Article
Plant Sciences
Takashi Yamano, Chihana Toyokawa, Daisuke Shimamura, Toshiki Matsuoka, Hideya Fukuzawa
Summary: Most microalgae use a CO2-concentrating mechanism (CCM) to acquire inorganic carbon in aquatic environments. This study found that the localization of a specific protein LCIB in the green alga Chlamydomonas reinhardtii undergoes changes in response to different CO2 concentrations, and this process is regulated by LCIC.
Article
Marine & Freshwater Biology
Baohai Zheng, Yuxin Du, Yuting Deng, Teng Zhao, Peichang Dong, Junqiong Shi, Zhongxing Wu
Summary: Different genotypes and colonial morphologies of Microcystis showed varying responses to different levels of CO2, with the bicA genotype performing better at higher CO2 levels and the sbtA genotype performing better at lower CO2 levels. The colonial morphology of Microcystis weakens the response of different genotypes to CO2 levels.
Article
Plant Sciences
Ashwani K. Rai, Timothy Chen, James Moroney
Summary: Chlamydomonas reinhardtii can grow photosynthetically using CO2, with the CO2 concentrating mechanism (CCM) playing a crucial role. Research suggests that mitochondrial carbonic anhydrases CAH4 and CAH5 are involved in maintaining optimal photosynthesis in C. reinhardtii.
Article
Microbiology
Jie Tang, Huizhen Zhou, Dan Yao, Sadaf Riaz, Dawei You, Anna Klepacz-Smolka, Maurycy Daroch
Summary: This study investigated the inorganic carbon-concentrating mechanism (CCM) of thermophilic cyanobacteria using genome-based approaches. The results revealed distinct molecular components and organization of CCM in different genera of thermophilic cyanobacteria, providing fundamental knowledge for further research on improving photosynthesis and biomass yield in these organisms.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Chun Sing Lau, Adam Dowle, Gavin H. Thomas, Philipp Girr, Luke C. M. Mackinder
Summary: Researchers have developed a proximity labeling technique using TurboID to identify the protein composition of a crucial organelle in Chlamydomonas reinhardtii called the pyrenoid. The resulting high-confidence proteome revealed new insights into the role of the pyrenoid in RNA-associated processes and redox-sensitive iron-sulfur cluster metabolism.
Article
Multidisciplinary Sciences
M. Aguila Ruiz-Sola, Serena Flori, Yizhong Yuan, Gaelle Villain, Emanuel Sanz-Luque, Petra Redekop, Ryutaro Tokutsu, Anika Kuken, Angeliki Tsichla, Georgios Kepesidis, Guillaume Allorent, Marius Arend, Fabrizio Iacono, Giovanni Finazzi, Michael Hippler, Zoran Nikoloski, Jun Minagawa, Arthur R. Grossman, Dimitris Petroutsos
Summary: Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. Depletion of CO2 can drive photoprotection and carbon acquisition even in the absence of light, previously believed to be indispensable for these processes.
NATURE COMMUNICATIONS
(2023)
Review
Plant Sciences
Elena V. Kupriyanova, Natalia A. Pronina, Dmitry A. Los
Summary: This review summarizes recent advances in the study of intracellular accumulation of inorganic carbon (C-i) in microalgae and cyanobacteria, revealing the third CO2-concentrating mechanism (CCM) in addition to the known CCM schemes in CAM and C-4 higher plants. CCM enables efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle by coordinating carbonic anhydrases and CO2/HCO3- uptake systems. It functions as an add-on to the RPP cycle and as an important regulatory link in the interaction of dark and light reactions of photosynthesis.
Review
Biotechnology & Applied Microbiology
Hai-Yan Yu, Shu-Guang Wang, Peng-Fei Xia
Summary: Global warming is becoming a serious problem due to human activities, particularly the emission of carbon dioxide. To address this challenge, reducing reliance on fossil fuels and capturing CO2 from the atmosphere are crucial. Carbon-neutral and carbon-negative biotechnologies, specifically those based on CO2-metabolizing microorganisms, have shown promise in producing fuels and chemicals. CRISPR-Cas systems have been developed to engineer these microorganisms and advance carbon-negative biotechnology. This review focuses on recent advances in applying CRISPR-Cas systems for genome editing and interference/activation in specific microorganisms and discusses potential future innovations.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Energy & Fuels
Leonardo Micheli, Greg P. Smestad, Muhammad Zahid Khan, Katja Lange, Huda M. I. Almughary, Mounir Abraim, Yanal Alamat, Cody B. Anderson, Said Bentouba, Benjamin Figgis, Pavan Fuke, Ahmed Amine Hachicha, Mounia Karim, Anil Kottantharayil, Alfredo A. Martinez-Morales, Ahmed Alami Merrouni, Douglas Olivares, Giovanni Picotti, Jorge Rabanal-Arabach, Florian Wiesinger, Klemens Ilse
Summary: Image analysis has been proposed as a practical method to monitor the soiling on solar energy conversion devices, but different methodologies can lead to different results. This study examines the role of thresholding through the analysis of micrographs of soiled glass samples and provides some preliminary best practices for image-based soiling estimation.
Article
Chemistry, Physical
Miguel Fuentes-Cabrera, Jonathan K. Sakkos, Daniel C. Ducat, Maxim Ziatdinov
Summary: Carboxysomes are bacterial microcompartments found in cyanobacteria that play a crucial role in photosynthetic metabolism. The assembly and dynamics of carboxysomes are not well understood, partly due to the limitations of microscopy in analyzing subtle changes in carboxysome morphology. In this study, deep learning techniques were used to analyze fluorescence microscopy images of cyanobacteria and quantitatively evaluate the impact of carboxysome shell remodelling on microcompartment morphology over time. The results suggest that this approach can accelerate the analysis of carboxysome assembly and dynamics.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Plant Sciences
Md Intesaful Haque, Shahrukh A. Siddiqui, B. Jha, Mangal S. Rathore
Summary: Under salt stress conditions, S. monoica showed better growth and biomass accumulation compared to S. fruticosa, along with improved photosynthetic performance at elevated CO2 levels.
JOURNAL OF PLANT GROWTH REGULATION
(2022)
Article
Biotechnology & Applied Microbiology
Songcui Wu, Wenhui Gu, Shuao Jia, Lepu Wang, Lijun Wang, Xuehua Liu, Lu Zhou, Aiyou Huang, Guangce Wang
Summary: The study revealed the carbon metabolism strategies of Phaeodactylum tricornutum under different CO2 concentrations, suggesting that LC conditions may induce a mitochondria-mediated C4-like CCM and enhance glycolysis and tricarboxylic acid cycle activities, while HC conditions increase photosynthesis and central carbon metabolism activity.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Review
Engineering, Marine
Jingyi Sun, Chunyan Zhao, Shuang Zhao, Wei Dai, Jinlin Liu, Jianheng Zhang, Juntian Xu, Peimin He
Summary: This paper provides a summary of the carbon concentrating mechanisms (CCM) in macroalgae, including important components and their functions. It introduces several indexes for evaluating the relative function of CCMs and summarizes methods for determining the carbon sequestration pathway, CCM responses under different carbon sources, and related genes involved in CCM operation. This work is important for understanding the CCMs of macroalgae and advancing research on the inorganic carbon utilization strategy of Ulva sp.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Lingaswamy Bantu, Suraj Chauhan, Afshan Srikumar, Yoshihisa Hirakawa, Iwane Suzuki, Martin Hagemann, Jogadhenu S. S. Prakash
Summary: A cAMP-dependent transcription factor, SyCRP1, is found to mediate the response to inorganic carbon (C-i) in Synechocystis. The mutant delta sycrp1 displays a slow-growth phenotype and reduced photosynthetic electron transport rate under limited CO2. The number of carboxysomes is significantly decreased in the mutant, consistent with its reduced photosynthetic activity. DNA microarray analysis reveals the upregulation of C-i transporter genes in the mutant. The membrane-localized SyCRP1 is released into the cytosol under sufficient CO2 or cAMP treatment. These findings suggest that SyCRP1 may be a regulator of the carbon concentrating mechanism by sensing C-i levels through cAMP signaling.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Review
Biochemistry & Molecular Biology
Shan He, Victoria L. Crans, Martin C. Jonikas
Summary: The pyrenoid is a segregated organelle that enhances carbon assimilation in algae and plants, and its function is driven by CO2 availability and light. The understanding of pyrenoid mainly comes from the model organism Chlamydomonas.
Article
Engineering, Electrical & Electronic
Mark Dong, Niall M. Mangan, J. Nathan Kutz, Steven T. Cundiff, Herbert G. Winful
IEEE JOURNAL OF QUANTUM ELECTRONICS
(2017)
Article
Plant Sciences
Tobias G. Boatman, Niall M. Mangan, Tracy Lawson, Richard J. Geider
JOURNAL OF EXPERIMENTAL BOTANY
(2018)
Article
Multidisciplinary Sciences
Christopher M. Jakobson, Danielle Tullman-Ercek, Niall M. Mangan
SCIENTIFIC REPORTS
(2018)
Article
Multidisciplinary Sciences
N. M. Mangan, T. Askham, S. L. Brunton, J. N. Kutz, J. L. Proctor
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2019)
Article
Optics
Chang Sun, Niall Mangan, Mark Dong, Herbert G. Winful, Steven T. Cundiff, J. Nathan Kutz
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS
(2019)
Article
Engineering, Electrical & Electronic
Chang Sun, Mark Dong, Niall M. Mangan, Herbert G. Winful, Steven T. Cundiff, J. Nathan Kutz
IEEE JOURNAL OF QUANTUM ELECTRONICS
(2020)
Article
Biochemical Research Methods
Kate E. Dray, Joseph J. Muldoon, Niall M. Mangan, Neda Bagheri, Joshua N. Leonard
Summary: Mathematical modeling is crucial for understanding and designing synthetic biological systems. However, the model development process is complex and nonintuitive, requiring iteration and comparison with experimental data. To address these challenges, we introduce the GAMES workflow, which combines automated and human-in-the-loop processes. This workflow enables biologists to more easily build and analyze models for various applications.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Mathematics, Applied
H. Ribera, S. Shirman, A. Nguyen, N. M. Mangan
Summary: Many natural systems exhibit chaotic behavior, but characterizing these systems can be challenging due to sensitivity to initial conditions and difficulties in differentiating chaotic behavior from noise. We present a method combining variational annealing with sparse-optimization methods to perform model identification for chaotic systems with unmeasured variables.
Article
Microbiology
Nolan W. Kennedy, Carolyn E. Mills, Charlotte H. Abrahamson, Andre G. Archer, Sasha Shirman, Michael C. Jewett, Niall M. Mangan, Danielle Tullman-Ercek
Summary: Bacterial microcompartments are protein-based organelles that house the enzymatic machinery for metabolism. A protein called PduB is found to be responsible for linking the shell of the microcompartment to its enzymatic core. The assembly of the shell can be separate from the encapsulation of the enzymes. These findings provide insight into the mechanism of enzyme encapsulation and shell assembly in bacterial microcompartments.
JOURNAL OF BACTERIOLOGY
(2022)
Correction
Biochemical Research Methods
Kate E. Dray, Joseph J. Muldoon, Niall M. Mangan, Neda Bagheri, Joshua N. Leonard
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Carolyn E. Mills, Curt Waltmann, Andre G. Archer, Nolan W. Kennedy, Charlotte H. Abrahamson, Alexander D. Jackson, Eric W. Roth, Sasha Shirman, Michael C. Jewett, Niall M. Mangan, Monica Olvera de la Cruz, Danielle Tullman-Ercek
Summary: The study investigates how the shell protein PduN changes the morphology of the Pdu metabolosome and the impact of this morphological shift on Pdu function.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Brianna N. Ruggiero, Kenzie M. Sanroman Gutierrez, Jithin D. George, Niall M. Mangan, Justin M. Notestein, Linsey C. Seitz
Summary: This study investigates the impact of electrolyte composition on the kinetics and mechanism of the oxygen reduction reaction (ORR) by monitoring local pH changes. The results demonstrate that local pH strongly dictates changes in mechanisms and performance, while the cation identity modulates local pH to influence these trends.
JOURNAL OF CATALYSIS
(2022)
Article
Multidisciplinary Sciences
Kotaro Tsuboyama, Justas Dauparas, Jonathan Chen, Elodie Laine, Yasser Mohseni Behbahani, Jonathan J. Weinstein, Niall M. Mangan, Sergey Ovchinnikov, Gabriel J. Rocklin
Summary: Advances in DNA sequencing and machine learning have enabled the investigation of protein sequences and structures on a large scale. However, the energetics driving protein folding remain largely unknown. In this study, a method called cDNA display proteolysis was developed to measure the folding stability of a large number of protein domains. The method allowed for the characterization of the thermodynamic properties of over 900,000 protein domains, providing insights into factors influencing protein fitness, thermodynamic couplings between sites, and the relationship between amino acid usage and protein folding stability.
Article
Plant Sciences
Chenyi Fei, Alexandra T. Wilson, Niall M. Mangan, Ned S. Wingreen, Martin C. Jonikas
Summary: Enhancing CO2 uptake by concentrating it in the pyrenoid is a potential method to increase crop yields. This study develops a computational model based on the assumed mechanism in green algae, revealing the biophysical principles and proposing an engineering pathway for introducing this mechanism into crops.
Proceedings Paper
Engineering, Electrical & Electronic
Mark Dong, Niall Mangan, J. Nathan Kutz, Steven T. Cundiff, Herbert G. Winful
2017 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO)
(2017)