Article
Biotechnology & Applied Microbiology
Lina Heistinger, Juliane C. Dohm, Barbara G. Paes, Daniel Koizar, Christina Troyer, Oezge Ata, Teresa Steininger-Mairinger, Diethard Mattanovich
Summary: By characterizing 25 natural isolates from all seven described Komagataella species, this study identified strains with differences in tolerance to high pH, high temperature, and growth on xylose. The genotypic and phenotypic diversity within this genus provides a basis for utilizing neglected Komagataella strains with interesting characteristics and understanding genetic determinants for improved growth and stress tolerance.
MICROBIAL CELL FACTORIES
(2022)
Article
Microbiology
Dalin Rifat, Liang Chen, Barry N. Kreiswirth, Eric L. Nuermberger
Summary: Using transposon mutagenesis and deep sequencing, this study comprehensively analyzed essential genes in M. abscessus and found that most of them have homology with essential genes in M. tuberculosis, providing valuable insights for understanding M. abscessus pathogenicity and drug development.
Article
Microbiology
Delphine Lariviere, Laura Wickham, Kenneth Keiler, Anton Nekrutenko
Summary: Our work provides an assessment of the currently available tools for TIS data analysis. It offers ready-to-use workflows that can be invoked by anyone in the world using our public Galaxy platform. To lower the entry barriers, we have also developed interactive tutorials explaining details of TIS data analysis procedures.
Article
Immunology
Fan Yin, Yan Hu, Zixuan Bu, Yuying Liu, Hui Zhang, Yawen Hu, Ying Xue, Shaowen Li, Chen Tan, Xiabing Chen, Lu Li, Rui Zhou, Qi Huang
Summary: In this study, a transposon (Tn) mutagenesis library and a mouse infection model were used to identify important genes involved in the in vivo fitness of porcine ExPEC. Several genes, including Delta fimG, were found to be critical for in vivo fitness and adhesion to host cells. Additionally, metabolic genes and regulatory genes were also identified as important determinants of in vivo fitness. This study provides insights into the pathogenicity of porcine ExPEC.
Article
Biology
Binyang Deng, Yu Yue, Jun Yang, Mingjun Yang, Qiong Xing, Hang Peng, Fei Wang, Ming Li, Lixin Ma, Chao Zhai
Summary: In this study, highly glycosylated IsPETase enzyme was obtained by controlling the glycosylation modification of PETase in Pichia pastoris, improving the enzyme's specific activity and thermostability. The partially deglycosylated IsPETase still maintained high thermostability and could completely degrade PET flakes at 50 degrees C. This study provides a strategy to modulate the thermostable IsPETase through glycosylation engineering, promoting PET biodegradation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Fidan Erden-Karaoglan, Mert Karaoglan
Summary: This study investigated the applicability of heterologous yeast promoters in Pichia pastoris, and found inducible and constitutive regulation modes as well as the optimal carbon sources for these promoters. The study also determined the DNA region with the highest activity for all promoters through promoter deletion analysis.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biology
Yoichiro Ito, Misa Ishigami, Goro Terai, Yasuyuki Nakamura, Noriko Hashiba, Teruyuki Nishi, Hikaru Nakazawa, Tomohisa Hasunuma, Kiyoshi Asai, Mitsuo Umetsu, Jun Ishii, Akihiko Kondo
Summary: This study presents a method to improve protein production in the non-conventional yeast Komagataella phaffii. The method involves gene knockout screening, combining gene disruptions, and adaptive evolution to recover growth reduction. The researchers used a multiwell-formatted screening system to evaluate a large number of mutant strains and identified multiple gene disruptions that increased antibody production. They also found that the target protein and promoter could be interchangeable for the effects of gene knockouts. Adaptive evolution was used to recover reduced cell growth caused by multiple gene knockouts and explore the possibility of further enhancing protein secretion. The overall approach holds promise for improving protein production in non-conventional microorganisms.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maria Carmela Bonaccorsi di Patti, Antimo Cutone, Zuzana Pakanova, Marek Nemcovic, Peter Barath, Giovanni Musci
Summary: Ceruloplasmin is crucial for iron metabolism in vertebrates, and the production of high-quality recombinant human ceruloplasmin represents a significant advancement. Further improvement in productivity and glycoengineering is necessary for potential therapeutic use in aceruloplasminemia patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Tianpeng Chen, Shimeng Wang, Huanqing Niu, Guanjia Yang, Sinan Wang, Yuqi Wang, Chaowei Zhou, Bin Yu, Pengpeng Yang, Wenjun Sun, Dong Liu, Hanjie Ying, Yong Chen
Summary: A biofilm-based fermentation system was constructed in P. pastoris by combining the surface display of beta-galactosidase and biofilm formation. The results showed a catalytic conversion rate of 50.3% for GOS with a maximum enzyme activity of 5125 U/g. This study provides a basis for developing biofilm-based surface display methods in P. pastoris.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Xihao Liao, Lu Li, Aysha Jameel, Xin-Hui Xing, Chong Zhang
Summary: A CRISPR-based toolbox for gene editing and transcriptional regulation in P. pastoris was developed, allowing efficient and flexible gene expression control. This toolkit will accelerate the application of P. pastoris in metabolic engineering and synthetic biology by providing a simple and multifunctional system for genetic engineering.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Nai-Xin Lin, Rui-Zhen He, Yan Xu, Xiao-Wei Yu
Summary: The robust P. pastoris mutant demonstrates higher expression levels of not only lipase but also other heterogeneous proteins under methanol induction conditions. The mutant shows lower intracellular ROS levels compared to the WT. RNA-seq analysis revealed upregulation of key pathways related to antioxidant, MAPK pathway, ergosterol synthesis pathway, transcription factors, and the peroxisome pathway in the robust mutant, contributing to its enhanced oxidative stress tolerance and high heterologous protein expression efficiency.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Microbiology
Hongbaek Cho
Summary: Transposon insertion site sequencing (TIS) is a powerful technique for determining the insertion profile of a transposon mutant library, providing insights into the fitness contributions of genetic loci in bacterial genomes under specific growth conditions. Despite being relatively new, TIS has emerged as a crucial tool in bacterial genetics research.
JOURNAL OF MICROBIOLOGY
(2021)
Article
Microbiology
Yaxing Su, Yanan Xu, Hailing Liang, Gaoqing Yuan, Xiaogang Wu, Dehong Zheng
Summary: This study identified key genes required for R. solanacearum survival in tomato plants using transposon insertion sequencing technology, highlighting the importance of genes related to cell wall/membrane/envelope biogenesis, amino acid transport and metabolism, energy production and conversion, posttranslational modification, protein turnover, and chaperones in the pathogenic mechanism of this bacterium.
Article
Microbiology
Yasmin Nabilah Binti Mohd Fauzee, Yuki Yoshida, Yukio Kimata
Summary: In eukaryotic species, dysfunction of the endoplasmic reticulum (ER) triggers a cellular protective response called the unfolded protein response (UPR). This response is initiated by ER stress sensors, including Ire1, which splices and matures mRNA encoding the transcription factor Hac1. Through analyzing the methylotrophic yeast Pichia pastoris, researchers discovered a previously unknown function of Ire1. They found that Ire1 not only regulates UPR but also controls protein aggregation and the heat shock response, conferring heat stress resistance to the cells.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Xiaobing Hu, Yulong Fan, Chengfeng Mao, Hui Chen, Qiang Wang
Summary: Microalgae, a group of organisms capable of producing various useful substances through photosynthesis, can be genetically modified at the molecular level to serve as Chassis Cells for food, medicine, energy, and environmental protection purposes, thus tapping into the benefits of microalgae resources. This manuscript provides theoretical and technical support for the application of transposons in studying microalgae gene function, by summarizing the sequencing method of transposon insertion sites.
FRONTIERS IN MICROBIOLOGY
(2023)