1
|
Belilla J, Moreira D, Jardillier L, Reboul G, Benzerara K, López-García JM, Bertolino P, López-Archilla AI, López-García P. Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area. Nat Ecol Evol 2019; 3:1552-1561. [PMID: 31666740 PMCID: PMC6837875 DOI: 10.1038/s41559-019-1005-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/16/2019] [Indexed: 11/13/2022]
Abstract
Microbial life has adapted to various individual extreme conditions; yet, organisms simultaneously adapted to very low pH, high salt and high temperature are unknown. We combined environmental 16S/18S rRNA-gene metabarcoding, cultural approaches, fluorescence-activated cell sorting, scanning electron microscopy and chemical analyses to study samples along such unique polyextreme gradients in the Dallol-Danakil area (Ethiopia). We identify two physicochemical barriers to life in the presence of surface liquid water defined by: i) high chaotropicity-low water activity in Mg2+/Ca2+-dominated brines and ii) hyperacidity-salt combinations (pH~0/NaCl-dominated salt-saturation). When detected, life was dominated by highly diverse ultrasmall archaea widely distributed across phyla with and without previously known halophilic members. We hypothesize that high cytoplasmic K+-level was an original archaeal adaptation to hyperthermophily, subsequently exapted during multiple transitions to extreme halophily. We detect active silica encrustment/fossilization of cells but also abiotic biomorphs of varied chemistry. Our work helps circumscribing habitability and calls for cautionary interpretations of morphological biosignatures on Earth and beyond.
Collapse
Affiliation(s)
- Jodie Belilla
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Ludwig Jardillier
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guillaume Reboul
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | | | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France.
| |
Collapse
|
3
|
Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA, Maywood ES, Hastings MH, Baliga NS, Merrow M, Millar AJ, Johnson CH, Kyriacou CP, O’Neill JS, Reddy AB. Peroxiredoxins are conserved markers of circadian rhythms. Nature 2012; 485:459-64. [PMID: 22622569 PMCID: PMC3398137 DOI: 10.1038/nature11088] [Citation(s) in RCA: 622] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 03/26/2012] [Indexed: 11/16/2022]
Abstract
Cellular life emerged ∼3.7 billion years ago. With scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the Earth's rotation. The advantage conferred on organisms that anticipate such environmental cycles has driven the evolution of endogenous circadian rhythms that tune internal physiology to external conditions. The molecular phylogeny of mechanisms driving these rhythms has been difficult to dissect because identified clock genes and proteins are not conserved across the domains of life: Bacteria, Archaea and Eukaryota. Here we show that oxidation-reduction cycles of peroxiredoxin proteins constitute a universal marker for circadian rhythms in all domains of life, by characterizing their oscillations in a variety of model organisms. Furthermore, we explore the interconnectivity between these metabolic cycles and transcription-translation feedback loops of the clockwork in each system. Our results suggest an intimate co-evolution of cellular timekeeping with redox homeostatic mechanisms after the Great Oxidation Event ∼2.5 billion years ago.
Collapse
Affiliation(s)
- Rachel S. Edgar
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | - Edward W. Green
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Yuwei Zhao
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Gerben van Ooijen
- Synthetic and Systems Biology (SynthSys), Mayfield Road, EH9 3JD, Edinburgh, UK
| | - Maria Olmedo
- Department of Molecular Chronobiology, Center for Life Sciences, University of Groningen, The Netherlands
| | - Ximing Qin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Yao Xu
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Min Pan
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Utham K. Valekunja
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | - Kevin A. Feeney
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | | | | | - Nitin S. Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Martha Merrow
- Department of Molecular Chronobiology, Center for Life Sciences, University of Groningen, The Netherlands
| | - Andrew J. Millar
- Synthetic and Systems Biology (SynthSys), Mayfield Road, EH9 3JD, Edinburgh, UK
- School of Biological Sciences, University of Edinburgh, Mayfield Road, EH9 3JR, Edinburgh, UK
| | - Carl H. Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | | | - John S. O’Neill
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | - Akhilesh B. Reddy
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| |
Collapse
|
4
|
Biochemical characteristics of the novel haloalkane dehalogenase DatA, isolated from the plant pathogen Agrobacterium tumefaciens C58. Appl Environ Microbiol 2010; 77:1881-4. [PMID: 21193677 DOI: 10.1128/aem.02109-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the biochemical characterization of a novel haloalkane dehalogenase, DatA, isolated from the plant pathogen Agrobacterium tumefaciens C58. DatA possesses a peculiar pair of halide-stabilizing residues, Asn-Tyr, which have not been reported to play this role in other known haloalkane dehalogenases. DatA has a number of other unique characteristics, including substrate-dependent and cooperative kinetics, a dimeric structure, and excellent enantioselectivity toward racemic mixtures of chiral brominated alkanes and esters.
Collapse
|