Functional decomposition of metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-39724-7
Download full text from publisher
References listed on IDEAS
- Conghui You & Hiroyuki Okano & Sheng Hui & Zhongge Zhang & Minsu Kim & Carl W. Gunderson & Yi-Ping Wang & Peter Lenz & Dalai Yan & Terence Hwa, 2013. "Coordination of bacterial proteome with metabolism by cyclic AMP signalling," Nature, Nature, vol. 500(7462), pages 301-306, August.
- David W. Erickson & Severin J. Schink & Vadim Patsalo & James R. Williamson & Ulrich Gerland & Terence Hwa, 2017. "A global resource allocation strategy governs growth transition kinetics of Escherichia coli," Nature, Nature, vol. 551(7678), pages 119-123, November.
- Hugo Dourado & Martin J. Lercher, 2020. "An analytical theory of balanced cellular growth," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
- H. Jeong & B. Tombor & R. Albert & Z. N. Oltvai & A.-L. Barabási, 2000. "The large-scale organization of metabolic networks," Nature, Nature, vol. 407(6804), pages 651-654, October.
- Iván Domenzain & Benjamín Sánchez & Mihail Anton & Eduard J. Kerkhoven & Aarón Millán-Oropeza & Céline Henry & Verena Siewers & John P. Morrissey & Nikolaus Sonnenschein & Jens Nielsen, 2022. "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Benjamin D. Towbin & Yael Korem & Anat Bren & Shany Doron & Rotem Sorek & Uri Alon, 2017. "Optimality and sub-optimality in a bacterial growth law," Nature Communications, Nature, vol. 8(1), pages 1-8, April.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Robert Planqué & Josephus Hulshof & Bas Teusink & Johannes C Hendriks & Frank J Bruggeman, 2018. "Maintaining maximal metabolic flux by gene expression control," PLOS Computational Biology, Public Library of Science, vol. 14(9), pages 1-20, September.
- Manlu Zhu & Xiongfeng Dai, 2023. "Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Manlu Zhu & Xiongfeng Dai, 2024. "Shaping of microbial phenotypes by trade-offs," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Gaoyang Li & Li Liu & Wei Du & Huansheng Cao, 2023. "Local flux coordination and global gene expression regulation in metabolic modeling," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun, 2006. "Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-10, November.
- Zihan Wang & Akshit Goyal & Veronika Dubinkina & Ashish B. George & Tong Wang & Yulia Fridman & Sergei Maslov, 2021. "Complementary resource preferences spontaneously emerge in diauxic microbial communities," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- Zhou, Wei-Xing & Jiang, Zhi-Qiang & Sornette, Didier, 2007. "Exploring self-similarity of complex cellular networks: The edge-covering method with simulated annealing and log-periodic sampling," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 375(2), pages 741-752.
- Manlu Zhu & Yiheng Wang & Haoyan Mu & Fei Han & Qian Wang & Yongfu Pei & Xin Wang & Xiongfeng Dai, 2024. "Plasmid-encoded phosphatase RapP enhances cell growth in non-domesticated Bacillus subtilis strains," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Jorge Peña & Yannick Rochat, 2012. "Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-13, September.
- Sgrignoli, P. & Agliari, E. & Burioni, R. & Schianchi, A., 2015.
"Instability and network effects in innovative markets,"
Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 108(C), pages 260-271.
- Paolo Sgrignoli & Elena Agliari & Raffaella Burioni & Augusto Schianchi, 2014. "Instability And Network Effects In Innovative Markets," Working Papers 16/2014, University of Verona, Department of Economics.
- Paolo Sgrignoli & Elena Agliari & Raffaella Burioni & Augusto Schianchi, 2014. "Instability and network effects in innovative markets," Papers 1409.3837, arXiv.org.
- Long Ma & Xiao Han & Zhesi Shen & Wen-Xu Wang & Zengru Di, 2015. "Efficient Reconstruction of Heterogeneous Networks from Time Series via Compressed Sensing," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-12, November.
- Christian F A Negre & Hayato Ushijima-Mwesigwa & Susan M Mniszewski, 2020. "Detecting multiple communities using quantum annealing on the D-Wave system," PLOS ONE, Public Library of Science, vol. 15(2), pages 1-14, February.
- Daphna Rothschild & Erez Dekel & Jean Hausser & Anat Bren & Guy Aidelberg & Pablo Szekely & Uri Alon, 2014. "Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-9, May.
- Biggiero, Lucio & Angelini, Pier Paolo, 2015. "Hunting scale-free properties in R&D collaboration networks: Self-organization, power-law and policy issues in the European aerospace research area," Technological Forecasting and Social Change, Elsevier, vol. 94(C), pages 21-43.
- Tamás Nepusz & Tamás Vicsek, 2013. "Hierarchical Self-Organization of Non-Cooperating Individuals," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-9, December.
- Aslam, Faheem & Aziz, Saqib & Nguyen, Duc Khuong & Mughal, Khurrum S. & Khan, Maaz, 2020.
"On the efficiency of foreign exchange markets in times of the COVID-19 pandemic,"
Technological Forecasting and Social Change, Elsevier, vol. 161(C).
- Faheem Aslam & Saqib Aziz & Duc K. Nguyen & Khurram S. Mughal & Maaz Khan, 2020. "On the Efficiency of Foreign Exchange Markets in Times of the COVID-19 Pandemic," Working Papers 2020-010, Department of Research, Ipag Business School.
- Aslam, Faheem & Aziz, Saqib & Nguyen, Duc Khuong & Mughal, Khurram S. & Khan, Maaz, 2020. "On the Efficiency of Foreign Exchange Markets in times of the COVID-19 Pandemic," MPRA Paper 102458, University Library of Munich, Germany, revised Jul 2020.
- Faheem Aslam & Saqib Aziz & Duc Khuong Nguyen & Khurrum Mughal & Maaz Khan, 2020. "On the efficiency of foreign exchange markets in times of the COVID-19 pandemic," Post-Print hal-02966920, HAL.
- Semi Min & Juyong Park, 2019. "Modeling narrative structure and dynamics with networks, sentiment analysis, and topic modeling," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-20, December.
- Jiang, Jingchi & Zheng, Jichuan & Zhao, Chao & Su, Jia & Guan, Yi & Yu, Qiubin, 2016. "Clinical-decision support based on medical literature: A complex network approach," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 459(C), pages 42-54.
- Ida Lauritsen & Pernille Ott Frendorf & Silvia Capucci & Sophia A. H. Heyde & Sarah D. Blomquist & Sofie Wendel & Emil C. Fischer & Agnieszka Sekowska & Antoine Danchin & Morten H. H. Nørholm, 2021. "Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
- Gerhardt, Günther J.L. & Lemke, Ney & Corso, Gilberto, 2006. "Network clustering coefficient approach to DNA sequence analysis," Chaos, Solitons & Fractals, Elsevier, vol. 28(4), pages 1037-1045.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39724-7. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.