Article
Microbiology
Purnendu Bhowmik, Nagakumar Bharatham, Satoshi Murakami, Vasanthi Ramachandran, Santanu Datta
Summary: OqxB, a member of the RND efflux pump family, is widely recognized as a major contributor to antimicrobial resistance. It is predominantly present in Klebsiella spp. and contributes to resistance against antibiotics like nitrofurantoin, quinolones, b-lactams, and colistin. In addition to Klebsiella spp., oqxB has been found to occur via horizontal gene transfer in other bacterial genera. The crystal structure and key amino acid residues involved in the substrate binding domain of OqxB have been characterized, revealing their importance in efflux and resistance development against fluoroquinolones.
RESEARCH IN MICROBIOLOGY
(2023)
Article
Microbiology
Emily C. Hoedt, Francesca Bottacini, Nora Cash, Roger S. Bongers, Kees van Limpt, Kaouther Ben Amor, Jan Knol, John MacSharry, Douwe van Sinderen
Summary: Members of the genus Bifidobacterium are difficult to genetically manipulate due to their extensive and variable Restriction-Modification systems. A modified suicide vector, pFREM28, was developed to target specific genes in B. breve by removing known restriction sites, reducing the time, effort, and resources required for generating site-directed mutants. This approach could be applied to other (bifido)bacterial species as well.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Tyll Stocker, Lena Altrogge, Caroline Marcon, Yan Naing Win, Frank Hochholdinger, Heiko Schoof
Summary: Insertional mutagenesis is a powerful tool for creating loss-of-function mutations on a genome-wide scale. MuWU is an automated Mutant-seq workflow utility that efficiently identifies insertion sites and handles complex bioinformatic tasks, making it a valuable resource for functional genomics studies.
Article
Agriculture, Multidisciplinary
Su-Jin Jun, Jung-A Lee, Young-Wan Kim, Sang-Ho Yoo
Summary: Through site-directed mutagenesis, a robust mutant Bifidobacterium thermophilum (BtAS) strain BtAS(Y414F/P200R) with enhanced turanose productivity was successfully developed, showing an increase in turanose yield by two times compared to the wild type BtAS and completing the reaction in half the time.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Soroosh Pouyan, Milad Lagzian, Mohammad Hossein Sangtarash
Summary: This study characterized a new alpha-amylase from Bacillus cereus GL96 and used an in-silico approach to redesign the enzyme for improved thermal stability. The engineered enzyme showed higher stability and activity at elevated temperatures compared to the wild-type enzyme. Specifically, the D162K mutation resulted in the best performance, with increased optimum temperature and improved stability. This mutant enzyme holds promise for further investigation and industrial applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Plant Sciences
Xia Li, Geng Chen, Qing-Qing Gao, Chun-Fan Xiang, Cheng-Xiao Yuan, Xiao-Ning Li, Yan-Yu Shu, Guang-Hui Zhang, Yan-Li Liang, Sheng-Chao Yang, Chen-Xi Zhai, Yan Zhao
Summary: This study explored the key enzymes involved in cucurbitacins biosynthesis in the Chinese traditional medicinal plant Hemsleya chinensis. Using AlphaFold2 and molecular docking, the researchers successfully predicted the 3D structure of HcOSC6 and its binding features to 2,3-oxidosqualene. Mutagenesis experiments identified three key amino acid residues, E246, M261, and D490, which significantly affected the activity of HcOSC6. This study not only characterized three potential key residues for producing cucurbitacins, but also provided insights into their significant role in metabolic engineering.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Lena Goshayeshi, Sara Yousefi Taemeh, Nima Dehdilani, Mohammadreza Nasiri, Mohammad M. Ghahramani Seno, Hesam Dehghani
Summary: The study demonstrates the use of an RNA-guided piggyBac transposase and dual sgRNAs for site-directed integrations in the human ROSA26 safe harbor region. This methodology shows promise for targeting specific genomic regions, such as in cancer cells for inserting sequences into target regions or activating tumor suppressor genes.
Article
Agriculture, Multidisciplinary
Cheng-Hua Wang, Wu-Ping Xiong, Cheng Huang, Xiao-Ming Li, Qing-Yan Wang, Ri-Bo Huang
Summary: This study successfully increased the catalytic activity and efficiency of an exoinulinase under acidic conditions through rational site-directed mutagenesis. The mutants showed improved substrate preference for inulin and may serve as promising candidates for industrial inulin hydrolysis. The study demonstrates the potential of mutating non-conserved substrate recognition residues for industrial enzyme improvements.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Review
Plant Sciences
Olawale Samuel Adeyinka, Bushra Tabassum, Brice Landry Koloko, Ifedayo Victor Ogungbe
Summary: The improvement of CRISPR-Cas gene editing technology has facilitated genetic modification of desirable agronomic traits in crops, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits. This presents a significant opportunity for precise genetic diversification in plants.
Article
Biochemistry & Molecular Biology
Satoru Watanabe, Masahiro Ito, Takanori Kigawa
Summary: DiRect is a novel PCR-based mutagenesis method that achieves high quality product (>99% substitution) without the use of recombinant DNA technology. It has been successfully applied in the study of an industrially relevant enzyme, showing simplicity, efficiency, and potential scalability in site-directed mutagenesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Chemistry, Organic
Houchao Xu, Jeroen S. Dickschat
Summary: In the past three decades, numerous terpene synthases have been characterized from various life kingdoms. The mechanisms of terpene synthases have been investigated through site-directed mutagenesis, providing valuable insights into their catalysis and resulting in mutants with improved yields.
SYNTHESIS-STUTTGART
(2022)
Article
Computer Science, Software Engineering
Madhavi Latha Yadav Bangaru, Ravi Kumar Medabalimi, Sobhan Babu, Nidhanapati K. Raghavendra
Summary: Silent mutations allowing for restriction site modification can aid in screening successful mutants during site-directed mutagenesis. However, introducing a new restriction site requires the analysis of degenerate sequences within mutant primers, which becomes increasingly laborious, time-consuming, and prone to errors as the number of degenerate codons increases. A software named 'REMP' was developed to instantly generate degenerate sequences with restriction sites that are 6-8 base pairs in length, allowing users to edit the list of restriction sites without the need for writing computer code or knowing a program language.
Article
Biochemistry & Molecular Biology
Qiuya Gu, Yu Lu, Jianli Zhou, Wenhua Yang, Ke Wang, Xiaobo Liu, Xiaobin Yu
Summary: Combinational mutagenesis was used to improve the catalytic efficiency and adaptability of alginate lyase from Pseudoalteromonas sp. Alg6B, which showed significant potential for the production of AOS from marine alginate.
PROCESS BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Krzysztof Michalski, Christian Hertig, Dariusz R. Mankowski, Jochen Kumlehn, Janusz Zimny, Anna M. Linkiewicz
Summary: Cas endonuclease-mediated genome editing offers a long-awaited molecular biological approach for modifying predefined genomic target sequences in living organisms. The implementation of this technology can be challenging for species like triticale, but pre-validated cas9/gRNA constructs provide a strong foundation for the targeted induction of heritable modifications in triticale genes. The study also demonstrates that in-del induction frequency in triticale can be increased by TREX2 nuclease activity, regardless of gRNA performance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Miguel O. Suarez-Barrera, Lydia Visser, Efrain H. Pinzon-Reyes, Paola Rondon Villarreal, Juan S. Alarcon-Aldana, Nohora Juliana Rueda-Forero
Summary: This study investigated the cytotoxic effects of Parasporin 2 on colon cancer cell lines, particularly the promising mutant 3-35 which exhibited higher cytotoxicity than PS2Aa1. The study also explored the possible involvement of residues 256 and 257 in the interaction of PS2Aa1 and APN.
