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
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
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
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
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
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
Biochemical Research Methods
Lishan Zhang, Zujie Yao, Huamei Tang, Qingli Song, Huanhuan Song, Jindong Yao, Zhen Li, Xiaofang Xie, Yuexu Lin, Xiangmin Lin
Summary: Protein lysine acetylation (Kac) modification plays an important role in bacterial antibiotic resistance. The downregulation of Aha1 protein and decreased abundance of Kac peptides were observed in the oxytetracycline resistance strains. Mutations in Aha1 increased antibiotic resistance and displayed multidrug resistance features.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biotechnology & Applied Microbiology
Pengfei Gu, Qianqian Ma, Shuo Zhao, Qiang Li, Juan Gao
Summary: In this study, the enzymatic properties, gene characteristics, and potential application of AlaDHs from BsAlaDH, BcAlaDH, MsAlaDH, and GsAlaDH were comprehensively evaluated. A high-yielding strain M-6 was constructed by blocking competitive pathways for L-alanine synthesis.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2023)
Article
Multidisciplinary Sciences
Yongqiang Gao, Jeremy D. Amon, Lior Artzi, Fernando H. Ramirez-Guadiana, Kelly P. Brock, Joshua C. Cofsky, Deborah S. Marks, Andrew C. Kruse, David Z. Rudner
Summary: Bacterial spores can stay dormant for long periods of time, but can quickly germinate and resume growth when nutrients are available. Receptors in the spore membrane act as nutrient-gated ion channels, initiating germination and exit from dormancy. Mutations that widen the channels induce germination in the absence of nutrients, while narrowing the channels prevents ion release and germination in response to nutrients.
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
Immunology
Yafan Hu, Mengna Zhao, Zhaoxin Lu, Fengxia Lv, Haizhen Zhao, Xiaomei Bie
Summary: L. johnsonii, L. plantarum, and L. rhamnosus were found to regulate and improve the structure of intestinal flora and alleviate diarrhea caused by EHEC infection.
MICROBIAL PATHOGENESIS
(2021)
Article
Biotechnology & Applied Microbiology
Nga Yu Poon, Anthony J. Sinskey, Kang Zhou
Summary: The threat of global plastic waste accumulation has led to the exploration of bioplastics. A proposed pathway for assimilating 1,3-propanediol (1,3-PDO) into central carbon metabolism was investigated using beta-alanine as a surrogate substrate. The study successfully engineered E. coli to assimilate beta-alanine and identified two enzymes from Vibrio natriegens that completed the metabolic pathway.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
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
Nicola Pellicciotta, Matteo Paoluzzi, Dario Buonomo, Giacomo Frangipane, Luca Angelani, Roberto Di Leonardo
Summary: By modulating bacterial motility with light, researchers have found a way to control the transport direction and speed of microscopic particles by adjusting the active pressure gradients. This discovery provides new insights into the potential use of active pressure for controlled transport of microscopic objects.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Helena Massana-Cid, Claudio Maggi, Giacomo Frangipane, Roberto Di Leonardo
Summary: Optical feedback can be used to confine and gather bacteria, forming dense high-activity regions. This method is general and scalable, making it versatile for microengineering applications and studying non-equilibrium phenomena in active systems.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Yui Uchida, Shuji Shigenobu, Hiroyuki Takeda, Chikara Furusawa, Naoki Irie
Summary: This study demonstrates that the phylotypic period, characterized by low potential for phenotypic variations, is developmentally stable and evolutionarily conserved. The results suggest that the intrinsic nature of organisms, specifically developmental stability, may limit the phenotypic variations and bias evolutionary outcomes.
Article
Developmental Biology
Takashi Takeuchi, Haruka Matsubara, Fumina Minamitani, Yukio Satoh, Sayo Tozawa, Tomoki Moriyama, Kohei Maruyama, Ken-ichi T. Suzuki, Shuji Shigenobu, Takeshi Inoue, Koji Tamura, Kiyokazu Agata, Toshinori Hayashi
Summary: This study generated mutants of Hox13 genes using the CRISPR/Cas9 system in newts and found that Hox13 genes are essential for digit formation in both development and regeneration. The predominant role of Hoxa13 in newt limbs, unlike in mouse limbs, suggests a potential contribution of Hoxa13 in the transition from fins to limbs. These findings demonstrate the conservation of Hox13 gene function in limb development and regeneration across taxa.
Article
Biochemistry & Molecular Biology
Chen-yo Chung, Shuji Shigenobu
Summary: Differentiation of the non-reproductive caste is a unique feature of eusocial insects, and apoptosis in oocytes plays a major role in constraining their reproductivity. This study investigated the soldier sterility in a hemipteran insect, the social aphid Ceratovacuna japonica, and found that soldiers possess ovaries and germaria but their ovarioles are small and lacking gastrulating embryos. The study also revealed apoptosis in the maternal nutritive cells of soldier ovaries and developmental failure of embryos.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Evolutionary Biology
Hajime Yaguchi, Shogo Suzuki, Naoto Kanasaki, Yudai Masuoka, Ryutaro Suzuki, Ryouhei H. Suzuki, Yoshinobu Hayashi, Shuji Shigenobu, Kiyoto Maekawa
Summary: In this study, the researchers investigated the role of vitellogenin (Vg) in nonreproductive castes of termites. They found that Vg4 plays an important role in the nonreproductive functions of termites. This suggests that Vg genes have undergone functionalization during the eusocial transition of termites.
JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Satoshi Ishishita, Shumpei Kitahara, Mayuko Takahashi, Sakura Iwasaki, Shoji Tatsumoto, Izumi Hara, Yoshiki Kaneko, Keiji Kinoshita, Katsushi Yamaguchi, Akihito Harada, Yasushige Ohmori, Yasuyuki Ohkawa, Yasuhiro Go, Shuji Shigenobu, Yoichi Matsuda, Takayuki Suzuki
Summary: This study investigated the molecular basis of low protoporphyrin IX (PPIX) production in the uterus of a white eggshell phenotype in Japanese quails, using transcriptome analysis and genetic linkage analysis. The results showed that several genes involved in heme biosynthesis, including ALAS1, HEPHL1, and PITX3, were specifically upregulated in the wild-type uterus and downregulated in the mutant. Further biochemical analysis indicated that the restricted availability of 5'-aminolevulinic acid is the main cause of low PPIX production. These findings suggest that uterus-specific transcriptional regulation of heme-biosynthesis-related genes plays an important role in eggshell pigment production in Japanese quails.
Article
Multidisciplinary Sciences
Kohei Ihara, Ami Oguro, Hiromasa Imaishi
Summary: The study found that the cytochrome P450 inhibition assay can discriminate sera between patients with Parkinson's disease and healthy individuals. This is of great importance for the future development of liquid biopsy-based diagnostic methods for Parkinson's disease.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Tomonari Nozaki, Shuji Shigenobu
Summary: It has been discovered that aphid bacteriocytes exhibit hyper polyploidy, with different ploidy levels observed in different developmental stages and sexes of aphids. This finding provides a foundation for understanding the functional roles and biological significance of insect bacteriocyte polyploidy.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Shotaro Namba, Hisaaki Kato, Shuji Shigenobu, Takashi Makino, Hisao Moriya
Summary: The overexpression of EGFP, a harmless protein, causes cell elongation in yeast, and this phenomenon is associated with the content of cysteine. The abnormal cell morphology triggered by EGFP overexpression is observed in different types of yeast. The perturbation of the proteasome by the exposed cysteine of the overexpressed protein leads to cell elongation.
G3-GENES GENOMES GENETICS
(2022)
Editorial Material
Biology
Shuji Shigenobu
CURRENT OPINION IN INSECT SCIENCE
(2022)
Article
Robotics
Toru Miura, Kohei Oguchi, Haruka Yamaguchi, Mayuko Nakamura, Daisuke Sato, Kenta Kobayashi, Nobuyuki Kutsukake, Kyoko Miura, Yoshinobu Hayashi, Masaru Hojo, Kiyoto Maekawa, Shuji Shigenobu, Takeshi Kano, Akio Ishiguro
Summary: This article introduces the life patterns and recent research advances of superorganisms, explores the regulatory mechanisms of superorganism systems and animal species with unique developmental systems. It also discusses synthetic approaches based on robotics and mathematical modeling.
ARTIFICIAL LIFE AND ROBOTICS
(2022)
Article
Plant Sciences
Karin Okazaki, Imari Koike, Sayuri Kera, Katushi Yamaguchi, Shuji Shigenobu, Koichiro Shimomura, Mikihisa Umehara
Summary: The study used RNA-seq analysis to compare gene expression patterns in apical and basal regions of internodal segments before and after a week of culture for adventitious shoot formation. The results identified 8987 differentially expressed genes, with 276 genes being upregulated in the apical region after culture. These genes include phytohormone-response and shoot-formation-related genes, as validated by quantitative real-time PCR assay.
Article
Genetics & Heredity
Yuuki Kobayashi, Tomoko F. Shibata, Hideki Hirakawa, Tomoaki Nishiyama, Akiyoshi Yamada, Mitsuyasu Hasebe, Shuji Shigenobu, Masayoshi Kawaguchi
Summary: Mycorrhizae are an important symbiotic relationship between plants and fungi, with ectomycorrhizae being the most common in boreal forest ecosystems. The genomic changes associated with the transition to the ectomycorrhizal lifestyle are not well understood.
Article
Pharmacology & Pharmacy
Hiroki Kuwada, Kohei Ihara, Hiromasa Imaishi
Summary: Early diagnosis and treatment interventions are crucial to overcome bladder cancer, one of the most common and deadly cancers in the world. Researchers have developed a P450 inhibition assay that can detect changes in P450 relevant substances in the serum of bladder cancer patients, and experimental results show that this method can distinguish between the sera of bladder cancer patients and healthy individuals.
DRUG METABOLISM AND PHARMACOKINETICS
(2022)
Article
Biochemistry & Molecular Biology
Ryohei H. Suzuki, Takumi Hanada, Yoshinobu Hayashi, Shuji Shigenobu, Kiyoto Maekawa, Masaru K. Hojo
Summary: Termites have an intricate social system with cooperation and division of labor. The perception of chemical signals in this social system is still not well understood. This study identified chemosensory genes involved in signal transduction in termites and found that the expression levels of certain non-receptor genes are affected by both individual and collective behaviors among termite colony members.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Plant Sciences
Chihiro Miura, Yuki Furui, Tatsuki Yamamoto, Yuri Kanno, Masaya Honjo, Katsushi Yamaguchi, Kenji Suetsugu, Takahiro Yagame, Mitsunori Seo, Shuji Shigenobu, Masahide Yamato, Hironori Kaminaka
Summary: Orchids autoactivate the mycorrhizal symbiosis pathway through gibberellin inactivation to accept the fungal partner during seed germination.