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Santana de Carvalho D, Trovatti Uetanabaro AP, Kato RB, Aburjaile FF, Jaiswal AK, Profeta R, De Oliveira Carvalho RD, Tiwar S, Cybelle Pinto Gomide A, Almeida Costa E, Kukharenko O, Orlovska I, Podolich O, Reva O, Ramos PIP, De Carvalho Azevedo VA, Brenig B, Andrade BS, de Vera JPP, Kozyrovska NO, Barh D, Góes-Neto A. The Space-Exposed Kombucha Microbial Community Member Komagataeibacter oboediens Showed Only Minor Changes in Its Genome After Reactivation on Earth. Front Microbiol 2022; 13:782175. [PMID: 35369445 PMCID: PMC8970348 DOI: 10.3389/fmicb.2022.782175] [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: 09/23/2021] [Accepted: 02/01/2022] [Indexed: 11/23/2022] Open
Abstract
Komagataeibacter is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the K. oboediens genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of K. oboediens under extraterrestrial conditions during a long time. Our results suggest that the genomes of K. oboediens IMBG180 (ground sample) and K. oboediens IMBG185 (space-exposed) are remarkably similar in topology, genomic islands, transposases, prion-like proteins, and number of plasmids and CRISPR-Cas cassettes. Nonetheless, there was a difference in the length of plasmids and the location of cas genes. A small difference was observed in the number of protein coding genes. Despite these differences, they do not affect any genetic metabolic profile of the cellulose synthesis, nitrogen-fixation, hopanoid lipids biosynthesis, and stress-related pathways. Minor changes are only observed in central carbohydrate and energy metabolism pathways gene numbers or sequence completeness. Altogether, these findings suggest that K. oboediens maintains its genome stability and functionality in KMC exposed to the space environment most probably due to the protective role of the KMC biofilm. Furthermore, due to its unaffected metabolic pathways, this bacterial species may also retain some promising potential for space applications.
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Affiliation(s)
- Daniel Santana de Carvalho
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Paula Trovatti Uetanabaro
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Postgraduate Program in Biology and Biotechnology of Microorganisms, Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Brazil
| | - Rodrigo Bentes Kato
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávia Figueira Aburjaile
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Profeta
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Dias De Oliveira Carvalho
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwar
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anne Cybelle Pinto Gomide
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eduardo Almeida Costa
- Computational Biology and Biotechnological Information Management Center (NBCGIB), State University of Santa Cruz, Ilhéus, Brazil
| | - Olga Kukharenko
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Iryna Orlovska
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Pablo Ivan P. Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Institute Gonçalo Moniz, Oswaldo Cruz Foundation (FIOCRUZ-Bahia), Salvador, Brazil
| | - Vasco Ariston De Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Brazil
| | - Jean-Pierre P. de Vera
- German Aerospace Center (DLR) Berlin, Institute of Planetary Research, Planetary Laboratories, Astrobiological Laboratories, Berlin, Germany
| | | | - Debmalya Barh
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Aristóteles Góes-Neto
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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