Article
Engineering, Environmental
Vera Slaveykova, Sanghamitra Majumdar, Nicole Regier, Weiwei Li, Arturo A. Keller
Summary: Metabolomics was used to study the response of green alga to sublethal concentrations of inorganic mercury and monomethylmercury. The alga adjusted its metabolism by increasing levels of various metabolites involved in different pathways after exposure to low concentrations of mercury compounds. Exposure to inorganic mercury resulted in more pronounced metabolic perturbations in comparison to monomethylmercury, while most metabolic disturbances were common between the two treatments.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Zihui Huang, Liangliang Shen, Wenda Wang, Zhiyuan Mao, Xiaohan Yi, Tingyun Kuang, Jian-Ren Shen, Xing Zhang, Guangye Han
Summary: Photosystems I and II undergo state transitions to balance light energy distribution and optimize photosynthesis, with the cryo-EM structure of a PSI-LHCI-LHCII supercomplex from C. reinhardtii revealing subunit organization and energy transfer pathways.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Xiaosong Gu, Li Cao, Xiaoying Wu, Yanhua Li, Qiang Hu, Danxiang Han
Summary: This study identified galactosyl hydrolases (CrGH) in lipid bodies of Chlamydomonas reinhardtii and found that deficiency of CrGH led to an increase in MGDG and DGDG content and a decrease in TAG content under high light stress conditions. The up-regulation of CrGH under high light stress suggests its involvement in the conversion of photosynthetic membranes to TAGs, revealing a new paradigm for lipid metabolism in microalgae.
Article
Engineering, Environmental
Ivan Liakh, Darya Harshkova, Pavel Hrouzek, Katerina Bisova, Anna Aksmann, Bartosz Wielgomas
Summary: The use of unicellular algae for removing xenobiotics from wastewaters is a rapidly developing field in environmental protection. Efficient phycoremediation requires biosorption, bioaccumulation, and biotransformation. However, the potential toxicity of biotransformation products and the resistance of analyzed algae strains to the mixture of compounds need to be considered. In this study, Chlamydomonas reinhardtii showed promise in removing diclofenac, a non-steroidal anti-inflammatory drug, through biosorption, bioaccumulation, and biotransformation processes.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Cell Biology
Darya Harshkova, Ivan Liakh, Vitali Bialevich, Kamila Ondrejmiskova, Anna Aksmann, Katerina Bisova
Summary: The study aimed to verify the hypothesis that diclofenac affects cell cycle progression in green algae. The research demonstrated that diclofenac delays cell division in the algae, resulting in a decrease in the number of daughter cells produced.
Review
Cell Biology
Ulrich Kueck, Olga Schmitt
Summary: This article reviews RNA trans-splicing process in eukaryotes, focusing on trans-splicing of discontinuous group II introns in lower eukaryotes and plants' chloroplasts and mitochondria. It also discusses the origin of intronic sequences and the evolutionary relationship between chloroplast ribonucleoprotein complexes and the nuclear spliceosome.
Article
Biochemistry & Molecular Biology
Yong Zou, Igor Sabljic, Natalia Horbach, Adrian N. Dauphinee, Anna Asman, Lucia Sancho Temino, Elena A. Minina, Marcin Drag, Simon Stael, Marcin Poreba, Jerry Stahlberg, Peter Bozhkov
Summary: Plants possess a more ancient and broader class of proteases called MetaCaspases (MCAs) in contrast to the animal-specific Caspases. This study investigates a single type-II MCA called CrMCA-II from the model chlorophyte Chlamydomonas reinhardtii. Surprisingly, CrMCA-II dimerizes like Caspases, and its activation is correlated with dimerization. Most of CrMCA-II in the cell is in the form of a proenzyme attached to the plasma membrane. Deletion of CrMCA-II compromises thermotolerance, but adding back either wild-type or catalytically dead CrMCA-II restores thermoprotection, suggesting that its proteolytic activity is not essential for its thermotolerance effect. Furthermore, CrMCA-II's non-proteolytic role is found to be related to the modulation of plasma membrane fluidity.
Article
Multidisciplinary Sciences
Rachel A. Schomaker, Jeffry L. Dudycha
Summary: Ankistrodesmus falcatus, a globally distributed freshwater chlorophyte, has been studied for biofuel production, aquatic toxins, and zooplankton research. Researchers created a reference transcriptome using NextGen sequencing, de novo assembly methods, and annotation tools, providing valuable genomic resources for various research fields.
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
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
Multidisciplinary Sciences
Asuka Tanno, Ryutaro Tokutsu, Yoko Arakaki, Noriko Ueki, Jun Minagawa, Kenjiro Yoshimura, Toru Hisabori, Hisayoshi Nozaki, Ken-Ichi Wakabayashi
Summary: Photo-induced behavioral responses are crucial for motile phototrophic organisms to survive in changing light conditions. Studying different types of green algae, researchers found that they exhibit various photobehaviors, such as phototaxis and photoshock responses. Interestingly, a four-celled algae Tetrabaena socialis did not show immediate photobehaviors after light exposure but instead slowly accumulated towards the light source.
Article
Biology
Yutaro Oishi, Rie Otaki, Yukari Iijima, Eri Kumagai, Motohide Aoki, Mikio Tsuzuki, Shoko Fujiwara, Norihiro Sato
Summary: Oishi et al. discovered that a green alga Chlorella kessleri synthesized a betaine lipid DGTS to replace phosphatidylcholine and phosphatidylethanolamine during phosphate deprivation. This study sheds light on the phosphorus-deficiency acclimation strategies in lower green plants through lipid remodeling.
COMMUNICATIONS BIOLOGY
(2022)
Article
Plant Sciences
Mithun Kumar Rathod, Sreedhar Nellaepalli, Shin-Ichiro Ozawa, Hiroshi Kuroda, Natsumi Kodama, Sandrine Bujaldon, Francis-Andre Wollman, Yuichiro Takahashi
Summary: Chlamydomonas reinhardtii's LHCs play a vital role in the function of photosystems. The protein Alb3.1 plays a key role in the assembly of LHCs, interacting with cpSRP43 and cpSRP54 proteins to form an assembly apparatus for most LHCs in the thylakoid membranes.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wei Liang, Junjie Qiu, Mengping Zhang, Chuan Wang
Summary: This study is the first attempt to express human CRP in Chlamydomonas reinhardtii, providing new insights into obtaining active CRP. The nuclear transformation system of C. reinhardtii has broad market prospects and huge application potential.
JOURNAL OF FOOD BIOCHEMISTRY
(2022)
Article
Microbiology
Akihito Nakanishi, Nanami Ozawa, Masahiko Watanabe
Summary: UV-C irradiation can efficiently collect intracellular lipids from green algae cells without cell burst and microbial contamination, while also potentially affecting lipid synthesis and degradation pathways. This study provides the first report on the transcriptional response of C. reinhardtii to UV-C irradiation.
Article
Plant Sciences
Birte Schwarz, Christina B. Azodi, Shin-Han Shiu, Petra Bauer
Article
Biotechnology & Applied Microbiology
Peipei Wang, Fanrui Meng, Bethany M. Moore, Shin-Han Shiu
Summary: This study identified factors contributing to variable coverage regions in plant genome assemblies, particularly in tomato. High coverage regions were found to have higher simple sequence repeat and tandem gene densities, with a significant proportion potentially misassembled due to duplicate sequences. Additionally, a predictive model showed that misassembled, high coverage regions were often surrounded by simple sequence repeats, pseudogenes, and transposon elements. Further testing is needed to determine the generality of these factors in other species.
Article
Biochemistry & Molecular Biology
Siobhan A. Cusack, Peipei Wang, Serena G. Lotreck, Bethany M. Moore, Fanrui Meng, Jeffrey K. Conner, Patrick J. Krysan, Melissa D. Lehti-Shiu, Shin-Han Shiu
Summary: Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene does not show an apparent phenotype until one or more paralogs are also knocked out. Machine learning models were established to predict whether a gene pair is likely redundant in Arabidopsis thaliana, with features such as recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and similar expression patterns under stress conditions being important predictors.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Peipei Wang, Bethany M. Moore, Sahra Uygun, Melissa D. Lehti-Shiu, Cornelius S. Barry, Shin-Han Shiu
Summary: Plant metabolites from various pathways play important roles in plant survival, human nutrition, and medicine. This study explores different data combinations and strategies to predict plant pathway memberships accurately, emphasizing the importance of data quality. Unsupervised learning performs better in prediction, and models based on gene-to-pathway expression similarities outperform those based solely on expression levels.
Article
Multidisciplinary Sciences
Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong Won Kim, Yibing Zeng, Christine H. O'Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia Krasileva, John L. Portwood, Ethalinda K. S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe
Summary: The study reports de novo genome assemblies, transcriptomes, annotations, and methylomes for 26 maize inbreds, with over 103,000 pangenes identified. It shows that the ancient tetraploid character of maize continues to degrade by fractionation, and reveals variation in DNA methylation levels across genotypes.
Article
Biochemistry & Molecular Biology
Bethany M. Moore, Yun Sun Lee, Peipei Wang, Christina Azodi, Erich Grotewold, Shin-Han Shiu
Summary: The modeling and experimental validation of transcriptional response to wounding and jasmonic acid identified temporal cis-regulatory codes and new regulatory sequences important for wound response. The study provides a global predictive model for wound response and highlights the significance of regulatory factors and open chromatin regions in different types of wound response.
Article
Microbiology
Zebulun W. Arendsee, Jennifer Chang, David E. Hufnagel, Alexey Markin, Alicia Janas-Martindale, Amy L. Vincent, Tavis K. Anderson
Summary: In the United States, Influenza A virus (IAV) is monitored in swine through a surveillance system administered by the U.S. Department of Agriculture. An interactive Web tool has been developed to visualize and explore trends in the genetic and geographic diversity of IAV derived from this surveillance system.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Review
Plant Sciences
Peipei Wang, Ally M. Schumacher, Shin-Han Shiu
Summary: Predicting plant metabolic pathways is crucial for metabolic engineering and the production of plant metabolite-derived medicine. Recent progress has been made in using multi-omics data and computational approaches to predict the pathways, complementing traditional genetic and biochemical approaches.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Plant Sciences
Peipei Wang, Fanrui Meng, Paityn Donaldson, Sarah Horan, Nicholas L. Panchy, Elyse Vischulis, Eamon Winship, Jeffrey K. Conner, Patrick J. Krysan, Shin-Han Shiu, Melissa D. Lehti-Shiu
Summary: This study measured fitness traits in Arabidopsis using image segmentation and object detection methods, and found fitness effects for certain genes. The object detection-based algorithm yielded more accurate results compared to the segmentation-based method, providing near-perfect seed counts and highly accurate fruit counts.
Article
Plant Sciences
Rihong Jiang, Xinlian Chen, Xuezhu Liao, Dan Peng, Xiaoxu Han, Changsan Zhu, Ping Wang, David E. Hufnagel, Li Wang, Kaixiang Li, Cheng Li
Summary: This study presents a high-quality chromosome-scale genome of the camphor tree. It reveals the phylogenetic position of magnoliids and identifies ancient whole-genome duplications. The study also shows that temperature and precipitation affect the accumulation of volatile compounds.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Wen-Yu Liu, Chun-Ping Yu, Chao-Kang Chang, Hsiang-June Chen, Meng-Yun Li, Yi-Hua Chen, Shin-Han Shiu, Maurice S. B. Ku, Shih-Long Tu, Mei-Yeh Jade Lu, Wen-Hsiung Li
Summary: The superior photosynthetic efficiency of C-4 leaves over C-3 leaves is due to their unique Kranz anatomy. This study identified the regulators and underlying molecular mechanisms of Kranz anatomy development in maize leaves. The researchers analyzed transcriptomic data and identified transcription factors and auxin transporter genes that are involved in early Kranz development. They constructed a gene regulatory network and provided insights into the regulation of early leaf development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Virology
J. Brian Kimble, Carine K. Souza, Tavis K. Anderson, Zebulun W. Arendsee, David E. Hufnagel, Katharine M. Young, Nicola S. Lewis, C. Todd Davis, Sharmi Thor, Amy L. Vincent Baker
Summary: During the last decade, swine H1 influenza A viruses have caused zoonotic infections in humans. The genetic diversity of these viruses was evaluated and it was found that certain clades showed strong cross-reactivity to human seasonal vaccines, while others demonstrated reduced cross-reactivity. These findings help prioritize the risk of swine influenza viruses and inform further research on their transmission and infectivity to humans.
Article
Virology
Carine K. K. Souza, J. Brian Kimble, Tavis K. K. Anderson, Zebulun W. W. Arendsee, David E. E. Hufnagel, Katharine M. M. Young, Phillip C. C. Gauger, Nicola S. S. Lewis, C. Todd Davis, Sharmi Thor, Amy L. Vincent L. Baker
Summary: Human-to-swine transmission of influenza A (H3N2) virus is significant in the evolution and diversity of swine influenza A virus (IAV). The introduction of human seasonal H3 IAVs into swine has led to the formation of different lineages and clades. Variant viruses from these lineages have caused zoonotic cases and pose a public health concern. The study indicates that existing vaccine strains offer limited protection against swine H3N2 infection, particularly the widespread 1990.4.A viruses associated with multiple zoonotic cases.
Article
Multidisciplinary Sciences
Yun Sun Lee, Shin-Han Shiu, Erich Grotewold
Summary: The association of bHLH and ACT-like domains is unique to the plantae kingdom, suggesting a common origin. The ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. The evolution of the ACT-like domains is constrained by the bHLH domains.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Amy Baetsen-Young, Huan Chen, Shin-Han Shiu, Brad Day
Summary: The study compared the response of Fusarium virguliforme in maize and soybean hosts, revealing that induction of senescence dampening transcriptional regulators occurred in infected maize, while senescence-associated processes were observed in soybean, suggesting root senescence as a key factor in symptomatic versus asymptomatic host-fungal interactions. This process supports the lifestyle and virulence of F. virguliforme during biotrophy to necrotrophy transitions, indicating a transcriptomic reprogramming favoring susceptibility and induction of pathways associated with senescence during the necrotrophic stage of fungal development within symptomatic hosts.