Gnaiger 2019 MitoFit Preprints: Difference between revisions

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{{Publication
|title=Gnaiger E, Aasander Frostner E, Abdul Karim N, Abdel-Rahman EA, Abumrad NA, Acuna-Castroviejo D, Adiele RC, ''et al'' (2019) Mitochondrial respiratory states and rates. https://doi.org/10.26124/mitofit:190001.v6. — '''''Published''': 2020-05-20 Mitochondrial physiology. Bioenerg Commun 2020.1. https://doi.org/10.26124/bec:2020-0001.v1''
|info=MitoFit Preprint Arch 2019.1.v6 [[File:MitoFit Preprint Arch pdf.png|left|160px|link=https://www.mitofit.org/images/4/46/Gnaiger_2019_MitoFit_Preprint_Arch_doi_10.26124_mitofit_190001.pdf |MitoFit pdf]] '''[https://www.mitofit.org/images/4/46/Gnaiger_2019_MitoFit_Preprint_Arch_doi_10.26124_mitofit_190001.pdf Mitochondrial respiratory states and rates]'''
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{{MITOEAGLE}}
|authors=MitoFit Prep 2019.1.v6.
|year=2019
|journal=MitoFit Prep
|abstract=Version 6 ('''v6''') '''2019-08-30''' [https://www.mitofit.org/images/4/46/Gnaiger_2019_MitoFit_Preprint_Arch_doi_10.26124_mitofit_190001.pdf doi:10.26124/mitofit:190001.v6]
::: <small>Versions ('''v5''') 2019-07-24; ('''v4''') 2019-05-20; ('''v3''') 2019-04-24; ('''v2''') 2019-03-15; ('''v1''') 2019-02-12 - [https://www.mitofit.org/index.php/File:Gnaiger_2019_MitoFit_Preprint_Arch_doi_10.26124_mitofit_190001.pdf#Links_to_all_versions »Link to all versions«]</small>
::: <big>'''Published online''': 2020-05-20
:::» Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1.  '''»[[BEC_2020.1 doi10.26124bec2020-0001.v1 |Bioblast link]]«'''</big>


{{Publication
As the knowledge base and importance of mitochondrial physiology to human health expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow guidelines of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols to the nomenclature of classical bioenergetics. We endeavour to provide a balanced view on mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of databases of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery.
|title=MitoEAGLE preprint 2018-03-16(34) Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology
Part 1. - http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08.
|info=<big>'''Last update 2018-03-16''':</big> [[File:PDF.jpg|120px|link=http://www.mitoeagle.org/images/4/49/MitoEAGLE_preprint_2018-02-08.pdf |Bioblast pdf]] - » [http://www.mitoeagle.org/index.php/File:MitoEAGLE_preprint_2018-02-08.pdf Versions]
|authors='''''Corresponding author:''''', Gnaiger E, '''''Co-authors:''''', Aasander Frostner E, Acuna-Castroviejo D, Ahn B, Alves MG, Amati F, Aral C, Arandarcikaite O, Bailey DM, Bakker BM, Bastos Sant'Anna Silva AC, Battino M, Beard DA, Ben-Shachar D, Bernardi P, Bishop D, Boetker HE, Boros M, Borsheim E, Borutaite V, Bouillaud F, Bouitbir J, Breton S, Brown GC, Brown RA, Buettner GR, Burtscher J, Calabria E, Calbet JA, Calzia E, Cardoso LHD, Carvalho E, Casado Pinna M, Cavalcanti-de-Albuquerque JP, Cervinkova Z, Chang SC, Chaurasia B, Chen Q, Chicco AJ, Chinopoulos C, Clementi E, Coen PM, Coker RH, Collin A, Crisostomo L, Das AM, Davis MS, De Palma C, Dias TR, Distefano G, Doerrier C, Drahota Z, Dubouchaud H, Duchen MR, Durham WJ, Dyrstad SE, Ehinger J, Elmer E, Endlicher R, Engin AB, Fell DA, Ferko M, Ferreira JCB, Ferreira R, Fessel JP, Filipovska A, Fisar Z, Fischer M, Fisher JJ, Fornaro M, Galkin A, Gan Z, Garcia-Roves PM, Garcia-Souza LF, Garlid KD, Garten A, Gastaldelli A, Genova ML, Giovarelli M, Gonzalez-Armenta JL, Gonzalo H, Goodpaster BH, Gorr TA, Gourlay CW, Granata C, Grefte S, Haas CB, Haavik J, Haendeler J, Han J, Hand SC, Harrison DK, Hellgren KT, Hepple RT, Hernansanz-Agustin P, Hickey AJ, Hoel F, Holland OJ, Hoppel CL, Houstek J, Hunger M, Iglesias-Gonzalez J, Irving BA, Iyer S, Jackson CB, Jadiya P, Jang DH, Jang YC, Jansen-Duerr P, Jespersen NR, Jha RK, Jurk D, Kaambre T, Kainulainen H, Kane DA, Kappler L, Karabatsiakis A, Keijer J, Keppner G, Khamoui AV, Klingenspor M, Komlodi T, Koopman WJH, Kopitar-Jerala N, Kowaltowski AJ, Krajcova A, Krako Jakovljevic N, Kuang J, Kucera O, Kwak HB, Kwast K, Labieniec-Watala M, Lai N, Lane N, Laner V, Larsen TS, Lee HK, Lemieux H, Leeuwenburgh C, Lerfall J, Li PA, Liu J, Lucchinetti E, Macedo MP, MacMillan-Crow LA, Makrecka-Kuka M, Malik AN, Markova M, Mazat JP, Menze MA, Meszaros AT, Methner A, Michalak S, Moisoi N, Molina AJA, Montaigne D, Moore AL, Mracek T, Muntane J, Muntean DM, Murray AJ, Nemec M, Neufer PD, Neuzil J, Newsom S, Nozickova K, O'Gorman D, Oliveira MF, Oliveira MT, Oliveira PF, Oliveira PJ, Orynbayeva Z, Pak YK, Pallotta ML, Palmeira CM, Parajuli N, Passos JF, Patel HH, Pecina P, Pelnena D, Pereira da Silva Grilo da Silva F, Pesta D, Petit PX, Pettersen IKN, Pichaud N, Piel S, Pino MF, Pirkmajer S, Porter C, Porter RK, Pranger F, Prochownik EV, Pulinilkunnil T, Puurand M, Radenkovic F, Radi R, Ramzan R, Rattan S, Reboredo P, Renner-Sattler K, Robinson MM, Roesland GV, Rohlena J, Rolo AP, Ropelle ER, Rossiter HB, Rybacka-Mossakowska J, Saada A, Safaei Z, Salin K, Salvadego D, Sandi C, Sazanov LA, Scatena R, Schartner M, Scheibye-Knudsen M, Schilling JM, Schlattner U, Schoenfeld P, Schwarzer C, Scott GR, Shabalina IG, Sharma P, Sharma V, Shevchuk I, Siewiera K, Silber AM, Silva AM, Singer D, Skolik R, Smenes BT, Soares FAA, Sobotka O, Sokolova I, Sonkar VK, Sparks LM, Spinazzi M, Stankova P, Stary C, Stier A, Stocker R, Sumbalova Z, Suravajhala P, Swerdlow RH, Swiniuch D, Szabo I, Tanaka M, Tandler B, Tavernarakis N, Tepp K, Thyfault JP, Tomar D, Towheed A, Tretter L, Trifunovic A, Trivigno C, Tronstad KJ, Trougakos IP, Tyrrell DJ, Urban T, Valentine JM, Velika B, Vendelin M, Vercesi AE, Victor VM, Vieyra A,Villena JA, Vitorino RMP, Vogt S, Volani C, Votion DM, Vujacic-Mirski K, Wagner BA, Ward ML, Wasserman DH, Watala C, Wei YH, Wieckowski MR, Williams C, Wohlwend M, Wolff J, Wuest RCI, Zaugg K, Zaugg M, Zischka H, Zorzano A
|year=2018
|journal=MitoEAGLE preprint
|abstract=As the knowledge base and importance of mitochondrial physiology to human health expands, the necessity for harmonizing nomenclature concerning mitochondrial respiratory states and rates has become increasingly apparent. Clarity of concept and consistency of nomenclature are key trademarks of a research field. These features facilitate effective transdisciplinary communication, education, and ultimately further discovery. Peter Mitchell’s chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow IUPAC guidelines on terminology in physical chemistry, extended by considerations on open systems and irreversible thermodynamics. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols to the nomenclature of classical bioenergetics. In the frame of COST Action MitoEAGLE open to global bottom-up input, we endeavour to provide a balanced view on mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately support the development of databases of mitochondrial respiratory function in species, tissues, and cells.
|keywords=Mitochondrial respiratory control, coupling control, mitochondrial preparations, protonmotive force, uncoupling, oxidative phosphorylation, OXPHOS, efficiency, electron transfer, ET; proton leak, LEAK, residual oxygen consumption, ROX, State 2, State 3, State 4, normalization, flow, flux, O<sub>2</sub>
|keywords=Mitochondrial respiratory control, coupling control, mitochondrial preparations, protonmotive force, uncoupling, oxidative phosphorylation, OXPHOS, efficiency, electron transfer, ET; proton leak, LEAK, residual oxygen consumption, ROX, State 2, State 3, State 4, normalization, flow, flux, O<sub>2</sub>
|editor=[[Gnaiger E]]
|editor=[[Gnaiger E]]
}} __TOC__
}}
 
__TOC__
== Executive summary ==
== Authors: MitoEAGLE Task Group ==
 
[[File:Respiration.png|thumb|right|400px|'''Figure 1. Internal and external respiration.''' Mitochondrial respiration is the oxidation of fuel substrates (electron donors) and reduction of O<sub>2</sub> catalysed by the electron transfer system, ETS: ('''mt''') mitochondrial catabolic respiration; ('''ce''') total cellular O<sub>2</sub> consumption; and ('''ext''') external respiration. All chemical reactions, r, that consume O<sub>2</sub> in the cells of an organism, contribute to cell respiration, ''J''<sub>rO2</sub>. In addition to mitochondrial catabolic respiration, O<sub>2</sub> is consumed by: (1) Mitochondrial residual oxygen consumption, ''Rox''. (2) Non-mitochondrial O<sub>2</sub> consumption by catabolic reactions, particularly peroxisomal oxidases and microsomal cytochrome P450 systems. (3) Non-mitochondrial ''Rox'' by reactions unrelated to catabolism. (4) Extracellular ''Rox''. (5) Aerobic microbial respiration. Bars are not at a quantitative scale.]]
  Updated 2018-03-03
:::* '''Corresponding author'''  
 
:::::: [[Gnaiger E |Erich Gnaiger]]
[[File:Respiration.png|thumb|right|400px|'''Figure 1. Mitochondrial respiration with reduction of oxygen catalysed by the electron transfer system (''a''), catabolic respiration (including non-mitochondrial oxidation reactions, ''b''), and oxygen balance of internal (''c'') and external (''d'') respiration.''' All chemical reactions, r, that consume O<sub>2</sub> in the cells of an organism, contribute to cell respiration, ''J''<sub>rO2</sub>. (1) Non-mitochondrial contribution to O<sub>2</sub> consumption by catabolic reactions, particularly peroxisomal oxidases (* the reactions k have to be defined specifically for ''a'' and ''b''; Figure 1); (2) mitochondrial residual oxygen consumption, ''Rox'', after blocking the electron transfer system; (3) non-mitochondrial ''Rox''; (4) extracellular O<sub>2</sub> consumption; (5) aerobic microbial respiration. Bars are not at a quantitative scale.]]
:::::: Chair COST Action CA15203 MitoEAGLE
 
:::::: T +43 512 566796 15, F +43 512 566796 20
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:::::: mitoeagle@i-med.ac.at | www.mitoeagle.org  
 
:::* '''Coauthors''' (listed in alphabetical order); number of coauthors (2019-09-16): '''621'''
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:::::: ''Many coauthors have made significant additions and suggestions for improvement of the manuscript. All coauthors confirm to have read the final manuscript, and to agree to implement the recommendations into future manuscripts, presentations and teaching materials.''         
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:::::: Disclaimer: This article was prepared while Joshua P. Fessel was employed at Vanderbilt University Medical Center. The opinions expressed in this article are the author's own and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government.
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:::* '''Copyright''': © 2019 Gnaiger et al.  
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:::::: This is an [[Open Access]] [[preprint]] (not peer-reviewed) distributed under the terms of the [[Creative Commons Attribution License]], which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. © remains with the authors, who have granted MitoFit an Open Access preprint licence in perpetuity.
::::#In view of broad implications on health care, mitochondrial researchers face an increasing responsibility to disseminate their fundamental knowledge and novel discoveries to a wide range of stakeholders and scientists beyond the group of specialists. This requires implementation of a commonly accepted terminology within the discipline and standardization in the translational context. Authors, reviewers, journal editors, and lecturers are challenged to collaborate with the aim to harmonize the nomenclature in the growing field of mitochondrial physiology and bioenergetics.
:::* '''Mailing list'''
::::#Aerobic respiration depends on the coupling of phosphorylation (ADP → ATP) to O<sub>2</sub> flux in catabolic reactions. Coupling in oxidative phosphorylation is mediated by translocation of protons across the inner mitochondrial membrane through proton pumps generating or utilizing the protonmotive force, measured between the mitochondrial matrix and intermembrane compartment. Compartmental coupling distinguishes vectorial oxidative phosphorylation from glycolytic fermentation as the counterpart of cellular core energy metabolism ('''Fig. 1''').
:::::: If you have read this paper and wish to be included in our mailing list, then see » [[MitoEAGLE#MitoEAGLE_Newsletter |MitoEAGLE Newsletter]]
::::#To exclude fermentation and other cytosolic interactions from exerting an effect on mitochondrial metabolism, the barrier function of the plasma membrane must be disrupted. Selective removal or permeabilization of the plasma membrane yields mitochondrial preparations—including isolated mitochondria, tissue and cellular preparations—with structural and functional integrity. Then extra-mitochondrial concentrations of fuel substrates, ADP, ATP, inorganic phosphate, and cations including H<sup>+</sup> can be controlled to determine mitochondrial function under a set of conditions defined as coupling control states. A concept-driven terminology of bioenergetics incorporates in its terms and symbols explicitly information on the nature of respiratory states, that makes the technical terms readily recognized and more easy to understand.
::::#Mitochondrial coupling states are defined according to the control of respiratory oxygen flux by the protonmotive force. Capacities of oxidative phosphorylation and electron transfer are measured at kinetically saturating concentrations of fuel substrates, ADP and inorganic phosphate, or at optimal uncoupler concentrations, respectively. Respiratory capacity is a measure of the upper bound of the rate of respiration, depends on the substrate type undergoing oxidation, and provides reference values for the diagnosis of health and disease, and for evaluation of the effects of '''E'''volutionary background, '''A'''ge, '''G'''ender and sex, '''L'''ifestyle and '''E'''nvironment (EAGLE).
::::#Incomplete tightness of coupling, ''i.e.'', some degree of uncoupling relative to the substrate-dependent coupling stoichiometry, is a characteristic of energy-transformations across membranes. Uncoupling is caused by a variety of physiological, pathological, toxicological, pharmacological and environmental conditions that exert an influence not only on the proton leak and cation cycling, but also on proton slip within the proton pumps and the structural integrity of the mitochondria. A more loosely coupled state is induced by stimulation of mitochondrial superoxide formation and the bypass of proton pumps. In addition, uncoupling by application of protonophores represents an experimental intervention for the transition from a well-coupled to the noncoupled state of mitochondrial respiration.
::::#Respiratory oxygen consumption rates have to be carefully normalized to enable meta-analytic studies beyond the specific question of a particular experiment. Therefore, all raw data should be published in a supplemental table or open access data repository. Normalization of rates for the volume of the experimental chamber (the measuring system) is distinguished from normalization for: (''1'') the volume or mass of the experimental sample; (''2'') the number of objects (cells, organisms); and (''3'') the concentration of mitochondrial markers in the chamber.  
::::#The consistent use of terms and symbols discussed in this MitoEAGLE position statement will facilitate transdisciplinary communication and support further development of a database on bioenergetics and mitochondrial physiology. The present considerations are focused on studies with mitochondrial preparations. These will be extended in a series of reports on pathway control of mitochondrial respiration, the protonmotive force, respiratory states in intact cells, and harmonization of experimental procedures.       
 
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== Section 2: Oxidative phosphorylation and coupling states in mitochondrial preparations ==
 
[[File:Cell respiration and OXPHOS.png|left|600px|Cell respiration and OXPHOS]] '''Figure 2. Cell respiration and oxidative phosphorylation (OXPHOS)'''. Mitochondrial respiration is the utilization of fuel substrates for electron transfer to O<sub>2</sub> as the electron acceptor. For explanation of symbols see also Figure 1. ('''A''') Respiration in intact cells: Mitochondrial fuel substrates are the products of extra-mitochondrial catabolism of macrofuels or are taken up by the cell as small molecules. Many fuel substrates are catabolized to acetyl-CoA or glutamate, and further electron transfer reduces nicotinamide adenine dinucleotide to NADH or flavin adenine dinucleotide to FADH<sub>2</sub>. In aerobic respiration, electron transfer is coupled to the phosphorylation of ADP to ATP, with energy transformation mediated by the protonmotive force, ∆''p''. Anabolic reactions are linked to catabolism, both by ATP as the intermediary energy currency and by small organic precursor molecules as building blocks for biosynthesis (not shown). Glycolysis involves substrate-level phosphorylation of ADP to ATP in fermentation without utilization of O<sub>2</sub>. In contrast, extra-mitochondrial oxidation of fatty acids and amino acids proceeds partially in peroxisomes without coupling to ATP production: acyl-CoA oxidase catalyzes the oxidation of FADH<sub>2</sub> with electron transfer to O<sub>2</sub>; amino acid oxidases oxidize flavin mononucleotide FMNH<sub>2</sub> or FADH<sub>2</sub>. Coenzyme Q, Q, and the cytochromes ''b'', ''c'', and ''aa''<sub>3</sub> are redox systems of the mitochondrial inner membrane, mtIM. Dashed arrows indicate the connection between the redox proton pumps (respiratory Complexes CI, CIII and CIV) and the transmembrane ∆''p''. Mitochondrial outer membrane, mtOM; glycerol-3-phosphate, Gp; tricarboxylic acid cycle, TCA cycle.
 
('''B''') Respiration in mitochondrial preparations: The mitochondrial electron transfer system (ETS) is fuelled by diffusion and transport of substrates across the mitochondrial outer and inner membrane and consists of the matrix-ETS and membrane-ETS. ET-pathways are coupled to the phosphorylation-pathway. ET-pathways converge at the N-junction and Q-junction. Additional arrows indicate electron entry into the Q-junction through electron transferring flavoprotein, glycerophosphate dehydrogenase, dihydro-orotate dehydrogenase, choline dehydrogenase, and sulfide-ubiquinone oxidoreductase. The dotted arrow indicates the branched pathway of oxygen consumption by alternative quinol oxidase (AOX). The H<sup>+</sup><sub>pos</sub>/O<sub>2</sub> ratio is the outward proton flux from the matrix space to the positively (pos) charged vesicular compartment, divided by catabolic O<sub>2</sub> flux in the NADH-pathway. The H<sup>+</sup><sub>neg</sub>/P» ratio is the inward proton flux from the inter-membrane space to the negatively (neg) charged matrix space, divided by the flux of phosphorylation of ADP to ATP. These are not fixed stoichiometries due to ion leaks and proton slip.
 
('''C''') Phosphorylation-pathway catalyzed by the proton pump F<sub>1</sub>F<sub>O­</sub>-ATPase (F-ATPase, ATP synthase), adenine nucleotide translocase, and inorganic phosphate transporter. The H<sup>+</sup><sub>neg</sub>/P» stoichiometry is the sum of the coupling stoichiometry in the F-ATPase reaction (­2.7 H<sup>+</sup><sub>pos</sub> from the positive intermembrane space, 2.7 H<sup>+</sup><sub>neg</sub> to the matrix, ''i.e.'', the negative compartment) and the proton balance in the translocation of ADP<sup>3­-</sup>, ATP<sup>4-</sup> and P<sub>i</sub><sup>2-</sup>. Modified from (B) [[Lemieux_2017_Sci_Rep|Lemieux et al 2017]] and (C) [[Gnaiger_2014_MitoPathways#Chapter_1._Real-time_OXPHOS_analysis|Gnaiger 2014 MitoPathways]].
 
<gallery heights="350px" mode="default" perrow="4" widths="350px">
File:Coupling in OXPHOS 1.png |'''Figure 3. Coupling in oxidative phosphorylation (OXPHOS)'''. Modified after [[Gnaiger_2014_MitoPathways#Chapter_1._Real-time_OXPHOS_analysis |Gnaiger 2014 MitoPathways]].
File:Uncoupling.png |'''Figure 4. Mechanisms of respiratory uncoupling.'''
File:OXPHOS compartments 1.png |'''Figure 5. Four-compartmental model of oxidative phosphorylation''' with respiratory states (ET, OXPHOS, LEAK) and corresponding rates (''E, P, L''). Modified from Gnaiger (2014).
File:LPE states.png |'''Figure 6. Respiratory coupling states.'''
File:Table Coupling states 1.png
File:Table Coupling terms.png
File:Table Chance states.png
</gallery>
 
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== Section 3: Normalization: fluxes and flows ==
 
<gallery heights="350px" mode="default" perrow="4" widths="350px">
File:Rate.png |'''Figure 7. Flow and flux, and normalization in structure-function analysis.''' '''(A)''' Different meanings of rate may lead to confusion, if the normalization is not sufficiently specified.
File:Flow in structure-function analysis.png |'''Figure 7B. O<sub>2</sub> flow''', ''I''<sub>O2/''X''</sub>, is the product of performance per functional element (element function, mitochondria-specific flux), element density (mitochondrial density, ''D<sub>mtE</sub>''), and and size of entity ''X'' (mass ''M<sub>X</sub>'').
File:Table Sample concentrations and normalization of flux.png
File:Table Sample types.png
</gallery>
 
== Concept ==
 
[[Gentle_Science#Preprints_for_Gentle_Science|'''Preprints for Gentle Science''']]
 
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::::Citation:  
::::MitoEAGLE preprint 2018-02-08(Version 34). Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology Part 1. - [http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08 http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08]     
 
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::::Acknowledgements: We thank M. Beno for management assistance. This publication is based upon work from [[MitoEAGLE|COST Action CA15203 MitoEAGLE]], supported by COST (European Cooperation in Science and Technology), and K-Regio project [[K-Regio_MitoFit|MitoFit]] (E.G.).     
 
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::::'''To co-authors, editors, reviewers, and readers'''  
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::::::The global MitoEAGLE network made it possible to collaborate with more than 250 co-authors to reach consensus on the present manuscript. Nevertheless, we do not consider scientific progress to be supported by ‘declaration’ statements (other than on ethical or political issues). Our manuscript aims at providing arguments for further debate rather than pushing opinions. We hope to initiate a much broader process of discussion and want to raise the awareness on the importance of a consistent terminology for the reporting of scientific data in the field of bioenergetics, mitochondrial physiology and pathology. Quality of research requires quality of communication. Some established researchers in the field may not want to re-consider the use of jargon which has become established despite deficiencies of accuracy and meaning. In the long run, superior standards will become accepted. We hope to contribute to this evolutionary process, with an emphasis on harmonization rather than standardization.         
 
=== Authors ===
 
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::::'''This is an open invitation to scientists and students to join as co-authors''', to provide a balanced view on mitochondrial respiratory control and a consensus statement on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes.     
 
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::::*'''Co-authors''': ''Confirming to have read the final manuscript, possibly to have made additions or suggestions for improvement, and to agree to implement the recommendations into future manuscripts, presentations and teaching materials. (alphabetical)''       
 
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::::*'''Supporting''': ''Confirming to have read the final manuscript, and to agree to implement the recommendations into future manuscripts, presentations and teaching materials; not included in journal-publication.''         
 
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::::We continue to invite comments and suggestions, particularly if you are an '''early career investigator adding an open future-oriented perspective''', or an '''established scientist providing a balanced historical basis'''. Your critical input into the quality of the manuscript will be most welcome, improving our aims to be educational, general, consensus-oriented, and practically helpful for students working in mitochondrial respiratory physiology.
::::To join as a co-author, please feel free to focus on a particular section, providing direct input and references, and contributing to the scope of the manuscript from the perspective of your expertise. Your comments will be largely posted on the [[Talk:MitoEAGLE_preprint_2018-02-08|discussion page of the MitoEAGLE preprint website]].
::::If you prefer to submit comments in the format of a referee's evaluation rather than a contribution as a co-author, we will be glad to distribute your views to the updated list of co-authors for a balanced response. We would ask for your consent on this open bottom-up policy.     
 
=== Progress ===
 
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::::*Phase 1: [[The_protonmotive_force_and_respiratory_control|44 versions until 2017-09-18]] / [[Talk:The_protonmotive_force_and_respiratory_control|Discussion]] 
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::::::*This manuscript on ‘Mitochondrial respiratory states and rates’ is a position statement in the frame of COST Action CA15203 MitoEAGLE. The list of co-authors evolved beyond phase 1 in the '''bottom-up spirit''' of COST.            
 
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::::*Phase 2: '''2017-09-21''' [[MitoEAGLE_preprint_2017-09-21|21 versions until 2018-02-06]] ‘The protonmotive force and respiratory control’ / [[Talk:MitoEAGLE_preprint_2017-09-21|Discussion]]
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::::::*2017-09-21 -: MitoEAGLE preprint'''- with updates on route to let the final publication fly.'''
::::::*2017-11-11: Print version (16) for MiP2017 and MitoEAGLE workshop in Hradec Kralove
::::::*[[MiP2017/MitoEAGLE_Hradec_Kralove_CZ|MiP2017/MitoEAGLE Hradec Kralove CZ]] - Discussion of manuscript submission for journal publication.           
 
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::::*Phase 3: '''2018-02-08''' (Version 22 - 23) Feedback, suggestions, and confirmation from co-authors. Contact the editor(s) of our finally targeted journal(s), to obtain a first opinion if submission to this journal will be adequate. Cell Metabolism and BBA have been mentioned as possible preferences. / [[Talk:MitoEAGLE_preprint_2018-02-08|Discussion]]       
 
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::::*Phase 4: '''2018-02-15''' (Version 24 - ) Preparation of manuscript for submission to a preprint server, such as [[BioRxiv|BioRxiv]], and submission to CELL METABOLISM, aiming at indexing by ''The Web of Science'' and ''PubMed''.       
 
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::::::We plan a series of follow-up reports by the expanding MitoEAGLE Network, to increase the scope of harmonization and facilitate global communication and collaboration. Further discussions: [[COST_Action_MitoEAGLE#Chronological_list_of_MitoEAGLE_Events|MitoEAGLE events]], various conferences ([[EBEC2018_Budapest_HU|EBEC 2018 in Budapest]]).         
 
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== Letter to the Editors of scientific journals ==


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[[File:SI-units.png|left|120px]]
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== From Version 4 to 5 ==
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On [https://www.euramet.org/publications-media-centre/news/?tx_news_pi1%5Bnews%5D=787&tx_news_pi1%5Baction%5D=detail&tx_news_pi1%5Bcontroller%5D=News World Metrology Day] (2019-05-20) the redefinition of the SI units came into force. At this occasion, Version 4 of the MitoEAGLE preprint on 'Mitochondrial respiratory rates and states' was released, in line with our emphasis on SI units for reporting data on mitochondrial respiratory physiology.
::::Dear Editors:     


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::::We would like to ask you for your opinion about the increasingly urgent issue of '''nomenclature in mitochondrial physiology'''.     


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== Preprints for [[Gentle Science]] ==
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{{MitoFit preprint}}
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::::With your collaboration our goal is to make publications with data on mitochondrial respiration more generally comprehensible and data more universally useful by bringing better standardization of nomenclature and data presentation to the field.     


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== References ==
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::::'''As the knowledge base and importance of mitochondrial physiology to human health expand, the necessity for harmonizing nomenclature concerning mitochondrial respiratory states and rates has become increasingly apparent. In the frame of COST Action MitoEAGLE, we endeavour to provide a balanced view on mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration. Uniform standards for evaluation of respiratory states and rates will ultimately support the development of databases of mitochondrial respiratory function in species, tissues, and cells.'''     


:
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::::A Working Group of the COST Action MitoEAGLE is preparing a document on ‘'''Mitochondrial respiratory states and rates'''’. The group is working on it with Open Access as a ‘MitoEAGLE preprint’ and the ultimate aim of publication in a scientific journal:  
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::::*'''pdf preprint''':&nbsp;» [http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08 http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08]  
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::::*'''Executive summary''':&nbsp;» [http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08#Executive_summary http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2018-02-08#Executive_summary]        
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:
::
:::
::::We would like to include your opinion as editor. We aim at providing a list of journals, from whom we received valuable feedback:
::::#Do you recognize a general need for a consensus on nomenclature and standards of reporting in the field of mitochondrial respiratory physiology?
::::#Can you provide comments and suggestions for the MitoEAGLE preprint: 'Mitochondrial respiratory states and rates’ from your point of view as an editor?
::::#Which further steps do you suggest towards implementing a harmonized terminology on mitochondrial states and rates in your editorial policy?       


:
== Corrigendum ==
::
:::
::::I thank you for your considerations.
::::With kind regards,     


[[File:MITOEAGLE-logo.jpg|left|100px|COST Action MITOEAGLE|link=http://www.mitoglobal.org/index.php/MITOEAGLE]]
::::* Section 2.5.4: Sulfur dioxygenase is related to ET, hence should not be listed here in relation to ''Rox''.


:
== Comments and communication ==
::
:::
::::Erich Gnaiger, Ao.Univ.-Prof., Ph.D.
::::''Chair COST Action CA15203 MitoEAGLE'' - [http://www.mitoeagle.org http://www.mitoeagle.org]
::::''Chair Mitochondrial Physiology Society'' - [http://www.mitophysiology.org http://www.mitophysiology.org]
::::Medical University of Innsbruck
::::Department of Visceral, Transplant and Thoracic Surgery
::::D. Swarovski Research Laboratory
::::A-6020 Innsbruck, Austria
::::Email: [email protected]     


&nbsp;
::::» [[Talk:Gnaiger_2019_MitoFit_Preprint_Arch#2019-07-22_Circular_to_coauthors |2019-07-22 Circular to coauthors]]
::::» [[Talk:Gnaiger_2019_MitoFit_Preprint_Arch#2019-03-12_Circular_to_coauthors |2019-03-12 Circular to coauthors]]
::::» [[Talk:Gnaiger_2019_MitoFit_Preprint_Arch#2019-02-12_Circular_to_coauthors |2019-02-12 Circular to coauthors]]


:
::::* [[Talk:Gnaiger_2019_MitoFit_Preprint_Arch#Comments |Comments]]
::
:::
::::
::::*[[Talk:MitoEAGLE_preprint_2018-02-08#Contacted_editors|Editors contacted by MitoEAGLE]]        


=== Answers ===


:
== Linking COST Actions and MiP''society'' ==
::
:::: [[File:MITOEAGLE-logo.jpg|60px|link=http://www.bioblast.at/index.php/COST_Action_MitoEAGLE|COST Action MitoEAGLE]] [[File:COST Logo.jpg|160px|link=http://www.cost.eu/COST_Actions/ca/CA15203|e-COST MitoEAGLE]] [[File:EU-logo.jpg|80px|link=http://www.cost.eu/COST_Actions/ca/CA15203?parties|e-COST MitoEAGLE countries]] [[Image:MiPsocietyLOGO.JPG|100px|link=http://www.mitoglobal.org/index.php/Mitochondrial_Physiology_Society|MiP''society'']]
:::
::::* [http://www.cost.eu/COST_Actions/ca/CA15203 COST Action CA15203 MitoEAGLE]
::::
::::* [http://www.cost.eu/COST_Actions/ca/CA16225 COST Action CA16225 EU-CARDIOPROTECTION]
::::*Dear Prof. Gnaiger 
::::* [http://www.cost.eu/COST_Actions/ca/CA17129 COST Action CA17129 CardioRNA]
:::::it is with great interest that I read your email. Indeed a more harmonised and well explained terminology in mitochondrial research would be excellent. I, as Editor in chief of Chemico-Biological Interactions, would support such a open source publication.  
:::::If we at CBI can support you, e.g. in publishing this terminology review paper as an open source publication in CBI, please do contact me directly.  
:::::Sincerely, Prof. Dr. Daniel Dietrich, Ph.D., FATS, DGPT, ERT Editor-in-Chief Chemico-Biological Interactions [http://ees.elsevier.com/chembioint http://ees.elsevier.com/chembioint]        


:
::
:::
::::
::::*Dear Dr. Gnaiger, 
:::::Thank you for forwarding us a copy of your manuscript under preparation. Since that the editors have already invited a submission, we recommend you submit the full paper via Editorial Manager for in-depth editorial evaluation when you are ready.
:::::Thank you for your support of Cell Metabolism.
:::::Best, Jennifer Estrompa - Journal Associate Cell Metabolism, Structure, and Cell Chemical Biology - Cell Press       


&nbsp;
== The MitoFit preprint ==
{{MitoEAGLE preprint 1 Phases}}
{{NextGen-O2k H2020-support}}
::::* [http://www.mitoeagle.org/index.php/File:MitoEAGLE_preprint_States_and_rates.pdf Versions towards the MitoFit Preprint]
::::* [http://www.mitoeagle.org/index.php/Talk:MitoEAGLE_Task_Group_States_and_rates Discussion towards the MitoFit Preprint]


:
== Cited by ==
::
{{Template:Cited by Gnaiger 2019 MitoFit Preprints}}
:::
::::
::::*Dear Dr. Sharma, 
:::::Thank you for asking us to consider your paper, “Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology”, for Cell Metabolism. In principle, we find the topic to be relevant and the work to be of interest. It is, however, somewhat difficult for us, based on the information you sent, to determine whether the paper would be a strong candidate for Cell Metabolism. I would therefore recommend you send us the full paper to be evaluated as part of our in-house editorial review system.
:::::Before submission of the article online at our EM site, please make sure that the article conforms to the format guidelines for the journal. Please mention this correspondence in the cover letter.
:::::We look forward to reading the full paper.
:::::Sincerely, Nikla Emambokus, Ph.D. - Editor-in-Chief, Cell Metabolism
:::::[[Talk:MitoEAGLE_preprint_2018-02-08#Phase_3.1:_Discussion|Discussion see ''2018-02-15 Sharma P'']]       
 
&nbsp;
 
:
::
:::
::::
::::*Dear Dr. Sokolova 
:::::I have given this some thought and, after some delay for which I apologize, would like to offer a response. It is a personal one that in no way represents the views of editors of the JEB.
:::::I can understand why some would wish to standardize nomenclature in mitochondrial physiology. Over the years, I have come across submissions and published papers that make claims about rates measured in "state 4" when the conditions actually did not fit the definition of state 4 established decades ago and widely accepted by mitochondrial biochemists.
:::::However, there are terms in the list provided that are not generally accepted and I doubt whether these should be 'made standard by official declaration'. Adopting standard nomenclature would mean that deviation from it would be frowned upon by reviewers and editors. I would be more comfortable with the idea of having authors refer to (cite) your document should they wish to use any or all the terms in it.&nbsp;::::: If, over time, people in the field choose to use the terms and cite the document, then the terms become accepted by consensus, rather than by declaration. This would be consistent with our wish for clarity and precision in the use of language in papers concerning mitochondrial physiology and biochemistry.
:::::I hope this feedback shall be of some use.
:::::With best wishes, Raul - Editor 'Journal of Experimental Biology'       
 
{{Labeling
|area=Respiration, mt-Awareness
|preparations=Permeabilized cells, Permeabilized tissue, Homogenate, Isolated mitochondria
|enzymes=Marker enzyme
|topics=Coupling efficiency;uncoupling, Flux control, mt-Membrane potential, Uncoupler
|couplingstates=LEAK, OXPHOS, ET
|pathways=ROX
|additional=MitoFitPublication
}}

Latest revision as of 08:27, 8 January 2023


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Gnaiger 2019 MitoFit Preprints

Publications in the MiPMap
Gnaiger E, Aasander Frostner E, Abdul Karim N, Abdel-Rahman EA, Abumrad NA, Acuna-Castroviejo D, Adiele RC, et al (2019) Mitochondrial respiratory states and rates. https://doi.org/10.26124/mitofit:190001.v6. — Published: 2020-05-20 Mitochondrial physiology. Bioenerg Commun 2020.1. https://doi.org/10.26124/bec:2020-0001.v1

» MitoFit Preprint Arch 2019.1.v6

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Mitochondrial respiratory states and rates



MitoFit Prep 2019.1.v6. (2019) MitoFit Prep

Abstract: Version 6 (v6) 2019-08-30 doi:10.26124/mitofit:190001.v6

Versions (v5) 2019-07-24; (v4) 2019-05-20; (v3) 2019-04-24; (v2) 2019-03-15; (v1) 2019-02-12 - »Link to all versions«
Published online: 2020-05-20
» Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. »Bioblast link«

As the knowledge base and importance of mitochondrial physiology to human health expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow guidelines of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols to the nomenclature of classical bioenergetics. We endeavour to provide a balanced view on mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of databases of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery. • Keywords: Mitochondrial respiratory control, coupling control, mitochondrial preparations, protonmotive force, uncoupling, oxidative phosphorylation, OXPHOS, efficiency, electron transfer, ET; proton leak, LEAK, residual oxygen consumption, ROX, State 2, State 3, State 4, normalization, flow, flux, O2 • Bioblast editor: Gnaiger E

Authors: MitoEAGLE Task Group

Figure 1. Internal and external respiration. Mitochondrial respiration is the oxidation of fuel substrates (electron donors) and reduction of O2 catalysed by the electron transfer system, ETS: (mt) mitochondrial catabolic respiration; (ce) total cellular O2 consumption; and (ext) external respiration. All chemical reactions, r, that consume O2 in the cells of an organism, contribute to cell respiration, JrO2. In addition to mitochondrial catabolic respiration, O2 is consumed by: (1) Mitochondrial residual oxygen consumption, Rox. (2) Non-mitochondrial O2 consumption by catabolic reactions, particularly peroxisomal oxidases and microsomal cytochrome P450 systems. (3) Non-mitochondrial Rox by reactions unrelated to catabolism. (4) Extracellular Rox. (5) Aerobic microbial respiration. Bars are not at a quantitative scale.
  • Corresponding author
Erich Gnaiger
Chair COST Action CA15203 MitoEAGLE
T +43 512 566796 15, F +43 512 566796 20
[email protected] | www.mitoeagle.org
  • Coauthors (listed in alphabetical order); number of coauthors (2019-09-16): 621
Many coauthors have made significant additions and suggestions for improvement of the manuscript. All coauthors confirm to have read the final manuscript, and to agree to implement the recommendations into future manuscripts, presentations and teaching materials.
Disclaimer: This article was prepared while Joshua P. Fessel was employed at Vanderbilt University Medical Center. The opinions expressed in this article are the author's own and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government.
  • Copyright: © 2019 Gnaiger et al.
This is an Open Access preprint (not peer-reviewed) distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. © remains with the authors, who have granted MitoFit an Open Access preprint licence in perpetuity.
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From Version 4 to 5

On World Metrology Day (2019-05-20) the redefinition of the SI units came into force. At this occasion, Version 4 of the MitoEAGLE preprint on 'Mitochondrial respiratory rates and states' was released, in line with our emphasis on SI units for reporting data on mitochondrial respiratory physiology.


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Corrigendum

  • Section 2.5.4: Sulfur dioxygenase is related to ET, hence should not be listed here in relation to Rox.


Comments and communication

» 2019-07-22 Circular to coauthors
» 2019-03-12 Circular to coauthors
» 2019-02-12 Circular to coauthors


Linking COST Actions and MiPsociety

COST Action MitoEAGLE e-COST MitoEAGLE e-COST MitoEAGLE countries MiPsociety


The MitoFit preprint


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» Manuscript phases and versions

Manuscript phases and versions - an open-access apporach

COST Action MitoEAGLE
This manuscript on ‘Mitochondrial respiratory states and rates’ is a position statement in the frame of COST Action CA15203 MitoEAGLE. The list of coauthors evolved beyond phase 1 in the bottom-up spirit of COST.
The global MitoEAGLE network made it possible to collaborate with a large number of coauthors to reach consensus on the present manuscript. Nevertheless, we do not consider scientific progress to be supported by ‘declaration’ statements (other than on ethical or political issues). Our manuscript aims at providing arguments for further debate rather than pushing opinions. We hope to initiate a much broader process of discussion and want to raise the awareness on the importance of a consistent terminology for reporting of scientific data in the field of bioenergetics, mitochondrial physiology and pathology. Quality of research requires quality of communication. Some established researchers in the field may not want to re-consider the use of jargon which has become established despite deficiencies of accuracy and meaning. In the long run, superior standards will become accepted. We hope to contribute to this evolutionary process, with an emphasis on harmonization rather than standardization.
  • Phase 1: The protonmotive force and respiratory control
» The protonmotive force and respiratory control - Discussion
» MitoEAGLE preprint 2017-09-21 - Discussion
  • Phase 2: Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology Part 1
» MitoEAGLE Task Group States and rates - Discussion
  • Phase 4: Journal submission
  • Target: CELL METABOLISM, aiming at indexing by The Web of Science and PubMed.
Coauthors
  • 2017-09-21 Version 01: 105 coauthors
  • 2017-10-15 Version 10: 131 coauthors
  • 2018-01-18 Version 20: 168 coauthors
  • 2018-02-26 Version 30: 225 coauthors
  • 2018-08-20 Version 40: 350 coauthors - EBEC Poster
  • 2018-10-17 Version 44: 426 coauthors - MiPschool Tromso-Bergen 2018
  • 2018-12-12 Version 50: 517 coauthors - Submission to the preprint server bioRxiv not successful
  • 2019-02-12 Preprint version 1: 530 coauthors
  • 2019-03-15 Preprint version 2: 533 coauthors
  • 2019-04-24 Preprint version 3: 533 coauthors
  • 2019-05-20 Preprint version 4: 542 coauthors
  • 2019-07-24 Preprint version 5: 612 coauthors
  • 2019-08-30 Preprint version 6: 622 coauthors - Preprint publication doi:10.26124/mitofit:190001.v6
  • BEC 2020.1. - Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. - »Bioblast link«


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Gnaiger 2019 MitoFit Preprints


Gnaiger E (2019) Editorial: A vision on preprints for mitochondrial physiology and bioenergetics. MitoFit Preprint Arch doi:10.26124/mitofit:190002.v2.
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