Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions

Round 1

Reviewer 1 Report

The authors present an excellent review of the current state of knowledge on the function of mitochondria as energy generating organelles focusing on the oxidative phosphorylation system and the detailed experiments that have been performed in the last 30 years to elucidate the assembly of the complexes and structure-function relationships. This review will be an important contribution to the literature as there is currently no one source of information that is so extensive regarding the current state of knowledge of the oxidative phosphorylation complexes.  However, there were some minor English wording issues in the manuscript and suggested improvements are indicated below.

 

Comment 1: In Figure 1, the small non-coding region between ATP6 and ATP8 genes should be colored white instead of pink.

Comment 2: In Fig. 1, it appears that the serine tRNA(UCN) is coded in an overlapping genetic location, but on the opposite strand of the COI gene, which is not correct. The serine tRNA(UCN) is located on the opposite strand adjacent to COI, so there should be some white non-coding space present to the left of tRNA D(Asp).

 

Line 45: Figure 1.1 -> Figure 1

Line 76: 1.2 -> 2

Line 79: freely -> freely through

Line 80: is at the base of -> forms the basis for

Line 85: in -> into

Line 95: You indicate there are 2 additional MICOS proteins in mammals compared to yeast, but list 3 proteins, one that is paralogous to yeast. You should delete “paralog of Mic19 in metazoans [18],” or explain this better if it needs to be present.

Line 98: directly -> directly to

Line 98: 1.3 -> 3

Line 102: at -> at the

Line 149: main -> the main

Lines 153-156 should be single spaced, not double spaced.

Line 170: in -> into

Line 172: in -> into

Line 191: Adenosine -> adenosine

Line 194: hydrogen -> hydrogen atoms

Line 196: one -> one molecule

Line 199: 1.4 -> 4

Line 203: the term “chetoacid” is antiquated; please use “ketoacid” instead

Line 206: lead in the mitochondrial matrix to -> in the mitochondrial matrix lead to

Line 220: forming the initial molecule -> hydrolyzed from the acyl chain

Line 237: cellular components degradation -> the degradation of cellular components

Line 241: subsequent -> subsequently

Line 248: as -> as the

Line 260: Remove the words “through a series of reactions both in the mitochondria and in the cytosol,” [redundant]

Line 262: The 85% -> 85%

Line 264:  Since all cells need heme for the electron transport chain complexes, don’t all cells synthesize heme? Or do cells in most tissues import heme that has been exported by the liver or RBCs?

Line 275: Most of -> Most

Line 278: cluster -> clusters

Line 279: outside -> from

Line 280: of -> of the

Line 283: cysteines -> cysteine

Line 295: cartoon -> Cartoon

Line 325: graphic -> Graphic

Line 334: to one -> from one

Line 343: the time -> a time

Line 347: with -> of

Line 348: reduction -> oxidation

Line 349: reductase -> dehydrogenase [FAD is reduced to FADH2, while succinate is oxidized to fumarate]

Line 356: as -> as the

Line 371 and 372: of cytochrome -> for cytochrome

Line 375: reaction -> the reaction

Line 379: schematic -> Schematic

Line 384: other -> the other

Line 388: bound -> bond

Line 394: in -> into

Line 404: 2.4 -> 8

Line 406: representation -> Representation

Lines 416 and 417:  Change font from “imported” to “protein”

Line 422: proteins -> protein

Line 424:  in a -> into the

Line 440: modules intermediate -> module intermediate

Line 442: in -> into

Line 466: central -> a central

Line 466: reduces ubiquinone to ubiquinol producing FADH2 -> reduces FAD to FADH2, which then reduces ubiquinone to ubiquinol

Line 470: representation -> Representation

Line 471: showed -> shown

Line 472: ubiquinone -> the ubiquinone

Line 477: It is indicated in the text that there are two ubiquinone binding sites in CII, but only one (QP) is shown in Figure 9.

Line 480: in -> into

Line 486: assembly -> assemble

Line 487: synthesised and inserted in -> and insert into

Line 494: clusters -> cluster

Line 501: of -> from

Line 508: 2.6 -> 10

Line 510: representation -> Representation

Line 525: heterodecamer -> heterodecamers

Line 527: details -> detail

Line 527: Crassa -> crassa

Line 528: Cerevisiae -> cerevisiae

Line 530: in -> into

Line 531: acids -> acid

Line 540: CIII -> The CIII

Line 545: in -> into

Line 553: nuclear -> nuclear-encoded

Line 560: it -> them

Line 562: including -> including those with

Line 567: Cbp3 -> The Cbp3

Line 576: Qcr7, and -> Qcr7, or

Line 579: Remove the words “in mammals” [redundant]

Line 596:  Remove the words: “and there are no known mammalian ortholog” [redundant]

Line 604: supercomplexes -> supercomplex

Line 605: enzyme complete biogenesis -> complete biogenesis of the enzyme

Line 606: 2.7 -> 11

Line 607: An essential passage -> A requirement

Line 616: in a second moment -> later

Line 621: in -> into

Line 624: N-terminal -> N-terminus

Line 635: in -> into

Line 640: in -> into

Line 641: UQCRFS1 -> the UQCRFS1

Lines 645 and 646: acids -> acid

Line 646: target -> targeting

Line 659: dues -> owes

Line 664: third -> the third

Line 666: process -> a process

Line 667: model of -> model of the

Line 668: 2.7 -> 11

Line 671: schematic -> Schematic

Line 671: Remove the bold typeface

Lines 672 and 677: please italicize S. cerevisiae

Line 692: 2.8 -> 12

Line 703: representation -> Representation

Line 708: evidences -> evidence

Line 709: indicated -> indicates

Line 726: proven -> shown

Table 2.6: bottom row, the word MTCO2 is duplicated

Line 764: 2.9. -> 13. The

Line 767: by -> of

Line 782: conversion -> conversion of

Line 785: subunits -> subunit

Line 788: representation -> Representation

Line 788: Please italicize Saccharomyces cerevisiae

Line 789: showed -> shown

Line 789: Remove one of the two periods at the end.

Line 796: moment -> step

Line 808: MT-ATP8 -> and MT-ATP8

Table 2.8: Second from bottom row (ATP5F1E), please change font in the third column

Line 838: last -> the last

Lines 849-855: please change font and spacing

Line 857: enzyme -> enzymes

Line 857: in time -> over time

Line 862: specie -> species

Line 869: native -> native PAGE

Line 870: a more -> more

Line 890: membrane -> IMS

Line 904: among -> with

Line 911: supercomplexe -> supercomplex

Line 915: native -> native PAGE

Line 921: 2.10 -> 14

Line 922: side -> hand

Line 925: not to -> not

Line 928: overall -> Overall

Line 929. Remove one of the two periods

Line 945: seem -> seems

Line 964: phospholipids -> phospholipid

Line 965: has been -> was

Line 994: role -> a role

Line 1001: position -> a position

Line 1018: inhibit -> inhibits

 

 

 

 

 

Author Response

• Figure 1 was modified as indicated.
• All the English wording issues indicated were addressed.
• Line 262: changed ‘85% of heme production takes place in erythroid progenitors, while the remaining 15% is generated in the liver…’ into ‘Most of heme production takes place in erythroid progenitors, followed by the liver for the formation of heme-containing enzymes.’
• Line 466: ‘…reduces ubiquinone to ubiquinol producing FADH2…’ was modified into ‘…reduces FAD to FADH2, which then reduces ubiquinone to ubiquinol…’
• Legend Figure 9: added ‘ubiquinone binding site facing the matrix (Qp)’ to specify which of the two binding sites is shown.
• In Table 2.6, bottom row, the word MTCO2 is not duplicated, it is repeated in two different columns, with different purposes.

 

Reviewer 2 Report

In the first part of their review, Protasoni and Zeviani bring information regarding mitochondria origins, structure and major functions. Then, they deeply and precisely go into the complexity of mitochondrial protein assembly (from complex I to V, as well as supercomplex formation). For each respiratory chain complex, they provide a list of gene mutations and related pathologies. Overall, this is a well-written and very interesting review with a view that has not been commonly published. This review is also well-illustrated. Here are my comments:

 

General comments:

-In their first part “1. Mitochondria”, the authors give information that will help the readers to better understand structure and functions of mitochondria. However, it is not clear why they describe mitochondrial dynamics unless they further describe mutations and related diseases, as done for mitochondrial complexes. To me, it is not clear either why they decided to mention specifically apoptosis. Indeed, mitochondria are now involved in other cell death pathways such as ferroptosis and necroptosis. Finally, line 187, the authors mention calcium homeostasis but they do not develop this specific part. Overall, the aim of the first part may be somehow confusing. In line, in the abstract, the aim of the review in not clearly stated. There is also no conclusion, no take home message at the end of their manuscript.

-Are there any links between supercomplex assembly and pathologies?

-Any therapeutic strategies to restore mitochondrial complex/supercomplex formation? It would refer to the last sentence of their abstract stating the challenge of discovering drug targets.

 

 

Minor comments:

• Abstract: it is very unusual to find references in the abstract.
• Discrepancy between figure numbers in the text and in the legends.
• Figure 2: Define abbreviations in the legend.
• L55: Which amount of mutant DNA can induce a visible phenotype?
• L151-152: Bring more details on why the protein import is driven by membrane potential.
• L154-155: What is the basis for the increasing affinities of precursor proteins?
• L163 and L166: Definition of mitophagy indicated L166 while first used in L163.
• L172-173: Please precise that Drp1 interacts with Fis1.
• L203: Name the pyruvate transporter MPC.
• L213: Indicate here that complex V is the ATPsynthase.
• L214: Add a reference indicating the amount of ATP produced.
• Figure 4: Show that glycolysis brings pyruvate which is then converted into Acetyl-coA. The top CoA-SH arrow should connect with the one between OAO and citrate.
• L229-L251: the apoptotic extrinsic pathway can connect to mitochondria through Bid cleavage.
• Figure 5: it seems that this figure is not cited in the manuscript. Cytochrome c should not be displayed as an inner membrane protein but should be in the IMS, in contact with IMM. Please define the abbreviations in the legend.
• L356: “cytochrome c a soluble carrier”: does that mean water-soluble?
• L404 figure 8: Is this the mammalian or murine complex I? Is complex I identical in all mammals?

 

Author Response

General comments:

 

• A section about mitochondria and calcium was added (1.7.3).
• A conclusive section was added.
• There are no clear evidences yet of direct link between SC deficiencies that are not a consequence of complexes assembly defects and pathologies.

 

Minor comments:

• Discrepancy between figure numbers in the text and in the legends.

The problem was addressed

• Figure 2: Define abbreviations in the legend.

The definitions of the abbreviations were added in the legend

• L55: Which amount of mutant DNA can induce a visible phenotype?

Different mutations can require different levels of heteroplasmy to induce a visible phenotype.

• L151-152: Bring more details on why the protein import is driven by membrane potential.

‘…responsible for an electrophoretic effect on the positively charged targeting sequences of these proteins…’ was added.

• L154-155: What is the basis for the increasing affinities of precursor proteins?

‘…compared with the affinities to the cis side…’ was added to better explain this concept.

• L163 and L166: Definition of mitophagy indicated L166 while first used in L163.

Mitophagy in L163 was substitute with ‘mitochondrial clearance’ and explained then in L166.

• L172-173: Please precise that Drp1 interacts with Fis1.

‘…via interaction with fission protein 1 (Fis1) and mito-chondrial fission factor (Mff)’ was added.

• L203: Name the pyruvate transporter MPC.

Modified in ‘Pyruvate enters through the mitochondrial pyruvate carrier (MPC) into the mitochondrial matrix [48]…’

• L213: Indicate here that complex V is the ATPsynthase.

Indicated

• L214: Add a reference indicating the amount of ATP produced.

The reference was added.

• Figure 4: Show that glycolysis brings pyruvate which is then converted into Acetyl-coA. The top CoA-SH arrow should connect with the one between OAO and citrate.

The figure was modified as suggested.

• Figure 5: it seems that this figure is not cited in the manuscript. Cytochrome c should not be displayed as an inner membrane protein but should be in the IMS, in contact with IMM. Please define the abbreviations in the legend.

The figure was corrected as indicated and cited in the text. Abbreviations were indicated in the figure legend.

• L356: “cytochrome c a soluble carrier”: does that mean water-soluble?

Yes, cytochrome c is a water-soluble molecule of the IMS, in opposition to the other hydrophobic OXPHOS proteins in the IMM.

• L404 figure 8: Is this the mammalian or murine complex I? Is complex I identical in all mammals?

Yes, while there are differences in the CI core and accessory subunits between plants, mammals, yeast and bacteria, mammalian structures are highly comparable.