Quantitative Connection between Cell Size and Growth Rate by Phospholipid Metabolism
Authors: Hualin Shi
Qing Zhang
Zhichao Zhang
Shaohua Guan
Journal: Cells (2020)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Escherichia coli; cell size; flux balance analysis; genome-scale metabolic network.
Affiliations: School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China., CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.

Abstract:  The processes involved in cell growth are extremely complicated even for a single cell organism such as Escherichia coli, while the relationship between growth rate and cell size is simple. We aimed to reveal the systematic link between them from the aspect of the genome-scale metabolic network. Since the growth rate reflects metabolic rates of bacteria and the cell size relates to phospholipid synthesis, a part of bacterial metabolic networks, we calculated the cell length from the cardiolipin synthesis rate, where the cardiolipin synthesis reaction is able to represent the phospholipid metabolism of Escherichia coli in the exponential growth phase. Combined with the flux balance analysis, it enables us to predict cell length and to examine the quantitative relationship between cell length and growth rate. By simulating bacteria growing in various nutrient media with the flux balance analysis and calculating the corresponding cell length, we found that the increase of the synthesis rate of phospholipid, the cell width, and the protein fraction in membranes caused the increase of cell length with growth rate. Different tendencies of phospholipid synthesis rate changing with growth rate result in different relationships between cell length and growth rate. The effects of gene deletions on cell size and growth rate are also examined. Knocking out the genes, such as Œî tktA, Œî tktB, Œî yqaB, Œî pgm, and Œî cysQ, affects growth rate largely while affecting cell length slightly. Results of this method are in good agreement with experiments. 

Retracted: No

PubPeer comments:
 FBA has limitations, however. Because it does not use kinetic parameters, **it cannot predict metabolite concentrations.** It is also only suitable for determining fluxes at steady state. Except in some modified forms, FBA does not account for regulatory effects such as activation of enzymes by protein kinases or regulation of gene expression, so its predictions may not always be accurate. Fromu201cWhat is flux balance analysis?u201duff0chttps: www.ncbi.nlm.nih.gov pmc articles PMC3108565 , 
 As the work  [What is flux balance analysis] ? states: FBA has limitations, however. **Because it does not use kinetic parameters, it cannot predict metabolite concentrations. **It is also only suitable for determining fluxes at steady state. Except in some modified forms, FBA does not account for regulatory effects such as activation of enzymes by protein kinases or regulation of gene expression, so its predictions may not always be accurate. But in this work [Quantitative Connection between Cell Size and Growth Rate by Phospholipid Metabolism]  .Aruthors predicted concentration of [PG], according to experimental value.   , 
  Why does E.coli have 3.4 capsuff1f , 
 We noticed Figure 3  Authors stated that the experimental data were cited from Basan et at. [10].uff0c and authors supposed that the cell width is a constant. But we check it in work[10] . We found that:  In the experimental data, the cell width is different in e different growth conditions. Authors should explain the reason why authors supposed that the cell width is a constant. , 
 This is the Author Response, which includes a brief introduction and replies to all the above comments. Please check the attached files. My (HualinShi s) email address is shihl@itp.ac.cn instead of h***i@i***c.cn shown on PubPeer website. Please use the correct email address to contact me. Thank you!        , 
 #5  Can the author cite any examples or references? , 
 #5 The author did not realize that the kinetic parameter of the Michaelis-Mentenion reaction is a quantity related to the growth rate. This is why the flux balance analysis cannot predict the concentration of metabolites. , 
 #6  I am also confused that there are 3.4 caps on average in a cell division cycle. I really can t imagine what this is like. , 
 This is the Author Response to Comment #6,7,8. Thanks for these comments and thank the Managing Editor of the journal for reminding me again.      , 
 #9 This picture is from [Cell-Size Control and Homeostasis in Bacteria]  The generation time is about 18min. How can we conclude from this picture that the average caps is 3.4? , 
 This is the Author Response to Comment #10. Thank Ischnura Senegalensis for this comments and thank the Managing Editor of the journal for reminding me again.    , 
 The definition of cell size in the theoretical part of the article is inconsistent with the definition of cell size in experimental data.  As shown in Equation 20, the cell length herein is the average cell length in a cell cycle. The experimental data used in Figure 2 in this article comes from the literatureuff1a[Cell-Size Control and Homeostasis in Bacteria ] . In this reference, cell size refers to the size of birth cells. For example, Figure 2uff1a  The same error also occurred in the articleuff1a[Cell Size Is Coordinated with Cell Cycle by Regulating Initiator Protein DnaA in E. coli]https: pubpeer.com publications E1BAD599BBA44AC2E5A2FDE50EB750#) by the same aurthors. , 
 I am puzzled by the inconsistent expression of the parameters km and Vamx. 1 In the text, the author thinks that KM is a constant and Vmax is related to strain.  2 However, in the author s reply #9, the author believes that km and Vmax are constants.  3 In the author s reply #11, the author changed the values of KM and Vmax at the same time.  , 
 The author s assumptions about cell width and growth rate under the two models (SEFBA and the reduced model of SEFBA) are contradictory. SEFBA: Cell width D changes linearly with the growth rate based on experiments data [6,9,13]. But in the reduced model of SEFBA, t he author assumes that the cell width has nothing to do with the growth rate and is a constant. , 
 This is an Author Response to the comment #13, #14 and #12, which should have appeared almost three weeks ago. The managing editor of Cells want to seek the advice of their academic editors before we reply. Two days ago (September 3), the managing editor informed us that their academic editor recommended that we put the reply on PubPeer. We respect the procedure of the journal in dealing with such things, and we are very grateful to the academic editors for their work. While waiting for feedback from the academic editor, an anonymous email was sent to many of my colleagues, which made a non-academic personal attack on me. So far, I have replied to all comments. As it has gone beyond academic discussion now, I will not reply here in the future.       , 
 The manuscript by Zhang et al reported a model that describes a relationship between growth rate and cell size via lipid biosynthesis. The claim of this study u201cCell size correlated to growth by metabolic networku201d was not supported by this manuscript following reasons. Tautology. The rate for the cardiolipin biosynthesis (rCLPNS) was linearly correlated with the growth rate due to a rule of FBA (fig. 1E). As shown in Eqn 17, the cell size L was correlating with rCLPNS. It means that cell size correlated with growth rate because the growth rate correlated with cell size. Arbitrary selection of cardiolipin biosynthesis. There is no biological reason to focus on the cardiolipin biosynthesis instead of other membrane lipids such as PG. Since PG is also important membrane lipid, a similar formulation could be done by the metabolic reaction in the PG biosynthetic pathway. The cardiolipin biosynthesis seems to be selected arbitrary, to introduce a nonlinear relationship in equation 7 that has no biological justification. What is wCLPNS? By introducing Eqn 18, and allowing negative values for wCLPNS, a negative correlation between growth rate and rate for the cardiolipin biosynthesis could be introduced without a biological basis. Fig. 3 means that cell size and growth rates were negatively correlated because parameter E (=wCLPNS) was set to a negative value. , 
 The authors calculations of the proportion of proteins on the membrane in the SEFBA model and the simplified SEFBA model are contradictory. In the SEFBA model, the authors assert that u201c*we assumed that the ratio of the surface area covered by protein to the surface area covered by phospholipid in membranes was in proportion to the ratio of facilitated diffusion rate (rfac) to simple diffusion rate (rsim)*,u201d written as equation (24). The author gets However, in the simplified SEFBA model, it is assumed that both fPG and KM are about constant, the value of C is 2.96 under different growth stresses. ,