Article
Biochemistry & Molecular Biology
Natalia Gabrielli, Christoniki Maga-Nteve, Eleni Kafkia, Mandy Rettel, Jakob Loeffler, Stephan Kamrad, Athanasios Typas, Kiran Raosaheb Patil
Summary: By using C-13 isotope tracing, we identified cross-fed metabolites in co-cultures of Saccharomyces cerevisiae and Lactococcus lactis. Our results showed that the yeast utilized galactose and lactic acid as carbon sources, and revealed a complex pattern of amino acid exchange between the two species. This study demonstrates the utility of C-13-based proteomics for uncovering microbial interactions.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Debra N. Brunson, Ling Ning Lam, Jose A. Lemos
Summary: A new study reveals that the heme released by Staphylococcus aureus can enhance the growth and biofilm biomass of Enterococcus faecalis, supporting the theory of metabolite cross feeding in shaping polymicrobial biofilm interactions.
TRENDS IN MICROBIOLOGY
(2022)
Editorial Material
Oncology
Chi Chun Wong, Winnie Fong, Jun Yu
Summary: This study tracked gut bacteria and metabolites in rectal cancer patients undergoing neoadjuvant chemoradiotherapy and identified Bacteroides vulgatus as a driver bacterium of therapeutic resistance by supplying tumors with nucleotides.
Article
Multidisciplinary Sciences
Sammy Pontrelli, Rachel Szabo, Shaul Pollak, Julia Schwartzman, Daniela Ledezma-Tejeida, Otto X. Cordero, Uwe Sauer
Summary: A study on a model marine microbial community that degrades chitin reveals that chitinases secreted by the degraders produce specific chain length oligomers, which select for specialized consumers and influence the metabolites secreted by these consumers. Each species in the breakdown cascade exhibits unique hierarchical preferences for substrates, leading to sequential colonization of metabolically distinct groups over time. This study uncovers a hierarchical cross-feeding structure that allows biopolymer degraders to shape the dynamics of community assembly.
Review
Microbiology
James B. McKinlay
Summary: The metabolism of bacterial cells can extend beyond their boundaries, forming extended metabolic networks across communities and the globe. Intracellular metabolites can be externalized through mechanisms such as active and passive transporters, rather than simple diffusion across membranes. The externalization of metabolites can be influenced by competition and can initiate a positive-feedback loop of reciprocal cross-feeding.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Christian Dusny, Andreas Schmid
Summary: Novel cultivation technologies require adaptation of analytical concepts, such as metabolic flux analysis (MFA), which traditionally relies on stable-isotope labeling of biomass-bound protein. This study introduces a non-disruptive approach using secreted protein as an information carrier for C-13-based metabolic flux analysis. Results show faster incorporation of isotope information from labeled glucose into recombinant reporter protein compared to biomass-bound protein, suggesting potential for analyzing fast metabolic dynamics under isotopically nonstationary conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Samir Giri, Leonardo Ona, Silvio Waschina, Shraddha Shitut, Ghada Yousif, Christoph Kaleta, Christian Kost
Summary: The study reveals that metabolic dissimilarity between bacterial genotypes is a key factor determining the establishment of metabolic cross-feeding interactions in microbial communities. Results showed that a greater phylogenetic distance and metabolic network dissimilarity between donor and recipient were associated with better growth of auxotrophic recipients, indicating that interacting with metabolically dissimilar partners benefits recipient genotypes.
Article
Biochemistry & Molecular Biology
Jiayu Sun, Zhimin Huang, Yifei Du, Pinou Lv, Xinqi Fan, Peng Dai, Xing Chen
Summary: It was found that per-O-acetylated clickable unnatural sugars used in metabolic glycan labeling (MGL) for analyzing glycans were cytotoxic to cultured primary neurons. This cytotoxicity was due to the non-enzymatic S-glyco-modification reactions of the sugars with protein cysteines, resulting in modified proteins associated with biological functions related to microtubule cytoskeleton organization and neuron projection development. By using S-glyco-modification-free unnatural sugars, MGL without cytotoxicity was established in cultured primary neurons, allowing for visualization of cell-surface sialylated glycans and large-scale identification of sialylated N-linked glycoproteins and modification sites.
ACS CHEMICAL BIOLOGY
(2023)
Article
Plant Sciences
Valeria F. Lima, Alexander Erban, Andre G. Daubermann, Francisco Bruno S. Freire, Nicole P. Porto, Silvio A. Candido-Sobrinho, David B. Medeiros, Markus Schwarzlaender, Alisdair R. Fernie, Leticia dos Anjos, Joachim Kopka, Danilo M. Daloso
Summary: C-13 metabolic flux analysis has advanced our understanding of plant metabolic regulation, but detailed in vivo flux mapping remains challenging. NMR-based flux investigations offer high accuracy for small networks, while mass spectrometry approaches have broader potential but are limited by lack of atomic level position information.
Article
Microbiology
Jessica A. Lee, Alyssa C. Baugh, Nicholas J. Shevalier, Brandi Strand, Sergey Stolyar, Christopher J. Marx
Summary: The research team developed a model microbial consortium for studying lignocellulose degradation with the specific goal of reducing formaldehyde production, by including various bacteria to simulate ecological dynamics and metabolite exchange. Experimental results suggest that this study lays the foundation for future eco-evolutionary research and optimization of biomass transformation efficiency.
Article
Biology
Digar Singh, Sang Hee Lee, Choong Hwan Lee
Summary: This study investigates the ecological interactions between Bacillus amyloliquefaciens and Aspergillus oryzae through a pairwise metabolite cross-feeding experiment. The results show that cross-feeding Aspergillus metabolites benefit the growth and biofilm formation of Bacillus, while cross-feeding Bacillus extracts suppress the mycelial growth and conidiation of Aspergillus.
COMMUNICATIONS BIOLOGY
(2022)
Article
Ecology
Leonardo Ona, Samir Giri, Neele Avermann, Maximilian Kreienbaum, Kai M. Thormann, Christian Kost
Summary: The study shows that obligate cross-feeding among bacteria can expand their metabolic niche space, especially between specialist taxa, and is positively correlated with the phylogenetic distance between interaction partners.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Chemistry, Analytical
Bo Wang, Jamey D. Young
Summary: The study evaluated the efficacy of several commonly used metabolic quenching methods, demonstrating that rapid filtration followed by 100% cold methanol quenching exhibited the highest efficiency. However, mixing cell samples with a partially frozen 30% methanol slurry was slightly less effective but enabled less laborious sample processing. Mixing the cells with a saline ice slurry or 60% cold methanol prior to centrifugation was found to be less effective and caused significant metabolite loss.
ANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Shingo Noguchi, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu
Summary: This study compared the metabolic phenotypes of cancer cells cultured in 2D and 3D environments using C-13 metabolic flux analysis. The results demonstrated distinct metabolic characteristics of cells cultured in 3D, showing significant differences in metabolic pathways compared to 2D cultures.
METABOLIC ENGINEERING
(2022)
Editorial Material
Plant Sciences
Thomas Wieloch, Johann Rohwer
Summary: C-13-INST-MFA is an emerging technique for estimating metabolic fluxes and pool sizes, with two studies in plant science utilizing this method to characterize carbon metabolism. It is recommended that researchers working with C-13-INST-MFA enter a phase of model validation to ensure robust estimations of specific fluxes.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Biochemical Research Methods
Alexander J. Connor, Runye H. Zha, Mattheos Koffas
Summary: Research suggests the necessity to develop and deploy next-generation antiviral treatments, with biomacromolecules potentially serving as potent antiviral agents. Modern advances in technology can enable the production of tailored biomacromolecules for targeted antiviral applications.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Hyun Gyu Hwang, Myung Hyun Noh, Mattheos A. G. Koffas, Sungho Jang, Gyoo Yeol Jung
Summary: Recombinant microbes provide a promising alternative for producing naringenin, a key molecular scaffold for flavonoids. In this study, a systematic strategy for multi-level optimization of biosynthetic pathways was introduced, resulting in a significant increase in naringenin production. Through the construction of a combinatorial library covering both transcription and translation stages, improved strains were identified, leading to a 3-fold increase in naringenin production compared to traditional methods.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Guoqiang Xu, Xiangliu Shi, Yuhao Gao, Jiyue Wang, Hui Cheng, Yang Liu, Yuanyuan Chen, Jiayu Li, Xiaopeng Xu, Jian Zha, Ke Xia, Robert J. Linhardt, Xiaomei Zhang, Jinsong Shi, Mattheos A. G. Koffas, Zhenghong Xu
Summary: This study demonstrates the improvement of pyruvate carboxylase activity through mutation and codon optimization to enhance the synthesis of fumaric acid. The results showed that the strategy significantly increased fumaric acid production and provided a effective way for elevating PYC activity.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Agriculture, Multidisciplinary
Yingpeng Xu, Lijun Geng, Yiwen Zhang, J. Andrew Jones, Meihong Zhang, Yuan Chen, Ronghui Tan, Mattheos A. G. Koffas, Zhengtao Wang, Shujuan Zhao
Summary: Salvianolic acid B (SAB), a water-soluble phenolic acid, has various biological activities and is clinically used for cardio- and cerebrovascular diseases. This study successfully engineered a heterologous rosmarinic acid biosynthetic pathway in yeast, enabling de novo biosynthesis of SAB through cooperation with the native metabolism of the yeast strain.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Xiao Bu, Jing-Yuan Lin, Chang-Qing Duan, Mattheos A. G. Koffas, Guo-Liang Yan
Summary: In this study, a strategy using exogenous oleic acid and metabolic engineering approaches was developed to efficiently accumulate beta-carotene in Saccharomyces cerevisiae. By increasing storage capacity and redirecting metabolic flux, the engineered strain achieved a significant increase in beta-carotene production compared to the parent strain.
MICROBIAL CELL FACTORIES
(2022)
Review
Environmental Sciences
Zhen Fang, Jun Zhou, Xiangtong Zhou, Mattheos A. G. Koffas
Summary: The conversion of CO2 into sustainable fuels, such as CH4, is significant in addressing carbon emissions and the energy crisis. The use of abiotic-biotic hybrid systems for CO2 biomethanation with renewable electric/solar energy shows promise, but efficiency may be limited. This review highlights the design of abiotic-biotic hybrids and synthetic biology strategies for tunable methanogenic microorganisms or enzymes, pointing towards a bright future for sustainable fuel production through CO2 biomethanation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Biochemical Research Methods
Joshua Finkelstein, James Swartz, Mattheos Koffas
Summary: Bioelectrosynthesis (BES) systems utilize extracellular electron transport pathways to enhance cellular metabolism, improving economic viability and reducing carbon footprint in biomanufacturing processes. To efficiently channel electrons towards biosynthesis, a better understanding of electron transport mechanisms and comprehensive evaluation of process performance is necessary.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Zhen Fang, Yinjie J. Tang, Mattheos A. G. Koffas
Summary: This review discusses the importance of electrical-to-biochemical conversion (E2BC) in driving cell metabolism for biosynthesis, including the natural processes, development of artificial E2BC, design of electrobiochemical systems, and synthetic biology methods for efficient microbial electrosynthesis.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Microbiology
Pattsarun Cheawchanlertfa, Suwalak Chitcharoen, Nachon Raethong, Qing Liu, Pramote Chumnanpuen, Panyawarin Soommat, Yuanda Song, Mattheos Koffas, Kobkul Laoteng, Wanwipa Vongsangnak
Summary: This study enhanced the genome-scale metabolic model of Cordyceps militaris and found key metabolic responses in alteration of lipid metabolism upon different carbon sources. The study provides a comprehensive basis for sphingolipid biosynthesis in Cordyceps militaris, which can be further applied in medicinal and functional food fields.
Article
Biology
Jinjin Diao, Rhiannon Carr, Tae Seok Moon
Summary: In this study, we identified and studied the transcription factors involved in aromatic degradation in Rhodococcus opacus using GFP-based sensors and comprehensive deletion analyses. Our results indicate that the funneling pathways for different aromatic compounds are regulated by transcriptional activators or repressors. Additionally, the substrate hierarchy in R. opacus may be due to the transcriptional cross-regulation of different aromatic funneling pathways.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yu Xiu, Ni Zhang, Pranesha Prabhakaran, Sungho Jang, Qipeng Yuan, Curt M. Breneman, Gyoo Yeol Jung, Wanwipa Vongsangnak, Mattheos A. G. Koffas
Summary: A parallel screening and physicochemical analysis of various flavonoids and chalcones were conducted to study the relationship between their binding affinity and specificity with artificial riboswitches. It was found that increased electronegativity and hydrophilicity of the flavonoid structures enhanced their binding affinity, while the position and number of hydroxyl groups played a crucial role in the binding with different riboswitches.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhengyang Xiao, Alexander J. Connor, Alyssa M. Worland, Yinjie J. Tang, R. Helen Zha, Mattheos Koffas
Summary: This study investigates the metabolic flexibility and limitations in the production of recombinant silk proteins in Escherichia coli. It reveals that metabolic burden leads to metabolic flux redistribution and changes in the Ent-ner-Doudoroff pathway. Additionally, accumulation of acetate is highly toxic to silk-producing strains, resulting in decreased silk protein production. The study proposes three solutions to address these issues and discusses other strategies.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Nisit Watthanasakphuban, Luan Van Nguyen, Yu-Shen Cheng, Pau-Loke Show, Malinee Sriariyanun, Mattheos Koffas, Kittipong Rattanaporn
Summary: The Agrobacterium-mediated transient gene expression system is a fast and efficient method for expressing recombinant proteins in plants. However, the high cost of Agrobacterium suspension production limits its application on an industrial scale. This study found that using sugarcane molasses as a low-cost carbon and nitrogen source can significantly reduce the production cost, without the need for antibiotic supplementation.
FERMENTATION-BASEL
(2023)
Review
Biotechnology & Applied Microbiology
Adeola E. Awofiranye, Jon Hudson, Aditi Dey Tithi, Robert J. Linhardt, Wanwipa Vongsangnak, Mattheos A. G. Koffas
Summary: This review discusses the structure, medical significance, and limitations of current extraction methods of chondroitin sulfate (CS). It explores alternative production strategies for CS, including chemical synthesis and chemoenzymatic synthesis, with a focus on the successful metabolic engineering of strains. Microbial engineering is presented as the optimal option for modern production of chondroitin and CS, and the biosynthetic pathway for chondroitin production in various microbes is also discussed. Manipulation of pathway genes has led to the biosynthesis of chondroitin derivatives.
FERMENTATION-BASEL
(2022)
Review
Biochemistry & Molecular Biology
Philippe Jeandet, Alessandro Vannozzi, Eduardo Sobarzo-Sanchez, Md. Sahab Uddin, Roque Bru, Ascension Martinez-Marquez, Christophe Clement, Sylvain Cordelier, Azadeh Manayi, Seyed Fazel Nabavi, Mahsa Rasekhian, Gaber El-Saber Batiha, Haroon Khan, Iwona Morkunas, Tarun Belwal, Jingjie Jiang, Mattheos Koffas, Seyed Mohammad Nabavi
Summary: Phytostilbenes, despite being a limited chemical family, represent a significant group of molecules among natural compounds. Research interest in these compounds has continuously grown, leading to a vast literature development and tens of thousands of references. The various aspects of phytostilbenes, including their chemistry, biosynthesis regulation, biological activities, molecular engineering, and biotechnological production, have been extensively covered in over 500 articles.
NATURAL PRODUCT REPORTS
(2021)
