Review
Biochemistry & Molecular Biology
Simon C. Kessler, Yit-Heng Chooi
Summary: This article discusses the current state of research on ribosomally synthesized and post-translationally modified peptides (RiPPs) from fungi, categorizing fungal RiPPs into three families based on their biosynthetic characteristics. The authors hope that by systematically outlining the structural and gene cluster features of fungal RiPPs, more comprehensive genome mining efforts can be facilitated in the future.
NATURAL PRODUCT REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Yong Gao, Yanan Zhang, Chen Feng, Honglong Chu, Chao Feng, Haibo Wang, Lifang Wu, Si Yin, Chao Liu, Huanhuan Chen, Zhumei Li, Zhengrong Zou, Lizhou Tang
Summary: In this study, a chromosome-level genome assembly of Amorphophallus konjac was generated, revealing the mechanisms underlying the large genome size and the key genes involved in glucomannan biosynthesis. The expansion of transposable elements was found to contribute to the large genome size, and valuable candidate genes for molecular breeding of this crop were identified.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Plant Sciences
Xiaoming Song, Haibin Liu, Shaoqin Shen, Zhinan Huang, Tong Yu, Zhuo Liu, Qihang Yang, Tong Wu, Shuyan Feng, Yu Zhang, Zhiyuan Wang, Weike Duan
Summary: The study reported a chromosome-level pepino genome, revealing chromosome rearrangements, fusions, and gene loss after WGT events, and the loss of disease resistance genes in pepino and eggplant. While disease resistance genes are scarce in pepino and eggplant, genes related to anthocyanin biosynthesis like CHS are significantly expanded in grapes.
Review
Biochemistry & Molecular Biology
Taro Shiraishi, Tomohisa Kuzuyama
Summary: Phosphonates are organic phosphorus compounds with a characteristic C-P bond, which serve as lead compounds for drug development. Fosfomycin, a widely-used antibacterial drug, has a complex biosynthetic pathway with recent breakthroughs. Genome mining and chemoenzymatic synthesis have expanded the repertoire of phosphonates and their biosynthetic machinery in recent years.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Therese Horch, Evelyn M. Molloy, Florian Bredy, Veit G. Haensch, Kirstin Scherlach, Kyle L. Dunbar, Jonathan Franke, Christian Hertweck
Summary: This study reports a previously overlooked biosynthetic pathway for benzoxazoles in anaerobic bacteria, expanding their chemical space and distribution range. The research reveals differences in biosynthesis between anaerobic bacteria and actinomycetes, and demonstrates the synthetic utility of the discovered pathway.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Stella T. Lima, Brigitte G. Ampolini, Ethan B. Underwood, Tyler N. Graf, Cody E. Earp, Imani C. Khedi, Michael A. Pasquale, Jonathan R. Chekan
Summary: Cyclopeptide alkaloids, a class of abundant plant cyclic peptides, have diverse bioactivities and over 200 analogs described. The biosynthetic basis of these natural products has remained unclear until now. Through transcriptome mining, researchers linked cyclopeptide alkaloids from Ceanothus americanus to dedicated RiPP precursor peptides and identified new gene clusters containing split BURP peptide cyclases. The discovery of arabipeptins from Coffea arabica and validation of BURP enzyme activity in the biosynthesis of arabipeptin A further expand our understanding of the biosynthetic pathways responsible for cyclic plant peptides.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Plant Sciences
Ling Guo, Fangjie Xie, Xue Huang, Zhengrong Luo
Summary: A high-quality genome of 'Xiaobaixing' apricot was obtained, and it was found to be closely related to 'Yinxiangbai'. Functional annotation and enrichment analysis revealed significant differences in the expansion and contraction of genes related to amygdalin synthesis in 'Xiaobaixing' compared to other species. A key gene for the identification of sweet/bitter kernels of apricots was also discovered.
Correction
Plant Sciences
Jingrui Li, Yiming Wang, Yanmei Dong, Wenying Zhang, Di Wang, Hongtong Bai, Kui Li, Hui Li, Lei Shi
Summary: A correction to the paper has been published.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Xiangyu Qi, Huadi Wang, Shuangshuang Chen, Jing Feng, Huijie Chen, Ziyi Qin, Ikram Blilou, Yanming Deng
Summary: In this study, the draft genome of Jasminum sambac cultivar 'Danbanmoli' was obtained and its genome size, gene number, origin time, and genes related to heat stress tolerance were identified. The study provides important fundamental knowledge for studying the molecular mechanism and fragrance of Jasmine flowers.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Fan Wu, Zhen Duan, Pan Xu, Qi Yan, Minghui Meng, Mingshu Cao, Chris S. Jones, Xifang Zong, Pei Zhou, Yimeng Wang, Kai Luo, Shengsheng Wang, Zhuanzhuan Yan, Penglei Wang, Hongyan Di, Zifeng Ouyang, Yanrong Wang, Jiyu Zhang
Summary: This study presents the chromosome-scale assembly of the Melilotus albus genome, providing insights into genetic diversity, population structure, and candidate genes associated with coumarin biosynthesis. The research also identified a beta-glucosidase (BGLU) gene cluster contributing to coumarin biosynthesis.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Xiao Wang, Sen Wang, Qiang Lin, Jianjun Lu, Shiyou Lv, Yanxin Zhang, Xuefang Wang, Wei Fan, Wanfei Liu, Liangxiao Zhang, Xiurong Zhang, Jun You, Peng Cui, Peiwu Li
Summary: This study investigates the genetic basis and adaptive evolution of wild and cultivated sesame by constructing high-quality genomes. The findings reveal the strong environmental adaptability and high sesamolin content of wild sesame, as well as the positive selection and gene family expansion in stress response genes. This study provides valuable insights into sesame evolution and improvement.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Plant Sciences
Jingrui Li, Yiming Wang, Yanmei Dong, Wenying Zhang, Di Wang, Hongtong Bai, Kui Li, Hui Li, Lei Shi
Summary: This study presented a high-quality reference genome for the Chinese lavender cultivar, revealing expanded gene families related to terpenoid biosynthesis in lavender compared to other species in Lamiaceae. The comprehensive analysis of the genetic basis of volatile production in lavender could serve as a foundation for future research into lavender evolution, phytochemistry, and ecology.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Aidi Zhang, Hui Zhou, Xiaohan Jiang, Yuepeng Han, Xiujun Zhang
Summary: The study successfully assembled the draft genome of a flat peach cultivar '124 Pan' and found an expansion of genes encoding enzymes involved in terpene biosynthesis. This research outcome provides a valuable genomic resource for improving the quality of flat peaches and conducting molecular breeding.
Article
Biochemistry & Molecular Biology
Zijiang Yang, Shanshan Chen, Shufen Wang, Ying Hu, Guanghui Zhang, Yang Dong, Shengchao Yang, Jianhua Miao, Wei Chen, Jun Sheng
Summary: A high-quality genome assembly of Siberian ginseng was reported, revealing a high proportion of transposable elements and a large number of predicted protein-coding genes. Comparative analysis with other plant genomes showed that whole-genome duplication events and a burst expansion of chromoviral elements may have contributed to adaptation in the Araliaceae family.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Niu Yu, Haixi Sun, Jinchang Yang, Rongsheng Li
Summary: This study presents a high-quality chromosome-scale assembly of the Sindora glabra genome and provides insights into its genomic features and gene expression. The genome of S. glabra underwent ancient genome triplication and further whole-genome duplication, which is important for understanding genome evolution. The study also identified genes involved in stress responses and secondary metabolite biosynthesis, as well as genes related to the diversity and specificity of terpene compounds. These findings offer new resources for studying gene function and oleoresin production in S. glabra.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Daniel A. Grajales-Hernandez, Susana Velasco-Lozano, Mariana A. Armendariz-Ruiz, Jorge A. Rodriguez-Gonzalez, Rosa Maria Camacho-Ruiz, Ali Asaff-Torres, Fernando Lopez-Gallego, Juan Carlos Mateos-Diaz
JOURNAL OF BIOTECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Daniel Grajales-Hernandez, Mariana Armendariz-Ruiz, Susana Velasco-Lozano, Fernando Lopez-Gallego, Juan Carlos Mateos-Diaz
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Review
Chemistry, Multidisciplinary
Juan M. Bolivar, Fernando Lopez-Gallego
CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Susana Velasco-Lozano, Erienne Jackson, Magdalena Ripoll, Fernando Lopez-Gallego, Lorena Betancor
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2020)
Article
Public, Environmental & Occupational Health
Antonio Lopez-Gay, Jeroen Spijker, Helen V. S. Cole, Antonio G. Marques, Margarita Triguero-Mas, Isabelle Anguelovski, Marc Mari-Dell'Olmo, Juan A. Modenes, Dolores alamo-Junquera, Fernando Lopez-Gallego, Carme Borrell
Summary: This study investigated the relationship between COVID-19 incidence and sociodemographic factors in Barcelona. The findings showed that areas with higher population density, an aged population structure, a high presence of nursing homes, a higher proportion of people who left their residential areas during lockdown, and a higher proportion of people working in health-related occupations were more likely to have a higher number of COVID-19 cases. On the other hand, COVID-19 incidence was negatively associated with the percentage of residents with post-secondary education and the population born in countries with a high Human Development Index.
JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH
(2022)
Article
Biochemistry & Molecular Biology
Luigi Tavernini, Oscar Romero, Carla Aburto, Fernando Lopez-Gallego, Andres Illanes, Lorena Wilson
Summary: Hybrid bioinorganic biocatalysts have drawn much attention for their simple synthesis, high efficiency, and structural features that enhance enzyme activity and stability. In this study, a biomineralization strategy was utilized to form hybrid nanocrystals from beta-galactosidase, showing high specific activity and remarkable thermal stability. This new biocompatible and inexpensive nanobiocatalyst demonstrated promising industrial applications with high enzyme recovery and stability.
Article
Chemistry, Physical
Guillermo Garcia-Marquina, Reyes Nunez-Franco, Francesca Peccati, Yi Tang, Gonzalo Jimenez-Oses, Fernando Lopez-Gallego
Summary: This study reveals that mutation clusters in the acyltransferase LovD9 can enhance enzyme kinetics and stability, providing a theoretical basis for simvastatin synthesis. By combining rational mutation clusters, we successfully generated the variant LovD-BuCh2 with catalytic efficiency close to LovD9.
Article
Chemistry, Multidisciplinary
Lorena Betancor, Fernando Lopez-Gallego
Summary: This review explores the combination of isolated enzymes and whole cells for chemical biomanufacturing. Both isolated enzymes and whole-cell biocatalysis have their own advantages, which can be synergistically utilized to improve efficiency and sustainability in bioprocesses. Different architectural approaches, such as combining extracellular enzymes and microorganisms, displaying enzymes on whole cell walls, and integrating enzymes and microorganisms into different materials, are presented as available alternatives for tandem enzyme-cell systems' biotransformations.
CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Susana Velasco-Lozano, Javier Santiago-Arcos, Maria Grazia Rubanu, Fernando Lopez-Gallego
Summary: In this study, a cell-free enzyme system with self-sufficient cofactor recycling was used for efficient transformation of aliphatic diols into omega-hydroxy acids. Two compatible alcohol dehydrogenases were selected as specialist biocatalysts to maximize the efficiency of the biosynthetic route. The cell-free system achieved high conversion rates and exhibited excellent enantioselectivity. It also demonstrated superior sustainability compared to traditional metal catalysts and whole cells. Moreover, the system allowed for enzyme reutilization.
Editorial Material
Chemistry, Multidisciplinary
Lorena Betancor, Fernando Lopez-Gallego
CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Guillermo Garcia-Marquina, Judith Langer, Mercedes Sanchez-Costa, Gonzalo Jimenez-Oses, Fernando Lopez-Gallego
Summary: This study focuses on optimizing the continuous synthesis of simvastatin by immobilizing an engineered acyltransferase enzyme on controlled porous glass particles functionalized with Fe3+-catechol complexes. The immobilized enzyme showed improved thermal stability and maintained high product yield during multiple operational cycles. Under optimal flow conditions, the system achieved a 100% simvastatin yield with improved reaction mass efficiency and atom economy compared to previous studies.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Eleftheria Diamanti, Susana Velasco-Lozano, Daniel Grajales-Hernandez, Alejandro H. Orrego, Desire Di Silvio, Jose Maria Fraile, Fernando Lopez-Gallego
Summary: Self-sufficient heterogeneous biocatalysts (ssHB) are potential candidates for cofactor-dependent enzymes in chemical biomanufacturing. By immobilizing adenylated cofactors on agarose microbeads through reversible covalent bonds formed between the cis-diol of the ribose in the cofactor backbone and boronic acid, the limitations of current ssHBs in high ionic strength conditions are overcome. The functionality and stability of these ssHBs are demonstrated in reductive aminations, and the immobilized enzymes and cofactors can be reused multiple times.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Physical
Alejandro H. Orrego, Daniel Andres-Sanz, Susana Velasco-Lozano, Mercedes Sanchez-Costa, Jose Berenguer, Jose M. Guisan, Javier Rocha-Martin, Fernando Lopez-Gallego
Summary: The research demonstrates the importance of asymmetric reduction of beta-ketoesters with cell-free enzymes in the synthesis of functional products. By using a novel thermophilic enzyme, it was possible to achieve successful reuse of both the enzyme and co-immobilised cofactor in up to 10 reaction cycles.
CATALYSIS SCIENCE & TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Marcos Navascuez, Raquel Gracia, Marco Marradi, Natividad Diaz, Javier Rodriguez, Iraida Loinaz, Fernando Lopez-Gallego, Jordi Llop, Damien Dupin
Summary: In this study, dextran derivatives with hydrophobic or hydrophilic functional groups were evaluated as stabilizers for oil-in-water emulsions. The methacrylate-functionalized dextran showed the most promising results, requiring a minimum amount to achieve stable nanoemulsions that could be degraded by lipases.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Jose M. Guisan, Fernando Lopez-Gallego, Juan M. Bolivar, Javier Rocha-Martin, Gloria Fernandez-Lorente
IMMOBILIZATION OF ENZYMES AND CELLS: METHODS AND PROTOCOLS, 4TH EDITION
(2020)
