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
Chemistry, Medicinal
Clement Monsarrat, Guillaume Compain, Christophe Andre, Sylvain Engilberge, Isabelle Martiel, Vincent Olieric, Philippe Wolff, Karl Brillet, Marie Landolfo, Cyrielle Silva da Veiga, Jerome Wagner, Gilles Guichard, Dominique Y. Burnouf
Summary: A study was conducted on a series of peptides interacting with the Escherichia coli SC binding pocket, showing improved affinity through various modifications. X-ray structure analysis revealed new peptide-protein interactions that explained the enhanced binding mechanism.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Shuai Liu, Bing-Bing Wang, Jian-Zhong Xu, Wei-Guo Zhang
Summary: This study improved the production of L-tryptophan by metabolic engineering, optimizing the shikimate pathway and L-tryptophan branch. The resulting strain produced 53.65 g/L of L-tryptophan, with a yield of 0.238 g/g glucose, setting the basis for the development of other valuable aromatic compounds or derivatives.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Myriam Roth, Vincent Jaquet, Sylvain Lemeille, Eve-Julie Bonetti, Yves Cambet, Patrice Francois, Karl-Heinz Krause
Summary: This study investigated the impact of sublethal hydrogen peroxide (H2O2) concentration on gene expression in E. coli. It was found that H2O2 exposure led to specific antioxidant and general stress responses, but did not significantly affect bacterial survival.
Article
Biotechnology & Applied Microbiology
Zheng Chen, Qinyu Li, Peng Zhou, Baoguo Li, Zhijun Zhao
Summary: This study investigated the ability of Escherichia coli to produce L-serine by fermentation using glycerol and glucose. The results showed that L-serine accumulated to a maximum of 634.37 mg/L and 459.27 mg/L in glycerol and glucose medium, respectively. Transcriptome sequencing revealed differentially expressed genes mainly involved in amino acid biosynthesis and histidine metabolism. Key genes in the degradation of L-serine to pyruvate and pyruvate to branched-chain amino acids were down-regulated, while many up-regulated genes appeared in the glycine anabolic pathway and transcription levels of regulatory genes in histidine metabolism were down-regulated. This study provides genetic insights into the construction of high-yielding strains for L-serine synthesis using glycerol.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
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)
Review
Biotechnology & Applied Microbiology
Wenwei Li, Zhen Zhou, Dan Wang
Summary: This paper summarizes the advantages and disadvantages of chemical hydrolysis, enzymatic biotransformation, and fermentation for the synthesis of L-cysteine. It provides a detailed introduction to the biosynthesis of L-cysteine, metabolic engineering strategies, and the latest progress in reported L-cysteine fermentation bacteria. Insights are given on the future development of increasing the production of biosynthetic L-cysteine.
FERMENTATION-BASEL
(2023)
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
Biotechnology & Applied Microbiology
Xiaomei Zhang, Zhenhang Sun, Jinyu Bian, Yujie Gao, Dong Zhang, Guoqiang Xu, Xiaojuan Zhang, Hui Li, Jinsong Shi, Zhenghong Xu
Summary: This study successfully increased the production efficiency of l-cysteine by optimizing serine production, constructing a biosensor, and implementing adaptive laboratory evolution. The engineered strain achieved efficient biosynthesis of l-cysteine from glycerol conversion.
FERMENTATION-BASEL
(2022)
Article
Multidisciplinary Sciences
Bin Liu, Lingyan Jiang, Yutao Liu, Hongmin Sun, Jun Yan, Chenbo Kang, Bin Yang
Summary: The mammalian gastrointestinal tract is a complex environment that hosts a diverse microbial community. This study discovered that enterohemorrhagic Escherichia coli (EHEC) O157:H7 imports L-malate from the host and microbiota using the DcuABC transporters, converting it into fumarate to fuel anaerobic respiration and promote colonization. L-malate also acts as a signaling molecule to activate virulence gene expression in EHEC O157:H7.
NATURE COMMUNICATIONS
(2023)
Article
Polymer Science
Faizul Azam, Mohammed. H. H. Alqarni, Sulaiman Mohammed Alnasser, Prawez Alam, Talha Jawaid, Mehnaz Kamal, Shamshir Khan, Aftab Alam
Summary: In the past decade, researchers have developed gel-based formulations as alternatives to traditional hydrogels and emulgels. Anise, the main constituent of Pimpinella anisum L., was selected as the active ingredient due to its strong antibacterial properties. This study aimed to develop an herbal emulgel for treating skin infections caused by antibiotic-resistant bacteria. Tests and evaluations were conducted on an emulgel solution containing anise essential oil, which showed good stability and potential as an antibacterial formulation against Escherichia coli (E. coli) as a model organism.
Article
Biochemistry & Molecular Biology
Ryusei Yoshida, Shogo Ozaki, Hironori Kawakami, Tsutomu Katayama
Summary: This study describes the unwinding mechanisms of the DUE in the replication origin oriC of Escherichia coli, which are promoted by DnaA, IHF, and the structural homolog HU. IHF and HU promote DUE unwinding by promoting the binding of R1/R5M-bound DnaAs to ssDUE. Notably, HU binds the R1-R5M interspace stimulated by ATP-DnaA and ssDUE, suggesting a model of DUE unwinding triggered by DnaA interactions and stabilized by HU binding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Kyeong Rok Choi, Hye Eun Yu, Hoseong Lee, Sang Yup Lee
Summary: The fermentation process for high-level production of heme by the metabolically engineered Escherichia coli HAEM7 strain was optimized in this study. Various factors such as carbon sources, iron concentration, pH control, induction points, and iron content in the feeding solution were examined to improve heme production. Strategies of increasing cell density, regular iron supplementation, and supplying excess feeding solution were also developed. The optimized fermentation process resulted in a heme production of 1.03 g/L with a productivity of 21.5 mg/L/h. This research will expedite the establishment of industrial-scale production of heme.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Infectious Diseases
Tsvetelina Petkova, Nikolina Rusenova, Svetla Danova, Aneliya Milanova
Summary: Biofilm-forming bacteria pose a challenge in treating veterinary patients. N-acetyl-L-cysteine (NAC) has been shown to inhibit biofilm formation in combination with certain antibiotics. This study aimed to investigate the effect of NAC on doxycycline activity against biofilm-forming strains. The results suggest that NAC does not affect the inhibitory effect of doxycycline on biofilm formation by Staphylococcus aureus, but may stimulate the growth of planktonic cells of S. aureus and biofilm-forming Escherichia coli.
Article
Biotechnology & Applied Microbiology
Alaska Pokhrel, Hue Dinh, Liping Li, Karl A. Hassan, Amy K. Cain, Ian T. Paulsen
Summary: In this study, a novel LysR-type transcriptional regulator encoded by ABUW_1016 (cbl) in Acinetobacter baumannii was characterized using transcriptomics and bioinformatic analyses. It was found that Cbl is involved in controlling the expression of genes required for uptake and reduction of various sulfur sources in A. baumannii. A model of cysteine biosynthesis and its regulation by Cbl and GigC in A. baumannii was proposed.
MICROBIAL PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yuki Yoshikawa, Ryo Nasuno, Hiroshi Takagi
Summary: The study found that yeast cells lacking NADPH exhibited increased tolerance to oxidative and nitrosative stress. This was primarily due to the upregulation of Ctt1 expression in ZWF1-deficient cells, enhancing their antioxidant capacity.
Article
Biotechnology & Applied Microbiology
Shota Isogai, Tomonori Matsushita, Hiroyuki Imanishi, Jirasin Koonthongkaew, Yoichi Toyokawa, Akira Nishimura, Xiao Yi, Romas Kazlauskas, Hiroshi Takagi
Summary: In this study, a feedback inhibition-insensitive HCS variant was designed and analyzed using in silico docking and enzymatic assays. The engineered HCS showed significantly higher lysine production in yeast cells compared to the wild-type HCS and another variant, demonstrating the potential for rational engineering of key enzymes in metabolic engineering for improved amino acid productivity.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shota Isogai, Hiroshi Takagi
Summary: The study showed that lysine supplementation and enhancement of lysine biosynthesis improved the high-temperature stress tolerance of E. coli cells. Lysine-overproducing strains have the potential as stress-tolerant microorganisms and can be used as robust host cells for microbial production of useful compounds.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shota Isogai, Akira Nishimura, Atsushi Kotaka, Naoyuki Murakami, Natsuki Hotta, Hiroki Ishida, Hiroshi Takagi
Summary: The study found that a yeast strain with a specific mutation can lead to the accumulation of isoleucine, resulting in increased production of 2-methyl-1-butanol. This discovery is valuable for engineering yeast strains to enhance the production of isoleucine and its derived fusel alcohols.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Akira Nishimura, Shota Isogai, Naoyuki Murakami, Natsuki Hotta, Atsushi Kotaka, Kengo Matsumura, Yoji Hata, Hiroki Ishida, Hiroshi Takagi
Summary: The research identified a sake yeast mutant that accumulates phenylalanine and decreases 2-phenylethanol production, which may lead to the creation of unique new sake varieties.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Microbiology
Masataka Ohashi, Shota Isogai, Hiroshi Takagi
Summary: This study revealed the crucial role of key residues in the formation of the arginine-binding cavity for arginine recognition of NAGK. Additionally, novel arginine feedback inhibition-insensitive variants of NAGK in sake yeast mutants with ornithine overproduction were analyzed, suggesting that amino acid substitutions in the NAGK variants destabilize the arginine-binding cavity, leading to lower sensitivity to arginine feedback inhibition of NAGK activity.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biotechnology & Applied Microbiology
Jirasin Koonthongkaew, Nontawat Ploysongsri, Yoichi Toyokawa, Vithaya Ruangpornvisuti, Hiroshi Takagi
Summary: In this study, we successfully increased the production of branched-chain higher alcohols (BCHAs) by designing variants of Bat1 and Bat2 with altered enzyme activity. Our results showed that these engineered BCATs decreased catalytic activities and increased BCHA production. This study provides new insights into the functions of BCATs and has practical applications in the future construction of enzymes for high-level BCHAs production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ryoya Tanahashi, Akira Nishimura, Fumika Morita, Hayate Nakazawa, Atsuki Taniguchi, Kazuki Ichikawa, Kazuki Nakagami, Kyria Boundy-Mills, Hiroshi Takagi
Summary: Proline, the most abundant amino acid in wine and beer, is hardly assimilated by Saccharomyces cerevisiae during fermentation. The study found that arginine, ornithine, and lysine inhibit proline utilization by inducing endocytosis of the proline transporter Put4, while citrulline does not. By genetic screening, it was revealed that the arginine transporter Can1 is involved in the arginine-dependent inhibition of proline utilization. Further biochemical analyses showed that Can1 activates signaling cascades of protein kinase A in response to extracellular arginine, suggesting its role as a transceptor regulating proline utilization.
Editorial Material
Biochemistry & Molecular Biology
Andriy A. Sibirny, Terrance G. Cooper, Hiroshi Takagi
Article
Biotechnology & Applied Microbiology
Shota Isogai, Akira Nishimura, Naoyuki Murakami, Natsuki Hotta, Atsushi Kotaka, Yoichi Toyokawa, Hiroki Ishida, Hiroshi Takagi
Summary: This study identified a valine-accumulating sake yeast mutant and found a novel amino acid substitution. The mutant yeast accumulated valine and produced more isobutanol. This research provides insights for brewing distinctive Japanese sake by increasing the production of valine-derived compounds.
FEMS YEAST RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Akira Nishimura, Ryoya Tanahashi, Tomoki Oi, Kyoyuki Kan, Hiroshi Takagi
Summary: The current CRISPR/Cas9 systems in Saccharomyces cerevisiae cannot be considered non-genetic modification technology due to the need for plasmid expression systems. However, our study demonstrates that editing the yeast genome can be achieved without plasmid expression systems, using a commercially available protein transfection reagent and chemically modified sgRNAs.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Ryoya Tanahashi, Akira Nishimura, Minh Nguyen, Irnayuli Sitepu, Glen Fox, Kyria Boundy-Mills, Hiroshi Takagi
Summary: Proline contributes to taste and flavor of foods. Saccharomyces cerevisiae poorly assimilates proline during fermentation, resulting in its accumulation in fermented products. Our screening of 1138 yeasts revealed that Zygoascus, Galactomyces, and Magnusiomyces genera are better at utilizing proline.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Masatoshi Tsukahara, Shota Isogai, Haruna Azuma, Keiko Tsukahara, Yoichi Toyokawa, Hiroshi Takagi
Summary: A new strain of yeast, Saccharomyces cerevisiae 35a14, was isolated from banana stems in Okinawa. This strain did not belong to any industrial yeast groups and had high alcohol production. Furthermore, a mutant derived from 35a14, which overproduces l-leucine, resulted in a high concentration of isoamyl acetate when used in brewing awamori, an Okinawa's traditional distilled alcoholic beverage.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Akira Nishimura, Kazuki Nakagami, Kyoyuki Kan, Fumika Morita, Hiroshi Takagi
Summary: This study elucidated the inhibitory effect of arginine on yeast biofilm formation and its underlying mechanism, providing insights into the molecular mechanism and control of yeast biofilm formation.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Akira Nishimura, Kazuki Ichikawa, Hayate Nakazawa, Ryoya Tanahashi, Fumika Morita, Irnayuli Sitepu, Kyria Boundy-Mills, Glen Fox, Hiroshi Takagi
Summary: This study clarifies the inhibitory mechanism of proline utilization in yeast during wine-making processes, revealing the involvement of glucose response and the Ras/PKA pathway. The research indicates the existence of crosstalk between carbon and proline metabolisms and provides valuable insights and directions for developing wine yeast strains that can efficiently assimilate proline.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
