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Sato T, Utashima S(H, Yoshii Y, Hirata K, Kanda S, Onoda Y, Jin JQ, Xiao S, Minami R, Fukushima H, Noguchi A, Manabe Y, Fukase K, Atomi H. A non-carboxylating pentose bisphosphate pathway in halophilic archaea. Commun Biol 2022; 5:1290. [PMID: 36434094 PMCID: PMC9700705 DOI: 10.1038/s42003-022-04247-2] [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: 07/28/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.
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Affiliation(s)
- Takaaki Sato
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan ,grid.258799.80000 0004 0372 2033Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
| | - Sanae (Hodo) Utashima
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Yoshii
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kosuke Hirata
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Shuichiro Kanda
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yushi Onoda
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Jian-qiang Jin
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Suyi Xiao
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryoko Minami
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hikaru Fukushima
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ayako Noguchi
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yoshiyuki Manabe
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan ,grid.136593.b0000 0004 0373 3971Forefront Research Center, Osaka University, Osaka, Japan
| | - Koichi Fukase
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan ,grid.136593.b0000 0004 0373 3971Forefront Research Center, Osaka University, Osaka, Japan
| | - Haruyuki Atomi
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan ,grid.258799.80000 0004 0372 2033Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
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Perez MF, Saona LA, Farías ME, Poehlein A, Meinhardt F, Daniel R, Dib JR. Assessment of the plasmidome of an extremophilic microbial community from the Diamante Lake, Argentina. Sci Rep 2021; 11:21459. [PMID: 34728656 PMCID: PMC8563766 DOI: 10.1038/s41598-021-00753-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/15/2021] [Indexed: 12/02/2022] Open
Abstract
Diamante Lake located at 4589 m.a.s.l. in the Andean Puna constitutes an extreme environment. It is exposed to multiple extreme conditions such as an unusually high concentration of arsenic (over 300 mg L-1) and low oxygen pressure. Microorganisms thriving in the lake display specific genotypes that facilitate survival, which include at least a multitude of plasmid-encoded resistance traits. Hence, the genetic information provided by the plasmids essentially contributes to understand adaptation to different stressors. Though plasmids from cultivable organisms have already been analyzed to the sequence level, the impact of the entire plasmid-borne genetic information on such microbial ecosystem is not known. This study aims at assessing the plasmidome from Diamante Lake, which facilitates the identification of potential hosts and prediction of gene functions as well as the ecological impact of mobile genetic elements. The deep-sequencing analysis revealed a large fraction of previously unknown DNA sequences of which the majority encoded putative proteins of unknown function. Remarkably, functions related to the oxidative stress response, DNA repair, as well as arsenic- and antibiotic resistances were annotated. Additionally, all necessary capacities related to plasmid replication, mobilization and maintenance were detected. Sequences characteristic for megaplasmids and other already known plasmid-associated genes were identified as well. The study highlights the potential of the deep-sequencing approach specifically targeting plasmid populations as it allows to evaluate the ecological impact of plasmids from (cultivable and non-cultivable) microorganisms, thereby contributing to the understanding of the distribution of resistance factors within an extremophilic microbial community.
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Affiliation(s)
- María Florencia Perez
- grid.423606.50000 0001 1945 2152Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Tucumán Argentina
| | - Luis Alberto Saona
- grid.423606.50000 0001 1945 2152Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Tucumán Argentina
| | - María Eugenia Farías
- grid.423606.50000 0001 1945 2152Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Tucumán Argentina
| | - Anja Poehlein
- grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Friedhelm Meinhardt
- grid.5949.10000 0001 2172 9288Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms Universität Münster, Münster, Germany
| | - Rolf Daniel
- grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Julián Rafael Dib
- grid.423606.50000 0001 1945 2152Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Tucumán Argentina ,grid.108162.c0000000121496664Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán Argentina
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Zhang WY, Hu J, Pan J, Sun C, Wu M, Xu XW. Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine. Stand Genomic Sci 2015; 10:124. [PMID: 26664653 PMCID: PMC4675023 DOI: 10.1186/s40793-015-0113-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 11/24/2015] [Indexed: 12/13/2022] Open
Abstract
Halopiger salifodinae strain KCY07-B2(T), isolated from a salt mine in Kuche county, Xinjiang province, China, belongs to the family Halobacteriaceae. It is a strictly aerobic, pleomorphic, rod-shaped, Gram-negative and extremely halophilic archaeon. In this work, we report the features of the type strain KCY07-B2(T), together with the draft genome sequence and annotation. The draft genome sequence is composed of 83 contigs for 4,350,718 bp with 65.41 % G + C content and contains 4204 protein-coding genes and 50 rRNA genes.
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Affiliation(s)
- Wei-Yan Zhang
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Jing Hu
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Jie Pan
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Cong Sun
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Min Wu
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Xue-Wei Xu
- />Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012 P. R. China
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Williams D, Gogarten JP, Papke RT. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol 2013; 4:1223-44. [PMID: 23160063 PMCID: PMC3542582 DOI: 10.1093/gbe/evs098] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In vitro studies of the haloarchaeal genus Haloferax have demonstrated
their ability to frequently exchange DNA between species, whereas rates of homologous
recombination estimated from natural populations in the genus Halorubrum
are high enough to maintain random association of alleles between five loci. To quantify
the effects of gene transfer and recombination of commonly held (relaxed core) genes
during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history
of 21 genomes representing all major groups. Using a novel algorithm and a concatenated
ribosomal protein phylogeny as a reference, we created a directed horizontal genetic
transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed
that 90% of testable HGTs were by direct homologous replacement, rather than
nonhomologous integration followed by a loss. Network analysis revealed an inverse
log-linear relationship between HGT frequency and ribosomal protein evolutionary distance
that is maintained across the deepest divergences in Halobacteria. We use this
mathematical relationship to estimate the total transfers and amino acid substitutions
delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core
genes of each genome, we conservatively estimate that 11–20% of their
evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer
and homologous recombination of relaxed core genes between members of the class
Halobacteria disrupts the coevolution of genes; however, the generation of new
combinations of divergent but functionally related genes may lead to adaptive phenotypes
not available through cumulative mutations and recombination within a single
population.
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Affiliation(s)
- David Williams
- Department of Molecular and Cell Biology, University of Connecticut, CT, USA
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Dassarma S, Capes MD, Karan R, Dassarma P. Amino acid substitutions in cold-adapted proteins from Halorubrum lacusprofundi, an extremely halophilic microbe from antarctica. PLoS One 2013; 8:e58587. [PMID: 23536799 PMCID: PMC3594186 DOI: 10.1371/journal.pone.0058587] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/05/2013] [Indexed: 11/18/2022] Open
Abstract
The halophilic Archaeon Halorubrum lacusprofundi, isolated from the perennially cold and hypersaline Deep Lake in Antarctica, was recently sequenced and compared to 12 Haloarchaea from temperate climates by comparative genomics. Amino acid substitutions for 604 H. lacusprofundi proteins belonging to conserved haloarchaeal orthologous groups (cHOGs) were determined and found to occur at 7.85% of positions invariant in proteins from mesophilic Haloarchaea. The following substitutions were observed most frequently: (a) glutamic acid with aspartic acid or alanine; (b) small polar residues with other small polar or non-polar amino acids; (c) small non-polar residues with other small non-polar residues; (d) aromatic residues, especially tryptophan, with other aromatic residues; and (e) some larger polar residues with other similar residues. Amino acid substitutions for a cold-active H. lacusprofundi β-galactosidase were then examined in the context of a homology modeled structure at residues invariant in homologous enzymes from mesophilic Haloarchaea. Similar substitutions were observed as in the genome-wide approach, with the surface accessible regions of β-galactosidase displaying reduced acidity and increased hydrophobicity, and internal regions displaying mainly subtle changes among smaller non-polar and polar residues. These findings are consistent with H. lacusprofundi proteins displaying amino acid substitutions that increase structural flexibility and protein function at low temperature. We discuss the likely mechanisms of protein adaptation to a cold, hypersaline environment on Earth, with possible relevance to life elsewhere.
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Affiliation(s)
- Shiladitya Dassarma
- Department of Microbiology and Immunology, and Institute of Marine and Environmental Technology, University of Maryland, Baltimore, Maryland, United States of America.
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Lynch EA, Langille MGI, Darling A, Wilbanks EG, Haltiner C, Shao KSY, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One 2012; 7:e41389. [PMID: 22848480 PMCID: PMC3404096 DOI: 10.1371/journal.pone.0041389] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/20/2012] [Indexed: 12/13/2022] Open
Abstract
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ∼20×coverage and assembled to an average of 50 contigs (range 5 scaffolds-168 contigs). Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera. Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen. Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.
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Affiliation(s)
- Erin A. Lynch
- Microbiology Graduate Group, University of California Davis, Davis, California, United States of America
| | | | - Aaron Darling
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Elizabeth G. Wilbanks
- Microbiology Graduate Group, University of California Davis, Davis, California, United States of America
| | - Caitlin Haltiner
- Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
- Department of Forensic Science, University of California Davis, Davis, California, United States of America
| | - Katie S. Y. Shao
- Davis Senior High School, Davis, California, United States of America
| | - Michael O. Starr
- Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | - Clotilde Teiling
- 454 Life Sciences, a Roche Company, Branford, Connecticut, United States of America
| | | | - Robert A. Edwards
- Department of Computer Science, San Diego State University, San Diego, California, United States of America
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Jonathan A. Eisen
- Microbiology Graduate Group, University of California Davis, Davis, California, United States of America
- Genome Center, University of California Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
- * E-mail: (MTF); (JAE)
| | - Marc T. Facciotti
- Microbiology Graduate Group, University of California Davis, Davis, California, United States of America
- Genome Center, University of California Davis, Davis, California, United States of America
- Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
- * E-mail: (MTF); (JAE)
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