Article
Biochemical Research Methods
Gerrich Behrendt, Jonas Frohwitter, Maria Vlachonikolou, Steffen Klamt, Katja Bettenbrock
Summary: Zymo-Parts is a modular toolbox based on Golden-Gate cloning that enables efficient construction of genetically modified strains. It offers a collection of promoters, terminators, ribosomal binding sites, and reporter genes for achieving desired levels of gene expression. The GoldenBraid-based system allows for the assembly of operons with multiple genes. The utility of Zymo-Parts for metabolic engineering applications is demonstrated by overexpressing a heterologous lactate dehydrogenase gene in Z. mobilis.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Biochemical Research Methods
Jasmine E. Bird, Jon Marles-Wright, Andrea Giachino
Summary: Golden Gate assembly is a widely used technique for DNA part assembly. While there are different standards and toolboxes available, choosing the right tools can be a challenge for both new users and experienced scientists.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Endocrinology & Metabolism
Yinchuan Li, Panpan Mi, Xue Chen, Jiabao Wu, Weibing Qin, Yiqi Shen, Pingbao Zhang, Yunge Tang, C. Yan Cheng, Fei Sun
Summary: Using single-cell RNA-Sequencing, the expression dynamics of histone variants, writers, erasers, and readers of histone modifications during spermiogenesis were assessed, revealing the transcriptional ranks of specific genes and preferences of epigenetic regulation in spermatids. The impact of spermatid metabolic preferences on epigenetic modifications was highlighted in the study. Despite the rising trend in transcription levels of all encoding genes and histone variants, genes involved in histone modifications displayed a downward expression trend, indicating a gradual decrease in overall epigenetic activity during spermiogenesis.
Article
Biotechnology & Applied Microbiology
Matthias Windhagauer, Raffaela M. Abbriano, Justin Ashworth, Lorenzo Barolo, Ana Cristina Jaramillo-Madrid, Mathieu Pernice, Martina A. Doblin
Summary: Phaeodactylum tricornutum is a model pennate diatom with a sequenced genome, and this study investigated the expression profile of four endogenous constitutive promoter and terminator pairs in different growth conditions. The results showed that these novel promoters and terminators exhibited stable expression and are promising tools for fine tuning gene expression in P. tricornutum.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Neurosciences
Marta Maleszewska, Aleksandra Steranka, Magdalena Smiech, Beata Kaza, Paulina Pilanc, Michal Dabrowski, Bozena Kaminska
Summary: Microglia pre-exposed to glioma-conditioned medium acquire a transcriptional memory and display reduced expression of inflammatory genes after re-stimulation. Epigenetic mechanisms contribute to glioma-induced transcriptional memory in microglia, resulting in a tumor-supportive phenotype. GCM induces distinct histone modifications in microglia, with Hdac inhibitors blocking these changes and restoring inflammatory responses.
Article
Biochemical Research Methods
Sonja Billerbeck, Rianne C. Prins, Malte Marquardt
Summary: Candida glabrata is an emerging drug-resistant human pathogen that causes severe infections in immunocompromised individuals and is a valuable biotechnology host. However, there is a lack of well-characterized cloning toolkit for this yeast. In this study, a CgTK was developed by characterizing a yeast molecular cloning toolkit and adding missing components, which can be used for genome-wide library screens.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Dong Hun Kang, Sung Cheon Ko, Yu Been Heo, Hyun Jeong Lee, Han Min Woo
Summary: Efficient and versatile DNA assembly frameworks have had a significant impact on promoting synthetic biology. However, the traditional MoClo system for multiple DNA assemblies in a biofoundry workflow has limitations in terms of simplicity and feasibility. In this study, a robot-assisted MoClo (RoboMoClo) system was proposed to accelerate synthetic biology projects with multiple gene expressions. The RoboMoClo framework combines hierarchical gene assembly and iterative gene assembly strategies, and requires fewer destination vectors. The application of RoboMoClo in an industrial bacterium, C. glutamicum, demonstrated its potential in laboratory automation for synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Christopher Szent-Gyorgyi, Lydia A. Perkins, Brigitte F. Schmidt, Zhen Liu, Marcel P. Bruchez, Robert van de Weerd
Summary: There is a need in synthetic biology for flexible fully designed vectors to address challenging cloning strategies. This article presents a new method for plasmid synthesis that paves the way for exploring protein interactions.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Ashby J. Morrison
Summary: Cellular adaptation to nutrient environment is crucial for survival, failure to adapt can result in cell death and diseases. Metabolism alterations, particularly in cancer cells, play a significant role in the pathogenesis of diseases. Recent studies have shown the interplay between metabolic pathways, epigenetic modifications, and transcriptional regulation in cancer cells.
Article
Chemistry, Multidisciplinary
Zrinka Raguz Nakic, Christin Peters
Summary: The conventional cloning strategies for preparing expression vectors are time-consuming and laborious, which are not suitable for designing metabolic pathways or enzyme cascades. However, Modular Cloning, a novel cloning technique in synthetic biology, provides a rapid and efficient method for preparing individual expression vectors using Golden Gate assembly. This technique has successfully been used to generate strains capable of producing complex compounds involving up to 20 enzymes. Although industrial applications of Modular Cloning are still rare, the lack of high-throughput screening methods limits its potential. Future developments should address the bottleneck in screening capacity to promote the establishment of Modular Cloning in industrial applications.
Article
Marine & Freshwater Biology
Zhimei Zhu, Yuan Liu, Juan Qi, Zhenghong Sui
Summary: This study investigated the types and changes of histone modifications in A. pacificum cells and the regulation of related genes. The results showed that histone lysine methylation plays an important role in A. pacificum's response to conditions that induce harmful algal blooms. These findings are significant for further understanding the mechanisms and regulation of A. pacificum's rapid growth.
Review
Plant Sciences
Qin Mu, Xianyang Li, Jianhua Luo, Qinwei Pan, Yi Li, Tingting Gu
Summary: This study identified key expansin genes involved in strawberry fruit softening and investigated their transcriptional regulation by histone modifications. Transcriptome data suggested certain EXP genes were associated with fruit softening. EXP proteins in cultivated strawberries were found to be more structurally diverse compared to woodland strawberries.
Article
Plant Sciences
Guannan Qin, Suting Wu, Liying Zhang, Yanyao Li, Chunmei Liu, Jianghui Yu, Lihua Deng, Guoying Xiao, Zhiguo Zhang
Summary: The study developed a gene stacking system, GNS, which allows efficient assembly of multiple gene expression cassettes. The system is modular and standardized, making it suitable for complex metabolic pathway modification and pyramiding breeding strategies. Using the GNS system, researchers were able to construct a binary vector containing multiple foreign genes and obtain transgenic plants with the desired traits.
Article
Plant Sciences
Wai-Shing Yung, Qianwen Wang, Mingkun Huang, Fuk-Ling Wong, Ailin Liu, Ming-Sin Ng, Kwan-Pok Li, Ching-Ching Sze, Man-Wah Li, Hon-Ming Lam
Summary: This study observed the priming phenomenon in soybean seedlings exposed to salt stress, where the seedlings showed distinct transcriptional responses and altered histone marks that modulate stress responses and salt tolerance. The findings highlight the importance of histone modifications in forming the priming response.
Article
Biochemical Research Methods
Yingjia Tong, Jingwen Zhou, Liang Zhang, Peng Xu
Summary: Violacein, a naturally occurring anticancer therapeutic compound, was produced in Y. lipolytica using a library of strains constructed with Golden Gate assembly method. Gene expression analysis revealed that strong expression of VioB, VioC, and VioD favored violacein production, while weak expression of VioD was associated with high deoxyviolacein production. By optimizing culture conditions, violacein reached a maximum of 70.04 mg/L with 5.28 mg/L of deoxyviolacein in shake flasks.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Plant Sciences
Benjamin Spaniol, Julia Lang, Benedikt Venn, Lara Schake, Frederik Sommer, Matthieu Mustas, Stefan Geimer, Francis-Andre Wollman, Yves Choquet, Timo Muhlhaus, Michael Schroda
Summary: The study identified the role of the LPA2 protein in the biogenesis of photosystem II (PSII) in Chlamydomonas, revealing its importance in maintaining the stability and structure of PSII. Mutations in LPA2 resulted in slower growth, hypersensitivity to high light, and aberrant thylakoid membrane structures. Complexome profiling showed alterations in PSII subunit levels and dynamics, suggesting the critical role of LPA2 in PSII assembly and stability.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Neurosciences
Manuela Gries, Anne Christmann, Steven Schulte, Maximilian Weyland, Stephanie Rommel, Monika Martin, Marko Baller, Ralph Roeth, Stefanie Schmitteckert, Marcus Unger, Yang Liu, Frederik Sommer, Timo Muehlhaus, Michael Schroda, Jean-Pierre Timmermans, Isabel Pintelon, Gudrun A. Rappold, Markus Britschgi, Hilal Lashuel, Michael D. Menger, Matthias W. Laschke, Beate Niesler, Karl-Herbert Schaefer
Summary: The study identified potential biomarkers for early PD in A30P mice before hallmark symptoms appear, including delayed gut motility and early molecular dysregulation in the myenteric plexus. These biomarkers were also found in PD patients, suggesting a novel approach for biomarker identification in humans.
MOLECULAR NEURODEGENERATION
(2021)
Article
Biochemistry & Molecular Biology
Mona L. Knapp, Dalia Alansary, Vanessa Poth, Kathrin Foerderer, Frederik Sommer, David Zimmer, Yvonne Schwarz, Nicolas Kuenzel, Achim Kless, Khaled Machaca, Volkhard Helms, Timo Muehlhaus, Michael Schroda, Annette Lis, Barbara A. Niemeyer
Summary: Stim1A is a splice variant that acts as a negative regulator of SOCE and is prominently expressed in specific tissues. It regulates NFAT activation by interfering with cAMP-SOCE crosstalk.
Article
Genetics & Heredity
Justus Niemeyer, Michael Schroda
Summary: Synthetic Biology is revolutionizing biological research by introducing mechanical engineering principles into genetic research, particularly through the Modular Cloning (MoClo) strategy. This strategy allows rapid assembly of genes, especially in organisms with short generation times like Chlamydomonas reinhardtii. Researchers have simplified gene testing in Chlamydomonas by constructing five new destination vectors for direct assembly of genetic parts.
Article
Microbiology
Thomas Leisen, Janina Werner, Patrick Pattar, Nassim Safari, Edita Ymeri, Frederik Sommer, Michael Schroda, Ivonne Suarez, Isidro G. Collado, David Scheuring, Matthias Hahn
Summary: In this study, the researchers used the CRISPR/Cas technology to eliminate most of the known phytotoxic compounds in Botrytis cinerea strains. They found that these phytotoxic proteins play important roles in infection and host cell killing. The study provides insights into the functional complexity of fungal virulence factors and contributes to a comprehensive understanding of the infection mechanism of B. cinerea.
Article
Biology
Ningning Zhang, Erin M. Mattoon, Will McHargue, Benedikt Venn, David Zimmer, Kresti Pecani, Jooyeon Jeong, Cheyenne M. Anderson, Chen Chen, Jeffrey C. Berry, Ming Xia, Shin-Cheng Tzeng, Eric Becker, Leila Pazouki, Bradley Evans, Fred Cross, Jianlin Cheng, Kirk J. Czymmek, Michael Schroda, Timo Muehlhaus, Ru Zhang
Summary: Different intensities of high temperatures affect the growth of photosynthetic cells differently. This study investigated the responses of Chlamydomonas reinhardtii to 24-hour moderate (35°C) and acute (40°C) high temperatures. While both temperatures induced photoprotection, 35°C promoted growth and carbon uptake, while 40°C disrupted cell division and decreased photosynthetic efficiency. During recovery, DNA synthesis-related transcripts/proteins increased, while those involved in photosynthetic light reactions decreased.
COMMUNICATIONS BIOLOGY
(2022)
Review
Plant Sciences
Michael Schroda, Claire Remacle
Summary: Chlamydomonas reinhardtii has emerged as a production platform for biotechnology purposes due to significant advancements in nuclear transgene expression, synthetic biology strategies, and genome editing using CRISPR/Cas9. These developments have established Chlamydomonas as an ideal chassis for synthetic biology and offer the potential to rewire its metabolism for new capabilities.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Anna Maria Kiefer, Justus Niemeyer, Anna Probst, Gerhard Erkel, Michael Schroda
Summary: This study reports the successful production of full-length SARS-CoV-2 spike protein in the unicellular green alga Chlamydomonas reinhardtii. The spike protein is efficiently cleaved during synthesis in the alga and can be purified using ammonium sulfate precipitation. Chlamydomonas reinhardtii, with its advantages of low cost, simple cultivation, and large-scale production, is a promising platform for biopharmaceutical production in low-income countries.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Janick Peter, Marie Huleux, Benjamin Spaniol, Frederik Sommer, Jens Neunzig, Michael Schroda, Yonghua Li-Beisson, Katrin Philippar
Summary: In this study, the researchers found that Cr-FAX1 and Cr-FAX5 are key proteins involved in TAG production in Chlamydomonas, located in the chloroplast and ER membranes respectively. Decreasing the expression of these proteins led to a significant reduction in TAG content. Additionally, overexpression of Cr-FAX1 in the chloroplast doubled the TAG content.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Plant Sciences
Fei Wang, Korbinian Dischinger, Lisa Desiree Westrich, Irene Meindl, Felix Egidi, Raphael Troesch, Frederik Sommer, Xenie Johnson, Michael Schroda, Joerg Nickelsen, Felix Willmund, Olivier Vallon, Alexandra-Viola Bohne
Summary: In plants and cyanobacteria, the binding of chlorophyll to the D1 polypeptide of photosystem II (PSII) requires a complex involving HCF244/Ycf39 and OHP1/OHP2 proteins. In a Chlamydomonas mutant lacking the OHP2 protein, core PSII subunits, especially D1, fail to accumulate. However, extragenic suppressors suggest alternative pathways for chlorophyll association to PSII. The data indicate that OHP2 is not required for psbA translation in Chlamydomonas, but is necessary for stabilizing D1.
Article
Microbiology
S. Joke Lambrecht, Nils Stappert, Frederik Sommer, Michael Schroda, Claudia Steglich
Summary: The abundance and diversity of marine picocyanobacterium Prochlorococcus is influenced by viral infection. A cyanophage-encoded MarR-type transcription factor has been identified to induce the gene expression of host Prochlorococcus MED4 endoribonuclease E during phage infection. The transcription factor binds to an atypical activator site downstream of the start site and its binding is enhanced by the presence of Ca2+. The transcription factor interacts with the alpha subunit of RNA polymerase.
Article
Plant Sciences
Elena Kreis, Justus Niemeyer, Marco Merz, David Scheuring, Michael Schroda
Summary: In plant cells, the CLP/HSP100 chaperone family member HSP101 plays a crucial role in resolving heat-induced protein aggregates. However, the role of the chloroplast family member CLPB3 in this process remains unclear. In this study, two clpb3 mutants in Chlamydomonas reinhardtii were characterized, revealing that chloroplast CLPB3 is required for resolving heat-induced protein aggregates and conferring thermotolerance. CLPB3 was found to interact with HSP22E/F near the thylakoid membranes, suggesting a possible role in disentangling protein aggregates from the thylakoid membrane system.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Elena Kreis, Katharina Koenig, Melissa Misir, Justus Niemeyer, Frederik Sommer, Michael Schroda
Summary: This study used TurboID-mediated proximity labeling to confirm the known interactions of VIPP1 with VIPP2, HSP70B, and CDJ2 in the chloroplast of Chlamydomonas. It also identified a group of unknown function proteins, named VPL. These results demonstrate the robustness of TurboID-mediated proximity labeling technique in studying protein interaction networks in the chloroplast, and provide a foundation for analyzing the functions of VIPPs in thylakoid biogenesis and stress responses.
Article
Genetics & Heredity
Justus Niemeyer, Laura Fischer, Frank O'Neill Aylward, Michael Schroda
Summary: This study investigated the use of promoters from giant virus genomes in Chlamydomonas reinhardtii to drive gene expression. The results showed that the viral promoters were unable to effectively drive gene expression. Additionally, it was found that by mutating the start codons of mCherry and using the 5 '-UTR of beta TUB2, the problem of gene expression in Chlamydomonas could be overcome.
Article
Biochemistry & Molecular Biology
Justus Niemeyer, David Scheuring, Julian Oestreicher, Bruce Morgan, Michael Schroda
Summary: In this study, a genetically encoded fluorescent H2O2 sensor was developed for monitoring H2O2 levels in various subcompartments of a Chlamydomonas cell. The results indicate the establishment of steep intracellular H2O2 gradients under normal physiological conditions with limited diffusion into other compartments.