Editing of Mitochondrial Transcripts nad3 and cox2 by Dek10 Is Essential for Mitochondrial Function and Maize Plant Development
Authors: Rentao Song
Zhongrui Tian
Xinze Chen
Weiwei Qi
Xiuzu Chen
Lei Lu
Wei Zhang
Journal: Genetics (2017)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: RNA editing; Zea mays; dek10; mitochondrion; pentatricopeptide repeat protein
Affiliations: Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 200444, China., Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 200444, China ., National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China.

Abstract:  Respiration, the core of mitochondrial metabolism, depends on the function of five respiratory complexes. Many respiratory chain-related proteins are encoded by the mitochondrial genome and their RNAs undergo post-transcriptional modifications by nuclear genome-expressed factors, including pentatricopeptide repeat (PPR) proteins. Maize defective kernel 10 (dek10) is a classic mutant with small kernels and delayed development. Through positional cloning, we found that Dek10 encodes an E-subgroup PPR protein localized in mitochondria. Sequencing analysis indicated that Dek10 is responsible for the C-to-U editing at nad3-61, nad3-62, and cox2-550 sites, which are specific editing sites in monocots. The defects of these editing sites result in significant reduction of Nad3 and the loss of Cox2. Interestingly, the assembly of complex I was not reduced, but its NADH dehydrogenase activity was greatly decreased. The assembly of complex IV was significantly reduced. Transcriptome and transmission electron microscopy (TEM) analysis revealed that proper editing of nad3 and cox2 is critical for mitochondrial functions, biogenesis, and morphology. These results indicate that the E-subgroup PPR protein Dek10 is responsible for multiple editing sites in nad3 and cox2, which are essential for mitochondrial functions and plant development in maize. 

Retracted: No

PubPeer comments:
 The central claim of this paper has been fact-checked and rated  incorrect by *Climate Feedback*, a website from the fact-checking not-for-profit *Science Feedback* which is accredited by the *International Fact-Checking Network (IFCN) at The Poynter Institute*. They have provided an analysis of the paper by 6 scientific reviewers here: https: climatefeedback.org claimreview non-peer-reviewed-manuscript-falsely-claims-natural-cloud-changes-can-explain-global-warming This regards the paper s claim: During the last hundred years the temperature is increased about 0.1u00b0C because of carbon dioxide. The human contribution was about 0.01u00b0C. The summary of Climate Feedback s analysis is quoted here: Flawed Reasoning: The authors argument claims a correlation between cloud cover relative humidity and global temperature proves that the former caused the latter without investigating whether they have the relationship backwards. Inadequate support: The source of their claimed global cloud dataset is not given, and no research on their proposed mechanism for climate change is cited. Fails to provide correct physical explanation: The manuscript incorrectly claims that the rise of atmospheric carbon dioxide is caused by release from ocean waters. It also provides no explanation for the claim that an increase in relative humidity causes global cooling. I would like to encourage a response from the authors. , 
 #1 Our short paper  No experimental... is like a summary of our earlier papers. So the further details are given in those earlier papers, which are of course listed as references. It seems that the reviewers have not read those references. This is a reason why all their comments are wrong. For example  flawed Reasoning: The authors arguments claims a correlation... This is a lie. We have not used any correlation! In addition,  ...carbon dioxide is caused by release from ocean waters... This reveals that the reviewers do not know Henry`s law, which is the basic law between liquid and gas phases. , 
 In Figure 2 we see the observed global temperature anomaly (red) and global low cloud cover changes (blue). These experimental observations indicate that 1 % increase of the low cloud cover fraction decreases the temperature by 0.11u00b0C. The wording of this statement suggests that the correlation of low cloud cover change and temperate change indicates the former causes the latter. If this interpretation was unintended, perhaps the paper should be corrected accordingly. As it is written, the reviewers are right to point out that correlation does not imply causation. The reviewers state that the paper does not investigate whether the temperature change is what causes low cloud cover change. The author has replied that they need to read the referenced papers. Where in the referenced papers has this been investigated? , 
 #3 #3In this paper u201dNo experimental ...u201d We have not calculated the correlation between temperature and low cloud cover fraction! Note that the correlation is a bare number between -1 and +1 without any unit. In order to study how much the temperature changes due to the change of the low cloud cover fraction we have theoretically calculated u2206T, when we first change cloud fraction by u2206c. In addition, with the same way for the relative humidity u0278. The results are as follows: u2206T is about - 11u2103 u2206c or - 15u2103 u2206u0278, which give the second term in Equation (1) in this paper. Please read the whole chapter 2 in Ref (2). In addition, in Ref (3) the text after Equation (24). OBS! G depends on the relative humidity and a cloud cover, too. In Ref (4) Equation (34) gives the most accurate temperature change depending on u2206u0278. Already in the year 1972 S. H. Schneider calculated the term about -11u2103u2206c. See Ref(12) in Ref(2). If we go next to the inverse direction i.e. we warm the atmosphere by increasing CO2 (green house effect or the first term in Equation (1)), u2206T0 is Ru2206Q, where u2206Q is the increase of absorption due to CO2 . Now u2206T0 is positive and the total cloud amount c0 increases about 6.4% u2103, if the relative humidity is constant. Now we can write : u2206T = - 11u2103u2206c and u2206T 0 = + 15.6u2103u2206c0 and finally u2206c u2206c0 is about -14, because u2206T u2206T0 is typically about 10. This means that the first term in Equation (1) is typically 10 % of the second term. This will be in our next paper dealing with Henry`law. All the above relations can be calculated using Equation (14) in Ref(4), where Figure 5 describes the situation. Now it is clear that u2206T = - 11u2103u2206c is the correct case, because u2206T and u2206c are opposite phases due to the minus sign. This is clearly seen in Figure 2. Please note that in this case the reasons for changes in the low cloud cover fraction are outside of the earth like cosmic rays, the sun and so on. But in the other case the cause is inside the atmosphere. My conclusion is that the comments are not very serious, because all the answers are in the References. At the end I like to thank Steve Castro for his valuable comments, which will improve our presentation in the next step. And a good thing was that when writing this I found three tiny printing errors in the paper in Ref(2). These are as follows: in Equation (14) 10.89u2206cu2103 should be -10.89u2206cu2103, on the page 395 Erlykin and Wolfendale (12) should end (13), Schneider (11) should end (12). , 
 #2 Henry s law does not explain the increase in atmospheric CO2 observed over the last few centuries. I urge the authors to calculate by how much the oceans would have to warm to get the observed increase according to Henry s law, explain why this temperature increase has not been observed (off by at least an order of magnitude), why the TIC in the oceans has been observed to increase (outgassing would mean it would decrease), the pH observed to decrease (outgassing would mean it would increase) and explain what enormous sink has taken up all the CO2 released through anthropogenic activity. In the absence of credible answers to all these issues, the authors should retract their statement about the Climate Feedback reviewers not knowing about Henry s law, and instead apologise for not knowing about all the science that contradicts their claim about the observed CO2 increase, and acknowledge Henry s law directly contradicts the CO2 rise being due to ocean warming. , 
 #5 You are right that the ocean is a strong sink for the human CO2 release. However, there is the temperature dependent emission component, which is smaller than the uptake of CO2 from the atmosphere. So your comments do not disprove our claims. For a better explanation you should wait for our paper about this topic. I hope that it will come up within a few months. Please use your real name. , 
 #6 If the authors agree that the ocean is a strong sink for the human CO2 release, they accept that the current atmospheric increase in CO2 is *not* due to ocean outgassing, and thereby agree that their comment about the climate feedback reviewers being ignorant about Henry s law was unwarranted. It then means the authors have already pre-debunked their own forthcoming article. Of course, even the simplest of mass balance equations should have told the authors they were wrong in their assertions, and the additional observations I added merely cement the fact that the oceans are clearly not the cause of the increased atmospheric CO2 (increase in TIC, decrease in pH, lack of credible enormous net sink, lack of sufficient ocean temperature increase to explain the large increase in atmospheric CO2). Criticism is independent of a person s identity. , 
 Question for the authors and others: Henry s Law applies to systems at equilibrium. The ocean-atmosphere is not at equilibrium. Does this not impact the argument going on here? ,