.1123/jab.13.4.471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Westerblad H, Lännergren J, Allen DG. Slowed relaxation in fatigued skeletal muscle fibers of Xenopus and Mouse. Contribution of [Ca2+]i and cross-bridges. J Gen Physiol 1997; 109:385-99. [PMID: 9089444 PMCID: PMC2217069 DOI: 10.1085/jgp.109.3.385] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/1996] [Accepted: 01/06/1997] [Indexed: 02/04/2023] Open
Abstract
Slowing of relaxation is an important characteristic of skeletal muscle fatigue. The aim of the present study was to quantify the relative contribution of altered Ca2+ handling (calcium component) and factors downstream to Ca2+ (cross-bridge component) to the slowing of relaxation in fatigued fibers of Xenopus and mouse. Two types of Xenopus fibers were used: easily fatigued, type 1 fibers and fatigue resistant, type 2 fibers. In these Xenopus fibers the free myoplasmic [Ca2+] ([Ca2+]i) was measured with indo-1, and the relaxation of Ca2(+)-derived force, constructed from tetanic [Ca2+]i records and in vivo [Ca2+]i-force curves, was analyzed. An alternative method was used in both Xenopus and mouse fibers: fibers were rapidly shortened during the initial phase of relaxation, and the time to the peak of force redevelopment was measured. These two methods gave similar results and showed proportional slowing of the calcium and cross-bridge components of relaxation in both fatigued type 1 and type 2 Xenopus fibers, whereas only the cross-bridge component was slowed in fatigued mouse fibers. Ca2+ removal from the myoplasm during relaxation was markedly less effective in Xenopus fibers as compared to mouse fibers. Fatigued Xenopus fibers displayed a reduced rate of sarcoplasmic reticulum Ca2+ uptake and increased sarcoplasmic reticulum Ca2+ leak. Some fibers were stretched at various times during relaxation. The resistance to these stretches was increased during fatigue, especially in Xenopus fibers, which indicates that longitudinal movements during relaxation had become less pronounced and this might contribute to the increased cross-bridge component of relaxation in fatigue. In conclusion, slowing of relaxation in fatigued Xenopus fibers is caused by impaired Ca2+ handling and altered cross-bridge kinetics, whereas the slowing in mouse fibers is only due to altered cross-bridge kinetics.
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Affiliation(s)
- H Westerblad
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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Buschman HP, van der Laarse WJ, Stienen GJ, Elzinga G. Force-dependent and force-independent heat production in single slow- and fast-twitch muscle fibres from Xenopus laevis. J Physiol 1996; 496 ( Pt 2):503-19. [PMID: 8910233 PMCID: PMC1160894 DOI: 10.1113/jphysiol.1996.sp021702] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
1. The origin of labile heat production, i.e. a heat component which rapidly decays after the onset of stimulation, and of stable (maintenance) heat production was investigated in intact single fast-twitch (type 1) and slow-twitch (type 3) iliofibularis muscle fibres from Xenopus laevis, at 20 degrees C, by varying stimulation frequency and by varying sarcomere length and the concentration of 2,3-butanedione 2-monoxime (BDM) added. 2. The labile heat produced consisted of a force-independent and a force-dependent part. The average parvalbumin (PA) content found in type 1 fibre bundles (0.84 +/- 0.08 mM; mean +/- S.E.M.; n = 5) and in type 3 fibre bundles (0.12 +/- 0.02 mM; n = 5) indicates that the force-independent labile heat is explained by Ca(2+)-Mg2+ exchange on PA, and amounts to a molar enthalpy change of -78 kJ (molPA)-1. 3. Force-dependent labile heat during fused contractions was similar to the calculated heat production resulting from the formation of force-generating cross-bridges, assuming an enthalpy change associated with cross-bridge formation of -30 kJ mol-1. 4. Activation heat, i.e. the part of the total stable heat that is not related to the contractile apparatus, and of which the calcium sequestration by the sarcoplasmic reticulum is the most important contributor, determined by varying sarcomere length or BDM concentration, was identical. For fused contractions the fraction activation heat of the stable maintenance rate of heat production was 34 +/- 4% (mean +/- S.E.M.; n = 13) in type 1 fibres, and 52 +/- 4% (n = 15) in type 3 fibres. In unfused contractions this was 48 +/- 5% (n = 13) in type 1 fibres, and 35 +/- 2% (n = 11) in type 3 fibres. 5. From the force-dependent stable rate of heat production the economy of cross-bridge cycling, expressed as the force-time integral for a single myosin head per ATP molecule hydrolysed, was calculated. It followed that cross-bridge interaction in type 3 fibres is more economical than in type 1 fibres, and that fused contractions are more economical than unfused contractions.
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Affiliation(s)
- H P Buschman
- Laboratory for Physiology, Vrije Universiteit, Amsterdam, The Netherlands.
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Dreessen J, Lutum C, Schäfer BW, Heizmann CW, Knöpfel T. Alpha-parvalbumin reduces depolarization-induced elevations of cytosolic free calcium in human neuroblastoma cells. Cell Calcium 1996; 19:527-33. [PMID: 8842520 DOI: 10.1016/s0143-4160(96)90062-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We investigated whether the expression of human alpha-parvalbumin affects depolarization-induced elevations of the cytosolic free calcium concentration ([Ca2+]i) in human neuroblastoma SKNBE2 cells. A full length human parvalbumin cDNA was cloned by PCR from human cerebellum and transiently transfected into SKNBE2 cells. Immunofluorescence staining using an antibody raised against parvalbumin revealed a transfection efficacy of about 14%. In parvalbumin-expressing SKNBE2 cells, parvalbumin concentration determined by quantitative Western blotting amounted to 0.42 mM. Transfected SKNBE2 cells were depolarized for 2 min by 50 mM K+. During this period, [Ca2+]i was monitored by video microfluorimetry using the Ca2+ indicator Fura-2. In a fraction of cells, depolarization induced a transient elevation in [Ca2+]i. The size of this elevation was compared with the immunofluorimetrically determined expression of parvalbumin on a cell-to-cell basis. Cells with a significant parvalbumin immunofluorescence responded to depolarization with smaller elevations in [Ca2+]i than non-parvalbumin-expressing cells. Resting [Ca2+]i did not differ between parvalbumin-expressing and control cells. These observations indicate that large depolarization-induced transient elevations of [Ca2+]i in neuroblastoma cells can be suppressed by parvalbumin.
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Affiliation(s)
- J Dreessen
- Department of Molecular and Cellular Neurobiology, CNS Research, Ciba, Basel, Switzerland
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Westerblad H, Allen DG. Slowing of relaxation and [Ca2+]i during prolonged tetanic stimulation of single fibres from Xenopus skeletal muscle. J Physiol 1996; 492 ( Pt 3):723-36. [PMID: 8734985 PMCID: PMC1158895 DOI: 10.1113/jphysiol.1996.sp021341] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
1. Parvalbumin (PA) has been proposed to take up Ca2+ and enhance skeletal muscle relaxation in brief contractions; as the duration of the contraction is increased, PA will become saturated with Ca2+ and no longer contribute to relaxation which therefore will be slowed. The rate of Ca2+ loading of PA is determined by the Mg2+ off rate (about 4 s-1 at 22 degrees C). In the present study we produced prolonged tetani in intact, single fibres of Xenopus frogs while measuring force and the free myoplasmic [Ca2+] ([Ca2+]i) with indo-1. 2. Mean rate constants of slowing of force relaxation with increasing tetanus duration ranged between 3.2 and 4.8 s-1, thus, similar to the Mg2+ off rate of PA. 3. The amplitude of the tail of [Ca2+]i after tetani increased with tetanus duration. This increase developed with a rate constant similar to the Mg2+ off rate of PA 4. Steady-state force-[Ca2+]i curves were produced from tetani of various frequencies and tetani produced when force was depressed after fatiguing stimulation. These curves were used to convert [Ca2+]i records into Ca(2+)-derived force. Relaxation of Ca(2+)-derived force was slowed following a time course similar to that of real force. The lag between Ca(2+)-derived and real force during relaxation was not affected by tetanus duration. 5. Tails of elevated [Ca2+]i after tetani were used to analyse the function of the SR Ca2+ pumps. This analysis showed a marked decline in the rate of Ca2+ uptake with prolonged tetani. 6. In conclusion, in Xenopus fibres the slowing of relaxation with increasing tetanus duration can be explained by altered Ca2+ handling due to PA Ca2+ loading and impaired SR Ca2+ uptake. This contrasts to our previous results in mouse fibres and the difference can be explained by a markedly lower rate of SR Ca2+ uptake resulting in higher tetanic [Ca2+]i in Xenopus fibres.
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Affiliation(s)
- H Westerblad
- Department of Physiology, University of Sydney, NSW, Australia
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Pauls TL, Cox JA, Berchtold MW. The Ca2+(-)binding proteins parvalbumin and oncomodulin and their genes: new structural and functional findings. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1306:39-54. [PMID: 8611623 DOI: 10.1016/0167-4781(95)00221-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- T L Pauls
- Institute of Histology and General Embryology, University of Fribourg, Switzerland
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Müntener M, Käser L, Weber J, Berchtold MW. Increase of skeletal muscle relaxation speed by direct injection of parvalbumin cDNA. Proc Natl Acad Sci U S A 1995; 92:6504-8. [PMID: 7604022 PMCID: PMC41546 DOI: 10.1073/pnas.92.14.6504] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Parvalbumin (PV) is a high affinity Ca(2+)-binding protein found at high concentration in fast-contracting/relaxing skeletal muscle fibers of vertebrates. It has been proposed that PV acts in the process of muscle relaxation by facilitating Ca2+ transport from the myofibrils to the sarcoplasmic reticulum. However, on the basis of metal-binding kinetics of PV in vitro, this hypothesis has been challenged. To investigate the function of PV in skeletal muscle fibers, direct gene transfer was applied in normal and regenerating rat soleus muscles which do not synthesize detectable amounts of PV. Two weeks after in vivo transfection with PV cDNA, considerable levels of PV mRNA and protein were detected in normal muscle, and even higher amounts were detected in regenerating muscle. Twitch half-relaxation time was significantly shortened in a dose-dependent way in transfected muscles, while contraction time remained unaltered. The observed shortening of half-relaxation time is due to PV and its ability to bind Ca2+, because a mutant protein lacking Ca(2+)-binding capacity did not promote any change in physiology. These results directly demonstrate the physiological function of PV as a relaxing factor in mammalian skeletal muscle.
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Affiliation(s)
- M Müntener
- Institute of Anatomy, University of Zürich-Irchel, Switzerland
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Stienen GJ, Zaremba R, Elzinga G. ATP utilization for calcium uptake and force production in skinned muscle fibres of Xenopus laevis. J Physiol 1995; 482 ( Pt 1):109-22. [PMID: 7730976 PMCID: PMC1157757 DOI: 10.1113/jphysiol.1995.sp020503] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
1. A method has been developed to discriminate between the rate of ATP hydrolysis associated with calcium uptake into the sarcoplasmic reticulum (SR) and force development of the contractile apparatus in mechanically or saponin-skinned skeletal muscle fibres. The rate of ATP hydrolysis was determined in fibres of different types from the iliofibularis muscle of Xenopus laevis by enzymatic coupling of ATP re-synthesis to the oxidation of NADH. 2. The ATPase activity was determined before and after exposure of the preparations for 30 min to a solution containing 0.5% Triton X-100, which effectively abolishes the SR ATPase activity. The fibres were activated in a solution containing 5 mM caffeine to ensure that calcium uptake into the SR was maximal. 3. At saturating Ca2+ concentrations the actomyosin (AM) and SR ATPase activities in fast-twitch fibres, at 4.3 degrees C, amounted to 1.52 +/- 0.07 and 0.58 +/- 0.10 mumol s-1 (g dry wt)-1, respectively (means +/- S.E.M.; n = 25). The SR ATPase activity was 25% of the total ATPase activity. At submaximal calcium concentrations the AM ATPase activity varied in proportion to the isometric force. 4. The calcium sensitivity of the SR ATPase was larger than that of the AM ATPase and its dependence on [Ca2+] was less steep. The AM ATPase activity was half-maximal at a pCa of 6.11 (pCa = -log [Ca2+]) whereas the SR ATPase activity was half-maximal at a pCa of 6.62. 5. In Triton X-100-treated fibres, at different 2,3-butanedione monoxime (BDM) concentrations, the AM ATPase activity and isometric force varied proportionally. The SR ATPase activity determined by extrapolation of the total ATPase activity in mechanically skinned or saponin-treated fibres to zero force, was independent of the BDM concentration in the range studied (0-20 mM). The values obtained for the SR ATPase activity in this way were similar to those obtained with Triton X-100 treatment. 6. The AM ATPase activity in slow-twitch fibres amounted to 0.74 +/- 0.13 mumol s-1 (g dry wt)-1, i.e. about a factor of two smaller than in fast-twitch fibres. The SR ATPase activity amounted to 0.47 +/- 0.07 mumol s-1 (g dry wt)-1, i.e. rather similar to the value in fast-twitch fibres. The proportion of the total ATPase activity that was due to SR ATPase (40%) was larger than in fast-twitch fibres. 7. The temperature dependence of the AM and SR ATPase activities in fast-twitch fibres differed. In the temperature range 5-10 degrees C, the relative changes in AM and SR ATPase activities for a 10 degrees C temperature change (Q10) were 3.9 +/- 0.3 and 7.2 +/- 1.5, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- G J Stienen
- Department of Physiology, Free University, Amsterdam, The Netherlands
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Westerblad H, Allen DG. Relaxation, [Ca2+]i and [Mg2+]i during prolonged tetanic stimulation of intact, single fibres from mouse skeletal muscle. J Physiol 1994; 480 ( Pt 1):31-43. [PMID: 7853224 PMCID: PMC1155775 DOI: 10.1113/jphysiol.1994.sp020338] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
1. In skeletal muscle there is generally a slowing of relaxation with increasing tetanus duration and it has been suggested that this is due to Ca2+ loading of parvalbumin (PA). To study this we have produced prolonged tetani in intact, single fibres from a mouse foot muscle which contain a high concentration of PA. We measured the rate of tension relaxation and also various aspects of Ca2+ handling. 2. During 'interrupted' tetani (15 repeated cycles of 100 ms with stimulation and 50 ms without) we observed a marked slowing of the relaxation both under control conditions and in acidosis (obtained by increasing the bath CO2 content). This slowing was not accompanied by any reduction of the initial rate of decline of the free myoplasmic Ca2+ concentration ([Ca2+]i), which was measured with indo-1. 3. The functioning of the sarcoplasmic reticulum (SR) pump after tetani of various durations was analysed by plotting d[Ca2+]i/dt vs. [Ca2+]i during the final slow decline of [Ca2+]i after tetani. This analysis showed that the rate of SR Ca2+ pumping after a 1 s tetanus is less than half of that after a 100 ms tetanus. 4. The amplitude of the tail of [Ca2+]i 250 ms into relaxation was measured after tetani of various durations. This amplitude increased with tetanus duration and could be fitted to the sum of one exponential and one linear function. The exponential component increased with a time constant of 0.17 s and probably reflects Ca2+ loading of PA. 5. Ca2+ binding to PA will displace Mg2+ and hence the free myoplasmic concentration of Mg2+ ([Mg2+]i) will increase. To study this we used the fluorescent Mg2+ indicator furaptra. The results showed an increase of [Mg2+]i during prolonged tetani which, after removing the Ca2+ component of the fluorescent signal, amounted to about 0.5 mM. 6. A model of Ca2+ movements and tension production in skeletal muscle was used. The model showed that the increase of the amplitude of [Ca2+]i tails after tetani of various durations can be explained by the combined effect of Ca2+ loading of PA and slowed SR Ca2+ pumping. In contrast to the experimental data, the model predicted a slight reduction of the initial rate of [Ca2+]i decline with increased tetanus duration. 7. In conclusion, we observed a marked slowing of relaxation during prolonged tetanic stimulation. Altered Ca2+ handling, including Ca2+ loading of PA, seems not to be important for this slowing. Thus, the slowing appears to be due to altered cross-bridge kinetics.
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Affiliation(s)
- H Westerblad
- Department of Physiology F13, University of Sydney, NSW, Australia
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