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Recent advances on the systems metabolically engineered Pseudomonas species as versatile biosynthetic platforms for the production of polyhydroxyalkanoates

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Systems Microbiology and Biomanufacturing 2024年第2期4卷 473-499页

作者： Hye Min Song Seo Young Jo Haeyoung Lee Subeen Jeon Dohye Yun Chaerin Kim Jina Son Yu Jung Sohn Jong-Il Choi Si Jae Park Department of Chemical Engineering and Materials Science Graduate Program in System Health Science and EngineeringEwha Womans UniversitySeoul 03760Republic of Korea Department of Biotechnology and Bioengineering Chonnam National UniversityGwangju 61186Republic of Korea

Pseudomonas *** been considered one of the most promising microbial platform strains due to its versatile metabolism,enabling the valorization of waste materials into value-added chemical *** the native producer of polyhydroxyal-kanoates(PHAs),the biodegradable biopolyesters,it has been widely engineered by various metabolic engineering tools for the production of PHAs composed of short-chain-length and medium-chain-length monomers with adjustable composition from diverse carbon sources,ranging from pure sugars to crude oils and fatty *** review discusses the feasibility of Pseudomonas *** the industrial host strain and the recent advances regarding the systems metabolic engineering strategies for PHAs production in Pseudomonas sp.

关键词： Pseudomonas sp. Polyhydroxyalkanoates Systems metabolic engineering Synthetic biology Fermentation

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TaxDiff: taxonomic-guided diffusion model for protein sequence generation

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science China(Information sciences) 2025年第4期68卷 385-386页

作者： Zongying LIN Hao LI Liuzhenghao LV Yu WANG Bin LIN Junwu ZHANG Zijun CHEN Calvin Yu-Chian CHEN Li YUAN Yonghong TIAN School of Electronic and Computer Engineering Peking University AI for Science (AI4S)-Preferred Program Peking University Shenzhen Graduate School Peng Cheng Laboratory School of Chemical Biology and Biotechnology Peking University

Protein design aims to generate protein variants with targeted biological functions, which is significant in multiple biological areas, including enzyme reaction catalysis, vaccine design, and fluorescence intensity. Protein design contains two paradigms: sequence generation and structure generation. Recently, EvoDiff [1] proposed a universal designing paradigm, combining structure and sequence generation using the diffusion framework, which improves the protein design efficiency.

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CRISPR/Cas genome editing in soybean: challenges and new insights to overcome existing bottlenecks

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Journal of Advanced Research 2025年 73卷 53-72页

作者： Freitas-Alves, Nayara Sabrina Moreira-Pinto, Clidia E. Távora, Fabiano T.P.K. Paes-de-Melo, Bruno Arraes, Fabricio B.M. Lourenço-Tessutti, Isabela T. Moura, Stéfanie M. Oliveira, Antonio C. Morgante, Carolina V. Qi, Yiping Fatima Grossi-de-Sa, Maria Embrapa Genetic Resources and Biotechnology DF Brasília Brazil Bioprocess Engineering and Biotechnology Graduate Program Federal University of Paraná (UFPR) PR Curitiba Brazil National Institute of Science and Technology INCT PlantStress Biotech EMBRAPA DF Brasília Brazil Federal University of Pelotas (UFPEL) RS Pelotas Brazil Embrapa Semi-Arid PE Petrolina Brazil Department of Plant Science and Landscape Architecture University of Maryland College Park MD United States Catholic University of Brasília Graduate Program in Genomic Sciences and Biotechnology DF Brasília Brazil Catholic University Dom Bosco Graduate Program in Biotechnology MS Campo Grande Brazil

Background: Soybean is a worldwide-cultivated crop due to its applications in the food, feed, and biodiesel industries. Genome editing in soybean began with ZFN and TALEN technologies;however, CRISPR/Cas has emerged and shortly became the preferable approach for soybean genome manipulation since it is more precise, easy to handle, and cost-effective. Recent reports have focused on the conventional Cas9 nuclease, Cas9 nickase (nCas9) derived base editors, and Cas12a (formally Cpf1) as the most commonly used genome editors in soybean. Nonetheless, several challenges in the complex plant genetic engineering pipeline need to be overcome to effectively edit the genome of an elite soybean cultivar. These challenges include (1) optimizing CRISPR cassette design (i.e., gRNA and Cas promoters, gRNA design and testing, number of gRNAs, and binary vector), (2) improving transformation frequency, (3) increasing the editing efficiency ratio of targeted plant cells, and (4) improving soybean crop production. Aim of review: This review provides an overview of soybean genome editing using CRISPR/Cas technology, discusses current challenges, and highlights theoretical (insights) and practical suggestions to overcome the existing bottlenecks. Key scientific concepts of review: The CRISPR/Cas system was discovered as part of the bacterial innate immune system. It has been used as a biotechnological tool for genome editing and efficiently applied in soybean to unveil gene function, improve agronomic traits such as yield and nutritional grain quality, and enhance biotic and abiotic stress tolerance. To date, the efficiency of gRNAs has been validated using protoplasts and hairy root assays, while stable plant transformation relies on Agrobacterium-mediated and particle bombardment methods. Nevertheless, most steps of the CRISPR/Cas workflow require optimizations to achieve a more effective genome editing in soybean plants. © 2024

关键词： Base editors Cas12a CRISPR/Cas9 Crops Genetic transformation Glycine max

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Rejuvenation of Meropenem by Conjugation with Tilapia Piscidin-4 Peptide Targeting NDM-1 Escherichia coli

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ACS Omega 2024年第27期9卷 29756-29764页

作者： Selvaraj, Sanjay Prasad Lin, Kuan-Hung Lin, Wen-Chun You, Ming-Feng Li, Tsung-Lin Chen, Jyh-Yih Molecular and Biological Agricultural Science Program Taiwan International Graduate Program Academia Sinica Graduate Institute of Biotechnology National Chung Hsing University Genomics Research Center Academia Sinica Marine Research Station Institute of Cellular and Organismic Biology Academia Sinica Biotechnology Center National Chung Hsing University The iEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine National Chung Hsing University

Gram-negative pathogens that produce β-lactamases pose a serious public health threat as they can render β-lactam antibiotics inactive via hydrolysis. This action contributes to the waning effectiveness of clinical antibiotics and creates an urgent need for new antimicrobials. Antimicrobial peptides (AMPs) exhibiting multimodal functions serve as a potential source in spite of a few limitations. Thus, the conjugation of conventional antibiotics with AMPs may be an effective strategy to leverage the advantages of each component. In this study, we conjugated meropenem to the AMP Tilapia piscidin 4 (TP4) using a typical coupling reaction. The conjugate was characterized by using HPLC-MS, HR-MS, and MS-MS fragmentation analysis. It was then evaluated in terms of antibacterial potency, hemolysis, and cytotoxicity toward RAW264.7 and CCD-966SK cell lines. The conjugation of meropenem with TP4 significantly reduced the cytotoxicity compared to TP4. Conjugation of unprotected TP4 with meropenem resulted in cross-linking at the N-terminal and lysine sites. The structural activity relationship of the two isomers of the TP4-meropenem conjugate was investigated. Both the isomers showed notable antibacterial activities against NDM-1 Escherichia coli and reduced red blood cell hemolysis as compared to TP4. Lysine conjugate (TP4-K-Mero) showed lesser hemolysis than the N-terminal conjugate (TP4-N-Mero). Molecular modeling further revealed that the conjugates can bind to lipopolysaccharides and inhibit NDM-1 β-lactamase. Together, these data show that conjugation of antibiotics with AMP can be a feasible approach to increase the therapeutic profile and effectively target multidrug-resistant pathogens. Furthermore, antibiotic conjugation at different AMP sites tends to show unique biological properties. © 2024 The Authors. Published by American Chemical Society.

关键词： Antimicrobial agents Show More

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Bioinformatics exploration into potential mechanisms of Calamus draco for colorectal cancer treatment 9th

Bioinformatics exploration into potential mechanisms of Cala...

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9th International Conference on Computer science and Computational Intelligence, ICCSCI 2024

作者： Kenneth, Christian Nirwantono, Rudi Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

As one of the cancer types with the highest incidence rates, colorectal cancer (CRC) would benefit from treatments with fewer side effects and reduced treatment-resistant potential. One of the options is to harness the anti-CRC potential of natural products. Previous studies have shown that Calamus draco exudate, dragon's blood, has anticancer activity in liver cancer and acute myeloid leukemia, but its bioactivity has not been studied in CRC. Here we conduct a bioinformatics study based on network pharmacology to explore the anti-CRC potential and mechanism of C. draco-derived compounds. The bioinformatics pipeline is composed of compound and target collection, biological network evaluation, and enrichment analysis. We found that there are 43 bioactive compounds from C. draco targeting 91 CRC-related targets, of which most compounds target MEN1, PTGS2, and IDH1. Further analyses show that the targets of C. draco are involved in the cellular response to hypoxia. By inhibiting those targets, C. draco bioactive compounds can potentially hinder angiogenesis and increase treatment response efficacy. © 2024 The Authors.

关键词： Lung cancer

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Evaluating mechanism of banana pseudo-stem retting using seawater:A cost-effective surface pre-treatment approach

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Journal of Bioresources and Bioproducts 2024年第3期9卷 322-335页

作者： Prince Hotor Ahmed H.Hassanin Osbert Akatwijuka Mohamed A.H.Gepreel Mitsuo Yamamoto Yukie Saito Ahmed Abdel-Mawgood Egypt-Japan University of Science and Technology Biotechnology ProgramAlexandria GovernorateNew Borg Al Arab 21934Egypt Alexandria University Department of Textile EngineeringAlexandria GovernorateBab Sharqi 5424041Egypt Egypt-Japan University of Science and Technology Material Science and EngineeringAlexandria GovernorateNew Borg Al Arab 21934Egypt Graduate School of Agricultural and Life Sciences The University of TokyoBunkyo-KuTokyo 113-8657Japan

Retting has been employed to extract natural fibers from agricultural wastes as a biological and cost-effective approach for *** its global abundance,banana pseudo-stem is a promising agro-waste for lignocellulosic fiber *** this study,fibers were extracted from the pseudo-stems after being pre-treated under four conditions using seawater at room temperature for up to 35 d Bacterial isolation from the fresh seawater sample and screening for ligninolytic ability were *** load as well as laccase and manganese peroxidase enzyme activity profile assay during the retting duration were *** transform infrared(FT-IR)and X-day diffraction(XRD)analyses were also examined for both pre-treated and untreated extracted *** results shows that six out of the eight bacterial isolates had the ability to degrade *** treatments(Raw stem+Raw seawater)and(Autoclaved stem+Raw seawater)recorded the highest viable bacterial load of 9.24×102 and 4.46×102 CFU,respectively,on the 14th day of the retting ***,the highest laccase and manganese peroxidase enzymes activity was recorded for(Raw stem+Raw seawater)and(Autoclaved stem+Raw seawater)treatments in the second to the third *** FT-IR spectra of the pre-treated fibers revealed relative reductions in peaks attributed to polysaccharides and other amorphous substances for all retting *** XRD diffractogram revealed that the crystallinity index(CI)of pre-treated fibers increased in all seawater retting treatment ***,the CI for fibers pre-treated under enzymatic conditions were enhanced even after five *** analysis for selected bacterial isolates showed homology to sequences of Bacillus velezensis,Shewanella sp.L8–5,and Citrobacter amalonaticus and Bacillus subtilis j8 *** these findings,it was suggested that physical,biological,and chemical actions were collectively involved in the seawater retting process of banana ps

关键词： Seawater retting Banana pseudo-stem Natural fiber Enzyme activity Colony forming unit

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NRC Immune receptor networks show diversified hierarchical genetic architecture across plant lineages

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Plant Cell 2024年第9期36卷 3399-3418页

作者： Goh, Foong-Jing Huang, Ching-Yi Derevnina, Lida Wu, Chih-Hang Institute of Plant and Microbial Biology Academia Sinica Taipei 115201 Taiwan Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program National Chung-Hsing University and Academia Sinica Taipei 115201 Taiwan Graduate Institute of Biotechnology National Chung-Hsing University Taichung 402202 Taiwan Crop Science Centre Department of Plant Science University of Cambridge Cambridge CB3 0LE United Kingdom Biotechnology Center National Chung-Hsing University Taichung 402202 Taiwan

Plants' complex immune systems include nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins, which help recognize invading pathogens. In solanaceous plants, the NRC (NLR required for cell death) family includes helper NLRs that form a complex genetic network with multiple sensor NLRs to provide resistance against pathogens. However, the evolution and function of NRC networks outside solanaceous plants are currently unclear. Here, we conducted phylogenomic and macroevolutionary analyses comparing NLRs identified from different asterid lineages and found that NRC networks expanded significantly in most lamiids but not in Ericales and campanulids. Using transient expression assays in Nicotiana benthamiana, we showed that NRC networks are simple in Ericales and campanulids, but have high complexity in lamiids. Phylogenetic analyses grouped the NRC helper NLRs into three NRC0 subclades that are conserved, and several family-specific NRC subclades of lamiids that show signatures of diversifying selection. Functional analyses revealed that members of the NRC0 subclades are partially interchangeable, whereas family-specific NRC members in lamiids lack interchangeability. Our findings highlight the distinctive evolutionary patterns of the NRC networks in asterids and provide potential insights into transferring disease resistance across plant lineages. © 2024 The Author(s).

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Cancer Prediction using Clinical and Genomic Data Fusion: A Systematic Review 6

Cancer Prediction using Clinical and Genomic Data Fusion: A ...

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6th International Conference on Cybernetics and Intelligent System, ICORIS 2024

作者： Julian, Kelvin Nugroho, Kuncahyo Setyo Nirwantono, Rudi Pardamean, Bens Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798331539603

This systematic review provides a comprehensive overview of the methods used to integrate genomic and clinical data in cancer prediction. The review includes 19 studies across various cancers, including breast, colorectal, melanoma, lung, pancreatic, and thyroid. The studies employed different methods to combine genomic and clinical data, including weighted polygenic risk scores, genetic and non-genetic risk scores, and different machine learning algorithms. The results show significant improvements in model prediction performance accuracy across multiple studies. The review highlights the potential benefits of integrating genetic and phenotypic information to improve disease risk prediction models and inform personalized healthcare strategies. © 2024 IEEE.

关键词： Lung cancer

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A versatile in situ cofactor enhancing system for meeting cellular demands for engineered metabolic pathways

A versatile in situ cofactor enhancing system for meeting ce...

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作者： Jaroensuk, Juthamas Sutthaphirom, Chalermroj Phonbuppha, Jittima Chinantuya, Wachirawit Kesornpun, Chatchai Akeratchatapan, Nattanon Kittipanukul, Narongyot Phatinuwat, Kamonwan Atichartpongkul, Sopapan Fuangthong, Mayuree Pongtharangkul, Thunyarat Hollmann, Frank Chaiyen, Pimchai Rayong Thailand Faculty of Science Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Mahidol University Bangkok Thailand Program in Applied Biological Sciences Chulabhorn Graduate Institute Bangkok Thailand Laboratory of Biotechnology Chulabhorn Research Institute Bangkok Thailand Faculty of Science Department of Biotechnology Mahidol University Bangkok Thailand Department of Biotechnology Delft University of Technology Delft Netherlands

Cofactor imbalance obstructs the productivities of metabolically engineered cells. Herein, we employed a minimally perturbing system, xylose reductase and lactose (XR/lactose), to increase the levels of a pool of sugar phosphates which are connected to the biosynthesis of NAD(P)H, FAD, FMN, and ATP in Escherichia coli. The XR/lactose system could increase the amounts of the precursors of these cofactors and was tested with three different metabolically engineered cell systems (fatty alcohol biosynthesis, bioluminescence light generation, and alkane biosynthesis) with different cofactor demands. Productivities of these cells were increased 2-4-fold by the XR/lactose system. Untargeted metabolomic analysis revealed different metabolite patterns among these cells, demonstrating that only metabolites involved in relevant cofactor biosynthesis were altered. The results were also confirmed by transcriptomic analysis. Another sugar reducing system (glucose dehydrogenase) could also be used to increase fatty alcohol production but resulted in less yield enhancement than XR. This work demonstrates that the approach of increasing cellular sugar phosphates can be a generic tool to increase in vivo cofactor generation upon cellular demand for synthetic biology. © 2023 The Authors

关键词： Biosynthesis

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Effect of hot water extraction process on schizophyllan from split gill mushroom

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Biomass Conversion and Biorefinery 2024年第1期14卷 1017-1026页

作者： Saetang, Nuttapong Rattanapot, Thiravat Manmai, Numchok Amornlerdpison, Doungporn Ramaraj, Rameshprabu Unpaprom, Yuwalee Program in Biotechnology Faculty of Science Maejo University Chiang Mai50290 Thailand Center of Excellence in Agricultural Innovation for Graduate Entrepreneur Maejo University Chiang Mai50290 Thailand Department of Forestry National Chung Hsing University Taichung402 Taiwan School of Renewable Energy Maejo University Chiang Mai50290 Thailand

The split gill mushroom or Schizophyllum commune (S. commune) is a therapeutic mushroom. For cell wall composition, it consists of rich β-glucans (schizophyllan). This mushroom is high in nutritional content and has a wide range of biological properties. In this research, it is interesting to study hot water extraction of this functional schizophyllan. Central composite design (CCD) of response surface methodology (RSM) was applied to optimize these extraction parameters, namely, temperature (80–121 °C) and time (1–3 h) of schizophyllan extract (polysaccharide from S. commune) with a greater degree of polymerization (DP), maximum total sugar content, minimum reducing sugar content, and appropriate extraction yield. The results revealed the highest yield obtained from polysaccharide and supernatant extract (from the separation of polysaccharide extraction) at an extraction temperature of 121 °C for 2–3 h. Moreover, the optimal extraction temperature and time of polysaccharide extracts were 106.5 °C and 126.7 min (total sugar content);103.1 °C and 177.0 min (reducing sugar content);and 104.1 °C and 175.5 min (DP value). This research shows that the optimum condition of schizophyllan extraction was around 100–110 °C for 2–3 h with the highest DP of about 6, including potential immune-enhancing and anticancer properties. As a result, the schizophyllan from the split gill mushroom is probably utilized as a functional ingredient with nutraceutical compounds and developed as other high value-added functional food products in further study. © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： Extraction

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