Article
Microbiology
Emma O. Fuentes-Ramirez, Miriam Vazquez-Acevedo, Alfredo Cabrera-Orefice, Sergio Guerrero-Castillo, Diego Gonzalez-Halphen
Summary: This study provides a morphological and proteomic characterization of the colorless alga Polytomella parva, identifying several plastid proteins involved in various metabolic pathways. The results contribute to a better understanding of the metabolism and biological activities of this unicellular, free-living alga.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sibaji K. Sanyal, Komal Sharma, Diksha Bisht, Sunita Sharma, Kumari Sushmita, Suneel Kateriya, Girdhar K. Pandey
Summary: Ca2+ signaling is crucial for perceiving and transmitting information in cells. The Ca2+-mediated CBL-CIPK module is a major sensor responder network for Ca2+ signaling, and its involvement in plant adaptation from aquatic to terrestrial habitats has been suggested. Experimental analysis showed that CrCBL1 protein interacts with Phototropin and Channelrhodopsin, and its expression is regulated by light. Comparing algal sequences, differences in CBL and CIPK proteins between aquatic and terrestrial plants were identified. Additionally, Klebsormidium CBL and CIPK genes were found to respond to abiotic stress, indicating their early role in terrestrial adaptations. Structure-based prediction and Ca2+-binding assays revealed a typical Ca2+-binding pocket in Klebsormidium's KnCBL1 protein. Overall, this study suggests that stress-responsive proteins facilitate crosstalk between Ca2+ and light signaling pathways during plant adaptation from aquatic to terrestrial habitats.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Microbiology
Jiale Qiu, Jie Zhang, Huihui Zhao, Cuiping Wu, Caoliang Jin, Xiangdong Hu, Jian Li, Xiuling Cao, Shenkui Liu, Xuejiao Jin
Summary: Carbonate stress has significant impacts on agriculture and industry, but the role of cell wall-related genes in resistance to carbonate remains poorly understood. This study reveals the critical role of cellulose in the NaHCO3 resistance of Chlorella JB17, and identifies a NaHCO3-tolerance gene that could be used for crop breeding and genetic modification of microalgae for biofuel production.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Vivien Hotter, David Zopf, Hak Joong Kim, Anja Silge, Michael Schmitt, Prasad Aiyar, Johanna Fleck, Christian Matthaus, Julian Hniopek, Qing Yan, Joyce Loper, Severin Sasso, Christian Hertweck, Jurgen Popp, Maria Mittag
Summary: The interaction between algae and bacteria involves a complex molecular strategy, with bacteria using protegencin and orfamide A to disrupt the visual system and behavior of algae. This study highlights the multifaceted ways in which microorganisms can impact the growth and development of algae in nature.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Tomokazu Kurita, Masako Iwai, Keishi Moroi, Kumiko Okazaki, Seiji Nomura, Fumihiko Saito, Shinichiro Maeda, Akihide Takami, Atsushi Sakamoto, Hiroyuki Ohta, Tetsushi Sakuma, Takashi Yamamoto
Summary: Algal lipids, produced through photosynthesis and carbon dioxide assimilation, are expected to be the basis for sustainable fuels. However, the use of genetically modified organisms (GMOs) in outdoor culture is restricted. Recent research has discovered that plasmids containing yeast centromere and autonomous replication sequence can behave as episomes in Nannochloropsis species. This study aims to develop a genome editing system that allows the removal of expression vectors after introducing mutations, thereby creating mutated Nannochloropsis without any transgenes.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Fan Bai, Yu Zhang, Jin Liu
Summary: bZIP transcription factors play important roles in lipid and pigment metabolisms in microalgae, as shown by the comparative analysis of crbzip2 mutant and wild-type strain in Chlamydomonas reinhardtii. The disruption of CrBZIP2 leads to reduced TAG accumulation, increased DGDG production, and up-regulated biosynthetic pathways of carotenoids and chlorophylls. These findings suggest that CrBZIP2 could be a potential target for genetic engineering to manipulate lipid and pigment production in microalgae.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Electrochemistry
Adnan Sayegh, Luca A. Perego, Marc Arderiu Romero, Louis Escudero, Jerome Delacotte, Manon Guille-Collignon, Laurence Grimaud, Benjamin Bailleul, Frederic Lemaitre
Summary: This study focuses on extracting energy from oxygenic photosynthesis by rerouting electron flow using intact photosynthetic organisms to generate photocurrent. Researchers found that some quinones can interact with the embedded photosynthetic chain, but the balance between toxicity and bioelectricity production needs to be considered.
Article
Microbiology
Zhao Peng, Gai Liu, Kaiyao Huang
Summary: Research shows that compared to a model organism from the same genus, snow algae exhibit higher growth rates and photosynthetic efficiency in cold environments, indicating better cold tolerance. Snow algae adapt to rapid temperature decrease by efficiently regulating transcription of specific genes to optimize resource assimilation and metabolic pathways. Additionally, horizontally transferred genes critical for cold adaptation in other psychrophiles are also identified in snow algae.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Monika Majewska, Darya Harshkova, Wojciech Pokora, Agnieszka Bascik-Remisiewicz, Szymon Tulodziecki, Anna Aksmann
Summary: Research found that DCF and atrazine had different effects on Chlamydomonas reinhardtii. Both substances decreased photosynthetic vitality of the cells, but for different reasons. Atrazine disrupted photosynthetic electron transport, leading to excessive ROS production and limited cell growth, while DCF silenced PSII reaction centers, preventing significant ROS overproduction.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biotechnology & Applied Microbiology
Akihito Nakanishi, Kohei Iritani, Akane Tsuruta, Naotaka Yamamoto, Marina Watanabe, Nanami Ozawa, Masahiko Watanabe, Kuan Zhang, Ayaka Tokudome
Summary: In this study, cell plastics were fabricated using only unicellular green alga Chlamydomonas reinhardtii as raw materials, and it was demonstrated that cells could be conjugated with intracellular contents to give mechanical strength to the cell plastics.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Medicinal
Mei-Li Zhao, Wen-Sheng Cai, Si-Qi Zheng, Jia-Lin Zhao, Jun-Liang Zhang, Ying Huang, Zhang-Li Hu, Bin Jia
Summary: This study successfully introduced a novel isopentenol utilization pathway into Chlamydomonas reinhardtii, leading to a significant increase in limonene production. With culture optimization, transgenic algae cultured under a light: dark regimen achieved the highest limonene production of 117μg/L.
Article
Engineering, Environmental
Youming Dong, Minling Gao, Weiwen Qiu, Zhengguo Song
Summary: Microplastic pollution was found to disrupt the phospholipid structure in Chlamydomonas reinhardtii cells, reducing the accumulation and efflux of arsenic, as well as inhibiting the detoxification process. This study demonstrated a significant impact of microplastics on arsenic accumulation in algae, potentially impeding its role in biogeochemical cycling in the earth's pedo- and hydrosphere.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biotechnology & Applied Microbiology
Joao Vitor Dutra Molino, Roberta Carpine, Karl Gademann, Stephen Mayfield, Simon Sieber
Summary: Cell-surface display systems are biotechnological techniques used to express heterologous proteins on the cell surface, and the choice of anchoring points depends on the cell system used. In this study, different anchoring points in the green algae Chlamydomonas were screened for efficiency and functionality, leading to the identification of two functional anchors. The use of GP1 protein in cell wall shedding provides a promising strategy for efficient protein release, supporting both cell biology studies and biotechnology applications.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Plant Sciences
Michela Cecchin, Jooyeon Jeong, Woojae Son, Minjae Kim, Seunghye Park, Luca Zuliani, Stefano Cazzaniga, Andrea Pompa, Chan Young Kang, Sangsu Bae, Matteo Ballottari, EonSeon Jin
Summary: This study generated lpa2 knockout mutants in Chlamydomonas reinhardtii using the CRISPR-Cas9 system and found that the absence of LPA2 protein resulted in impaired PSII assembly and function, leading to compromised photoautotrophic growth.
Article
Environmental Sciences
Aoxue Sun, Limei Xu, Gaoxiang Zhou, Erqin Yin, Tiantian Chen, Yong Wang, Xiaochen Li
Summary: This study investigated the impacts of micro-plastics as carriers on the toxicity of heavy metals. It found that nano-sized plastics showed higher adsorption capacities and lower desorption rates for Pb2+ compared to micro-sized plastics. The presence of micro-plastics decreased the bioavailability of Pb2+ to Chlamydomonas reinhardtii and suppressed membrane damage and oxidative stress. The study also observed that the size of micro-plastics influenced their capacity to carry heavy metal ions and their toxicity to C. reinhardtii.
Article
Biochemistry & Molecular Biology
Craig P. Barry, Rosemary Gillane, Gert H. Talbo, Manual Plan, Robin Palfreyman, Andrea K. Haber-Stuk, John Power, Lars K. Nielsen, Esteban Marcellin
Summary: The study demonstrates that utilizing a multi-omics approach in combination with antiSMASH allows for the assessment of the secondary metabolic potential of a Streptomyces strain producing mannopeptimycin, an important cyclic peptide effective against Gram-positive infections. By combining genomics, proteomics, and metabolomics, it is possible to rapidly evaluate a strain's performance in bioreactors for industrial production of secondary metabolites.
Review
Biochemical Research Methods
James K. Heffernan, Vishnu Mahamkali, Kaspar Valgepea, Esteban Marcellin, Lars K. Nielsen
Summary: Acetogens use the unique Wood-Ljungdahl Pathway to capture C1 close to the thermodynamic limit. Gas fermentation using acetogens has been applied on an industrial scale for CO2 to ethanol conversion and has the potential to convert various C1 and waste substrates to carboxylic acids and alcohols. Advances in analytical quantification and metabolic modelling have guided industrial gas fermentation designs, but further improvements in measuring difficult metabolites are needed.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Review
Medicine, Research & Experimental
Pouyan Ghaffari, Saeed Shoaie, Lars K. Nielsen
Summary: This article summarizes the research progress on the microbiome in irritable bowel syndrome (IBS), pointing out the lack of established microbial mechanisms and clear treatment methods for IBS. The review proposes a new treatment perspective, using data-driven approach and computational modeling to design microbiome-aware personalized treatment strategies.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Microbiology
Kaspar Valgepea, Gert Talbo, Nobuaki Takemori, Ayako Takemori, Christina Ludwig, Vishnuvardhan Mahamkali, Alexander P. Mueller, Ryan Tappel, Michael Kopke, Sean Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin
Summary: Microbes that can recycle C-1 greenhouse gases into fuels and chemicals are crucial for the sustainability of future industries. In this study, the absolute proteomics technique was used to quantify protein concentrations in the acetogen Clostridium autoethanogenum, revealing the importance of proteome allocation for C-1 fixation.
Review
Biochemical Research Methods
Esteban Marcellin, Largus T. Angenent, Lars K. Nielsen, Bastian Molitor
Summary: This review explores the potential of gas fermentation and synthetic biology to transform food production and achieve sustainability.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Medicine, Research & Experimental
Michael A. MacDonald, Matthias Nobel, Veronica S. Martinez, Kym Baker, Evan Shave, Peter P. Gray, Stephen Mahler, Trent Munro, Lars K. Nielsen, Esteban Marcellin
Summary: The development of death-resistant cell lines using CRISPR technology has proven to be beneficial for monoclonal antibody production. These cell lines showed advantages in fed-batch and perfusion bioreactors, with higher cell densities or longer culture durations in fed-batch, and the ability to culture without bleed in perfusion. This study highlights the potential of rationally engineered cell lines for improving mAb manufacturing processes.
Article
Biochemical Research Methods
Veronica S. Martinez, Pedro A. Saa, Jason Jooste, Kanupriya Tiwari, Lake-Ee Quek, Lars K. Nielsen
Summary: The topology of metabolic networks is modular, with weak connections between modules. This study defines metabolic modules using network topology and validates them using genome-scale metabolic models. The study also explores the role of reversible reactions in metabolic flexibility.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Lorena Azevedo de Lima, Kristina Reinmets, Lars Keld Nielsen, Esteban Marcellin, Audrey Harris, Michael Kopke, Kaspar Valgepea
Summary: RNA sequencing (RNA-seq) is a widely used technique for transcriptome analysis, but the choice of library preparation kits can significantly impact the results. Different commercial products show significant differences in rRNA removal, strand specificity, and transcript abundance distribution. Selecting appropriate sample processing workflows and products is crucial for RNA-seq studies.
MICROBIOLOGY SPECTRUM
(2022)
Article
Engineering, Chemical
Sarang S. Nath, Lars K. Nielsen, John Villadsen
Summary: A novel methodology is developed to convert chemical reactions into electrical circuits, allowing for the study of complex cyclic bionetworks. The approach is demonstrated using a pyramidal reaction network catalyzed by an important enzyme in cancer therapy. The analysis identifies the key mechanisms contributing to the overall reaction rate.
CHEMICAL ENGINEERING SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Tae Kwang Ha, Andreu Odena, Karen Julie la Cour Karottki, Che Lin Kim, Hooman Hefzi, Gyun Min Lee, Helene Faustrup Kildegaard, Lars K. Nielsen, Lise Marie Grav, Nathan E. Lewis
Summary: The use of a dual selection method can greatly improve the efficiency of Chinese hamster ovary (CHO) cell lines in producing biotherapeutic proteins, although it may lead to reduced growth rate and viability. By knocking out the Gs/Aspg genes, a novel dual selectable system was successfully constructed, which showed significantly improved productivity and titer compared to the standard Gs system under the same selection conditions. With further optimization of culture medium and selection conditions, this approach is expected to be an effective addition to industrial workflows for producing recombinant biotherapeutics.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Hanne H. Henriksen, Igor Marin de Mas, Lars K. Nielsen, Joseph Krocker, Jakob Stensballe, Sigurour T. Karvelsson, Niels H. Secher, Ottar Rolfsson, Charles E. Wade, Par I. Johansson
Summary: In trauma patients, shock-induced endotheliopathy (SHINE) is associated with poor prognosis. This study identified four metabolic phenotypes in trauma patients and analyzed their intracellular metabolic profiles using a computational network analysis. One of the phenotypes, characterized by an inability to maintain redox balance, was associated with increased mortality. This research highlights the importance of understanding metabolic patterns in trauma patients for prognosis and potential therapeutic interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Carmen Bedia, Nuria Dalmau, Lars K. Nielsen, Roma Tauler, Igor Marin de Mas
Summary: Although the dose-effect relationship between Endocrine disruptors (EDs) and tumor malignancy is supported by numerous studies, the impact of chronic exposure to non-lethal concentrations of EDs in cancer remains unknown. This study investigates the molecular processes underlying malignancy in prostate cancer using two complementary computational approaches. Experimental validation confirms predictions, revealing a disruption in metabolic and regulatory pathways.
Article
Biotechnology & Applied Microbiology
Igor Marin de Mas, Helena Herand, Jorge Carrasco, Lars K. Nielsen, Par I. Johansson
Summary: Genome-scale metabolic models (GEMs) are valuable tools for understanding human metabolism and have applications in studying diseases and designing metabolic engineering. This paper presents a novel algorithm-aided protocol that allows for the continuous updating of highly curated GEMs, overcoming the limitations of existing methods.
BIOENGINEERING-BASEL
(2023)
Article
Biotechnology & Applied Microbiology
Marina de Leeuw, Marta R. A. Matos, Lars Keld Nielsen
Summary: Kinetic models are important for understanding metabolic systems. This paper presents a detailed kinetic model for the central carbon metabolism of Escherichia coli, which has been validated and can be used for studying cellular metabolism and metabolic pathway design.
METABOLIC ENGINEERING
(2023)
Article
Engineering, Environmental
James K. Heffernan, Chun-Yu Lai, R. Axayacatl Gonzalez-Garcia, Lars Keld Nielsen, Jianhua Guo, Esteban Marcellin
Summary: Biogas production from anaerobic digestion is important for energy generation, nutrient recovery, and waste resource valorisation. Removing or altering carbon dioxide content facilitates biogas use as biomethane and can contribute to transitioning into a low carbon and circular economy. Gas fermentation utilising acetogens and renewable H2 offers an alternative for biogas upgrading, enriching the biogas and transforming CO2 into valuable fuels and chemicals in a one-step process.
CHEMICAL ENGINEERING JOURNAL
(2023)