DOCSLIB.ORG

Genes-496949 Resubmission Without Tracked

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genes-496949 Resubmission Without Tracked Diversity of “Ca. Micrarchaeota” in two distinct types of acidic ANGOR UNIVERSITY environments and their associations with Thermoplasmatales Golyshina, Olga; Bargiela, Rafael; Toshchakov, Stepan V.; Chernyh, Nikolay A.; Ramayah, Soshila; Korzhenkov, Aleksei A.; Kublanov, Ilya V.; Golyshin, Peter Genes DOI: 10.3390/genes10060461 PRIFYSGOL BANGOR / B Published: 15/06/2019 Publisher's PDF, also known as Version of record Cyswllt i'r cyhoeddiad / Link to publication Dyfyniad o'r fersiwn a gyhoeddwyd / Citation for published version (APA): Golyshina, O., Bargiela, R., Toshchakov, S. V., Chernyh, N. A., Ramayah, S., Korzhenkov, A. A., Kublanov, I. V., & Golyshin, P. (2019). Diversity of “Ca. Micrarchaeota” in two distinct types of acidic environments and their associations with Thermoplasmatales. Genes, 10(6), [461]. https://doi.org/10.3390/genes10060461 Hawliau Cyffredinol / General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. 25. Sep. 2021 1 Article 2 Diversity of “Ca. Micrarchaeota” in two distinct 3 types of acidic environments and their associations 4 with Thermoplasmatales 5 Olga V. Golyshina 1,2 #, Rafael Bargiela 1,2, Stepan V. Toshchakov 3, Nikolay A. Chernyh 3, Soshila 6 Ramayah1,2, Aleksei A. Korzhenkov 4 , Ilya V. Kublanov 3 and Peter N. Golyshin 1,2 7 1School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW, UK, [email protected]; 8 [email protected]; [email protected] 9 2Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor, LL57 2UW, UK 10 3Winogradsky Institute of Microbiology, Research Center for Biotechnology, Russian Academy of Sciences, 11 Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312, Russia, [email protected]; 12 [email protected]; [email protected] 13 4National Research Center "Kurchatov Institute", Akademika Kurchatova sq., 1, Moscow, 123182, Russia, 14 [email protected]; 15 Correspondence: Tel.: +44 1248 388607; Fax: +44 1248 382569; [email protected] 16 17 Abstract: “Candidatus Micrarchaeota” are widely distributed in acidic environments, however, their 18 cultivability and our understanding of their interactions with potential hosts are very limited. Their 19 habitats were so far attributed with acidic sites, soils, peats, freshwater systems and hypersaline 20 mats. Using cultivation and culture-independent approaches (16S rRNA gene clonal libraries, high- 21 throughput amplicon sequencing of V3-V4 region of 16S rRNA genes) we surveyed the occurrence 22 of these archaea in geothermal areas on Kamchatka Peninsula and Kunashir Island and assessed 23 their taxonomic diversity in relation with another type of low-pH environment, acid mine drainage 24 stream (Wales, UK). We detected “Ca. Micrarchaeota” in thermophilic heterotrophic enrichment 25 cultures of Kunashir and Kamchatka that appeared as two different phylotypes, namely “Ca. 26 Mancarchaeum acidiphilum”-, and ARMAN-2-related, alongside their potential hosts, 27 Cuniculiplasma spp. and other Thermoplasmatales archaea without defined taxonomic position. These 28 clusters of “Ca. Micrarchaeota” together with three other groups were also present in mesophilic 29 acid mine drainage community. Present work expands our knowledge on the diversity of “Ca. 30 Micrarchaeota” in thermophilic and mesophilic acidic environments, suggests cultivability patterns 31 of acidophilic archaea and establishes potential links between low-abundance species of 32 thermophilic “Ca. Micrarchaeota” and certain Thermoplasmatales, such as Cuniculiplasma spp. in situ. 33 Keywords: “Ca. Mancarchaeum acidiphilum”; ARMAN-2; “Ca. Micrarchaeota”; DPANN 34 superphylum; Thermoplasmatales; Cuniculiplasma; Acidic environments; Acid Mine Drainage sites; 35 Terrestrial hot springs 36 37 1. Introduction 38 Archaeal lineages represented in relatively low abundance in communities are still largely 39 underexplored, which leaves many gaps in our knowledge regarding their distribution patterns, 40 specific roles in the environment and interconnection with other community members. One example 41 of these organisms, often referred to as microbial “dark matter”, is a group of Archaeal Richmond 42 Mine Acidophilic Nanoorganisms (ARMAN), firstly detected in acid mine drainage systems of Iron 43 Mountain (CA, USA) and later confirmed to be widely distributed in numerous low pH settings as 44 well as in areas with neutral pH values 1, 2, 3, 4, 5, 6, 7, 8. Two names for candidate phyla were proposed Genes 2019, 10, x; doi: FOR PEER REVIEW www.mdpi.com/journal/genes Genes 2019, 10, x FOR PEER REVIEW 2 of 13 45 for these lineages with significantly reduced genome sizes, namely “Ca. Micrarchaeota” and “Ca. 46 Parvarchaeota” 1. 47 Based on the phylogenetic analysis of three concatenated protein sets these groups are placed 48 divergently 9. “Ca. Micrarchaeota” were shown to cluster with “Ca. Diapherotrites” and “Ca. 49 Parvarchaeota” to be associated with Nanoarchaeota 9. Both groups are included into a tentative 50 DPANN supercluster, incorporating also Nanoarchaeota and Candidate phyla “Aenigmarchaeota”, 51 “Altiarchaeota”, “Diapherotrites”, “Huberarchaeota”, “Nanohaloarchaeota”, “Pacearchaeota”, and 52 “Woesearchaeota” 10, 11. This group comprises organisms with reduced genome sizes and limited 53 metabolic potential, small dimensions of cells and reliance on symbiotic/mutualistic/commensalism- 54 based interactions with other species for some of these archaea 10. However, cultivated DPANN 55 members were only recorded for Nanoarchaeota and “Ca. Micrarchaeota”. Cultured thermophilic 56 associations between Nanoarchaeota and Crenarchaeota described and studied so far, are noteworthy 57 to mention. The very first example of a co-culture was Nanoarchaeum equitans and Ignicoccus hospitalis 58 12, followed by an association between Nanoobsidianus stetteri and Sulfolobales Acd1 13 a “Candidatus 59 Nanopusillus acidilobi” and Acidilobus sp. 7a 14 and finally by a stable co-culture of “Candidatus 60 Nanoclepta minutus” and Zestosphaera tikiterensis (representing a new member of the family 61 Desulfurococacceae) 15. For mesophilic and extremely acidophilic “Ca. Micrarchaeota” two cultured 62 associations were documented: “Ca. Mancarchaeum acidiphilum” Mia14 with Cuniculuplasma 63 divulgatum PM4 6 and “Ca. Micrarchaeota”, ARMAN-1-related organism in a co-culture with 64 consortium of two archaea (Cuniculiplasma divulgatum-like and another archaeon of the order 65 Thermoplasmatales) together with a fungus16. Nevertheless, the distribution of “Ca. Micrarchaeota” in 66 metagenomic data occurs at a global scale 8. 67 Estimation of phylogenetic diversity for “Ca. Micrarchaeota” 8 based on 16S rRNA gene sequence 68 identity cut-offs for genus (94.5 %) and family (86.5%) proposed by Yarza et al.17 suggested clustering 69 into 12 genera and 2 families. Relative abundance of “Ca. Micrarchaeota” in environmental 70 microbiomes was shown to constitute <1% in 17 of 25 genomes reconstructed from metagenomic 71 data, although an abundance of one assembly variant represented by FK_Sed_bin12_4 (Fankou AMD 72 sediment, China) was as high as 5.3-21.3% in certain subsamples 8. Two acidophilic biofilm 73 communities of Iron Mountain (CA, USA) accounted for ~7% “Ca. Micrarchaeota”/ ARMAN-2 reads 74 2. It was reported 8 that “Ca. Micrarchaeota” in comparison to “Ca. Parvarchaeota” possess wider 75 distribution patterns since signatures of this group were detected not in acidic settings only but in 76 soils, peats, freshwater systems and hypersaline mats. It may imply that “Ca. Micrarchaeota” 77 demonstrate enhanced resistance to selective pressure, which enables their spreading and genome 78 stability. Altogether, connection with Thermoplasmatales was predicted for 16 “Ca. Micrarchaeota” and 79 for 13 “Ca. Parvarchaeota” species 8. 80 Analysis of 39 ARMAN-related genomes with different levels of completeness from various 81 emplacements pointed at a certain variability in genome sizes (0.64-1.08 Mb) and predicted their 82 potential involvement in carbon, nitrogen and iron cycles 8. Furthermore, genomic analysis suggested 83 microaerophilic and anaerobic lifestyles for “Ca. Micrarchaeota”, based on aerobic respiratory chain, 84 fermentation potential and presence of cytochrome bd-II encoding genes 8. However, experimental 85 confirmations of certain predicted physiological traits are still due 6, 8, 16. 86 To understand further patterns of distribution and phylogenetic variance of these archaea in 87 particular environments, we focused our study on two types of acidic environments. 88 We surveyed the presence of “Ca. Micrarchaeota” -related sequences in acidic geothermal areas 89 via establishment of enrichment cultures with samples from terrestrial hydrothermal vents of 90 Kamchatka Peninsula and Kunashir Islands
Load more

Recommended publications
  • S41564-017-0083-5.Pdf
    CORRECTION https://doi.org/10.1038/s41564-017-0083-5 Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Donovan H. Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J. Woodcroft, Paul N. Evans, Philip Hugenholtz* and Gene W. Tyson* Correction to: Nature Microbiology https://doi.org/10.1038/s41564-017-0012-7 (2017); published online 11 September 2017. In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metage- nome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc. Natl Acad. Sci. USA 107, 8806–8811; 2010). The ARMAN-4 and ARMAN-5 MAGs are estimated to be 68.0% and 76.7% complete with 3.3% and 5.6% contamination, respectively, based on the archaeal-specific marker sets of CheckM. The 11 Parvarchaeota genomes identified in our study were obtained from different Richmond Mine metagenomes, but are highly similar to the ARMAN-4 (ANI of ~99.7%) and ARMAN-5 (ANI of ~99.6%) MAGs. The highest-quality uncultivated bacteria and archaea (UBA) MAGs with similarity to ARMAN-4 and ARMAN-5 are 82.5% and 83.3% complete with 0.9% and 1.9% contamination, respectively. The Parvarchaeota rep- resents only 0.23% of the archaeal genome tree and addition of the ARMAN-4 and ARMAN-5 MAGs do not change the conclusions of this Article, but do impact the phylogenetic gain for this phylum.
    [Show full text]
  • Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma Divulgatum
    microorganisms Article Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum Rafael Bargiela 1 , Karin Lanthaler 1,2, Colin M. Potter 1,2 , Manuel Ferrer 3 , Alexander F. Yakunin 1,2, Bela Paizs 1,2, Peter N. Golyshin 1,2 and Olga V. Golyshina 1,2,* 1 School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; [email protected] (R.B.); [email protected] (K.L.); [email protected] (C.M.P.); [email protected] (A.F.Y.); [email protected] (B.P.); [email protected] (P.N.G.) 2 Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK 3 Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain; [email protected] * Correspondence: [email protected]; Tel.: +44-1248-388607; Fax: +44-1248-382569 Received: 27 April 2020; Accepted: 15 May 2020; Published: 19 May 2020 Abstract: The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation.
    [Show full text]
  • And Femtogram-Input DNA Libraries for Microscale Metagenomics
    Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics Christian Rinke1, Serene Low1, Ben J. Woodcroft1, Jean-Baptiste Raina2, Adam Skarshewski1, Xuyen H. Le1, Margaret K. Butler1, Roman Stocker3, Justin Seymour2, Gene W. Tyson1,4 and Philip Hugenholtz1,5 1 Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia 2 Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia 3 Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland 4 Advanced Water Management Centre, University of Queensland, Brisbane, QLD, Australia 5 Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia ABSTRACT High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The Submitted 14 June 2016 main technical issues with the low input libraries were a greater potential for Accepted 24 August 2016 Published 22 September 2016 contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a Corresponding authors Christian Rinke, lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition [email protected] fidelity, and the inclusion of negative controls to identify reagent-specific Philip Hugenholtz, contaminants.
    [Show full text]
  • Unexpected Host Dependency of Antarctic Nanohaloarchaeota
    Unexpected host dependency of Antarctic Nanohaloarchaeota Joshua N. Hamma, Susanne Erdmanna,1, Emiley A. Eloe-Fadroshb, Allegra Angelonia, Ling Zhongc, Christopher Brownleed, Timothy J. Williamsa, Kirston Bartone, Shaun Carswelle, Martin A. Smithe,f, Sarah Brazendalea,2, Alyce M. Hancocka,3, Michelle A. Allena, Mark J. Rafteryc, and Ricardo Cavicchiolia,4 aSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; bDepartment of Energy, Joint Genome Institute, Walnut Creek, CA 94598; cBioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW 2052, Australia; dBiological Resources Imaging Laboratory, University of New South Wales, Sydney, NSW 2052, Australia; eKinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; and fSt. Vincent’s Clinical School, University of New South Wales, Sydney, Darlinghurst, NSW 2010, Australia Edited by Norman R. Pace, University of Colorado Boulder, Boulder, CO, and approved June 5, 2019 (received for review March 25, 2019) In hypersaline environments, Nanohaloarchaeota (Diapherotrites, acidilobi (<0.3-μmdiameter,∼0.6 Mb) (11), Candidatus Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarch- Parvarchaeum acidophilus (0.6-μm diameter, <1 Mb) (12), and aeota [DPANN] superphylum) are thought to be free-living Candidatus Mancarchaeum acidophilum (∼1-μmdiameter,∼1Mb) microorganisms. We report cultivation of 2 strains of Antarctic (13), have all been shown to possess small cell and genome sizes; Nanohaloarchaeota and show that they require the haloarchaeon these are traits that have been proposed to be typical of all Halorubrum lacusprofundi for growth. By performing growth us- DPANN phyla (3). Due to their reduced genomic capacity, these ing enrichments and fluorescence-activated cell sorting, we dem- – onstrated successful cultivation of Candidatus Nanohaloarchaeum Nanoarchaeota and Pavarchaeota require cell cell contact with – antarcticus, purification of Ca.
    [Show full text]
  • Archaea and the Origin of Eukaryotes
    REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative.
    [Show full text]
  • Metagenomic Insights Into the Metabolism and Ecologic Functions of the Widespread
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.12.946848; this version posted February 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Metagenomic insights into the metabolism and ecologic functions of the widespread 2 DPANN archaea from deep-sea hydrothermal vents 3 Ruining Cai1,2,3,4, Jing Zhang1,2,3,4, Rui Liu1,2,4, Chaomin Sun1,2,4* 4 1Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of 5 Sciences, Qingdao, China 6 2Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine 7 Science and Technology, Qingdao, China 8 3College of earth science, University of Chinese Academy of Sciences, Beijing, China 9 4Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China 10 11 * Corresponding author 12 Chaomin Sun Tel.: +86 532 82898857; fax: +86 532 82898857. 13 E-mail address: [email protected] 14 15 Keywords: DPANN, hydrothermal vents, metabolism, ecology significance 16 Running title: Metagenomic insights into DPANN 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.12.946848; this version posted February 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 18 ABSTRACT 19 Due to the particularity of metabolism and the importance of ecological roles, the archaea living 20 in deep-sea hydrothermal system always attract great attention. Included, the DPANN 21 superphylum archaea, which are massive radiation of organisms, distribute widely in 22 hydrothermal environment, but their metabolism and ecology remain largely unknown.
    [Show full text]
  • The Novel Extremely Acidophilic, Cell-Wall-Deficient Archaeon Cuniculiplasma Divulgatum Gen
    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 332–340 DOI 10.1099/ijsem.0.000725 The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales Olga V. Golyshina,1 Heinrich Lu¨nsdorf,2 Ilya V. Kublanov,3 Nadine I. Goldenstein,4 Kai-Uwe Hinrichs4 and Peter N. Golyshin1 Correspondence 1School of Biological Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK Olga V. Golyshina 2Central Unit of Microscopy, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, [email protected] Braunschweig 38124, Germany 3Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia 4MARUM – Center for Marine Environmental Sciences, University of Bremen, Leobener Str., Bremen 28359, Germany Two novel cell-wall-less, acidophilic, mesophilic, organotrophic and facultatively anaerobic archaeal strains were isolated from acidic streamers formed on the surfaces of copper-ore- containing sulfidic deposits in south-west Spain and North Wales, UK. Cells of the strains varied from 0.1 to 2 mm in size and were pleomorphic, with a tendency to form filamentous structures. The optimal pH and temperature for growth for both strains were 1.0–1.2 and 2 37–40 8C, with the optimal substrates for growth being beef extract (3 g l 1) for strain S5T and 2 beef extract with tryptone (3 and 1 g l 1, respectively) for strain PM4. The lipid composition was dominated by intact polar lipids consisting of a glycerol dibiphytanyl glycerol tetraether (GDGT) core attached to predominantly glycosidic polar headgroups.
    [Show full text]
  • UNIVERSITY of CALIFORNIA Los Angeles Discovery of a Novel
    UNIVERSITY OF CALIFORNIA Los Angeles Discovery of a Novel Mevalonate Pathway and its Potential to Produce Biofuels A dissertation submitted in the partial satisfaction of the requirements for the degree Doctor of Philosophy in Biochemistry, Molecular and Structural Biology by Jeffrey Michael Vinokur 2017 © Copyright by Jeffrey Michael Vinokur 2017 ABSTRACT OF THE DISSERTATION Discovery of a Novel Mevalonate Pathway and its Potential to Produce Biofuels by Jeffrey Michael Vinokur Doctor of Philosophy in Biochemistry, Molecular and Structural Biology University of California, Los Angeles, 2017 Professor James U. Bowie, Chair The mevalonate pathway is present in eukaryotes, archaea, and some bacteria, where it produces the building blocks used to make cholesterol, vitamin A, natural rubber, and over 25,000 other biomolecules collectively called isoprenoids. Here we report the discovery of a novel mevalonate pathway in archaea. We describe the identification and characterization of three new enzymes, two new metabolites, a novel structure, and a new mechanism. We also show that the new pathway is unique to extreme acidophiles that grow below pH 2. We attempt to re-design three mevalonate pathway enzymes (mevalonate 3-kinase, mevalonate 5- phosphate decarboxylase, and mevalonate 5-pyrophosphate decarboxylase) to produce isoprenol through the decarboxylation of mevalonate. Isoprenol is a 5-carbon alcohol that has a higher energy density than ethanol. Both rational design and random mutagenesis strategies are described. Finally, we report a new method for the soluble expression of recombinant proteins in E. coli through the co-expression of archaeal thermosomes and prefoldins. ii The dissertation of Jeffrey Michael Vinokur is approved. Todd O.
    [Show full text]
  • Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar De Huasco, Chile
    microorganisms Communication Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile Yoanna Eissler 1,* , Cristina Dorador 2,3 , Brandon Kieft 4 , Verónica Molina 5,6 and Martha Hengst 3,7 1 Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso 2360102, Chile 2 Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Avenida Universidad de Antofagasta s/n, Antofagasta 1240000, Chile; [email protected] 3 Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7), Santiago 8320000, Chile; [email protected] 4 Lab of Dr. Steven Hallam, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; [email protected] 5 Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso 2340000, Chile; [email protected] 6 HUB Ambiental UPLA, Universidad de Playa Ancha, Avenida Leopoldo Carvallo 200, Playa Ancha, Valparaíso 2340000, Chile 7 Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Av Angamos 0610, Antofagasta 1270709, Chile * Correspondence: [email protected]; Tel.: +56-32-250-8063 Received: 24 June 2020; Accepted: 3 July 2020; Published: 20 July 2020 Abstract: Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis.
    [Show full text]
  • Biosynthetic Capacity, Metabolic Variety and Unusual Biology in the CPR and DPANN Radiations Cindy J
    Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations Cindy J. Castelle 1,2, Christopher T. Brown 1, Karthik Anantharaman 1,5, Alexander J. Probst 1,6, Raven H. Huang3 and Jillian F. Banfield 1,2,4* 1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 2Chan Zuckerberg Biohub, San Francisco, CA, USA. 3Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA. 4Department of Environmental Science, Policy, and Management, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 5Department of Bacteriology, University of WisconsinMadison, Madison, WI, USA. 6Department of Chemistry, Biofilm Center, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany. *e-mail: [email protected] Abstract Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth’s environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living.
    [Show full text]
  • An Adaptation to Life in Acid Through a Novel Mevalonate Pathway
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by eScholarship - University of California UCLA UCLA Previously Published Works Title An Adaptation To Life In Acid Through A Novel Mevalonate Pathway. Permalink https://escholarship.org/uc/item/1j33k1mj Journal Scientific reports, 6(1) ISSN 2045-2322 Authors Vinokur, Jeffrey M Cummins, Matthew C Korman, Tyler P et al. Publication Date 2016-12-22 DOI 10.1038/srep39737 Peer reviewed eScholarship.org Powered by the California Digital Library University of California www.nature.com/scientificreports OPEN An Adaptation To Life In Acid Through A Novel Mevalonate Pathway Received: 18 August 2016 Jeffrey M. Vinokur*, Matthew C. Cummins*, Tyler P. Korman & James U. Bowie Accepted: 28 November 2016 Extreme acidophiles are capable of growth at pH values near zero. Sustaining life in acidic environments Published: 22 December 2016 requires extensive adaptations of membranes, proton pumps, and DNA repair mechanisms. Here we describe an adaptation of a core biochemical pathway, the mevalonate pathway, in extreme acidophiles. Two previously known mevalonate pathways involve ATP dependent decarboxylation of either mevalonate 5-phosphate or mevalonate 5-pyrophosphate, in which a single enzyme carries out two essential steps: (1) phosphorylation of the mevalonate moiety at the 3-OH position and (2) subsequent decarboxylation. We now demonstrate that in extreme acidophiles, decarboxylation is carried out by two separate steps: previously identified enzymes generate mevalonate 3,5-bisphosphate and a new decarboxylase we describe here, mevalonate 3,5-bisphosphate decarboxylase, produces isopentenyl phosphate. Why use two enzymes in acidophiles when one enzyme provides both functionalities in all other organisms examined to date? We find that at low pH, the dual function enzyme, mevalonate 5-phosphate decarboxylase is unable to carry out the first phosphorylation step, yet retains its ability to perform decarboxylation.
    [Show full text]
  • Microbial Metagenomic Analysis of Paddy Field Soil of Bario, the Kelabit Highland of Sarawak
    MICROBIAL METAGENOMIC ANALYSIS OF PADDY FIELD SOIL OF BARIO, THE KELABIT HIGHLAND OF SARAWAK SUPANG LAU MEI LING FACULTY OF SCIENCE UNIVERSITY OF MALAYA UniversityKUALA LUMPUR of Malaya 2018 MICROBIAL METAGENOMIC ANALYSIS OF PADDY FIELD SOIL OF BARIO, THE KELABIT HIGHLAND OF SARAWAK SUPANG LAU MEI LING THESIS SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE INSTITUTE OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE UNIVERSITY OF MALAYA UniversityKUALA LUMPUR of Malaya 2018 UNIVERSITY OF MALAYA ORIGINAL LITERARY WORK DECLARATION Name of Candidate: Supang Lau Mei Ling Matric No: SGR110123 Name of Degree: Master of Science Title of Thesis: Microbial Metagenomic Analysis of Paddy Field Soil of Bario, The Kelabit Highland of Sarawak Field of Study: Microbiology (Biology & Biochemistry) I do solemnly and sincerely declare that: (1) I am the sole author/writer of this Work; (2) This Work is original; (3) Any use of any work in which copyright exists was done by way of fair dealing and for permitted purposes and any excerpt or extract from, or reference to or reproduction of any copyright work has been disclosed expressly and sufficiently and the title of the Work and its authorship have been acknowledged in this Work; (4) I do not have any actual knowledge nor do I ought reasonably to know that the making of this work constitutes an infringement of any copyright work; (5) I hereby assign all and every rights in the copyright to this Work to the University of Malaya (“UM”), who henceforth shall be owner of the copyright in this Work and that any reproduction or use in any form or by any means whatsoever is prohibited without the written consent of UM having been first had and obtained; (6) I am fully aware that if in the course of making this Work I have infringed any copyright whether intentionally or otherwise, I may be subject to legal action or any other action as may be determined by UM.
    [Show full text]