Thermophiles and Thermozymes Edited by María-Isabel González-Siso Printed Edition of the Special Issue Published in Microorganisms www.mdpi.com/journal/microorganisms Thermophiles and Thermozymes Thermophiles and Thermozymes Special Issue Editor Mar´ıa-Isabel Gonz´alez-Siso MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editor Mar´ıa-Isabel Gonzalez-Siso´ Universidade da Coruna˜ Spain Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Microorganisms (ISSN 2076-2607) from 2018 to 2019 (available at: https://www.mdpi.com/journal/ microorganisms/special issues/thermophiles) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. 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Contents About the Special Issue Editor ...................................... vii Mar´ıa-Isabel Gonz´alez-Siso Editorial for the Special Issue: Thermophiles and Thermozymes Reprinted from: Microorganisms 2019, 7, 62, doi:10.3390/microorganisms7030062 ......... 1 Alba Blesa, Mercedes S´anchez, Eva Sacrist´an-Horcajada, Sandra Gonz´alez-de la Fuente, Ram´on Peir´o and Jos´e Berenguer Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp. Reprinted from: Microorganisms 2019, 7, 25, doi:10.3390/microorganisms7010025 ......... 3 Anders Schouw, Francesca Vulcano, Irene Roalkvam, William Peter Hocking, Eoghan Reeves, Runar Stokke, Gunhild Bødtker and Ida Helene Steen Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System Reprinted from: Microorganisms 2018, 6, 63, doi:10.3390/microorganisms6030063 ......... 18 Juan Miguel Gonzalez Molecular Tunnels in Enzymes and Thermophily: A Case Study on the Relationship to Growth Temperature Reprinted from: Microorganisms 2018, 6, 109, doi:10.3390/microorganisms6040109 ......... 39 Mar´ıa-Efigenia Alvarez-Cao,´ Roberto Gonz´alez, Mar´ıa A. Pernas and Mar´ıa Luisa Rua ´ Contribution of the Oligomeric State to the Thermostability of Isoenzyme 3 from Candida rugosa Reprinted from: Microorganisms 2018, 6, 108, doi:10.3390/microorganisms6040108 ......... 49 Mohit Bibra, Venkat Reddy Kunreddy and Rajesh K. Sani Thermostable Xylanase Production by Geobacillus sp. Strain DUSELR13, and Its Application in Ethanol Production with Lignocellulosic Biomass Reprinted from: Microorganisms 2018, 6, 93, doi:10.3390/microorganisms6030093 ......... 62 Mohamed Amine Gomri, Agust´ın Rico-D´ıaz, Juan-Jos´e Escuder-Rodr´ıguez, Tedj El Moulouk Khaldi, Mar´ıa-Isabel Gonz´alez-Siso and Karima Kharroub Production and Characterization of an Extracellular Acid Protease from Thermophilic Brevibacillus sp. OA30 Isolated from an Algerian Hot Spring Reprinted from: Microorganisms 2018, 6, 31, doi:10.3390/microorganisms6020031 ......... 87 Hiroyuki Hori, Takuya Kawamura, Takako Awai, Anna Ochi, Ryota Yamagami, Chie Tomikawa and Akira Hirata Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA Reprinted from: Microorganisms 2018, 6, 110, doi:10.3390/microorganisms6040110 .........103 Anthony J. Finch and Jin Ryoun Kim Thermophilic Proteins as Versatile Scaffolds for Protein Engineering Reprinted from: Microorganisms 2018, 6, 97, doi:10.3390/microorganisms6040097 .........149 Juan-Jos´e Escuder-Rodr´ıguez, Mar´ıa-Eugenia DeCastro, Mar´ıa-Esperanza Cerd´an, Esther Rodr´ıguez-Belmonte, Manuel Becerra and Mar´ıa-Isabel Gonz´alez-Siso Cellulases from Thermophiles Found by Metagenomics Reprinted from: Microorganisms 2018, 6, 66, doi:10.3390/microorganisms6030066 .........162 v About the Special Issue Editor Mar´ıa-Isabel Gonz´alez-Siso, Ph.D., is a Full Professor of Biochemistry and Molecular Biology at the University of A Coruna˜ (Spain). Dr. Gonzalez-Siso´ gained her PhD in Biology in 1989 from the University of Santiago de Compostela, Spain. Following a postdoctoral period in the CSIC (Vigo, Spain), since 1990, Prof. Gonzalez-Siso´ has served as an academician and has held various academic and administrative positions. Moreover, Prof. Gonzalez-Siso´ has over 100 research articles and reviews published in JCR journals, 20 books and book chapters, and eight patents to her name, and has supervised the writing of PhD and Masters’ degree theses as well as reviewing works by invited researchers. Her recent investigations are focused on enzyme bioengineering, metagenomics of thermophiles, bioprospection of new thermozymes, and biotechnological valorisation of food industry byproducts. vii microorganisms Editorial Editorial for the Special Issue: Thermophiles and Thermozymes María-Isabel González-Siso Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain; [email protected] Received: 22 February 2019; Accepted: 22 February 2019; Published: 27 February 2019 Heat-loving microorganisms or thermophiles arouse noticeable scientific interest nowadays, not only with the aim to elucidate the mystery of life at high temperatures, but also due to the huge field of biotechnological applications of the enzymes they produce or thermozymes, able to function under industrial harsh conditions. This Special Issue contains nine papers that study diverse aspects of thermophiles biology and their enzymes. Two research articles deal with the genomics of thermophilic microorganisms. Blesa et al. [1] describe the characterization of active and inactive insertion sequences spanning the genus Thermus. This work represents an interesting contribution both to the construction of new genetic engineering tools and to the knowledge of the genomic plasticity and capacity of adaptation of thermophilic microorganisms. Schouw et al. [2] analyze the genome of a fermentative new strain isolated from a deep-sea hydrothermal vent, which was reassigned to the genus Vallitalea and designated V. guaymasensis strain L81, showing interesting features for industrial application. Furthermore, the potential of these marine ecosystems for the bioprospection of new enzymes and antimicrobials is revealed in this work. Four other research articles deal with different aspects of thermozymes. J.M. González [3] presents a structural analysis of substrate tunnels in two types of enzymes (with low and high ◦ ◦ tunneling) from microorganisms living optimally at 15 Cto100 C. Molecular tunnel dimensions are reduced with increasing optimum growth temperatures, minimizing unnecessary spaces within the molecule. From this work, molecular channeling appears as a mechanism that helps to understand how thermophiles are adapted to live under high temperatures. Álvarez-Cao et al. [4], using the lipase LipE from Candida rugosa, show that oligomerization-dimerization is another structural feature that causes protein stabilization against temperature and pH, also expanding substrate specificity on soluble substrates. Domain swapping is the mechanism proposed to explain LipE homodimerization. Bibra et al. [5] report the statistical optimization of the production of a thermostable xylanase from a Geobacillus sp. strain isolated from a gold mine, its comparison (favorable) with commercial counterparts for lignocellulosic biomass hydrolysis, and the use of the strain in co-culture for ethanol fermentation of the biomass. Gomri et al. [6] depict the characterization of a new acid protease produced extracellularly by a thermophilic bacterium that was isolated from an Algerian hot spring and affiliated with Brevibacillus thermoruber species. The purified 32-F38 protease resulted to be thermostable and highly stable in the presence of different detergents and solvents, suggesting potential biotechnological applications. Three reviews complete this monograph. The one by Hori et al. [7] is a comprehensive study about modified nucleosides in tRNA and tRNA modification enzymes from thermophiles, in view of strategies to stabilize tRNA structures including RNA-binding proteins and polyamines. The one by Finch and Kim [8] focuses on the application of thermophilic proteins as scaffolds for protein engineering, proposed due to their robustness and evolvability, without forgetting the trade-off between protein activity and stability. Finally, the one by Escuder-Rodríguez et al. [9] introduces the Microorganisms 2019, 7, 621 www.mdpi.com/journal/microorganisms Microorganisms 2019, 7,62 metagenomics approach, in this case for the search of thermostable cellulases, a complex group of enzymes which is here unraveled. Altogether these papers allow us to go one step forward to explain how the thermophilic microorganisms and their enzymes are stable and functional at high temperatures, and to envisage new biotechnological applications and fields for bioprospection. Acknowledgments: Thank you to all the authors and reviewers for their excellent contributions to this Special Issue.