Article
Biochemistry & Molecular Biology
Satoshi Katsube, Keiichiro Sakai, Tasuke Ando, Ryuta Tobe, Hiroshi Yoneyama
Summary: D-amino acids are found at high levels in the extracellular environment and are thought to have physiological functions, but how they are secreted remains unknown. This study discovered several potential d-alanine exporters in Escherichia coli and developed a screening system to evaluate their efficacy. The results suggest that AlaE and YciC are involved in the export of d-alanine, and overexpression of AlaE can alleviate growth constraints caused by high levels of d-alanine. This study also identified YciC as a novel d-alanine exporter.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Sailesh Malla, Eric van der Helm, Behrooz Darbani, Stefan Wieschalka, Jochen Foerster, Irina Borodina, Morten Otto Alexander Sommer
Summary: The lack of an active export system limits the accumulation and purification of intracellular products in industrial bio-based production processes. In this study, a novel L-lysine exporter belonging to the uncharacterized EamA superfamily was identified using metagenomic functional selection. This exporter significantly improved L-lysine tolerance and enhanced the yield and production of L-lysine in an industrial strain. This approach allows for the discovery of novel exporters and can be used to increase the productivity of bioprocesses with toxicity limitations.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jun Liu, Li Cao, Paul C. Klauser, Rujin Cheng, Viktoriya Y. Berdan, Wei Sun, Nanxi Wang, Farid Ghelichkhani, Bingchen Yu, Sharon Rozovsky, Lei Wang
Summary: Introducing novel chemical bonds into proteins offers innovative possibilities, with the incorporation of latent bioreactive unnatural amino acids providing a powerful system for covalent targeting of natural residues. This approach has potential applications in biochemical research and protein engineering.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Analytical
Samantha Nunez, Maria Barra, Daniel Garrido
Summary: In this study, a molecular quantification method of free fucose was designed and developed using fluorescent Escherichia coli. The molecular circuit showed specificity against other monosaccharides and exhibited a linear response in the range of 0-45 mM. The biosensor was successfully tested on different concentrations of free fucose and the supernatant of Bifidobacterium bifidum JCM 1254, indicating its applicability in detecting free fucose.
Article
Biology
Gita Naseri, Hannah Raasch, Emmanuelle Charpentier, Marc Erhardt
Summary: In this study, a set of arabinose-inducible artificial transcription factors (ATFs) were developed using CRISPR/dCas9 and Arabidopsis-derived DNA-binding proteins to control gene expression in E. coli and Salmonella over a wide range of inducer concentrations. The transcriptional output of the ATFs varied greatly, particularly in Salmonella strains rewired for arabinose catabolism. The developed ATFs were used to engineer a Salmonella biosensor strain and regulate beta-carotene biosynthesis in E. coli, resulting in significantly higher production compared to traditional methods.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Swati Dubey, Puja Majumder, Aravind Penmatsa, Abhijit A. Sardesai
Summary: The study elucidated the membrane topology and export mechanism of LysO protein, suggesting that Thl may be exported in antiport with H+ while Lys may be a low-affinity export substrate. This finding provides insight into how LysO mediates Lys/Thl export and affords protection from Thl toxicity in Escherichia coli.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Microbiology
Harutaka Mishima, Hirokazu Watanabe, Kei Uchigasaki, So Shimoda, Shota Seki, Toshitaka Kumagai, Tomonori Nochi, Tasuke Ando, Hiroshi Yoneyama
Summary: In E. coli, stress-induced mutagenesis led to the emergence of L-alanine prototrophic mutants when grown in L-alanine-deficient medium, with the mutants carrying point mutations in key metabolic pathways. Addition of pyruvate relieved the starvation stress and prevented the emergence of L-alanine prototrophic mutants, highlighting the role of pyruvate in inducing L-alanine prototrophy.
Article
Chemistry, Multidisciplinary
Menghua Wang, Katherine S. Ryan
Summary: In this study, two new l-Alanosine-producing strains were discovered through genome mining. These strains lack the aspartate-nitrosuccinate pathway genes found in the original producer and use a unique set of nitrate-nitrite reductases to reduce nitrate instead. The repurposing of enzymes from the nitrogen cycle for specialized metabolite biosynthesis and the potential for the discovery of new nitric-oxide-derived natural products are demonstrated.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Microbiology
Kohei Ihara, Seryoung Kim, Tasuke Ando, Hiroshi Yoneyama
Summary: AlaE is the smallest amino acid exporter identified in Escherichia coli, functioning by forming homo-oligomers. It exports β-alanine using the proton motive force and plays a pivotal role in maintaining intracellular β-alanine homeostasis. The GxxxG motif in the TM4 region is important for substrate export but not involved in AlaE oligomer formation.
Article
Biotechnology & Applied Microbiology
Mengzhen Nie, Jingyu Wang, Kechun Zhang
Summary: A novel approach was developed to achieve high-yield production of L-arginine from N-acetylglutamate in E. coli by genetically modifying the bacteria and overexpressing specific genes. Co-production of pyruvate and L-arginine was also demonstrated to increase the utilization of input carbon sources.
MICROBIAL CELL FACTORIES
(2023)
Article
Multidisciplinary Sciences
Anna K. Orta, Nadia Riera, Yancheng E. Li, Shiho Tanaka, Hyun Gi Yun, Lada Klaic, William M. Clemons
Summary: In this study, the researchers used single-particle electron cryo-microscopy to uncover the mechanism by which bacteriophage can kill bacteria by encoding a protein antibiotic. The results were validated experimentally and provide a model for bacterial lysis and potential design of phage therapeutics.
Article
Biotechnology & Applied Microbiology
Ryota Hagihara, Shoto Ohno, Mikiro Hayashi, Kazuhiko Tabata, Hirofumi Endo
Summary: The study presents an efficient method for producing L-theanine without supplemental ethylamine, using engineered biosynthetic pathways in Escherichia coli. By optimizing gene expression and enhancing production capacity, successful large-scale production of L-theanine was achieved, laying the foundation for safe and economical production of this beneficial compound.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yinyin Ma, Josep Ramoneda, David R. Johnson
Summary: In this study, the researchers used consortia of Pseudomonas stutzeri strains to investigate the optimal timing of antibiotic administration to minimize the spread of antibiotic resistance-encoding plasmids within microbial communities. They found that plasmid transfer and transconjugant proliferation peaked at intermediate antibiotic administration times when the mixing between plasmid donors and potential recipients was maximal.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
Summary: The study analyzed the expression dynamics of thousands of genes with inducible promoters, revealing the impact of RNA polymerase and LacI repressor binding site strengths on gene expression. By fitting a statistical mechanics model, properties of theoretically optimal inducible promoters were accurately modeled. Through the examination of three alternative promoter architectures, the study showed how repositioning binding sites within promoters influences the combinatorial effects observed between promoter elements.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Guang Zeng, Yinzhen Zheng, Ya Xiang, Run Liu, Xiaofeng Yang, Zhanglin Lin
Summary: Our study successfully purified four proteins and peptides using a novel salt-inducible self-assembling peptide tag scheme, with yields ranging from 12 to 87 mg/L. The yield and purity (72-97%) were comparable to the classical His-tag method, but without using a His-tag.
MICROBIAL CELL FACTORIES
(2023)