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)
Review
Biotechnology & Applied Microbiology
Andrew Currin, Steven Parker, Christopher J. Robinson, Eriko Takano, Nigel S. Scrutton, Rainer Breitling
Summary: The ability to engineer biological systems is crucial in biotechnology and synthetic biology. Generating genetic diversity is essential to explore variations in phenotype, and recent advancements in DNA synthesis technology have enhanced our ability to create variant libraries. This review focuses on approaches to create diversity from enzyme level to entire pathways in vitro, emphasizing the creation of combinatorial libraries for significant improvements in function.
BIOTECHNOLOGY ADVANCES
(2021)
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
Biotechnology & Applied Microbiology
Malgorzata Witkowska, Robert P. Jedrzejczak, Andrzej Joachimiak, Onur Cavdar, Anna Malankowska, Piotr M. Skowron, Agnieszka Zylicz-Stachula
Summary: In this study, the authors successfully converted the [NiFeSe] Dmb H2ase to [NiFe] type through site-directed mutagenesis. They created a functional and optimized operon for the rapid production of the recombinant Dmb H2ase. By introducing a series of alterations within the native dmb genes, they obtained 4 recombinant [NiFe] Dmb enzyme variants capable of H2 evolution.
MICROBIAL CELL FACTORIES
(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.
Article
Biotechnology & Applied Microbiology
Larissa Maximiano Resende, Erica de Oliveira Mello, Mariana Carvalho de Lima Aguieiras, Celso Shiniti Nagano, Renata Pinheiro Chaves, Gabriel Bonan Taveira, Marciele Souza da Silva, Andre de Oliveira Carvalho, Rosana Rodrigues, Valdirene Moreira Gomes
Summary: This study investigated the antimicrobial peptides present in Capsicum chinense fruits and evaluated their enzymatic and antifungal activities. The results showed that these peptides exhibited inhibitory effects on various fungi and demonstrated enzyme inhibition potential. These findings suggest the biotechnological potential of these antimicrobial peptides in plant disease control.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Biochemical Research Methods
Ignazio Avella, Juan J. Calvete, Libia Sanz, Wolfgang Wuester, Fulvio Licata, Sarai Quesada-Bernat, Yania Rodriguez, Fernando Martinez-Freiria
Summary: This study analyzed the venom of Lataste's viper from different populations in Portugal and compared the differences in venom composition between juvenile and adult specimens. The results showed that there are ontogenetic changes in the venom composition and geographic variability in venom profiles. Factors such as body size and sex of the vipers were also found to be potentially related to venom variation.
JOURNAL OF PROTEOMICS
(2022)
Article
Biotechnology & Applied Microbiology
Marilucia C. Ribeiro, Rodrigo S. Gebara, Gabriel B. Taveira, Andre de O. Carvalho, Rosana Rodrigues, Erica O. Mello, Celso S. Nagano, Renata P. Chaves, Valdirene M. Gomes
Summary: This study purified and evaluated the antifungal peptides present in the fruits of Capsicum chinense Jacq. The results showed that the D2 fraction of these fruits significantly inhibited the growth of Candida albicans and C. tropicalis yeasts. Mass spectrometry analysis revealed that the 6 kDa peptide band of the HI9 fraction showed similarity with antimicrobial peptides belonging to the plant defensin family.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Biotechnology & Applied Microbiology
Adson Avila de Souza, Adrianne Maia Lima, Daniele Dede Oliveira BezerraSousa, Francisca Cristiane Nogueira, Jose Carlos do Sacramento Neto, Lucas Pinheiro Dias, Nadine Monteiro Salgueiro Araujo, Celso Shiniti Nagano, Helio Vitoriano Nobre Junior, Cecilia Rocha da Silva, Livia Gurgel do Amaral Valente Sa, Joao Batista de Andrade Neto, Fatima Daiana Dias Barroso, Maria Elisabete Amaral de Moraes, Hermogenes David de Oliveira
Summary: This study isolated and characterized a thermostable trypsin inhibitor from chia seeds, which showed antibacterial activity against Staphylococcus aureus sensitive and resistant to methicillin. The trypsin inhibitor, named ShTI, displayed competitive inhibition and 1:1 stoichiometry ratio for the ShTI:trypsin complex. ShTI exhibited antibacterial activity alone and in combination with oxacillin, and its antibacterial action involved overproduction of reactive oxygen species and plasma membrane pore formation.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Pharmacology & Pharmacy
Diana Mora-Obando, Bruno Lomonte, Davinia Pla, Jimmy Alexander Guerrero-Vargas, Santiago Ayerbe-Gonzalez, Jose Maria Gutierrez, Mahmood Sasa, Juan J. Calvete
Summary: Snake venoms are complex biological mixtures that contain proteins, peptides, and nucleotides. They are produced in specialized glands and have evolved over millions of years to serve defense, immobilization, and digestion purposes. The study of the variability in venom composition has become an important area of research in toxinology.
Article
Food Science & Technology
Carlos Correa-Netto, Marcelo A. Strauch, Marcos Monteiro-Machado, Ricardo Teixeira-Araujo, Juliana Guzzo Fonseca, Moema Leitao-Araujo, Maria Lucia Machado-Alves, Libia Sanz, Juan J. Calvete, Paulo A. Melo, Russolina Benedeta Zingali
Summary: Polyclonal antibodies have been the only scientifically validated treatment for snakebites for over a century, but there have been moderate innovations in this immunotherapy. New strategies and approaches are being explored to develop next-generation antivenoms.
Review
Spectroscopy
Juan J. Calvete, Bruno Lomonte, Anthony J. Saviola, Francisco Calderon Celis, Jorge Ruiz Encinar
Summary: The advent of soft ionization mass spectrometry-based proteomics in the 1990s allowed for integral analysis of whole proteomes. However, the analytical technique itself is inherently nonquantitative, leading to the development of strategies for proteomic quantification. The combination of elemental and molecular mass spectrometry systems holds potential for absolute quantification in various areas of proteomics.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Marciele Souza da Silva, Layrana de Azevedo dos Santos, Gabriel Bonan Taveira, Celso Shiniti Nagano, Renata Pinheiro Chaves, Andre de Oliveira Carvalho, Rosana Rodrigues, Valdirene Moreira Gomes
Summary: This study characterized and evaluated the antimicrobial activity of a family of serine protease inhibitors (PIs) from Capsicum chinense Jacq. seeds. The PIs showed inhibitory effects on various enzymes and had antifungal activity. They also induced oxidative stress and apoptosis in the fungi. These findings highlight the importance of PIs in plant defense against phytopathogenic fungi.
PROTEIN AND PEPTIDE LETTERS
(2023)
Article
Pharmacology & Pharmacy
Juan J. Calvete, Bruno Lomonte, Carolina Lorente, Davinia Pla, Michael Zollweg, Dietrich Mebs
Summary: Based on its relationship to other reptiles, the Chinese crocodile lizard has been classified as venomous. However, no data about its oral secretion have been reported. This study compared the mandibular gland of the Chinese crocodile lizard with a herbivorous lizard and found no evidence of venom-derived peptides or proteins, supporting the non-venomous nature of these lizards.
Article
Infectious Diseases
Tawanny K. B. Aguiar, Felipe P. Mesquita, Nilton A. S. Neto, Francisco I. R. Gomes, Cleverson D. T. Freitas, Romulo F. Carneiro, Celso S. Nagano, Luciana M. R. Alencar, Ralph Santos-Oliveira, Jose T. A. Oliveira, Pedro F. N. Souza
Summary: Mo-CBP3-PepII, a synthetic peptide, exhibits potent activity against multidrug-resistant Cryptococcus neoformans. It targets the cells through multiple mechanisms including induction of reactive oxygen species (ROS), inhibition of enzyme activities, disruption of energy metabolism and DNA/RNA metabolism, as well as impact on protein metabolism, cytoskeleton, and cell wall organization. These findings suggest that Mo-CBP3-PepII could be a promising molecule for the development of new drugs against C. neoformans infections.
Article
Biochemistry & Molecular Biology
Renata Pinheiro Chaves, Ana Katia Barbosa dos Santos, Alexandre Lopes Andrade, Aryane de Azevedo Pinheiro, Juliana Meneses de Sena Silva, Francisca Manuela Santos da Silva, Jucilene Pereira de Sousa, Ito Liberato Barroso Neto, Eduardo Henrique Salviano Bezerra, Jade Oliveira Abreu, Fatima Cristiane Teles de Carvalho, Oscarina Viana de Sousa, Bruno Lopes de Sousa, Bruno Anderson Matias da Rocha, Andre Luis Coelho Silva, Luiz Gonzaga do Nascimento Neto, Mayron Alves de Vasconcelos, Edson Holanda Teixeira, Romulo Farias Carneiror, Alexandre Holanda Sampaio, Celso Shiniti Nagano
Summary: The SfL-1 isoform from Solieria filiformis displayed similar hemagglutinating activity and inhibition to native SfL. Circular dichroism analysis revealed fi-strands structures for both lectins. The three-dimensional structure of rSfL-1 was determined, showing two fi-barrel domains formed by five antiparallel fi chains. Both SfL and rSfL-1 exhibited agglutination activity against Escherichia coli and Staphylococcus aureus, with rSfL-1 showing a greater reduction in colony-forming units.
Article
Biochemistry & Molecular Biology
Jessica de Assis Duarte, Jose Eduardo de Oliveira Neto, Renato Cezar Farias Torres, Andressa Rocha de Oliveira Sousa, Alexandre Lopes Andrade, Renata Pinheiro Chaves, Mayron Alves de Vasconcelos, Claudener Souza Teixeira, Edson Holanda Teixeira, Celso Shiniti Nagano, Alexandre Holanda Sampaio, Romulo Farias Carneiro
Summary: This study structurally characterized and evaluated the antibacterial potential of a lectin isolated from the marine sponge Aplysina lactuta (ALL). The lectin showed affinity for specific glycoproteins and exhibited antibacterial effects when combined with certain antibiotics, suggesting its potential for the development of new antibacterial drugs.
Article
Infectious Diseases
Milena Mechkarska, Taylor S. Cunning, Megan G. Taggart, Nigel G. Ternan, Jerome Leprince, Laurent Coquet, Thierry Jouenne, Jordi Tena-Garces, Juan J. Calvete, J. Michael Conlon
Summary: The venom of the Trinidad thick-tailed scorpion contains peptides with antimicrobial activity and potassium channel and sodium channel toxins. Among the peptides, TtAP-1 exhibits strong bactericidal activity against various bacteria and can rapidly kill clinically relevant bacteria. However, its high hemolytic activity limits its potential as an anti-infective agent.
Article
Multidisciplinary Sciences
Francisco R. N. Andrade, Pedro A. S. Tabosa, Renato C. F. Torres, Romulo F. Carneiro, Mayron A. Vasconcelos, Alexandre L. Andrade, Elielton Nascimento, Ulisses Pinheiro, Edson H. Teixeira, Celso S. Nagano, Alexandre H. Sampaio
Summary: A lectin (HiL) with galactose specificity was isolated from marine sponge Haliclona (Reniera) implexiformis using affinity chromatography. Potent inhibitors of HiL included glycoproteins porcine stomach mucin (PSM) and bovine stomach mucin (BSM). HiL showed maximal hemagglutinating activity at pH 5.0-9.0 and remained active up to 60 degrees C. It consists of a dimer with identical subunits linked by disulfide bonds and has a significant impact on Staphylococcus biofilms.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2023)
Article
Multidisciplinary Sciences
Alexandra S. De Almeida, Dayara N. M. Mendonca, Romulo F. Carneiro, Ulisses Pinheiro, Elielton Francisco Do Nascimento, Alexandre l. Andrade, Mayron A. De Vasconcelos, Edson H. Teixeira, Celso S. Nagano, Alexandre H. Sampaio
Summary: A new lectin IsL was isolated from the marine sponge Ircinia strobilina. It exhibited stable agglutination activity and had a specific secondary structure. IsL is calcium-dependent and able to inhibit biofilm formation of Staphylococcus aureus and Staphylococcus epidermidis.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2023)
