Article
Microbiology
Sadaf Riaz, Ying Jiang, Meng Xiao, Dawei You, Anna Klepacz-Smolka, Faiz Rasul, Maurycy Daroch
Summary: This study optimized the cultivation and natural transformation protocol for the important cyanobacterium Synechococcus elongatus PCC 7942. By adjusting agar concentration and overexpressing catalase gene, the growth of Synechococcus 7942 on solid media was improved. High temperature and phosphate depletion conditions resulted in fewer genome copies and potential to produce fully segregated mutants. Higher antibiotic concentrations improved the selection of homozygous transformants.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Amit K. Singh, Maria Santos-Merino, Jonathan K. Sakkos, Berkley J. Walker, Daniel C. Ducat
Summary: This study investigates the systemic changes in a model cyanobacterium caused by alterations in carbon availability. The results suggest that Rubisco activity and organization are key variables connected to regulatory pathways involved in metabolic balancing in cyanobacteria.
Article
Microbiology
Rees Rillema, Y. Hoang, Joshua S. MacCready, Anthony G. Vecchiarelli
Summary: Research shows that improper distribution of carboxysomes in cyanobacteria can result in slower cell growth, cell elongation, asymmetric cell division, and elevated levels of cellular Rubisco. Additionally, even wild-type S. elongatus undergoes cell elongation and asymmetric cell division when grown at lower temperatures or switched from high to ambient CO2 conditions. This suggests that the McdAB system plays a crucial role in maintaining the carbon fixation efficiency of Rubisco in cyanobacteria.
Article
Biotechnology & Applied Microbiology
Shu-Yan Wang, Xin Li, Shu-Guang Wang, Peng-Fei Xia
Summary: Cyanobacteria have the potential to convert atmospheric carbon dioxide into biofuels, chemicals, and food. However, the development of genome-editing tools for cyanobacteria has been slower compared to other microbial chassis. In this study, we successfully adapted base editing using the CRISPR-Cas system for cyanobacteria, enabling precise and efficient genome editing. We demonstrated multiplex base editing in a model cyanobacterium and manipulated the glycogen metabolic pathway to enhance the production of chemicals and food from carbon dioxide. This work represents the first report of base editing in cyanobacteria and provides a paradigm for using CRISPR-Cas systems in bacteria, with the potential to accelerate metabolic engineering and synthetic biology to address global climate change.
METABOLIC ENGINEERING
(2023)
Article
Immunology
Wen Peng, Qunjing Bao, Rui Jia, Peimin He
Summary: This study constructed transgenic cyanobacteria expressing recombinant protein VP28-mOrange using the receptor system of Synechococcus elongatus PCC 7942 and explored its metabolic cycle and protective effect against WSSV in Litopenaeus vannamei. The results showed that the recombinant protein had a weak fluorescence signal in the intestine after the shrimp stopped consuming transgenic cyanobacteria and its protective effect decreased with the time of WSSV challenge.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Maria Santos-Merino, Raquel Gutierrez-Lanza, Juan Nogales, Jose Luis Garcia, Fernando de la Cruz
Summary: This study analyzed enzymes in cyanobacteria related to fatty acid synthesis and found that increasing the expression of these enzymes can enhance the production of C18 fatty acids. However, coexpression with other desaturases did not improve the production of alpha-linolenic acid, and attempts to clone another enzyme for stearidonic acid synthesis were also unsuccessful.
Article
Biology
Jake N. Gonzales, Tanner R. Treece, Stephen P. Mayfield, Ryan Simkovsky, Shota Atsumi
Summary: This study investigates the potential of using the photoautotroph cyanobacterium Synechococcus elongatus PCC 7942 as a chassis organism for lignocellulosic chemical production. By modifying the cyanobacterium to import monosaccharides, it can grow well at high lysate concentrations and enhance carbon efficiency by fixing CO2. This study is important in enabling industrial scale production of commodity chemicals from a combination of sunlight, CO2, and lignocellulosic sugars.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Ryan Simkovsky, Rami Parnasa, Jingtong Wang, Elad Nagar, Eli Zecharia, Shiran Suban, Yevgeni Yegorov, Boris Veltman, Eleonora Sendersky, Rakefet Schwarz, Susan S. Golden
Summary: In this study, transcriptomics and phenomics screens were used to identify genes involved in biofilm formation and regulation in Synechococcus elongatus PCC 7942. The study also revealed the transcriptomic adaptation to the biofilm state and compared the effectiveness of these two approaches for gene discovery.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yu Dan, Jiahui Sun, Shanshan Zhang, Yannan Wu, Shaoming Mao, Guodong Luan, Xuefeng Lu
Summary: This study successfully regulated glycogen content in cyanobacteria by enhancing glycogen degradation, leading to increased sucrose production. These findings provide new insights into cyanobacterial glycogen metabolism engineering and will inspire the development of novel metabolic engineering approaches for efficient photosynthetic biosynthesis.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Julie A. Z. Zedler, Marlene Michel, Georg Pohnert, David A. A. Russo
Summary: This study describes a novel domesticated substrain of the model cyanobacterium S. elongatus PCC 7942, which exhibits a fast-sedimenting phenotype. The Group 3 alternative sigma factor F was found to play a key role in cell sedimentation through whole genome sequencing and gene deletion. Changes in cell surface structures and an increase in released polysaccharides were identified as the factors contributing to the fast-sedimenting phenotype. This research sheds light on the transition from planktonic to benthic forms and provides genetic targets for the development of fast-sedimenting strains for cost-effective cyanobacterial harvesting at scale.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anna Paola Casazza, Alessandro Lombardi, Barbara Menin, Stefano Santabarbara
Summary: The exogenous crtZ gene was expressed in Synechococcus elongatus PCC 7942 to engineer the carotenoid metabolic pathway and increase zeaxanthin content. However, this led to a growth impairment and cellular stress.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2023)
Article
Biochemical Research Methods
Mingyi Zhang, Quan Luo, Huili Sun, Jacques Fritze, Guodong Luan, Xuefeng Lu
Summary: This study developed an inducible cyanobacteria cell factory using the ssrADAS-SspB-ClpXPEc system to achieve rapid degradation of target proteins. Additionally, an efficient and stringent inducible gene expression system was obtained, laying the foundation for future dynamic metabolic engineering efforts.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Plant Sciences
Takayuki Sakamoto, Nobuyuki Takatani, Kintake Sonoike, Haruhiko Jimbo, Yoshitaka Nishiyama, Tatsuo Omata
Summary: In this study, it was found that the loss of P-II in cyanobacteria increased the sensitivity of PSII to ammonium and stimulated the formation of reactive oxygen species in mutant cells, leading to growth defects. The aberrant action of uncontrolled PipX impaired the electron transport reactions in both the reducing and oxidizing sides of Q(A), as shown by the unusual chlorophyll fluorescence profile observed in the targeted P-II mutant.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Microbiology
Maria Santos-Merino, Alvaro Gargantilla-Becerra, Fernando de la Cruz, Juan Nogales
Summary: In this study, a more comprehensive and functional model of a freshwater cyanobacterium was constructed, known as iMS837. The model provides detailed insights into the metabolism of the bacterium, including fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. The findings suggest that this model can be used to identify suitable metabolic engineering strategies to improve the production of non-native omega-3 fatty acids.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Hazuki Hasegawa, Ikki Kobayashi, Nachiketa Bairagi, Satoru Watanabe, Kan Tanaka
Summary: This study investigated the mechanism of the Hik2-Rre1 system in high-temperature shift and redox stress and found that overexpression of dnaK2 can alleviate these responses. The results suggest a negative feedback mechanism mediated by DnaK2 to maintain cellular homeostasis.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Microbiology
Yevgeni Yegorov, Eleonora Sendersky, Shaul Zilberman, Elad Nagar, Hiba Waldman Ben-Asher, Eyal Shimoni, Ryan Simkovsky, Susan S. Golden, Andy LiWang, Rakefet Schwarz
Summary: This study identifies novel components of cyanobacterial biofilm regulation and suggests that cyanobacteria may use the same complex for the assembly of motility appendages and protein secretion. This broadens the understanding of pilus assembly/secretion in diverse bacteria and aims to control the formation of cyanobacterial biofilms.
Article
Biochemistry & Molecular Biology
Madhurima Das, Nanhao Chen, Andy LiWang, Lee-Ping Wang
Summary: Metamorphic proteins are able to switch between different folds under native conditions. Uncovering the metamorphome requires computational screening and experimental validation. Understanding the properties of these proteins could lead to novel applications as sensors.
Editorial Material
Biochemistry & Molecular Biology
Patricia J. LiWang, Lee-Ping Wang, Andy LiWang
Summary: The study reveals that the ancestors of XCL1 developed metamorphic properties about 150 million years ago, and these properties are believed to be adaptive. The zigzagging evolutionary path also unveils three design principles that can be applied in technological applications.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Editorial Material
Biochemistry & Molecular Biology
Andy LiWang, Lauren L. Porter, Lee-Ping Wang
Article
Chemistry, Multidisciplinary
Gary K. Chow, Archana G. Chavan, Joel Heisler, Yong-Gang Chang, Ning Zhang, Andy LiWang, R. David Britt
Summary: In this study, the authors used EPR spectroscopy to identify and quantify two subpopulations of KaiC-bound KaiB, providing kinetic evidence for their intermediacy as bridges and nucleation sites. Furthermore, they showed that the relative abundance of these subpopulations is dependent on the phosphorylation state of KaiC and the presence of KaiA. Finally, the authors demonstrated that the interconversion between these subpopulations is linked to the phosphorylation cycle of KaiC.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Yuanpeng Janet Huang, Ning Zhang, Beate Bersch, Krzysztof Fidelis, Masayori Inouye, Yojiro Ishida, Andriy Kryshtafovych, Naohiro Kobayashi, Yutaka Kuroda, Gaohua Liu, Andy LiWang, G. V. T. Swapna, Nan Wu, Toshio Yamazaki, Gaetano T. Montelione
Summary: NMR studies provide unique information on protein conformations in solution, with CASP14 showing varying prediction results for targets with NMR-based structures. By comparing prediction models and experimental NMR data, new methods were explored for guiding NMR data analysis.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biology
Pyonghwa Kim, Neha Thati, Shreya Peshori, Hye-In Jang, Yong-Ick Kim
Summary: The oscillatory phosphorylation/dephosphorylation of proteins in the cyanobacterial circadian clock is regulated by the interaction between KaiA, KaiB, and KaiC. KaiB plays a critical role in dephosphorylating hyperphosphorylated KaiC, independent of KaiA's effect, by inducing a conformational change in the A-loop of KaiC. Additionally, KaiB's binding to KaiC contributes to the robustness of cyclic KaiC phosphorylation by inhibiting it during the dephosphorylation phase, effectively keeping the clock in the correct phase.
Article
Biochemistry & Molecular Biology
Jeffrey A. Swan, Colby R. Sandate, Archana G. Chavan, Alfred M. Freeberg, Diana Etwaru, Dustin C. Ernst, Joseph G. Palacios, Susan S. Golden, Andy LiWang, Gabriel C. Lander, Carrie L. Partch
Summary: This work uncovers the mechanism of phosphorylation-dependent day/night signaling by KaiC in the cyanobacterial circadian clock. Cryogenic-electron microscopy analysis reveals that the C-terminal domain of KaiC undergoes structural changes, causing destabilization during the day and rigidification at night, leading to the binding of clock proteins and regulation of circadian rhythms. The phosphorylation-dependent KaiB association is coupled to ATPase activity, providing insights into the overall regulation of cyanobacterial circadian rhythms.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Analytical
Yongling Ai, Harsha P. Gunawardena, Xuanwen Li, Yong-Ick Kim, Howard D. Dewald, Hao Chen
Summary: This study developed a method for absolute quantitation of proteins without using standards, based on the electrochemical oxidation of surrogate peptides and mass spectrometry measurement of the peptide oxidation yield. The method was successfully applied for quantitation of multiple proteins in a mixture and for quantitation of low-level target proteins in the presence of highly abundant proteins. Additionally, the study demonstrated the unprecedented quantitative analysis of deamidated peptide products arising from a specific reaction.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Mingxu Fang, Archana G. Chavan, Andy LiWang, Susan S. Golden
Summary: In this study, the researchers used the IVC reactions and massively parallel experiments to study entrainment, the synchronization of the circadian clock with the environment. The results showed that the IVC better explains the in vivo clock-resetting phenotypes of wild-type and mutant strains, and the output components are deeply engaged with the core oscillator, affecting the way input signals entrain the core pacemaker. These findings blur the line between input and output pathways and support the previous demonstration that key output components are fundamental parts of the clock.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Hye -In Jang, Pyonghwa Kim, Yong-Ick Kim
Summary: Most organisms have circadian clocks to ensure the synchronization of the metabolic cycle with environmental changes. Cyanobacteria, the oldest and simplest form of life, has a KaiABC-based central oscillator that can be reconstituted in vitro. Mutating a phosphorylation site in KaiC, Thr-432, to Ser results in a damping effect on the oscillatory phosphoryl transfer reaction. The mutant KaiC loses its autonomous running ability and remains phosphorylated after several cycles in vitro.
Article
Biochemistry & Molecular Biology
Archana Chavan, Joel Heisler, Yong-Gang Chang, Susan S. Golden, Carrie L. Partch, Andy LiWang
Summary: Circadian clocks, which regulate metabolic processes based on local time, are important for the health of diverse life forms. However, studying their mechanisms in vivo is challenging. Recent research has successfully reconstituted the circadian clock of cyanobacteria in vitro, allowing real-time observation of clock proteins and DNA under controlled conditions. This breakthrough provides protocols for other labs to investigate how changing environments impact the core oscillator and transcriptional regulation.
Meeting Abstract
Biophysics
Andy LiWang, Archana G. Chavan, Jeffrey A. Swan, Joel C. Heisler, Cigdem Sancar, Dustin Ernst, Mingxu Fang, Clive R. Bagshaw, Sarvind Tripathi, Priya Crosby, Susan S. Golden, Carrie L. Partch
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Alfred M. Freeberg, Jeffrey A. Swan, Colby Sandate, Archana G. Chavan, Dustin Ernst, Diana Etwaru, Joseph G. Palacios, Susan Golden, Andy LiWang, Gabriel C. Lander, Carrie L. Partch
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Jeffrey A. Swan, Colby R. Sandate, Alfred M. Freeberg, Joel C. Heisler, Diana L. Etwaru, Cigdem Sancar, Dustin C. Ernst, Joseph G. Palacios, Clive R. Bagshaw, Archana G. Chavan, Susan S. Golden, Andy LiWang, Gabriel C. Lander, Carrie L. Partch
BIOPHYSICAL JOURNAL
(2022)