Review
Biotechnology & Applied Microbiology
Atrayee Chattopadhyay, Mohor Mitra, Mrinal K. Maiti
Summary: Research is currently focusing on several nonconventional oleaginous yeast species for developing renewable and sustainable biolipid feedstock. Significant progress has been made in recent years in understanding metabolic pathways, implementing engineering strategies, and improving genetic tools for various yeast genera, which will benefit future studies in strain improvement and metabolic engineering for enhanced lipid production.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Biotechnology & Applied Microbiology
Abhishek Joshi, Krishan K. Verma, Vishnu D. Rajput, Tatiana Minkina, Jaya Arora
Summary: Addressing climate change and energy supply issues requires the use of renewable biofuels as a replacement for petroleum fuels. However, the cost-effective conversion of lignocellulose into biofuels remains a challenge. Recent research has focused on lignocellulose feedstock and microbial engineering, with some success in improving metabolic pathways and creating robust microbial hosts. Future advancements should focus on designing more efficient pathways and screening and engineering novel enzymes to achieve economically feasible lignocellulosic-based biofuel production.
Review
Plant Sciences
Ralph Bock
Summary: The technology of plastid genome transformation has great significance in metabolic engineering due to the ability of plastid genomes to accommodate large amounts of foreign DNA and the unique mode of inheritance. The absence of epigenetic gene silencing mechanisms in plastids and the high expression levels achieved further enhance its attractiveness. This review focuses on the engineering principles, tools, and recent applications of plastid genome transformation in metabolic engineering.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jin Liu, Meijing Liu, Yufang Pan, Ying Shi, Hanhua Hu
Summary: Research on the marine alga Nannochloropsis oceanica showed that introducing potent DGATs with strong activity on EPA-CoA and overexpressing elongase genes involved in EPA biosynthesis can drastically increase EPA abundance in TAG, providing insights for enriching other desired fatty acids in TAG.
METABOLIC ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Zihua Li, Yufei Dong, Yu Liu, Xuecong Cen, Dehua Liu, Zhen Chen
Summary: In this study, an efficient C. glutamicum strain for the production of 1,3-propanediol (1,3-PDO) from glucose and xylose was developed using systems metabolic engineering approaches. Through the construction and optimization of glycerol and 1,3-PDO synthesis modules, as well as pathway engineering to reduce toxic byproducts, the engineered strain demonstrated high production of 1,3-PDO. This study highlights the potential of C. glutamicum as a chassis for the industrial production of 1,3-PDO from lignocellulosic feedstocks.
METABOLIC ENGINEERING
(2022)
Article
Biochemical Research Methods
Drew M. DeLorenzo, Jinjin Diao, Rhiannon Carr, Yifeng Hu, Tae Seok Moon
Summary: The study developed a simple gene repression system based on CRISPR interference, which demonstrated improved repression efficiency compared to previous systems and allowed for parallel construction of multiple plasmids without PCR steps, facilitating engineering of the GC-rich nonmodel organism. Utilizing this system, the researchers confirmed the annotated roles of four metabolic pathway genes and successfully demonstrated the tool's utility.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Energy & Fuels
Rituparna Saha, Mainak Mukhopadhyay
Summary: The use of fossil fuels is increasingly associated with detrimental environmental effects, making renewables such as biodiesel highly attractive. Research into oleaginous microorganisms for lipid synthesis has shown promise, but low lipid production has been a limiting factor in industrial biodiesel production. Engineering robust strains of these microbes has increased their lipid production capacity and led to commercialization.
BIOMASS CONVERSION AND BIOREFINERY
(2021)
Article
Agricultural Engineering
Huarong Zhou, Zhaoxian Xu, Chenggu Cai, Jie Li, Mingjie Jin
Summary: This study deciphered the metabolic distribution of vanillin in Rhodoccous opacus PD630 and identified several vanillin reductases. By manipulating the genes involved in vanillin metabolism, the conversion of vanillin to muconic acid was significantly increased. Furthermore, the existence of vanillin reductases in other bacteria was demonstrated.
BIORESOURCE TECHNOLOGY
(2022)
Review
Microbiology
Wei Jiang, Chao Li, Yanjun Li, Huadong Peng
Summary: Microbial lipids have gained significant attention in the field of metabolic engineering and synthetic biology due to their market growth and versatile applications. This review provides an overview of lipid synthesis modules in yeast and discusses various metabolic engineering strategies for enhancing lipid production. It also explores the potential impact of lipid pathway engineering on cellular physiological properties and suggests future trends for enhancing intracellular lipid production in yeast.
Article
Microbiology
Varsha Patil, Vikas Jain
Summary: This study found that deletion of one copy of the atpD gene in M. smegmatis leads to an energy-compromised state, resulting in a major routing shift in electron flux through less efficient respiratory chain complexes and an increased reduced state. This alteration further modulates the biosynthesis of cell wall associated lipids and triacylglycerol (TAG), with an accumulation of TAG-containing lipid bodies. Moreover, the mutant shows overexpression of TAG-degrading lipase genes, indicating a shift towards utilizing TAG as an energy source.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Leonie Benninghaus, Tatjana Walter, Melanie Mindt, Joe Max Risse, Volker F. Wendisch
Summary: This study demonstrates the production of L-theanine using metabolic engineering techniques with Pseudomonas putida KT2440 from various carbon sources, showcasing the efficiency of the process utilizing heterologous enzymes. Fed-batch bioreactor cultures yielded significant titers of L-theanine, proving the feasibility of the approach for commercial production.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Hai-De Wang, Jian-Zhong Xu, Wei-Guo Zhang
Summary: In this study, a high L-arginine (L-Arg) producing E. coli strain was obtained through metabolic engineering. The genes speC and speF were found to play important roles in L-Arg accumulation. Feedback inhibition of the L-Arg pathway in E. coli was successfully overcome by combining gene mutations/deletions. Additionally, the insertion of a gene cluster from Corynebacterium glutamicum enhanced the metabolic flux of the L-Arg pathway. The final strain achieved the highest reported level of L-Arg production by E. coli.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Xiaoxin Zhai, Jiaoqi Gao, Yunxia Li, Martin Grininger, Yongjin J. Zhou
Summary: Methanol is an ideal feedstock for chemical and biological manufacturing. Constructing an efficient cell factory is essential for producing complex compounds through methanol biotransformation. This study demonstrates that compartmentalizing fatty alcohol biosynthesis and methanol utilization in peroxisomes significantly improves fatty alcohol production in methylotrophic yeast.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yuichi Kato, Kosuke Inabe, Yuji Haraguchi, Tatsuya Shimizu, Akihiko Kondo, Tomohisa Hasunuma
Summary: To develop a sustainable animal cell culture system, researchers introduced the lldD gene from Escherichia coli into Synechococcus sp. PCC 7002, enabling the strain to consume l-lactate. This consumption was accelerated by the expression of the lldP gene and an increase in culture temperature. The study provides new insight into the treatment of l-lactate by photosynthetic microorganisms, potentially enhancing the feasibility of animal cell culture industries.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Helena A. Saunders, Pablo Calzadilla, Jean-Marc Schwartz, Giles N. Johnson
Summary: The accumulation of fumarate, catalyzed by the fumarase isoform FUM2, is necessary for photosynthetic acclimation in Arabidopsis. Using the Failure Mode and Effect Analysis (FMEA) technique, researchers have identified fumarate as a low-risk metabolite and malate as a high-risk metabolite that can cause system instability. FUM2 is suggested to provide a fail-safe mechanism to control malate concentration and maintain stability in a changing environment.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biotechnology & Applied Microbiology
Martina Oberhofer, Fabian Malfent, Martin Zehl, Ernst Urban, Judith Wackerlig, Gottfried Reznicek, Gabriel A. Vignolle, Christian Rueckert, Tobias Busche, Daniel Wibberg, Sergey B. Zotchev
Summary: Endophytic fungi have the potential to produce diverse secondary metabolites. In this study, a Helotiales isolate from Bergenia pacumbis was found to produce bioactive secondary metabolites. Genome sequencing revealed numerous secondary metabolite biosynthesis gene clusters, and heterologous gene expression in Streptomyces bacteria showed the production of terpenoids. The study highlights the importance of a comprehensive approach combining traditional methods and genome mining to investigate the biosynthetic potential of endophytic fungi.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Lena Ullmann, Daniel Wibberg, Tobias Busche, Christian Rueckert, Andreas Muesgens, Jorn Kalinowski, Lars M. Blank
Summary: The Ustilaginaceae family, a type of Basidiomycetes, not only causes plant diseases but also produces valuable compounds. Through genome sequencing and analysis, it was found that the reclassification of Ustilaginaceae might be necessary. The study also revealed potential biotechnological applications of secondary metabolite clusters.
Article
Microbiology
Thomas Schafhauser, Daniel Wibberg, Antonia Binder, Christian Rueckert, Tobias Busche, Wolfgang Wohlleben, Joern Kalinowski
Summary: This study presents the genome sequence of the pleuromutilin-producing fungus Clitopilus passeckerianus and identifies the biosynthetic gene clusters for pleuromutilin. The findings lay the foundation for improving the yield of pleuromutilin through metabolic strain engineering.
Article
Chemistry, Multidisciplinary
Yi-Ming Shi, Jan J. Crames, Laura Czech, Kenan A. J. Bozhuyuk, Yan-Ni Shi, Merle Hirschmann, Stefanie Lamberth, Peter Claus, Nicole Paczia, Christian Ruckert, Jorn Kalinowski, Gert Bange, Helge B. Bode
Summary: This study reveals the biosynthetic potential of a widespread benzobactin gene cluster and identifies the acyl AMP-ligase responsible for the last cyclization step. Genome mining of Pseudomonas chlororaphis uncovered the presence of the gene cluster in different bacterial species, highlighting the regulatory mechanisms and structural diversity of benzobactin biosynthesis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Microbiology
Olha Schneider, Martin Zehl, Reiko Ueoka, Christian Ruckert, Tobias Buche, Yi Jiang, Qin-Yuan Li, Jorn Piel, Sergey B. Zotchev
Summary: In their natural habitats, bacteria encounter a wide variety of organic compounds, including antibiotics produced by other members of the microbial community. This study identified and characterized an enzyme that is apparently involved in the biosynthesis of a siderophore, but also has the ability to modify and inactivate structurally diverse antibiotics. This discovery highlights additional capabilities of bacteria to withstand antibiotic treatment and suggests that enzymes involved in secondary metabolism may have an additional function in the natural environment.
Article
Chemistry, Medicinal
Fazlin Pheiffer, Yannik K. -H. Schneider, Espen Holst Hansen, Jeanette Hammer Andersen, Johan Isaksson, Tobias Busche, Christian Rueckert, Joern Kalinowski, Leonardo van Zyl, Marla Trindade
Summary: This study investigates the bioactive potential of the marine invertebrate symbiont Thalassomonas actiniarum, identifying its antibacterial and cytotoxic activities, as well as their ability to produce cholic acid and 3-oxo cholic acid through hydrolysis of conjugated bile acids. The findings provide a foundation for further research on the bioactivities and ecological role of Thalassomonas sp. in the marine environment.
Article
Multidisciplinary Sciences
Melissa E. Reardon-Robinson, Minh Tan Nguyen, Belkys C. Sanchez, Jerzy Osipiuk, Christian Ruckert, Chungyu Chang, Bo Chen, Rahul Nagvekar, Andrzej Joachimiak, Andreas Tauch, Asis Das, Hung Ton-That
Summary: In many gram-positive Actinobacteria, MdbA plays a crucial role in bacterial viability by catalyzing oxidative folding of exported proteins. However, in Corynebacterium diphtheriae, the deletion of mdbA only affects cell growth at 37°C, suggesting the existence of alternative oxidoreductase enzymes. Through genetic suppressor mutations, we discovered that elevated expression of tsdA can compensate for the loss of mdbA by mediating oxidative folding of pilin and toxin substrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Simone Kann, Gustavo Concha, Felix Weinreich, Andreas Hahn, Christian Rueckert, Joern Kalinowski, Olfert Landt, Hagen Frickmann
Summary: This study compared the performance of two commercial real-time PCR assays for identifying Trypanosoma cruzi DNA in serum. The results showed that both assays had a similar diagnostic accuracy for detecting T. cruzi from human serum, with slightly higher specificity observed for the TibMolBiol assay. The RealStar assay exhibited cross-reactions with T. rangeli, a non-pathogenic parasite, which may be a disadvantage in areas where T. cruzi and T. rangeli co-circulate.
Article
Microbiology
Daniel Siebert, Tobias Busche, Ezgi Saydam, Jorn Kalinowski, Christian Rueckert-Reed, Bastian Blombach
Summary: Pseudomonas carboxydohydrogena is a lithoautotrophic and obligate aerobic alphaproteobacterium that can utilize CO, CO2, H-2, and mixtures thereof as sole carbon and energy sources. The complete genome sequence of type strain DSM 1083 is reported, and its close relation to Afipia carboxidovorans strain OM5 is discussed.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Meeting Abstract
Oncology
Cassandra Cieslak, Christian Rueckert, Tobias Busche, Carsten Hain, Joern Kalinowski, Katrin Schaper-Gerhardt, Ralf Gutzmer, Rudolf Stadler
EUROPEAN JOURNAL OF CANCER
(2023)
Article
Biotechnology & Applied Microbiology
Selma Beganovic, Christian Rueckert-Reed, Hilda Sucipto, Wei Shu, Lars Glaeser, Thomas Patschkowski, Ben Struck, Joern Kalinowski, Andriy Luzhetskyy, Christoph Wittmann
Summary: In this study, a multiomics analysis of Streptomyces rimosus was performed to gain insights into the metabolic and regulatory networks driving oxytetracycline formation. The study compared wild-type and hyperproducing strains and revealed key traits influencing oxytetracycline production. Using these traits, the researchers successfully synthesized bhimamycin and created a novel microbial chassis strain with enhanced production. The mutagenized hyperproducer strain exhibited complex mutations, impacting gene expression and complicating rational engineering. This study highlights the importance of precursor supply and genetic stability in improving antibiotic production.
MICROBIAL CELL FACTORIES
(2023)
Article
Infectious Diseases
Leonie Sagurna, Sascha Heinrich, Lara-Sophie Kaufmann, Christian Rueckert-Reed, Tobias Busche, Alexander Wolf, Jan Eickhoff, Bert Klebl, Joern Kalinowski, Julia E. Bandow
Summary: Bacteria of the genus Streptomyces produce various specialized metabolites. Single biosynthetic gene clusters (BGCs) can give rise to different products with varying biological activities. In this study, alnumycin and 1,6-dihydro 8-propylanthraquinone were isolated from a Streptomyces strain containing the alnumycin BGC. Both compounds exhibited antimicrobial activity, with 1,6-dihydro 8-propylanthraquinone showing higher activity against E. coli & UDelta;tolC compared to alnumycin. The modes of action of these compounds are worth further investigation.
Article
Biotechnology & Applied Microbiology
Felix Werner, Lynn S. Schwardmann, Daniel Siebert, Christian Ruckert-Reed, Joern Kalinowski, Marie-Theres Wirth, Katharina Hofer, Ralf Takors, Volker F. Wendisch, Bastian Blombach
Summary: This study achieved efficient fatty alcohol production in C. glutamicum from wheat straw hydrolysate for the first time through targeted metabolic engineering and adaptive laboratory evolution (ALE). The study provides useful metabolic engineering principles to tailor C. glutamicum for other products from second-generation feedstock.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2023)
Article
Biochemical Research Methods
Rahmi Lale, Lisa Tietze, Maxime Fages-Lartaud, Jenny Nesje, Ingerid Onsager, Kerstin Engelhardt, Che Fai Alex Wong, Madina Akan, Niklas Hummel, Joern Kalinowski, Christian Rueckert, Martin Frank Hohmann-Marriott
Summary: In this study, a universal approach called Gene Expression Engineering (GeneEE) was developed to create artificial expression systems in various organisms, including bacteria and yeast, resulting in a wide range of expression levels.
Meeting Abstract
Dermatology
C. Cieslak, C. Hain, C. Ruckert, L. J. Klages, K. Schaper-Ger-Hardt, J. Kalinowski, R. Gutzmer
JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT
(2022)
Article
Biotechnology & Applied Microbiology
Nicolas Huber, Edgar Alberto Alcala-Orozco, Thomas Rexer, Udo Reichl, Steffen Klamt
Summary: Cell-free production systems are commonly used for synthesizing industrial chemicals and biopharmaceuticals. This study presents a model-based optimization framework for cell-free enzyme cascades, taking into account parameter uncertainties. The approach was exemplified using the synthesis of GDP-fucose, resulting in significant improvements in the process.
METABOLIC ENGINEERING
(2024)
