Article
Plant Sciences
Zhong-Qing Li, Yao Zhang, He Li, Ting-Ting Su, Cheng-Gong Liu, Zi-Chao Han, Ai-Ying Wang, Jian-Bo Zhu
Summary: In this study, a genome-wide identification and characterization of FBA genes in cotton was conducted, revealing 17 GhFBA genes that were classified into two subgroups. The expression of GhFBAs was found to be tissue-specific and responsive to various abiotic stress and phytohormonal treatments.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Horticulture
Hailiang Zhao, Zicun Zhang, Yi Zhang, Longqiang Bai, Xiaohui Hu, Xiaojing Li, Lu Zhang, Yanxiu Miao, Yuping Wang
Summary: Melatonin reduces photoinhibition in cucumber seedlings during chilling by regulating the Calvin-Benson cycle.
SCIENTIA HORTICULTURAE
(2022)
Article
Multidisciplinary Sciences
Yuan Xu, Thomas Wieloch, Joshua A. M. Kaste, Yair Shachar-Hill, Thomas D. Sharkey
Summary: This study presents a carbon-13 washout model for leaf metabolism and identifies three processes that contribute to the labeling of Calvin-Benson cycle (CBC) metabolites. The model integrates CBC, cytosolic sugar pools, the glucose-6-phosphate shunt, and vacuolar sugars into a single system, providing a more complete understanding of carbon movement in photosynthetic metabolism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Cell Biology
Martha Ludwig, James Hartwell, Christine A. Raines, Andrew J. Simkin
Summary: The Calvin-Benson-Bassham (CBB) cycle is found in all photosynthetic organisms and acts as the ancestral CO2 assimilation pathway. Biochemical extensions to this cycle, such as C4 photosynthesis and Crassulacean acid metabolism (CAM), allow for CO2 concentrating mechanisms. However, further research is needed to understand the integration and regulation of C4 and CAM pathways with the CBB cycle.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Plant Sciences
Christine A. Raines
Summary: The Calvin-Benson-Bassham (CBB) cycle is the most important pathway on earth, capturing and converting CO2 into organic molecules for the basis of life. This cycle has been extensively studied and is highly conserved in nature. The enzymes in this cycle regenerate the CO2 acceptor molecule RuBP. Manipulating RuBP regeneration has the potential to improve photosynthesis and increase crop yields.
Article
Chemistry, Multidisciplinary
Jia Feng, Ding Ma, Siyuan Gao, Yang Liao, Jiao Feng, Sheng Xu, Xin Wang, Kequan Chen
Summary: Global climate change caused by greenhouse gas emission is the fundamental challenge facing mankind. Recently, biological carbon dioxide fixation has received much attention, with the Calvin-Benson-Bassham (CBB) cycle being the most studied pathway. This paper reviews the understanding of the CBB cycle, summarizes the progress in assembling the CBB cycle in heterotrophic microorganisms, and discusses the strategies to enhance carbon fixation efficiency. The potential applications of the engineered microorganisms in green biomanufacturing and synthetic autotrophs are also discussed.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Plant Sciences
Theo Le Moigne, Libero Gurrieri, Pierre Crozet, Christophe H. Marchand, Mirko Zaffagnini, Francesca Sparla, Stephane D. Lemaire, Julien Henri
Summary: Thioredoxins (TRXs) are a class of disulfide oxidoreductases with a highly conserved fold, plant TRXs evolved into seven types, with z-type TRX having a distinct electronegative surface that can activate the photosynthetic enzyme phosphoribulokinase.
Review
Cell Biology
Vittoria Clapero, Stephanie Arrivault, Mark Stitt
Summary: The Calvin-Benson cycle has undergone massive selection and co-evolution with carbon-concentrating mechanisms due to changing environmental factors. Metabolite profiling reveals species-specific variations in the operation of the cycle, indicating the influence of different modes of photosynthesis. Connectivity analysis identifies constraints and driving factors for cross-species diversity in the cycle.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2024)
Review
Cell Biology
Thomas D. Sharkey
Summary: The pentose phosphate pathway (PPP) consists of an oxidative branch and a non-oxidative branch, with the latter playing a crucial role in the Calvin-Benson cycle. The non-oxidative branch can convert CO2 into sugar through metabolic reversal, involving reactions that consume ATP in photosynthesis. The oxidative branch forms a shunt with the non-oxidative branch, leading to an unusual labeling pattern in the cytosol and a potential stress-induced response in the stroma.
Review
Chemistry, Physical
Filippo Federici, Enrico Orsi, Pablo Ivan Nikel
Summary: This review discusses the opportunities and challenges of using the Calvin-Benson-Bassham cycle (CBBc) to engineer microbial cell factories for the utilization of CO2, highlighting its potential to advance a circular carbon bioeconomy. By studying and engineering the CBBc, further exploration of biomanufacturing using CO2 as a feedstock can be achieved.
Review
Plant Sciences
Mark Stitt, Gian Luca Borghi, Stephanie Arrivault
Summary: Understanding the interspecies diversity and evolution of photosynthesis is crucial for increasing crop yield. Metabolite profiling can help uncover differences between species and reveal key factors in photosynthesis.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Maureen Saint-Sorny, Pawel Brzezowski, Stephanie Arrivault, Jean Alric, Xenie Johnson
Summary: This study utilized a Chlamydomonas reinhardtii RuBisCO-less mutant, Delta rbcL, to investigate carbohydrate metabolism in the absence of atmospheric carbon fixation. The results showed that in Delta rbcL, ATP is generated via photosynthetic electron transfer reactions at the onset of illumination, and metabolites of the CBB cycle are responsive to light.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Environmental Sciences
Yating Chen, Xiaomin Li, Tongxu Liu, Fangbai Li, Weimin Sun, Lily Y. Young, Weilin Huang
Summary: In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) were enriched from paddy soil under microoxic conditions, and their capacity for Fe(II) oxidation and carbon assimilation was investigated. The results showed that the highest rate of Fe(II) oxidation was obtained in the FeCO3 tubes, and cells grown in the Fe3(PO4)2 tubes yielded the maximum assimilation amounts of 13C-NaHCO3 on Day 15.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Biochemistry & Molecular Biology
Cassy Gerard, Frederic Carriere, Veronique Receveur-Brechot, Helene Launay, Brigitte Gontero
Summary: The CP12 protein, an intrinsically disordered protein, plays a key role in the regulation of CO2 assimilation and may have additional functions. Its structure is influenced by the redox state of its cysteine residues.
Review
Biochemistry & Molecular Biology
Kezhen Qin, Alisdair R. Fernie, Youjun Zhang
Summary: Recent studies have shown that enzymes from various biological pathways can form larger supramolecular structures known as super-complexes, including those found in the mitochondrial respiratory chain complexes. These dynamically assembled super-complexes can switch between participating in larger complexes and existing in a free state, potentially reducing oxidative damage and increasing metabolic efficiency.
Article
Multidisciplinary Sciences
Anika Kueken, Damoun Langary, Zoran Nikoloski
Summary: Understanding the complexity of metabolic networks can be characterized by identifying multi-reaction dependencies. Concordant complexes can capture these dependencies and reduce the apparent complexity of metabolic networks. The metabolic network of Escherichia coli is more tightly coordinated than expected by chance.
Article
Developmental Biology
Timon W. Matz, Yang Wang, Ritika Kulshreshtha, Arun Sampathkumar, Zoran Nikoloski
Summary: In this study, the authors used a network representation of live cell imaging data from shoot apical meristems (SAMs) in Arabidopsis thaliana to predict cell division events and their consequences at the tissue level. They found that a support vector machine classifier based on the SAM network properties is able to predict cell division events with high accuracy. Furthermore, the combination of topological and biological properties can improve the prediction accuracy of resulting changes in tissue topology triggered by cell division. The study also highlights the importance of microtubule-mediated cell-to-cell growth coordination in influencing tissue-level topology.
Editorial Material
Plant Sciences
Andrew D. Hanson, A. Harvey Millar, Zoran Nikoloski, Danielle A. Way
Review
Plant Sciences
Philipp Wendering, Zoran Nikoloski
Summary: Plant respiration is important for supporting cellular processes and the global carbon cycle. Modulating plant respiration can increase plant yield and mitigate climate change effects. Modeling plant respiration has seen less effort compared to photosynthesis, but recent advances have improved the understanding of the process. The review highlights the need for coupling biochemical models of respiration with acclimation and adaptation models for effective usage in breeding and climate scenario modeling.
Review
Biochemistry & Molecular Biology
Isabella osterlund, Staffan Persson, Zoran Nikoloski
Summary: Filamentous structures are widely present in nature and studied in various scientific fields. They play important roles in biological systems and form dynamic networks. Automated methods for tracing and tracking of filamentous structures have been developed, and this review categorizes and discusses the state-of-the-art methods for tracing and tracking of filamentous structures in sparse and dense networks, highlighting the mathematical approaches, assumptions, and outstanding challenges for future research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Seirana Hashemi, Roosa Laitinen, Zoran Nikoloski
Summary: Accumulating evidence has shown the importance of trade-offs involving metabolic traits in organism evolution. Different levels of complexity in metabolic models have been used to investigate and explain various metabolic trade-offs. This review discusses the modelling approaches used to study trade-offs in enzyme properties, reaction rates, pathway and network rates and yields, metabolic objectives, and metabolic concentrations. Insights into these trade-offs are provided by constraint-based metabolic modelling, highlighting their relationship to the classical black box Y-model and identifying concerns and future research perspectives.
Article
Multidisciplinary Sciences
Qiao Wen Tan, Peng Ken Lim, Zhong Chen, Asher Pasha, Nicholas Provart, Marius Arend, Zoran Nikoloski, Marek Mutwil
Summary: The response of plants to the combination of multiple stresses occurring simultaneously is not well understood. This study investigates how gene expression in Marchantia polymorpha is affected by different combinations of seven abiotic stresses and provides online resources for data visualization and usability.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Marius Arend, Yizhong Yuan, M. Aguila Ruiz-Sola, Nooshin Omranian, Zoran Nikoloski, Dimitris Petroutsos
Summary: Using a transcriptomic data compendium of Chlamydomonas reinhardtii, we reconstructed a gene regulatory network and identified transcriptional regulators of photoprotection. Our study showed that the CCM regulator LCR1 also controls photoprotection, and QER7, a Squamosa Binding Protein, suppresses photoprotection and CCM-gene expression under the control of Phototropin. This study provides insights into gene expression regulation in microalgae.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Philipp Wendering, Marius Arend, Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Turnover numbers of enzymes are a key property that can improve the prediction accuracy of cellular phenotypes in metabolic modeling. However, in vitro and in vivo turnover numbers alone do not lead to accurate predictions of condition-specific growth rates of E. coli and S. cerevisiae, especially when considering protein abundances. By correcting turnover numbers using proteomics and physiological data, we demonstrate improved predictions of condition-specific growth rates. Our approach provides a means to correct turnover numbers and catalog kcatomes of other organisms.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Hao Tong, Roosa A. E. Laitinen, Zoran Nikoloski
Summary: Plants can adapt to suboptimal growth environments and mitigate the effects on their fitness-related traits through phenotypic plasticity. However, accurate genomic prediction models for plasticity of fitness-related traits, especially for rosette growth under nitrogen availability changes, are still lacking. In this study, metabolic and statistical modeling were combined to explore and predict the genetic variation and predictability of flux plasticity in Arabidopsis thaliana. The results showed significant genetic variation in key metabolic pathways and photorespiration reactions, and the genomic prediction of growth plasticity improved the predictability of fresh weight under low nitrogen conditions.
Article
Multidisciplinary Sciences
Sandra Correa Cordoba, Hao Tong, Asdrubal Burgos, Feng Zhu, Saleh Alseekh, Alisdair R. Fernie, Zoran Nikoloski
Summary: This study constructed a plant lipid module for Arabidopsis rosette and integrated it into other plant metabolic models to dissect the genetic architecture of lipid metabolism. This research is important because it provides a mechanistic description model for studying the component modulation of lipid metabolism.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Marius Arend, David Zimmer, Rudan Xu, Frederik Sommer, Timo Muehlhaus, Zoran Nikoloski
Summary: Metabolic engineering of microalgae can be improved by integrating enzyme turnover numbers and quantitative protein abundance data, which provides valuable information on enzyme catalytic rates and improves predictions on enzyme usage and allocation.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Alain J. Mbebi, Zoran R. Nikoloski
Summary: Reconstruction of cellular networks based on molecular profiles is a challenging task in systems biology. In this study, we focused on inferring gene regulatory networks (GRNs) and proposed two novel approaches that simultaneously model multiple target genes. The results show that these models outperform existing methods and provide improved inference of GRNs.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Research findings suggest that steady-state flux distributions derived from maximizing multi-reaction dependencies principle are more accurate and precise compared to traditional predictions. This indicates that other cellular principles may influence the distribution of intracellular fluxes. Data on intracellular fluxes provide snapshots of the rates of underlying reactions and metabolic pathway activity, but capturing this data is resource-intensive.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Mauricio Alexander de Moura Ferreira, Wendel Batista da Silveira, Zoran Nikoloski
Summary: This study explores the allocation of proteins in cellular pathways and proposes a method, called PARROT, to predict enzyme allocation based on the minimization of differences between growth conditions. The results suggest that minimizing protein allocation adjustments is a key principle in microorganisms under alternative growth conditions.
PLOS COMPUTATIONAL BIOLOGY
(2023)
