Talk:MitoEAGLE preprint 2017-09-21

» MitoEAGLE preprint 2017-09-21

Phase 2: Discussion

• 2017-10-09 Coen PM

• Please find attached some (minor) edits/suggestions on the joint MitoEAGLE manuscript. Overall, the manuscript is in great shape and I believe will be a very useful practice resource for both investigators who are new to mitochondrial energetics and those who are more experienced.

• 2017-10-06 Amati F:

• In the idea to add my experience, and participating as a co-author, I have carefully read the MitoEAGLE preprint, particularly focusing on the normalization issues which is what I thought my expertise could be, but it is so well written that I had nothing to add! The only small thing that I found was on page 18, line 446, there is a missing reference. Here is the paper (Greggio, Cell Metabolism, 2017) that I was mentioning in an earlier email where we have used the proposed nomenclature. While we were writing that manuscript, it was clear that a common language and protocols were needed. I struggled a fair amount with reviewers as I wanted to use unequivocal labels not referring to respiratory states. Still today, each time I present at a conference, I insist on the importance of having one language and relate to the MitoEAGLE guidelines. So as you see, even not being necessary active in the MitoEAGLE network and joined only later, I am one of the most fervent defenders!

• 2017-10-06 Lai N

• This is a very mice initiative which I am glad to be part of.

I have only few minor suggestions that you find in the attached document.

2017-10-04 MitoEAGLE preprint 2017-09-21 Version 06

• 'Electron transfer system' is changed to 'electron transfer pathways; ETS to ET pathways
• 'Phosphorylation system' is changed to 'phosphorylation pathway'
• 'OXPHOS system' is changed to 'OXPHOS pathway'
• 'ETS capacity' is changed to 'ET capacity' (compare: OXPHOS capacity)
• 'ETS state' is changed to 'ET state' (compare: OXPHOS state)

• 2017-10-04 Wuest RC

• It’s becoming a very nice paper, thanks so much for the input and all the work! I don’t have any further suggestions to the current version. Looking forward to seeing the final version!

• 2017-10-04 Breton S

• Here are a few more edits on the version preprint_2017-09-21

• 2017-10-01 Schoenfeld P

• after reading the new version of the manuscript, I feel that it has been further improved.

My minor comments is very brief.

p.6, line 181-182

For me sounds strange too write: As part of the OXPHOS system, these powerhouses of the cell...

Who are (besides mitochondria) the other part(s)?

My proposal is: In addition to the OXPHOS system, the powerhouses of the cell contain…

p.14, line 372

OXPHOS as abbreviation was already indroduced. Therefore, I propose to write: The capacity of OXPHOS….

p.12, line 405

I propose to substitute in F1F0, 0(zero) by O. Originally, O was used to indicate oligomycin-sensitivity.

p.50, line 1233

Sentence: Mitochondrial and cell respiration is the process of highly exothermic energy transformation….

According to my understanding, exothermic has to be substituted by exergonic.

• 2017-09-28 Trougakos IP

• Great effort.

• 2017-09-28 Pak YK

• On text of the MitoEAGLE manuscript, I like page 20~26 on OCR on different stages; Nowadays many scientists are using basal respiration, ATP turnover, maximum repiration to define the OCR. I wonder if you could put these definitions connected to your OCR, LEAK OXPHOS, ETS, ROX.

I like the manuscript very much and it is my honor to be a supporting co-author.

• 2017-09-27 Wohlwend M

• In my opinion the manuscripts reflects the current state of terminology very well and will serve excellently for teaching purposes. I would like to contribute by adding/challenging a couple of details from our experiences working with permeabilized muscle fibers.

Line 575: “In permeabilized muscle fibre bundles of high respiratory capacity, the apparent Km for ADP increases up to 0.5 mM (Saks et al. 1998), indicating that >90% saturation is reached only at >5 mM ADP.”

n our hands, performing two-step 2.5 - 5 mM ADP titrations has shown that 2.5 mM ADP is sufficient to achieve maximal OXPHOS (Malate+Glutamate+Pyurvate+Octanoyl carnitine+Succinate but also other substrate combinations) in permeabilized muscle fibers of both rat and human skeletal muscle. There is no additive respiratory effect beyond 2.5 mM ADP. However, for longer evaluation protocols it might be “safer” to use 5 mM ADP.

• 2017-09-27 Asander Frostner E:

• I focused on the sections that I felt are relevant to my level of knowledge. I think it's a very good and educational manuscript, very elaborate and structured. I don't have any input on the contents as such, only a few suggestions on minor text adjustments.

• 2017-09-27 Haavik J:

• I appreciate your efforts to increase the visibility and aid harmonization within this field. I support the initiative and you may well add my name to the growing list of supporters.

• 2017-09-27 Gorr TA:

• I added two text sections on pages 10+11 of the manuscript plus references, concerning protein-driven mechanisms of respiration control. Please have a look at the attached pdf and find the two text boxes within the mansucript´s on pp. 10+11.
• (6) Regulatory proteins, such as the inhibitory factor 1 (IF1), function in mitochondria of mammals challenged by severe O2 deprivation (hypoxia, anoxia, ischemia) to keep the reversal of proton pumping by complex V (ATP synthase), and, hence, the resulting ATP hydrolysis plus production of reactive oxygen species (ROS), at bay (Matic et al 2016; Esparza-Molto et al. 2017). HIF-1, on the other hand, coordinates access of mitochondrial substrates with hypoxia, in part through the transcriptional activation of the pyruvate dehydrogenase (PDH) inhibitor PDK1. This slow-down of the PDH reaction starves the tricarboxylic acid (TCA) cycle of pyruvate substrate, which, in turn, helps in decreasing respiration rates during conditions of low oxygen availability (Kim et al. 2006, Papandreou et al. 2006). As such, HIF-1 may well contribute in driving the switch from an oxy-regulated to an oxy-conforming mode of respiration (Gnaiger 2003; Gorr 2010; 2017).
• References:

1. Matic I, Cocco S, Ferraina C et al. Neuroprotective coordination of cell mitophagy by the F1Fo-ATPase inhibitory factor (IF1). Pharmacol Research 2016;103:56-68.
2. Esparza-Molto PB, Nuevo-Tapioles C and Cuezva JM. Regulation of the H+-ATP synthase by IF1: a role in mitohormesis. Cell Mol Life Sci 2017;74:2151-66.
3. Kim J-W, Tchernyshyov I, Semenza GL and Dang CV. HIF-1-mediated expression of pyruvate dehydrogenase kinase: A metabolic switch required for cellular adaptation to hypoxia 2006;3:177-85.
4. Papandreou I, Cairns RA, Fontana L, Lim AL and Denko NC. HIF-1 mediates adaptation to hypoxia by actively downregulating mitochondrial oxygen consumption. 2006;3:187-97.
5. Gnaiger E. Oxygen conformance of cellular respiration. A perspective of mitochondrial physiology. 2003;543:39-55.
6. Gorr TA, Wichmann D, Hu J et al. Hypoxia Tolerance in Animals: Biology and Application. Physiol Biochem Zool 2010;83:733-52.
7. Gorr TA. Hypometabolism as the ultimate defence in stress response: how the comparative approach helps understanding of medically relevant questions. Acta Physiol. 2017;219:409-440.

• EG: Great I added it quickly.

• 2017-09-27 O'Gorman D

• I have provided specific comments in the attached document. It is extremely comprehensive and will be very useful for a range of researchers investigating mitochondrial respiration.

In publishing this manuscript we should think as much as possible about the researchers that are very interested, but maybe not experts, in mitochondrial research. With this in mind I have suggested the simplification of some sections and the include of some additional introductory sentences in some sections to help provide more of a basis for the information being provided.

• 2017-09-26 Tomar D:

• I would like to introduce myself as an early career contributor in your excellent work to standardize the nomenclature for mitochondrial bioenergetics. Currently, I am working as a postdoctoral fellow at Temple University, Philadelphia USA and my work focused on the role of calcium in mitochondrial bioenergetics and functions. As a leading author, I discovered the molecular mechanism of one of mitochondrial calcium uniporter regulator (MCUR1) mediated regulation of uniporter function (Cell Reports, 2016). Recently, as a co-first author, I have shown that mitochondrial calcium uniporter senses the reactive oxygen species through the conserved cysteine residue (Molecular Cell, 2017). Besides these contributions in the field of mitochondrial biology, I was the part of the discovery of SPG7 as mitochondrial permeability transition pore from our group (Molecular Cell, 2015) and the association of small RNAs with mitochondria (PlosOne, 2012). I have thoroughly reviewed the preprint of the “The protonmotive force and respiratory control: Building blocks of mitochondrial physiology”. This is an excellent and comprehensive resource for the researchers working in the area of mitochondrial bioenergetics. I have three minor comments on Page 7 and Page 11. I hope these could be useful.

• 2017-09-26 Victor VM:

• Thank you very much for your invitation. I would like to sign the article with you. It is very interesting and accurated article.

• 2017-09-26 MacMillan-Crow LA:

• I think this reads very well. I have made a few comments that might be helpful.

2017-09-24 MitoEAGLE preprint 2017-09-21 Version 04

• 2017-09-23 Robinson MM, Newsom S:

• I reviewed the Preprint of the “Mitochondrial Respiratory Control” joint paper and found it to be quite a useful resource. There are minor editorial updates but overall the main theme and concepts are presented well and I have no major considerations at this point. Thank you for including us in the manuscript as it is very important for standardization of nomenclature.

2017-09-21 MitoEAGLE preprint 2017-09-21 Version 01

Phase 1: Work flow 44 versions until 2017-09-18

» Talk:The protonmotive force and respiratory control