1
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Soto J, Moro SL, Cocco MJ. Dynamics and thermal stability of the bypass polymerase, DinB homolog (Dbh). Front Mol Biosci 2024; 11:1364068. [PMID: 38745908 PMCID: PMC11091320 DOI: 10.3389/fmolb.2024.1364068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
The DinB homolog polymerase (Dbh) is a member of the Y-family of translesion DNA polymerases that can synthesize using a damaged DNA template. Since Dbh comes from the thermophilic archaeon Sulfolobus acidocaldarius, it is capable of functioning over a wide range of temperatures. Existing X-ray structures were determined at temperatures where the protein is least active. Here we use NMR and circular dichroism to understand how the structure and dynamics of Dbh are affected by temperature (2°C-65°C) and metal ion binding in solution. We measured hydrogen exchange protection factors, temperature coefficients, and chemical shift perturbations with and without magnesium and manganese. We report on regions of the protein that become more dynamic as the temperature is increased toward the functional temperature. Hydrogen exchange protection factors and temperature coefficients reveal that both the thumb and finger domains are very dynamic relative to the palm and little-finger (LF) domains. These trends remain true at high temperature with dynamics increasing as temperatures increase from 35°C to 50°C. Notably, NMR spectra show that the Dbh tertiary structure cold denatures beginning at 25°C and increases in denaturation as the temperature is lowered to 5°C with little change observed by CD. Above 35°C, chemical shift perturbation analysis in the presence and absence of magnesium and manganese reveals three ion binding sites, without DNA bound. In contrast, these bound metals are not apparent in any Dbh crystal structures of the protein without DNA. Two ion binding sites are confirmed to be near the active site, as reported in other Y-family polymerases, and we report a novel ion binding site in the LF domain. Thus, the solution-state structure of the Dbh polymerase is distinct from that of the solid-state structures and shows an unusually high cold denaturation temperature.
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Affiliation(s)
- Jenaro Soto
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, United States
| | - Sean L. Moro
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Melanie J. Cocco
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
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2
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Takemata N. How Do Thermophiles Organize Their Genomes? Microbes Environ 2024; 39:n/a. [PMID: 38839371 DOI: 10.1264/jsme2.me23087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
All cells must maintain the structural and functional integrity of the genome under a wide range of environments. High temperatures pose a formidable challenge to cells by denaturing the DNA double helix, causing chemical damage to DNA, and increasing the random thermal motion of chromosomes. Thermophiles, predominantly classified as bacteria or archaea, exhibit an exceptional capacity to mitigate these detrimental effects and prosper under extreme thermal conditions, with some species tolerating temperatures higher than 100°C. Their genomes are mainly characterized by the presence of reverse gyrase, a unique topoisomerase that introduces positive supercoils into DNA. This enzyme has been suggested to maintain the genome integrity of thermophiles by limiting DNA melting and mediating DNA repair. Previous studies provided significant insights into the mechanisms by which NAPs, histones, SMC superfamily proteins, and polyamines affect the 3D genomes of thermophiles across different scales. Here, I discuss current knowledge of the genome organization in thermophiles and pertinent research questions for future investigations.
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Affiliation(s)
- Naomichi Takemata
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
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3
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Manesh MJH, Willard DJ, Lewis AM, Kelly RM. Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us? BIORESOURCE TECHNOLOGY 2024; 391:129988. [PMID: 37949149 DOI: 10.1016/j.biortech.2023.129988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.
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Affiliation(s)
- Mohamad J H Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
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4
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Iacono R, De Lise F, Moracci M, Cobucci-Ponzano B, Strazzulli A. Glycoside hydrolases from (hyper)thermophilic archaea: structure, function, and applications. Essays Biochem 2023; 67:731-751. [PMID: 37341134 DOI: 10.1042/ebc20220196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/19/2023] [Accepted: 05/31/2023] [Indexed: 06/22/2023]
Abstract
(Hyper)thermophilic archaeal glycosidases are enzymes that catalyze the hydrolysis of glycosidic bonds to break down complex sugars and polysaccharides at high temperatures. These enzymes have an unique structure that allows them to remain stable and functional in extreme environments such as hot springs and hydrothermal vents. This review provides an overview of the current knowledge and milestones on the structures and functions of (hyper)thermophilic archaeal glycosidases and their potential applications in various fields. In particular, this review focuses on the structural characteristics of these enzymes and how these features relate to their catalytic activity by discussing different types of (hyper)thermophilic archaeal glycosidases, including β-glucosidases, chitinase, cellulases and α-amylases, describing their molecular structures, active sites, and mechanisms of action, including their role in the hydrolysis of carbohydrates. By providing a comprehensive overview of (hyper)thermophilic archaeal glycosidases, this review aims to stimulate further research into these fascinating enzymes.
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Affiliation(s)
- Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
| | - Federica De Lise
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
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5
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Medina-Chávez NO, Viladomat-Jasso M, Zarza E, Islas-Robles A, Valdivia-Anistro J, Thalasso-Siret F, Eguiarte LE, Olmedo-Álvarez G, Souza V, De la Torre-Zavala S. A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico. ASTROBIOLOGY 2023; 23:796-811. [PMID: 37279013 DOI: 10.1089/ast.2021.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.
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Affiliation(s)
- Nahui-Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, México
| | | | - Eugenia Zarza
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur, Tapachula, Mexico
- Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Africa Islas-Robles
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Irapuato, Irapuato, México
| | - Jorge Valdivia-Anistro
- Unidad Multidisciplinaria de Investigación Experimental Zaragoza, Facultad de Estudios Superiores Zaragoza, UNAM, Ciudad de México, México
| | - Frédéric Thalasso-Siret
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, UNAM, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Gabriela Olmedo-Álvarez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Irapuato, Irapuato, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, UNAM, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Susana De la Torre-Zavala
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, México
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6
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Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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7
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Biological role of the major AP (abasic site) endonuclease of an archaeon from geothermal environments. Extremophiles 2023; 27:1. [DOI: 10.1007/s00792-022-01286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
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8
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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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9
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Sulfolobus islandicus Employs Orc1-2-Mediated DNA Damage Response in Defense against Infection by SSV2. J Virol 2022; 96:e0143822. [PMID: 36448807 PMCID: PMC9769372 DOI: 10.1128/jvi.01438-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
All living organisms have evolved DNA damage response (DDR) strategies in coping with threats to the integrity of their genome. In response to DNA damage, Sulfolobus islandicus activates its DDR network in which Orc1-2, an ortholog of the archaeal Orc1/Cdc6 superfamily proteins, plays a central regulatory role. Here, we show that pretreatment with UV irradiation reduced virus genome replication in S. islandicus infected with the fusellovirus SSV2. Like treatment with UV or the DNA-damaging agent 4-nitroquinoline-1-oxide (NQO), infection with SSV2 facilitated the expression of orc1-2 and significantly raised the cellular level of Orc1-2. The inhibitory effect of UV irradiation on the virus DNA level was no longer apparent in the infected culture of an S. islandicus orc1-2 deletion mutant strain. On the other hand, the overexpression of orc1-2 decreased virus genomic DNA by ~102-fold compared to that in the parent strain. Furthermore, as part of the Orc1-2-mediated DDR response genes for homologous recombination repair (HRR), cell aggregation and intercellular DNA transfer were upregulated, whereas genes for cell division were downregulated. However, the HRR pathway remained functional in host inhibition of SSV2 genome replication in the absence of UpsA, a subunit of pili essential for intercellular DNA transfer. In agreement with this finding, lack of the general transcriptional activator TFB3, which controls the expression of the ups genes, only moderately affected SSV2 genome replication. Our results demonstrate that infection of S. islandicus by SSV2 triggers the host DDR pathway that, in return, suppresses virus genome replication. IMPORTANCE Extremophiles thrive in harsh habitats and thus often face a daunting challenge to the integrity of their genome. How these organisms respond to virus infection when their genome is damaged remains unclear. We found that the thermophilic archaeon Sulfolobus islandicus became more inhibitory to genome replication of the virus SSV2 after preinfection UV irradiation than without the pretreatment. On the other hand, like treatment with UV or other DNA-damaging agents, infection of S. islandicus by SSV2 triggers the activation of Orc1-2-mediated DNA damage response, including the activation of homologous recombination repair, cell aggregation and DNA import, and the repression of cell division. The inhibitory effect of pretreatment with UV irradiation on SSV2 genome replication was no longer observed in an S. islandicus mutant lacking Orc1-2. Our results suggest that DNA damage response is employed by S. islandicus as a strategy to defend against virus infection.
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10
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Wang G, Du Y, Ma X, Ye F, Qin Y, Wang Y, Xiang Y, Tao R, Chen T. Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology. Int J Mol Sci 2022; 23:ijms232314969. [PMID: 36499296 PMCID: PMC9738464 DOI: 10.3390/ijms232314969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.
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11
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Aulitto M, Martinez-Alvarez L, Fusco S, She Q, Bartolucci S, Peng X, Contursi P. Genomics, Transcriptomics, and Proteomics of SSV1 and Related Fusellovirus: A Minireview. Viruses 2022; 14:v14102082. [PMID: 36298638 PMCID: PMC9608457 DOI: 10.3390/v14102082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Saccharolobus spindle-shaped virus 1 (SSV1) was one of the first viruses identified in the archaeal kingdom. Originally isolated from a Japanese species of Saccharolobus back in 1984, it has been extensively used as a model system for genomic, transcriptomic, and proteomic studies, as well as to unveil the molecular mechanisms governing the host–virus interaction. The purpose of this mini review is to supply a compendium of four decades of research on the SSV1 virus.
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Affiliation(s)
- Martina Aulitto
- Dipartimento di Biologia, University of Naples Federico II, 80126 Naples, Italy
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA
| | - Laura Martinez-Alvarez
- Archaea Centre, Department of Biology, University of Copenhagen, DK-1165 Copenhagen, Denmark
| | - Salvatore Fusco
- Biochemistry and Industrial Biotechnology Laboratory, Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 250100, China
| | | | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, DK-1165 Copenhagen, Denmark
- Correspondence: (X.P.); (P.C.)
| | - Patrizia Contursi
- Dipartimento di Biologia, University of Naples Federico II, 80126 Naples, Italy
- BAT Center—Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80055 Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80126 Naples, Italy
- Correspondence: (X.P.); (P.C.)
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12
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Valorization of Biomasses from Energy Crops for the Discovery of Novel Thermophilic Glycoside Hydrolases through Metagenomic Analysis. Int J Mol Sci 2022; 23:ijms231810505. [PMID: 36142415 PMCID: PMC9505709 DOI: 10.3390/ijms231810505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The increasing interest for environmentally friendly technologies is driving the transition from fossil-based economy to bioeconomy. A key enabler for circular bioeconomy is to valorize renewable biomasses as feedstock to extract high value-added chemicals. Within this transition the discovery and the use of robust biocatalysts to replace toxic chemical catalysts play a significant role as technology drivers. To meet both the demands, we performed microbial enrichments on two energy crops, used as low-cost feed for extremophilic consortia. A culture-dependent approach coupled to metagenomic analysis led to the discovery of more than 300 glycoside hydrolases and to characterize a new α-glucosidase from an unknown hyperthermophilic archaeon. Aglu1 demonstrated to be the most active archaeal GH31 on 4Np-α-Glc and it showed unexpected specificity vs. kojibiose, revealing to be a promising candidate for biotechnological applications such as the liquefaction/saccharification of starch.
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13
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Sakai HD, Nakamura K, Kurosawa N. Stygiolobus caldivivus sp. nov., a facultatively anaerobic hyperthermophilic archaeon isolated from the Unzen hot spring in Japan. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hyperthermophilic, acidophilic and facultatively anaerobic archaeon, strain KN-1T, was isolated from Unzen hot spring in Japan and characterized. The cells of KN-1T were irregular cocci with a diameter of 1.0–3.0 µm that grew at 55–87.5 °C (optimum: 75 °C) and pH 1.0–5.5 (optimum: 3.0). Chemolithoautotrophic growth of KN-1T occurred in the presence of S0 or H2 under oxic conditions. Under anoxic conditions, KN-1T grew with S0, ferric citrate and FeCl3 as electron acceptors. A phylogenetic analysis of 16S rRNA gene sequences showed that the species most closely related to KN-1T was
Stygiolobus azoricus
JCM 9 021T, with 98.9 % sequence identity, indicating that strain KN-1T belongs to the genus
Stygiolobus
. This genus has been considered to consist of obligate anaerobes since its description in 1991. However, KN-1T grew under oxic, microoxic and anoxic conditions. Moreover, KN-1Tutilized various complex substrates and some sugars as carbon or energy sources, which is also different from
S. azoricus
JCM 9 021T. The average nucleotide identity and amino acid identity values between KN-1T and
S. azoricus
JCM 9 021T were 79.4 and 76.1 %, respectively, indicating that KN-1T represents a novel species. Its main polar lipids were calditoglycerocaldarchaeol and caldarchaeol, and its DNA G+C content was 40.1 mol%. We also found that
S. azoricus
JCM 9021T grew under microoxic conditions in the presence of H2 as an electron donor, indicating that this genus does not comprise obligate anaerobes. Based on this polyphasic taxonomic analysis, we propose the novel species, Stygiolobus caldivivus sp. nov., whose type strain is KN-1T (=JCM 34 622T=KCTC 4 293T).
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Affiliation(s)
- Hiroyuki D. Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Koichi Nakamura
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Norio Kurosawa
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, Japan
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14
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Nixon SL, Bonsall E, Cockell CS. Limitations of microbial iron reduction under extreme conditions. FEMS Microbiol Rev 2022; 46:6645348. [PMID: 35849069 PMCID: PMC9629499 DOI: 10.1093/femsre/fuac033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 01/09/2023] Open
Abstract
Microbial iron reduction is a widespread and ancient metabolism on Earth, and may plausibly support microbial life on Mars and beyond. Yet, the extreme limits of this metabolism are yet to be defined. To investigate this, we surveyed the recorded limits to microbial iron reduction in a wide range of characterized iron-reducing microorganisms (n = 141), with a focus on pH and temperature. We then calculated Gibbs free energy of common microbially mediated iron reduction reactions across the pH-temperature habitability space to identify thermodynamic limits. Comparing predicted and observed limits, we show that microbial iron reduction is generally reported at extremes of pH or temperature alone, but not when these extremes are combined (with the exception of a small number of acidophilic hyperthermophiles). These patterns leave thermodynamically favourable combinations of pH and temperature apparently unoccupied. The empty spaces could be explained by experimental bias, but they could also be explained by energetic and biochemical limits to iron reduction at combined extremes. Our data allow for a review of our current understanding of the limits to microbial iron reduction at extremes and provide a basis to test more general hypotheses about the extent to which biochemistry establishes the limits to life.
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Affiliation(s)
- Sophie L Nixon
- Corresponding author: Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
| | - Emily Bonsall
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
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15
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Fackler JR, Dworjan M, Gazi KS, Grogan DW. Diversity of SIRV-like Viruses from a North American Population. Viruses 2022; 14:v14071439. [PMID: 35891419 PMCID: PMC9319562 DOI: 10.3390/v14071439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
A small subset of acidic hot springs sampled in Yellowstone National Park yielded rod-shaped viruses which lysed liquid host cultures and formed clear plaques on lawns of host cells. Three isolates chosen for detailed analysis were found to be genetically related to previously described isolates of the Sulfolobus islandicus rod-shaped virus (SIRV), but distinct from them and from each other. Functional stability of the new isolates was assessed in a series of inactivation experiments. UV-C radiation inactivated one of the isolates somewhat faster than bacteriophage λ, suggesting that encapsidation in the SIRV-like virion did not confer unusual protection of the DNA from UV damage. With respect to high temperature, the new isolates were extremely, but not equally, stable. Several chemical treatments were found to inactivate the virions and, in some cases, to reveal apparent differences in virion stability among the isolates. Screening a larger set of isolates identified greater variation of these stability properties but found few correlations among the resulting profiles. The majority of host cells infected by the new isolates were killed, but survivors exhibited heritable resistance, which could not be attributed to CRISPR spacer acquisition or the loss of the pilus-related genes identified by earlier studies. Virus-resistant host variants arose at high frequency and most were resistant to multiple viral strains; conversely, resistant host clones generated virus-sensitive variants, also at high frequency. Virus-resistant cells lacked the ability of virus-sensitive cells to bind virions in liquid suspensions. Rapid interconversion of sensitive and resistant forms of a host strain suggests the operation of a yet-unidentified mechanism that acts to allow both the lytic virus and its host to propagate in highly localized natural populations, whereas variation of virion-stability phenotypes among the new viral isolates suggests that multiple molecular features contribute to the biological durability of these viruses.
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Affiliation(s)
- Joseph R. Fackler
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA
| | - Michael Dworjan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
| | - Khaled S. Gazi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Department of Biology, Faculty of Science and Arts in Almandaq, Al-Baha University, Almandaq 65756, Saudi Arabia
| | - Dennis W. Grogan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Correspondence:
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16
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Nuno de Sousa Machado J, Albers SV, Daum B. Towards Elucidating the Rotary Mechanism of the Archaellum Machinery. Front Microbiol 2022; 13:848597. [PMID: 35387068 PMCID: PMC8978795 DOI: 10.3389/fmicb.2022.848597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Motile archaea swim by means of a molecular machine called the archaellum. This structure consists of a filament attached to a membrane-embedded motor. The archaellum is found exclusively in members of the archaeal domain, but the core of its motor shares homology with the motor of type IV pili (T4P). Here, we provide an overview of the different components of the archaellum machinery and hypothetical models to explain how rotary motion of the filament is powered by the archaellum motor.
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Affiliation(s)
- João Nuno de Sousa Machado
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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17
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Yang MJ, Kim J, Lee Y, Lee W, Park CJ. NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus. Int J Mol Sci 2022; 23:ijms23063099. [PMID: 35328522 PMCID: PMC8954794 DOI: 10.3390/ijms23063099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.
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Affiliation(s)
- Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
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18
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Complete Genome Sequence of the Hyperthermophilic and Acidophilic Archaeon Saccharolobus caldissimus Strain HS-3 T. Microbiol Resour Announc 2022; 11:e0107821. [PMID: 35262381 PMCID: PMC9022530 DOI: 10.1128/mra.01078-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of the hyperthermophilic archaeon Saccharolobus caldissimus strain HS-3T was determined. The genome is 3,075,795 bp with a GC content of 32.9%. Genes for the complete semiphosphorylative Entner-Doudoroff pathway, gluconeogenesis, tricarboxylic acid cycle, pentose phosphate pathway, and 3-hydroxypropionate 4-hydroxybutylate cycle were present in the genome.
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19
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Malik L, Hedrich S. Ferric Iron Reduction in Extreme Acidophiles. Front Microbiol 2022; 12:818414. [PMID: 35095822 PMCID: PMC8790237 DOI: 10.3389/fmicb.2021.818414] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Biochemical processes are a key element of natural cycles occurring in the environment and enabling life on earth. With regard to microbially catalyzed iron transformation, research predominantly has focused on iron oxidation in acidophiles, whereas iron reduction played a minor role. Microbial conversion of ferric to ferrous iron has however become more relevant in recent years. While there are several reviews on neutrophilic iron reducers, this article summarizes the research on extreme acidophilic iron reducers. After the first reports of dissimilatory iron reduction by acidophilic, chemolithoautotrophic Acidithiobacillus strains and heterotrophic Acidiphilium species, many other prokaryotes were shown to reduce iron as part of their metabolism. Still, little is known about the exact mechanisms of iron reduction in extreme acidophiles. Initially, hypotheses and postulations for the occurring mechanisms relied on observations of growth behavior or predictions based on the genome. By comparing genomes of well-studied neutrophilic with acidophilic iron reducers (e.g., Ferroglobus placidus and Sulfolobus spp.), it became clear that the electron transport for iron reduction proceeds differently in acidophiles. Moreover, transcriptomic investigations indicated an enzymatically-mediated process in Acidithiobacillus ferrooxidans using respiratory chain components of the iron oxidation in reverse. Depending on the strain of At. ferrooxidans, further mechanisms were postulated, e.g., indirect iron reduction by hydrogen sulfide, which may form by disproportionation of elemental sulfur. Alternative scenarios include Hip, a high potential iron-sulfur protein, and further cytochromes. Apart from the anaerobic iron reduction mechanisms, sulfur-oxidizing acidithiobacilli have been shown to mediate iron reduction at low pH (< 1.3) under aerobic conditions. This presumably non-enzymatic process may be attributed to intermediates formed during sulfur/tetrathionate and/or hydrogen oxidation and has already been successfully applied for the reductive bioleaching of laterites. The aim of this review is to provide an up-to-date overview on ferric iron reduction by acidophiles. The importance of this process in anaerobic habitats will be demonstrated as well as its potential for application.
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Affiliation(s)
- Luise Malik
- Research Group Biohydrometallurgy and Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Sabrina Hedrich
- Research Group Biohydrometallurgy and Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
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20
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Matsuda R, Suzuki S, Kurosawa N. Genetic Study of Four Candidate Holliday Junction Processing Proteins in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Int J Mol Sci 2022; 23:ijms23020707. [PMID: 35054893 PMCID: PMC8775617 DOI: 10.3390/ijms23020707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/24/2021] [Accepted: 01/06/2022] [Indexed: 02/01/2023] Open
Abstract
Homologous recombination (HR) is thought to be important for the repair of stalled replication forks in hyperthermophilic archaea. Previous biochemical studies identified two branch migration helicases (Hjm and PINA) and two Holliday junction (HJ) resolvases (Hjc and Hje) as HJ-processing proteins; however, due to the lack of genetic evidence, it is still unclear whether these proteins are actually involved in HR in vivo and how their functional relation is associated with the process. To address the above questions, we constructed hjc-, hje-, hjm-, and pina single-knockout strains and double-knockout strains of the thermophilic crenarchaeon Sulfolobus acidocaldarius and characterized the mutant phenotypes. Notably, we succeeded in isolating the hjm- and/or pina-deleted strains, suggesting that the functions of Hjm and PINA are not essential for cellular growth in this archaeon, as they were previously thought to be essential. Growth retardation in Δpina was observed at low temperatures (cold sensitivity). When deletion of the HJ resolvase genes was combined, Δpina Δhjc and Δpina Δhje exhibited severe cold sensitivity. Δhjm exhibited severe sensitivity to interstrand crosslinkers, suggesting that Hjm is involved in repairing stalled replication forks, as previously demonstrated in euryarchaea. Our findings suggest that the function of PINA and HJ resolvases is functionally related at lower temperatures to support robust cellular growth, and Hjm is important for the repair of stalled replication forks in vivo.
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21
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Charbonneau AA, Eckert DM, Gauvin CC, Lintner NG, Lawrence CM. Cyclic Tetra-Adenylate (cA 4) Recognition by Csa3; Implications for an Integrated Class 1 CRISPR-Cas Immune Response in Saccharolobus solfataricus. Biomolecules 2021; 11:biom11121852. [PMID: 34944496 PMCID: PMC8699464 DOI: 10.3390/biom11121852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 01/09/2023] Open
Abstract
Csa3 family transcription factors are ancillary CRISPR-associated proteins composed of N-terminal CARF domains and C-terminal winged helix-turn-helix domains. The activity of Csa3 transcription factors is thought to be controlled by cyclic oligoadenyate (cOA) second messengers produced by type III CRISPR-Cas surveillance complexes. Here we show that Saccharolobus solfataricus Csa3a recognizes cyclic tetra-adenylate (cA4) and that Csa3a lacks self-regulating "ring nuclease" activity present in some other CARF domain proteins. The crystal structure of the Csa3a/cA4 complex was also determined and the structural and thermodynamic basis for cA4 recognition are described, as are conformational changes in Csa3a associated with cA4 binding. We also characterized the effect of cA4 on recognition of putative DNA binding sites. Csa3a binds to putative promoter sequences in a nonspecific, cooperative and cA4-independent manner, suggesting a more complex mode of transcriptional regulation. We conclude the Csa3a/cA4 interaction represents a nexus between the type I and type III CRISPR-Cas systems present in S. solfataricus, and discuss the role of the Csa3/cA4 interaction in coordinating different arms of this integrated class 1 immune system to mount a synergistic, highly orchestrated immune response.
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Affiliation(s)
- Alexander A. Charbonneau
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.A.C.); (C.C.G.); (N.G.L.)
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - Debra M. Eckert
- School of Medicine, University of Utah, Salt Lake City, UT 84112, USA;
| | - Colin C. Gauvin
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.A.C.); (C.C.G.); (N.G.L.)
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - Nathanael G. Lintner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.A.C.); (C.C.G.); (N.G.L.)
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - C. Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; (A.A.C.); (C.C.G.); (N.G.L.)
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
- Correspondence: ; Tel.: +1-406-994-5382
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22
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Liu LJ, Jiang Z, Wang P, Qin YL, Xu W, Wang Y, Liu SJ, Jiang CY. Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea. Front Microbiol 2021; 12:768283. [PMID: 34721370 PMCID: PMC8551704 DOI: 10.3389/fmicb.2021.768283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.
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Affiliation(s)
- Li-Jun Liu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Xu
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yang Wang
- School of Basic Medical Science, the Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, China.,Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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23
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Abstract
A large number of fuselloviruses have been found in acidic hot springs around the globe. They share a set of highly conserved genes (core genes) and possess a varying number of less-conserved genes (non-core genes). However, the functions of most of these genes are unknown. Recent studies show that as many as half of these genes tolerate mutation. In this study, we conducted a genetic analysis on Saccharolobus spindle-shaped virus 22 (SSV22), an alphafusellovirus with fewer open reading frames (ORFs) than most of the isolated fuselloviruses. Both deletion and frame-shift mutations were introduced into nearly all of the 26 ORFs of the viral genome. A total of 17 ORFs were indispensable, and two additional ORFs were required for the optimal infectivity of the virus. Deletion of either VP2 or VP3, the two structural proteins, did not affect the morphology or infectivity of the virus. An infectious SSV22 derivative carrying a minimal genome of 20 ORFs was obtained. The SSV22 capsid was capable of accommodating a genome as large as ∼18 kb, or ∼7 kb larger than that of the wild-type virus. The viral capsid varied in both the length and width, but not in shape, with the size of the genome. Our results will facilitate the analysis of crucial protein-protein interactions between SSV22 and the host during viral infection and help explore the use of SSV22 as a vector for DNA delivery in potential applications.
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Affiliation(s)
- Junxia Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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24
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Complete Genome Sequence of a Novel Thermoacidophilic and Facultatively Anaerobic Crenarchaeon, Stygiolobus sp. Strain KN-1. Microbiol Resour Announc 2021; 10:e0058121. [PMID: 34591670 PMCID: PMC8483694 DOI: 10.1128/mra.00581-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of the thermoacidophilic crenarchaeon Stygiolobus sp. strain KN-1 was determined and annotated. The genome was 2,958,410 bp in size, with a GC content of 40.1%. It contained 2,973 coding sequences, a single copy of the 16S-23S rRNA operon, 47 tRNA genes, and 9 CRISPR repeat sequences.
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25
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Complete Genome Sequence of a Novel Sulfolobales Archaeon Strain, HS-7, Isolated from the Unzen Hot Spring in Japan. Microbiol Resour Announc 2021; 10:e0058221. [PMID: 34553995 PMCID: PMC8459659 DOI: 10.1128/mra.00582-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The order Sulfolobales includes thermoacidophilic archaea that thrive in acidic geothermal environments. A novel Sulfolobales archaeon strain, HS-7, which may represent a novel genus, was isolated from an acidic hot spring in Japan. We report the 2.15-Mb complete genome sequence of strain HS-7.
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26
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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Counts JA, Willard DJ, Kelly RM. Life in hot acid: a genome-based reassessment of the archaeal order Sulfolobales. Environ Microbiol 2021; 23:3568-3584. [PMID: 32776389 PMCID: PMC10560490 DOI: 10.1111/1462-2920.15189] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 01/07/2023]
Abstract
The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re-organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.
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Affiliation(s)
- James A. Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
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Banerjee R, Chaudhari NM, Lahiri A, Gautam A, Bhowmik D, Dutta C, Chattopadhyay S, Huson DH, Paul S. Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae. Front Microbiol 2021; 12:639995. [PMID: 34248865 PMCID: PMC8267890 DOI: 10.3389/fmicb.2021.639995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/06/2021] [Indexed: 11/21/2022] Open
Abstract
Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO2 fixation for Sulfolobaceae. Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain-loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.
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Affiliation(s)
- Rachana Banerjee
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Narendrakumar M. Chaudhari
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Abhishake Lahiri
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anupam Gautam
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Debaleena Bhowmik
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chitra Dutta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sujay Chattopadhyay
- JIS Institute of Advanced Studies and Research, JIS University, Kolkata, India
| | - Daniel H. Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Cluster of Excellence: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Sandip Paul
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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30
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Dai X, Wang Y, Luo L, Pfiffner SM, Li G, Dong Z, Xu Z, Dong H, Huang L. Detection of the deep biosphere in metamorphic rocks from the Chinese continental scientific drilling. GEOBIOLOGY 2021; 19:278-291. [PMID: 33559972 DOI: 10.1111/gbi.12430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
It is generally accepted that there is a vast, well-populated biosphere in the subsurface, but the depth limit of the terrestrial biosphere has yet to be determined, largely because of the lack of access to the subsurface. Here as part of the Chinese Continental Scientific Drilling (CCSD) project in eastern China, we acquired continuous rock cores and endeavored to probe the depth limit of the biosphere and the depth-dependent distribution of microorganisms at a geologically unique site, that is, a convergent plate boundary. Microbiological analyses of ultra-high-pressure metamorphic rock cores taken from the ground surface to 5,158-meter reveal that microbial distribution was continuous up to a depth of ~4,850 m, where temperature was estimated to be ~137°C. The metabolic state of these organisms at such great depth remains to be determined. Microbial abundance, ranging from 103 to 108 cells/g, was also related to porosity, but not to the depth and rock composition. In addition, microbial diversity systematically decreased with depth. Our results support the notion that temperature is a key factor in determining the lower limit of the biosphere in the continental subsurface.
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Affiliation(s)
- Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanliang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liqiang Luo
- National Research Center for Geoanalysis, Chinese Academy of Geological Sciences, Beijing, China
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - Guangyu Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiqin Xu
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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31
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Yang MJ, Lee W, Park CJ. Resonance assignments and secondary structure of thermophile single-stranded DNA binding protein from Sulfolobus solfataricus at 323K. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:159-164. [PMID: 33405014 DOI: 10.1007/s12104-020-09999-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Single-stranded DNA (ssDNA)-binding proteins (SSBs) are essential for DNA replication, recombination, and repair processes in all organisms. Sulfolobus solfataricus (S. solfataricus), a hyperthermophilic species, overexpresses its SSB (S. solfataricus SSB (SsoSSB)) to protect ssDNA during DNA metabolisms. Even though the crystal structure of apo SsoSSB and its ssDNA-bound solution structure have been reported at room temperature, structural information at high temperature is not yet available. To find out how SsoSSB maintains its structure and ssDNA binding affinity at high temperatures, we performed multidimensional NMR experiments for SsoSSB at 323K. In this study, we present the backbone and side chain chemical shifts and predict the secondary structure of SsoSSB from the chemical shifts. We found that SsoSSB is ordered, even at high temperatures, and has the same fold at high temperature as at room temperature. Our data will help improve structural analyses and our understanding of the features of thermophilic proteins.
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Affiliation(s)
- Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO, 80217-3364, USA.
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea.
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32
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Curci N, Strazzulli A, Iacono R, De Lise F, Maurelli L, Di Fenza M, Cobucci-Ponzano B, Moracci M. Xyloglucan Oligosaccharides Hydrolysis by Exo-Acting Glycoside Hydrolases from Hyperthermophilic Microorganism Saccharolobus solfataricus. Int J Mol Sci 2021; 22:3325. [PMID: 33805072 PMCID: PMC8037949 DOI: 10.3390/ijms22073325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
In the field of biocatalysis and the development of a bio-based economy, hemicellulases have attracted great interest for various applications in industrial processes. However, the study of the catalytic activity of the lignocellulose-degrading enzymes needs to be improved to achieve the efficient hydrolysis of plant biomasses. In this framework, hemicellulases from hyperthermophilic archaea show interesting features as biocatalysts and provide many advantages in industrial applications thanks to their stability in the harsh conditions encountered during the pretreatment process. However, the hemicellulases from archaea are less studied compared to their bacterial counterpart, and the activity of most of them has been barely tested on natural substrates. Here, we investigated the hydrolysis of xyloglucan oligosaccharides from two different plants by using, both synergistically and individually, three glycoside hydrolases from Saccharolobus solfataricus: a GH1 β-gluco-/β-galactosidase, a α-fucosidase belonging to GH29, and a α-xylosidase from GH31. The results showed that the three enzymes were able to release monosaccharides from xyloglucan oligosaccharides after incubation at 65 °C. The concerted actions of β-gluco-/β-galactosidase and the α-xylosidase on both xyloglucan oligosaccharides have been observed, while the α-fucosidase was capable of releasing all α-linked fucose units from xyloglucan from apple pomace, representing the first GH29 enzyme belonging to subfamily A that is active on xyloglucan.
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Affiliation(s)
- Nicola Curci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Roberta Iacono
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
| | - Federica De Lise
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Luisa Maurelli
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
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33
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Miyabayashi H, Sakai HD, Kurosawa N. DNA Polymerase B1 Binding Protein 1 Is Important for DNA Repair by Holoenzyme PolB1 in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Microorganisms 2021; 9:microorganisms9020439. [PMID: 33672533 PMCID: PMC7923795 DOI: 10.3390/microorganisms9020439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 11/16/2022] Open
Abstract
DNA polymerase B1 (PolB1) is a member of the B-family DNA polymerase family and is a replicative DNA polymerase in Crenarchaea. PolB1 is responsible for the DNA replication of both the leading and lagging strands in the thermophilic crenarchaeon Sulfolobus acidocaldarius. Recently, two subunits, PolB1-binding protein (PBP)1 and PBP2, were identified in Saccharolobus solfataricus. Previous in vitro studies suggested that PBP1 and PBP2 influence the core activity of apoenzyme PolB1 (apo-PolB1). PBP1 contains a C-terminal acidic tail and modulates the strand-displacement synthesis activity of PolB1 during the synthesis of Okazaki fragments. PBP2 modestly enhances the DNA polymerase activity of apo-PolB1. These subunits are present in Sulfolobales, Acidilobales, and Desulfurococcales, which belong to Crenarchaea. However, it has not been determined whether these subunits are essential for the activity of apo-PolB1. In this study, we constructed a pbp1 deletion strain in S. acidocaldarius and characterized its phenotypes. However, a pbp2 deletion strain was not obtained, indicating that PBP2 is essential for replication by holoenzyme PolB1. A pbp1 deletion strain was sensitive to various types of DNA damage and exhibited an increased mutation rate, suggesting that PBP1 contribute to the repair or tolerance of DNA damage by holoenzyme PolB1. The results of our study suggest that PBP1 is important for DNA repair by holoenzyme PolB1 in S. acidocaldarius.
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Affiliation(s)
- Hiroka Miyabayashi
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan;
| | - Hiroyuki D. Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan;
| | - Norio Kurosawa
- Department of Environmental Engineering for Symbiosis, Graduate School of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan;
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan;
- Correspondence: ; Tel.: +81-42-691-8175
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34
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Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 2021; 49:D274-D281. [PMID: 33167031 DOI: 10.1093/nar/gkaa1018] [Citation(s) in RCA: 342] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014. The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI's gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for >200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Roberto Vera Alvarez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Wolf J, Koblitz J, Albersmeier A, Kalinowski J, Siebers B, Schomburg D, Neumann-Schaal M. Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response. Front Microbiol 2021; 11:587032. [PMID: 33488537 PMCID: PMC7820114 DOI: 10.3389/fmicb.2020.587032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022] Open
Abstract
Present in many industrial effluents and as common degradation product of organic matter, phenol is a widespread compound which may cause serious environmental problems, due to its toxicity to animals and humans. Degradation of phenol from the environment by mesophilic bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation at high temperatures or low pH. In this work we studied phenol degradation in the thermoacidophilic archaeon Saccharolobus solfataricus P2 (basonym: Sulfolobus solfataricus) under extreme conditions (80°C, pH 3.5). We combined metabolomics and transcriptomics together with metabolic modeling to elucidate the organism’s response to growth with phenol as sole carbon source. Although S. solfataricus is able to utilize phenol for biomass production, the carbon source induces profound stress reactions, including genome rearrangement as well as a strong intracellular accumulation of polyamines. Furthermore, computational modeling revealed a 40% higher oxygen demand for substrate oxidation, compared to growth on glucose. However, only 16.5% of oxygen is used for oxidation of phenol to catechol, resulting in a less efficient integration of carbon into the biomass. Finally, our data underlines the importance of the phenol meta-degradation pathway in S. solfataricus and enables us to predict enzyme candidates involved in the degradation processes downstream of 2-hydroxymucconic acid.
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Affiliation(s)
- Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Julia Koblitz
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology-CeBiTec, Universität Bielefeld, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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36
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Wu Y, Jaremko WJ, Wilson RC, Pata JD. Heterotrimeric PCNA increases the activity and fidelity of Dbh, a Y-family translesion DNA polymerase prone to creating single-base deletion mutations. DNA Repair (Amst) 2020; 96:102967. [PMID: 32961405 DOI: 10.1016/j.dnarep.2020.102967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 11/15/2022]
Abstract
Dbh is a Y-family translesion DNA polymerase from Sulfolobus acidocaldarius, an archaeal species that grows in harsh environmental conditions. Biochemically, Dbh displays a distinctive mutational profile, creating single-base deletion mutations at extraordinarily high frequencies (up to 50 %) in specific repeat sequences. In cells, however, Dbh does not appear to contribute significantly to spontaneous frameshifts in these same sequence contexts. This suggests that either the error-prone DNA synthesis activity of Dbh is reduced in vivo and/or Dbh is restricted from replicating these sequences. Here, we test the hypothesis that the propensity for Dbh to make single base deletion mutations is reduced through interaction with the S. acidocaldarius heterotrimeric sliding clamp processivity factor, PCNA-123. We first confirm that Dbh physically interacts with PCNA-123, with the interaction requiring both the PCNA-1 subunit and the C-terminal 10 amino acids of Dbh, which contain a predicted PCNA-interaction peptide (PIP) motif. This interaction stimulates the polymerase activity of Dbh, even on short, linear primer-template DNA, by increasing the rate of nucleotide incorporation. This stimulation requires an intact PCNA-123 heterotrimer and a DNA duplex length of at least 18 basepairs, the minimal length predicted from structural data to bind to both the polymerase and the clamp. Finally, we find that PCNA-123 increases the fidelity of Dbh on a single-base deletion hotspot sequence 3-fold by promoting an increase in the rate of correct, but not incorrect, nucleotide addition and propose that PCNA-123 induces Dbh to adopt a more active conformation that is less prone to creating deletions during DNA synthesis.
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Affiliation(s)
- Yifeng Wu
- Wadsworth Center, New York State Department of Health, Albany, NY, United States; Department of Biomedical Sciences, University at Albany, Albany, NY, United States
| | - William J Jaremko
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Ryan C Wilson
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Janice D Pata
- Wadsworth Center, New York State Department of Health, Albany, NY, United States; Department of Biomedical Sciences, University at Albany, Albany, NY, United States.
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37
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Suleiman M, Krüger A, Antranikian G. Biomass-degrading glycoside hydrolases of archaeal origin. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:153. [PMID: 32905355 PMCID: PMC7469102 DOI: 10.1186/s13068-020-01792-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
During the last decades, the impact of hyperthermophiles and their enzymes has been intensively investigated for implementation in various high-temperature biotechnological processes. Biocatalysts of hyperthermophiles have proven to show extremely high thermo-activities and thermo-stabilities and are identified as suitable candidates for numerous industrial processes with harsh conditions, including the process of an efficient plant biomass pretreatment and conversion. Already-characterized archaea-originated glycoside hydrolases (GHs) have shown highly impressive features and numerous enzyme characterizations indicated that these biocatalysts show maximum activities at a higher temperature range compared to bacterial ones. However, compared to bacterial biomass-degrading enzymes, the number of characterized archaeal ones remains low. To discover new promising archaeal GH candidates, it is necessary to study in detail the microbiology and enzymology of extremely high-temperature habitats, ranging from terrestrial to marine hydrothermal systems. State-of-the art technologies such as sequencing of genomes and metagenomes and automated binning of genomes out of metagenomes, combined with classical microbiological culture-dependent approaches, have been successfully performed to detect novel promising biomass-degrading hyperthermozymes. In this review, we will focus on the detection, characterization and similarities of archaeal GHs and their unique characteristics. The potential of hyperthermozymes and their impact on high-temperature industrial applications have not yet been exhausted.
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Affiliation(s)
- Marcel Suleiman
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anna Krüger
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
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Febbraio F, Ionata E, Marcolongo L. Forty years of study on the thermostable β-glycosidase from S. solfataricus: Production, biochemical characterization and biotechnological applications. Biotechnol Appl Biochem 2020; 67:602-618. [PMID: 32621790 DOI: 10.1002/bab.1982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aim of this paper is to make the point on the fortieth years study on the β-glycosidase from Sulfolobus solfataricus. This enzyme represents one of the thermophilic biocatalysts, which is more extensively studied as witnessed by the numerous literature reports available since 1980. Comprehensive biochemical studies highlighted its broad substrate specificity for β-d-galacto-, gluco-, and fuco-sides and also showed its remarkable exo-glucosidase and transglycosidase activities. The enzyme demonstrated to be active and stable over a wide range of temperature and pHs, withstanding to several drastic conditions comprising solvents and detergents. Over the years, a great deal of studies were focused on its homotetrameric tridimensional structure, elucidating several structural features involved in the enzyme stability, such as ion pairs and post-translational modifications. Several β-glycosidase mutants were produced in the years in order to understand its peculiar behavior in extreme conditions and/or to improve its functional properties. The β-glycosidase overproduction was also afforded reporting numerous studies dealing with its production in the mesophilic host Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, and Lactococcus lactis. Relevant applications in food, beverages, bioenergy, pharmaceuticals, and nutraceutical fields of this enzyme, both in free and immobilized forms, highlighted its biotechnological relevance.
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Affiliation(s)
- Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, Italy
| | - Elena Ionata
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
| | - Loredana Marcolongo
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
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Feng X, Liu X, Xu R, Zhao R, Feng W, Liao J, Han W, She Q. A Unique B-Family DNA Polymerase Facilitating Error-Prone DNA Damage Tolerance in Crenarchaeota. Front Microbiol 2020; 11:1585. [PMID: 32793138 PMCID: PMC7390963 DOI: 10.3389/fmicb.2020.01585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Sulfolobus islandicus codes for four DNA polymerases: three are of the B-family (Dpo1, Dpo2, and Dpo3), and one is of the Y-family (Dpo4). Western analysis revealed that among the four polymerases, only Dpo2 exhibited DNA damage-inducible expression. To investigate how these DNA polymerases could contribute to DNA damage tolerance in S. islandicus, we conducted genetic analysis of their encoding genes in this archaeon. Plasmid-borne gene expression revealed that Dpo2 increases cell survival upon DNA damage at the expense of mutagenesis. Gene deletion studies showed although dpo1 is essential, the remaining three genes are dispensable. Furthermore, although Dpo4 functions in housekeeping translesion DNA synthesis (TLS), Dpo2, a B-family DNA polymerase once predicted to be inactive, functions as a damage-inducible TLS enzyme solely responsible for targeted mutagenesis, facilitating GC to AT/TA conversions in the process. Together, our data indicate that Dpo2 is the main DNA polymerase responsible for DNA damage tolerance and is the primary source of targeted mutagenesis. Given that crenarchaea encoding a Dpo2 also have a low-GC composition genome, the Dpo2-dependent DNA repair pathway may be conserved in this archaeal lineage.
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Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Liu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruyi Xu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruiliang Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenqian Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianglan Liao
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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40
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Pulschen AA, Mutavchiev DR, Culley S, Sebastian KN, Roubinet J, Roubinet M, Risa GT, van Wolferen M, Roubinet C, Schmidt U, Dey G, Albers SV, Henriques R, Baum B. Live Imaging of a Hyperthermophilic Archaeon Reveals Distinct Roles for Two ESCRT-III Homologs in Ensuring a Robust and Symmetric Division. Curr Biol 2020; 30:2852-2859.e4. [PMID: 32502411 PMCID: PMC7372223 DOI: 10.1016/j.cub.2020.05.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022]
Abstract
Live-cell imaging has revolutionized our understanding of dynamic cellular processes in bacteria and eukaryotes. Although similar techniques have been applied to the study of halophilic archaea [1-5], our ability to explore the cell biology of thermophilic archaea has been limited by the technical challenges of imaging at high temperatures. Sulfolobus are the most intensively studied members of TACK archaea and have well-established molecular genetics [6-9]. Additionally, studies using Sulfolobus were among the first to reveal striking similarities between the cell biology of eukaryotes and archaea [10-15]. However, to date, it has not been possible to image Sulfolobus cells as they grow and divide. Here, we report the construction of the Sulfoscope, a heated chamber on an inverted fluorescent microscope that enables live-cell imaging of thermophiles. By using thermostable fluorescent probes together with this system, we were able to image Sulfolobus acidocaldarius cells live to reveal tight coupling between changes in DNA condensation, segregation, and cell division. Furthermore, by imaging deletion mutants, we observed functional differences between the two ESCRT-III proteins implicated in cytokinesis, CdvB1 and CdvB2. The deletion of cdvB1 compromised cell division, causing occasional division failures, whereas the ΔcdvB2 exhibited a profound loss of division symmetry, generating daughter cells that vary widely in size and eventually generating ghost cells. These data indicate that DNA separation and cytokinesis are coordinated in Sulfolobus, as is the case in eukaryotes, and that two contractile ESCRT-III polymers perform distinct roles to ensure that Sulfolobus cells undergo a robust and symmetrical division.
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Affiliation(s)
| | - Delyan R Mutavchiev
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Kim Nadine Sebastian
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | | | | | | | - Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | - Chantal Roubinet
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Uwe Schmidt
- Center for System Biology Dresden (CSBD), 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), 01307 Dresden, Germany
| | - Gautam Dey
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, UCL, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, UCL, London WC1E 6BT, UK.
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Ceballos RM, Drummond CG, Stacy CL, Padilla-Crespo E, Stedman KM. Host-Dependent Differences in Replication Strategy of the Sulfolobus Spindle-Shaped Virus Strain SSV9 (a.k.a., SSVK1): Infection Profiles in Hosts of the Family Sulfolobaceae. Front Microbiol 2020; 11:1218. [PMID: 32760354 PMCID: PMC7372142 DOI: 10.3389/fmicb.2020.01218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
The Sulfolobus Spindle-shaped Virus (SSV) system has become a model for studying thermophilic virus biology, including archaeal host-virus interactions and biogeography. Several factors make the SSV system amenable to studying archaeal genetic mechanisms (e.g., CRISPRs) as well as virus-host interactions in high temperature acidic environments. Previously, we reported that SSVs exhibited differential infectivity on allopatric vs. sympatric hosts. We also noticed a wide host range for virus strain SSV9 (a.k.a., SSVK1). For decades, SSVs have been described as "non-lytic" double-stranded DNA viruses that infect species of the genus Sulfolobus and release virions via budding rather than host lysis. In this study, we show that SSVs infect hosts representing more than one genus of the family Sulfolobaceae in spot-on-lawn "halo" assays and in liquid culture infection assays. Growth curve analyses support the hypothesis that SSV9 virion release causes cell lysis. While SSV9 appears to lyse allopatric hosts, on a single sympatric host, SSV9 exhibits canonical non-lytic viral release historically reported SSVs. Therefore, the nature of SSV9 lytic-like behavior may be driven by allopatric evolution. The SSV9-infected host growth profile does not appear to be driven by multiplicity of infection (MOI). Greater stability of SSV9 vs. other SSVs (i.e., SSV1) in high temperature, low pH environments may contribute to higher transmission rates. However, neither higher transmission rate nor relative virulence in SSV9 infection seems to alter replication profile in susceptible hosts. Although it is known that CRISPR-Cas systems offer protection against viral infection in prokaryotes, CRISPRS are not reported to be a determinant of virus replication strategy. The mechanisms underlying SSV9 lytic-like behavior remain unknown and are the subject of ongoing investigations. These results suggest that genetic elements, potentially resulting from allopatric evolution, mediate distinct virus-host growth profiles of specific SSV-host strain pairings.
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Affiliation(s)
- Ruben Michael Ceballos
- Department of Biological Sciences, The University of Arkansas, Fayetteville, AR, United States
- Arkansas Center for Space and Planetary Sciences, Fayetteville, AR, United States
- Cell and Molecular Biology Program, The University of Arkansas, Fayetteville, AR, United States
| | - Coyne Gareth Drummond
- Departmento de Ciencias y Tecnología, Universidad Interamericana de Puerto Rico, Aguadilla, PR, United States
| | - Carson Len Stacy
- Cell and Molecular Biology Program, The University of Arkansas, Fayetteville, AR, United States
| | - Elizabeth Padilla-Crespo
- Departmento de Ciencias y Tecnología, Universidad Interamericana de Puerto Rico, Aguadilla, PR, United States
| | - Kenneth Mark Stedman
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
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42
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Jain R, Dhiman S, Grogan DW. Genetic Control of Oxidative Mutagenesis in Sulfolobus acidocaldarius. J Bacteriol 2020; 202:JB.00756-19. [PMID: 32482723 PMCID: PMC8404708 DOI: 10.1128/jb.00756-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/26/2020] [Indexed: 02/01/2023] Open
Abstract
To identify DNA-oxidation defenses of hyperthermophilic archaea, we deleted genes encoding the putative 7,8-dihydro-8-oxoguanine (oxoG)-targeted N-glycosylase of S. acidocaldarius (ogg; Saci_01367), the Y-family DNA polymerase (dbh; Saci_0554), or both, and measured the effects on cellular survival, replication accuracy, and oxoG bypass in vivo Spontaneous G:C to T:A transversions were elevated in all Δogg and Δdbh constructs, and the Δogg Δdbh double mutant lost viability at a faster rate than isogenic WT and ogg strains. The distribution of G:C to T:A transversions within mutation-detector genes suggested that reactivity of G toward oxidation and the effect on translation contribute heavily to the pattern of mutations that are recovered. An impact of the Ogg protein on overall efficiency of bypassing oxoG in transforming DNA was evident only in the absence of Dbh, and Ogg status did not affect the accuracy of bypass. Dbh function, in contrast, dramatically influenced both the efficiency and accuracy of oxoG bypass. Thus, Ogg and Dbh were found to work independently to avoid mutagenesis by oxoG, and inactivating this simple but effective defense system by deleting both genes imposed a severe mutational burden on S. acidocaldarius cells.IMPORTANCE Hyperthermophilic archaea are expected to have effective (and perhaps atypical) mechanisms to limit the genetic consequences of DNA damage, but few gene products have been demonstrated to have genome-preserving functions in vivo This study confirmed by genetic criteria that the S. acidocaldarius Ogg protein avoids the characteristic mutagenesis of G oxidation. This enzyme and the bypass polymerase Dbh have similar impacts on genome stability but work independently, and may comprise most of the DNA-oxidation defense of S. acidocaldarius The critical dependence of accurate oxoG bypass on the accessory DNA polymerase Dbh further argues that some form of polymerase exchange is important for accurate genome replication in Sulfolobus, and perhaps in related hyperthermophilic archaea.
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Affiliation(s)
- Rupal Jain
- Department of Biological Sciences, 614 Rieveschl Hall, ML0006, University of Cincinnati 513-556-9748
| | - Samuel Dhiman
- Department of Biological Sciences, 614 Rieveschl Hall, ML0006, University of Cincinnati 513-556-9748
| | - Dennis W Grogan
- Department of Biological Sciences, 614 Rieveschl Hall, ML0006, University of Cincinnati 513-556-9748
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43
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DeWerff SJ, Bautista MA, Pauly M, Zhang C, Whitaker RJ. Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism. mBio 2020; 11:e00404-20. [PMID: 32345641 PMCID: PMC7188992 DOI: 10.1128/mbio.00404-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/02/2020] [Indexed: 02/05/2023] Open
Abstract
Theory, simulation, and experimental evolution demonstrate that diversified CRISPR-Cas immunity to lytic viruses can lead to stochastic virus extinction due to a limited number of susceptible hosts available to each potential new protospacer escape mutation. Under such conditions, theory predicts that to evade extinction, viruses evolve toward decreased virulence and promote vertical transmission and persistence in infected hosts. To better understand the evolution of host-virus interactions in microbial populations with active CRISPR-Cas immunity, we studied the interaction between CRISPR-immune Sulfolobus islandicus cells and immune-deficient strains that are infected by the chronic virus SSV9. We demonstrate that Sulfolobus islandicus cells infected with SSV9, and with other related SSVs, kill uninfected, immune strains through an antagonistic mechanism that is a protein and is independent of infectious virus. Cells that are infected with SSV9 are protected from killing and persist in the population. We hypothesize that this infection acts as a form of mutualism between the host and the virus by removing competitors in the population and ensuring continued vertical transmission of the virus within populations with diversified CRISPR-Cas immunity.IMPORTANCE Multiple studies, especially those focusing on the role of lytic viruses in key model systems, have shown the importance of viruses in shaping microbial populations. However, it has become increasingly clear that viruses with a long host-virus interaction, such as those with a chronic lifestyle, can be important drivers of evolution and have large impacts on host ecology. In this work, we describe one such interaction with the acidic crenarchaeon Sulfolobus islandicus and its chronic virus Sulfolobus spindle-shaped virus 9. Our work expands the view in which this symbiosis between host and virus evolved, describing a killing phenotype which we hypothesize has evolved in part due to the high prevalence and diversity of CRISPR-Cas immunity seen in natural populations. We explore the implications of this phenotype in population dynamics and host ecology, as well as the implications of mutualism between this virus-host pair.
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Affiliation(s)
- Samantha J DeWerff
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Maria A Bautista
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Matthew Pauly
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
- Infection Genomics for One Health Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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Thermostable endoglucanase gene derived by amplification from the genomic DNA of a cellulose-enriched mixed culture from mudspring water of Mt. Makiling, Laguna, Philippines. World J Microbiol Biotechnol 2020; 36:51. [PMID: 32157408 DOI: 10.1007/s11274-020-02825-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/29/2020] [Indexed: 10/24/2022]
Abstract
Culture-independent molecular-based approaches can be used to identify genes of interest from environmental sources that have desirable properties such as thermo activity. For this study, a putative thermo stable endoglucanase gene was identified from a mixed culture resulting from the inoculation of Brock-CMcellulose (1%) broth with mudspring water from Mt. Makiling, Laguna, Philippines that had been incubated at 90 °C. Genomic DNA was extracted from the cellulose-enriched mixed culture and endo1949 forward and reverse primers were used to amplify the endoglucanase gene, which was cloned into pCR-script plasmid vector. Blastn alignment of the sequenced insert revealed 99.69% similarity to the glycosyl hydrolase, sso1354 (CelA1; Q97YG7) from Saccharolobus solfataricus. The endoglucanase gene (GenBank accession number MK984682) was determined to be 1,021 nucleotide bases in length, corresponding to 333 amino acids with a molecular mass of ~ 37 kDa. The endoglucanase gene was inserted into a pET21 vector and transformed in E. coli BL21 for expression. Partially purified recombinant Mt. Makiling endoglucanase (MM-Engl) showed a specific activity of 187.61 U/mg and demonstrated heat stability up to 80 °C. The thermo-acid stable endoglucanase can be used in a supplementary hydrolysis step to further hydrolyze the lignocellulosic materials that were previously treated under high temperature-dilute acid conditions, thereby enhancing the release of more glucose sugars for bioethanol production.
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Itoh T, Miura T, Sakai HD, Kato S, Ohkuma M, Takashina T. Sulfuracidifex tepidarius gen. nov., sp. nov. and transfer of Sulfolobus metallicus Huber and Stetter 1992 to the genus Sulfuracidifex as Sulfuracidifex metallicus comb. nov. Int J Syst Evol Microbiol 2020; 70:1837-1842. [DOI: 10.1099/ijsem.0.003981] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel, strictly aerobic, sulfur-dependent, thermoacidophilic strains, IC-006T and IC-007, were isolated from a solfataric field at Hakone Ohwaku-dani, Kanagawa, Japan. Cells of the two strains were irregular cocci with a diameter of 1.0–1.8 µm. They were strict aerobes and grew in a temperature range between 45 and 69 °C (optimally at 65 °C) and a pH range between 0.4 and 5.5 (optimally at pH 3.5). They required sulfur or a reduced sulfur compound, and sulfur was oxidized to sulfate. They grew autotrophically or mixotrophically utilizing several sugars and complex organic substances as carbon sources. The DNA G+C content was 42.4 mol%. A comparison of the 16S rRNA gene sequences among members of the order
Sulfolobales
indicated that they were closely related to
Sulfolobus metallicus
, forming an independent lineage within this order. The two isolates and
Sulfolobus metallicus
were also diffentiated based on their phenotypic properties from the other members of the order
Sulfolobales
. Detailed comparisons of the phenotypic properties and DNA–DNA hybridization study illustrated that the two isolates belong to a species different from
Sulfolobus metallicus
. On the basis of the phylogenetic and phenotypic comparisons, we propose a new genus and species, Sulfuracidifex tepidarius gen. nov., sp. nov. to accommodate strains IC-006T and IC-007. The type strain of Sulfuracidifex tepidarius is IC-006T (=JCM 16833T=DSM 104736T). In addition,
Sulfolobus metallicus
should be transferred to the new genus as Sulfuracidifex metallicus comb. nov.: the type strain is Kra23T (=DSM 6482T=JCM 9184T=NBRC 15436T).
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Affiliation(s)
- Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tatsuki Miura
- Graduate School of Life Sciences, Toyo University, Oura, Japan, Gunma 374-0193
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroyuki D. Sakai
- Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomonori Takashina
- Graduate School of Life Sciences, Toyo University, Oura, Japan, Gunma 374-0193
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Suzuki S, Kurosawa N. Participation of UV-regulated Genes in the Response to Helix-distorting DNA Damage in the Thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. Microbes Environ 2019; 34:363-373. [PMID: 31548441 PMCID: PMC6934391 DOI: 10.1264/jsme2.me19055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Several species of Sulfolobales have been used as model organisms in the study of response mechanisms to ultraviolet (UV) irradiation in hyperthermophilic crenarchaea. To date, the transcriptional responses of genes involved in the initiation of DNA replication, transcriptional regulation, protein phosphorylation, and hypothetical function have been observed in Sulfolobales species after UV irradiation. However, due to the absence of knockout experiments, the functions of these genes under in situ UV irradiation have not yet been demonstrated. In the present study, we constructed five gene knockout strains (cdc6-2, tfb3, rio1, and two genes encoding the hypothetical proteins, Saci_0951 and Saci_1302) of Sulfolobus acidocaldarius and examined their sensitivities to UV irradiation. The knockout strains exhibited significant sensitivities to UV-B irradiation, indicating that the five UV-regulated genes play an important role in responses to UV irradiation in vivo. Furthermore, Δcdc6-2, Δrio1, ΔSaci_0951, and Δtfb3 were sensitive to a wide variety of helix-distorting DNA lesions, including UV-induced DNA damage, an intra-strand crosslink, and bulky adducts. These results reveal that cdc6-2, tfb3, rio1, and Saci_0951 are play more important roles in broad responses to helix-distorting DNA damage than in specific responses to UV irradiation.
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Affiliation(s)
- Shoji Suzuki
- Department of Science and Engineering for Sustainable Development, Faculty of Science and Engineering, Soka University
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Development, Faculty of Science and Engineering, Soka University
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Couturier M, Gadelle D, Forterre P, Nadal M, Garnier F. The reverse gyrase TopR1 is responsible for the homeostatic control of DNA supercoiling in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 2019; 113:356-368. [PMID: 31713907 DOI: 10.1111/mmi.14424] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 11/28/2022]
Abstract
Maintaining an appropriate DNA topology with DNA-based processes (DNA replication, transcription and recombination) is crucial for all three domains of life. In bacteria, the homeostatic regulation for controlling DNA supercoiling relies on antagonistic activities of two DNA topoisomerases, TopoI and gyrase. In hyperthermophilic crenarchaea, the presence of such a regulatory system is suggested as two DNA topoisomerases, TopoVI and reverse gyrase, catalyze antagonistic activities. To test this hypothesis, we estimated and compared the number of the TopoVI with that of the two reverse gyrases, TopR1 and TopR2, in Sulfolobus solfataricus cells maintained either at 80 or at 88°C, or reciprocally shifted from one temperature to the other. From the three DNA topoisomerases, TopR1 is the only one exhibiting significant quantitative variations in response to the up- and down-shifts. In addition, the corresponding intrinsic activities of these three DNA topoisomerases were tested in vitro at both temperatures. Although temperature modulates the three DNA topoisomerases activities, TopR1 is the sole topoisomerase able to function at high temperature. Altogether, results presented in this study demonstrate, for the first time, that the DNA topological state of a crenarchaeon is regulated via a homeostatic control, which is mainly mediated by the fine-tuning of TopR1.
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Affiliation(s)
- Mohea Couturier
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France
| | - Danièle Gadelle
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France
| | - Marc Nadal
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France.,Institut Jacques Monod, UMR 8621 CNRS-Université Paris Diderot, Paris Cedex 13, France
| | - Florence Garnier
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France.,Institut Jacques Monod, UMR 8621 CNRS-Université Paris Diderot, Paris Cedex 13, France.,Biology Department, Université Versailles St-Quentin, Versailles, France
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48
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Perera HM, Trakselis MA. Amidst multiple binding orientations on fork DNA, Saccharolobus MCM helicase proceeds N-first for unwinding. eLife 2019; 8:46096. [PMID: 31661075 PMCID: PMC6831031 DOI: 10.7554/elife.46096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/23/2019] [Indexed: 11/13/2022] Open
Abstract
DNA replication requires that the duplex genomic DNA strands be separated; a function that is implemented by ring-shaped hexameric helicases in all Domains. Helicases are composed of two domains, an N- terminal DNA binding domain (NTD) and a C- terminal motor domain (CTD). Replication is controlled by loading of helicases at origins of replication, activation to preferentially encircle one strand, and then translocation to begin separation of the two strands. Using a combination of site-specific DNA footprinting, single-turnover unwinding assays, and unique fluorescence translocation monitoring, we have been able to quantify the binding distribution and the translocation orientation of Saccharolobus (formally Sulfolobus) solfataricus MCM on DNA. Our results show that both the DNA substrate and the C-terminal winged-helix (WH) domain influence the orientation but that translocation on DNA proceeds N-first.
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Affiliation(s)
- Himasha M Perera
- Department of Chemistry and Biochemistry, Baylor University, Waco, United States
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, United States
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Zeldes BM, Loder AJ, Counts JA, Haque M, Widney KA, Keller LM, Albers S, Kelly RM. Determinants of sulphur chemolithoautotrophy in the extremely thermoacidophilicSulfolobales. Environ Microbiol 2019; 21:3696-3710. [DOI: 10.1111/1462-2920.14712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/04/2019] [Accepted: 06/09/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin M. Zeldes
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Andrew J. Loder
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - James A. Counts
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Mashkurul Haque
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Karl A. Widney
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Lisa M. Keller
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Sonja‐Verena Albers
- Institute of Biology II – MicrobiologyUniversity of Freiburg Freiburg Germany
| | - Robert M. Kelly
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
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The Impact of Pyroglutamate: Sulfolobus acidocaldarius Has a Growth Advantage over Saccharolobus solfataricus in Glutamate-Containing Media. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2019; 2019:3208051. [PMID: 31178666 PMCID: PMC6507225 DOI: 10.1155/2019/3208051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/24/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022]
Abstract
Microorganisms are well adapted to their habitat but are partially sensitive to toxic metabolites or abiotic compounds secreted by other organisms or chemically formed under the respective environmental conditions. Thermoacidophiles are challenged by pyroglutamate, a lactam that is spontaneously formed by cyclization of glutamate under aerobic thermoacidophilic conditions. It is known that growth of the thermoacidophilic crenarchaeon Saccharolobus solfataricus (formerly Sulfolobus solfataricus) is completely inhibited by pyroglutamate. In the present study, we investigated the effect of pyroglutamate on the growth of S. solfataricus and the closely related crenarchaeon Sulfolobus acidocaldarius. In contrast to S. solfataricus, S. acidocaldarius was successfully cultivated with pyroglutamate as a sole carbon source. Bioinformatical analyses showed that both members of the Sulfolobaceae have at least one candidate for a 5-oxoprolinase, which catalyses the ATP-dependent conversion of pyroglutamate to glutamate. In S. solfataricus, we observed the intracellular accumulation of pyroglutamate and crude cell extract assays showed a less effective degradation of pyroglutamate. Apparently, S. acidocaldarius seems to be less versatile regarding carbohydrates and prefers peptidolytic growth compared to S. solfataricus. Concludingly, S. acidocaldarius exhibits a more efficient utilization of pyroglutamate and is not inhibited by this compound, making it a better candidate for applications with glutamate-containing media at high temperatures.
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