Article
Plant Sciences
Peter L. Cummins
Summary: RuBisCO is the carbon-fixing enzyme in most photosynthetic organisms, with the C4 pathway utilizing carbon concentrating mechanisms to increase CO2 levels, while the energy efficiency of C3 photosynthesis relies on chloroplast CO2 supply. RuBisCO possesses extensive kinetic plasticity for adaptation to changes in photorespiration under various environmental conditions.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Agricultural Engineering
Soo Rin Kim, Soo-Jung Kim, Sun-Ki Kim, Seung-Oh Seo, Sujeong Park, Jamin Shin, Jeong-Sun Kim, Bo-Ram Park, Yong-Su Jin, Pahn-Shick Chang, Yong-Cheol Park
Summary: This review summarizes the recent advances in metabolic engineering strategies for CO2 fixation in yeasts and discusses the potential of other natural and synthetic metabolic pathways independent of RuBisCO for developing CO2-fixing yeast strains capable of producing value-added biochemicals.
BIORESOURCE TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Dario Leister, Anurag Sharma, Natalia Kerber, Thomas Naegele, Bennet Reiter, Viviana Pasch, Simon Beeh, Peter Jahns, Roberto Barbato, Mathias Pribil, Thilo Ruehle
Summary: In this study, it was found that the activity of Rubisco, the major catalyst in carbon dioxide conversion, is impaired by inhibitory sugars. The loss of two phosphatases in plants negatively affects plant growth and photosynthesis, but this effect can be reversed by introducing a XuBP phosphatase from Rhodobacter sphaeroides. This finding demonstrates the physiological importance of a metabolite damage-repair system in degradation of Rubisco by-products and has implications for carbon fixation optimization in photosynthetic organisms.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yi-Chin Candace Tsai, Lynette Liew, Zhijun Guo, Di Liu, Oliver Mueller-Cajar
Summary: The CO2-fixing enzyme rubisco is responsible for almost all carbon fixation. Rubisco activase (Rca) machinery is often required for this process. However, characterized carboxysomal rubiscos are not prone to inhibition and do not require activase machinery. New research has identified two carboxysomal rubiscos that release the substrate RuBP at a slower rate. It has also been found that activases encoded in carboxysome gene clusters can remove RuBP from the corresponding rubiscos. These findings have implications for improving carbon fixation in crops and introducing biophysical CCMs into plants and other hosts.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Cell Biology
Qiong Li, Yong-Liang Jiang, Ling-Yun Xia, Yuxing Chen, Cong-Zhao Zhou
Summary: This study elucidated the structure of an assembly intermediate of RuBisCO enzyme in cyanobacteria and discovered that the proteins Raf1 and RbcX facilitate and regulate RuBisCO assembly by controlling the formation of RuBisCO condensates.
Review
Plant Sciences
Thomas D. Sharkey
Summary: This review discusses the discovery of the enzyme responsible for the initial step of converting carbon dioxide into sugars and its properties. Rubisco is considered possibly the most important enzyme, especially in terms of quantity, on Earth. The review describes the key findings related to Rubisco, including its quaternary structure, the need for post-translational modification, and its dual role as an oxygenase and a carboxylase. Furthermore, the review highlights the significant requirement for chaperonins in the assembly of Rubisco in plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
Stephen P. Long, Samuel H. Taylor, Steven J. Burgess, Elizabete Carmo-Silva, Tracy Lawson, Amanda P. De Souza, Lauriebeth Leonelli, Yu Wang
Summary: Studies have shown that it takes several minutes for photosynthesis to adjust under different light conditions in modern crop canopies to improve efficiency, and transgenic manipulation has shown potential for productivity increase.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Review
Plant Sciences
Kaining Jin, Guoxin Chen, Yirong Yang, Zhiguo Zhang, Tiegang Lu
Summary: This review summarizes the strategies for improving C-3 photosynthesis, including enhancing Rubisco properties and reducing photorespiratory limitations. It also discusses the potential of synthetic biology approaches in constructing photorespiratory bypasses. These strategies have the potential to enhance C-3 photosynthesis and boost crop production.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Biotechnology & Applied Microbiology
Zhao Zhang, Dongzhe Sun, Ka-Wing Cheng, Feng Chen
Summary: Mixotrophy in Chromochloris zofingiensis involves a dynamic balance between photosynthesis and glucose metabolism, with intermediates of glycolysis directly entering the chloroplast to provide carbon sources and bypass the photosynthesis rate-limiting enzyme RuBisCO, leading to reduced energy waste and increased cell growth. This finding paves the way for future studies on mixotrophic biomass production and photosynthetic metabolism.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Plant Sciences
Kazuma Sakoda, Shunsuke Adachi, Wataru Yamori, Yu Tanaka
Summary: This review discusses the processes and variations related to dynamic photosynthesis in crop plants under field environments. The study reveals that plant adaptations to different hydrological environments are explained by natural genetic variation in gas diffusion through stomata. The coordination of photosynthetic and stomatal dynamics is emphasized for optimizing the balance between carbon gain and water use efficiency. Future challenges include utilizing natural genetic variation and employing high-throughput phenotyping to evaluate the effects of genetic and environmental factors on dynamic photosynthesis.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Taiyu Chen, Saba Riaz, Philip Davey, Ziyu Zhao, Yaqi Sun, Gregory F. Dykes, Fei Zhou, James Hartwell, Tracy Lawson, Peter J. Nixon, Yongjun Lin, Lu-Ning Liu
Summary: Researchers have successfully replaced plant Rubisco with a faster Rubisco in tobacco chloroplasts, resulting in a higher carboxylation rate and similar growth rate of transgenic plants compared to the wild-type under 1% CO2 concentration. This study represents a step towards engineering a fast and highly active Rubisco in chloroplasts to improve crop photosynthesis and growth.
Article
Fisheries
Ilaria Mania, Martina Pellicciaro, Roberta Gorra
Summary: The study investigated autotrophic microbial communities in sediments of an oligotrophic freshwater pond in the Italian Alps, revealing the presence of RuBisCO genes at different depths, with abundance strongly correlated with total bacterial abundance and positively correlated with Ca2+ and Mg2+ concentrations. These findings provide initial insights into the distribution of autotrophic bacteria relying on the Calvin-Benson-Bassham cycle for carbon fixation in alpine pond sediments.
MARINE AND FRESHWATER RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Wojciech Wietrzynski, Eleonora Traverso, Francis-Andre Wollman, Katia Wostrikoff
Summary: Rubisco is a crucial enzyme present in all photosynthetic organisms, and this study elucidates the biogenesis pathway of Rubisco in Chlamydomonas reinhardtii using site-directed mutants. The research uncovers a major regulation process during Rubisco biogenesis, where LSU translation is controlled by its ability to assemble with SSU, and proposes a model where the LSU8-RAF1 complex acts as a platform for SSU binding.
Article
Biochemistry & Molecular Biology
Masayasu Fujii, Shigenori Tanaka
Summary: In this study, ab initio analyses of RuBisCO were conducted using the fragment molecular orbital (FMO) method on multiple structural datasets with the 2'-carboxylarabinitol 1,5-bisphosphate (2CABP) ligand as a substrate analog. The results revealed physicochemical relevant features similar to phylogenetic relationships based on sequence information, as well as identified residues that strongly interacted with the ligand and characteristics of the isoforms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Alexander P. Hertle, Benedikt Haberl, Ralph Bock
Summary: Recent research has shown that genomes can be transferred between cells in both plants and animals, with mechanisms still unknown. This study focuses on the mechanism of plastid genome transfer in plants through cell-to-cell movement, providing insights into horizontal genome transfer processes.
Editorial Material
Plant Sciences
Andrew D. Hanson, A. Harvey Millar, Zoran Nikoloski, Danielle A. Way
Article
Plant Sciences
Paulo V. L. Souza, Liang-Yu Hou, Hu Sun, Louis Poeker, Martin Lehman, Humaira Bahadar, Adilson P. Domingues-Junior, Avilien Dard, Laetitia Bariat, Jean-Philippe Reichheld, Joaquim Albenisio G. Silveira, Alisdair R. Fernie, Stefan Timm, Peter Geigenberger, Danilo M. Daloso
Summary: Plants have a NADPH-thioredoxin reductase (NTR) system consisting of three enzymes located in different cellular compartments with important metabolic functions. In this study, the effects of NTR deficiency were investigated using Arabidopsis mutants. The results showed that NTR deficiency led to reduced growth and metabolic alterations in sink leaves, especially under high CO2 conditions. Interestingly, the mutants lacking all NTRs showed higher photosynthetic efficiency and altered redox states, indicating a functional interaction between chloroplastic and extra-chloroplastic NTRs in photosynthesis regulation. Overall, the NTR system plays a previously unknown role in regulating sink leaf metabolism and plant acclimation to high CO2.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Paula da Fonseca-Pereira, Rita de Cassia Monteiro-Batista, Wagner L. Araujo, Adriano Nunes-Nesi
Summary: Cofactors play a fundamental role in enzyme catalytic activity. Plants are a critical source of cofactors, including vitamin precursors, for human nutrition. Numerous studies have explored the metabolism of coenzymes and vitamins in plants, revealing their significant impact on plant development, metabolism, and stress responses.
Article
Plant Sciences
Leonardo Perez de Souza, Elena Bitocchi, Roberto Papa, Takayuki Tohge, Alisdair R. Fernie
Summary: The process of crop domestication leads to a reduction in gene expression associated with metabolic diversity, particularly in genes involved in specialized metabolism. The reduction in diversity at the metabolite level has been assumed but never adequately assessed and quantified. This study used high coverage metabolomics to investigate metabolic diversity in common bean and found a shift towards lower diversity and specialization in domesticated bean accessions. Molecular networking analysis enabled a broader annotation of metabolites and revealed a metabolic shift from specialized metabolism to central metabolism upon domestication of this crop.
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
Josiane C. de Carvalho, Katharine D. Goncalves, Elmer Goncalves, Pedro Paulo dos Santos, Manoel de Jesus de S. Miranda, Adamir da R. Nina Junior, Adriano Nunes-Nesi, Wagner L. Araujo, Jose Francisco de. C. Goncalves
Summary: We investigated the morphophysiological changes related to germination and initial growth of wild and cultivated genotypes of Hevea spp., aiming to add value to new clones. Sterilized seeds from six genotypes were studied for imbibition curve, germination parameters, and initial seedling growth. Morphological differences in seeds/embryos, imbibition process, emergence, and seedling growth were observed. Seed coat patterns, imbibition, growth, and development processes can be used as markers for genotype identification and selection. This is the first morphophysiological study of Hevea spp. seeds and seedlings. Phenotypic variability in seed and seedling morphophysiology can be explored in rubber tree breeding programs.
Review
Plant Sciences
Mutsumi Watanabe, Takayuki Tohge
Summary: Functional genomics approaches have successfully detected key metabolic polymorphisms in plant specialized metabolism through comparative omics analyses of wild-accessions and cultivars/wild species, as well as comparative genomic analyses in plant species focusing on gene clusters. In recent decades, intra-species specific metabolic polymorphisms, new functionalization of tandem duplicated genes, and metabolic gene clusters have been found as the main factors creating metabolic diversity of specialized metabolites in plants. However, strategic approaches depending on the target metabolic pathways are required for gene identification in plant specialized metabolism. The increasing availability of plant genome sequences and transcriptome data has facilitated inter-specific comparative analyses, including genomic analysis and gene co-expression network analysis. Here, we introduce functional genomics approaches with the integration of inter-/intra-species comparative metabolomics, their key roles in providing genomic signatures of metabolic evolution, and discuss future prospects of functional genomics on plant specialized metabolism.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Plant Sciences
Yue Jing, Mutsumi Watanabe, Fayezeh Aarabi, Alisdair R. Fernie, Monica Borghi, Takayuki Tohge
Summary: This study comprehensively analyzed the responses of four Brassicaceae species to UV-B radiation, revealing a reprogramming of the central metabolic pathway and the production of specific classes of flavonoids with increased protection against UV-B radiation. The activation of the phenylpropanoid-acetate pathway and the increase in phenylacylated-flavonoid glucosides were also observed across species. Interestingly, the expression of acyltransferase genes of the SCPLs protein class was constitutive but downregulated in response to UV-B radiation, possibly independent of the HY5 signaling pathway.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Greice Leal Pereira, Vitor L. Nascimento, Rebeca Patricia Omena-Garcia, Beatriz Costa O. Q. Souza, Jose Francisco de Carvalho Goncalves, Dimas Mendes Ribeiro, Adriano Nunes-Nesi, Wagner L. Araujo
Summary: Boron stress affects physiological parameters in tomato plants and stimulates ethylene biosynthesis, leading to toxicity symptoms in roots and leaves.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
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)
