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Armstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, Kang JT, Redondo SA, Prost S, Barsh G, Kaelin C, Phalke S, Chugani A, Gilbert M, Miquelle D, Zachariah A, Borthakur U, Reddy A, Louis E, Ryder OA, Jhala YV, Petrov D, Excoffier L, Hadly E, Ramakrishnan U. Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection. Mol Biol Evol 2021; 38:2366-2379. [PMID: 33592092 PMCID: PMC8136513 DOI: 10.1093/molbev/msab032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world’s wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.
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Affiliation(s)
| | - Anubhab Khan
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA.,End2End Genomics, LLC, Davis, CA, USA
| | - Alexandre Gouy
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gili Greenbaum
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Ecology, Evolution & Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexandre Thiéry
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jonathan T Kang
- Department of Biology, Stanford University, Stanford, CA, USA.,Genome Institute of Singapore, A*STAR, Singapore
| | | | - Stefan Prost
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Gregory Barsh
- Hudsonalpha Institute, Hunstville, AL, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | | | - Martin Gilbert
- Wildlife Conservation Society, Russia Program, New York, NY, USA.,College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Dale Miquelle
- Wildlife Conservation Society, Russia Program, New York, NY, USA
| | | | | | - Anuradha Reddy
- Laboratory for Conservation of Endangered Species, CCMB, Hyderabad, India
| | - Edward Louis
- Department of Genetics, Omaha Zoo, Omaha, NE, USA
| | - Oliver A Ryder
- San Diego Zoo, Institute for Conservation Research, Escondido, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Elizabeth Hadly
- Wildlife Conservation Society, Russia Program, New York, NY, USA
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Rodríguez-Herrero V, Peris A, Camacho M, Bautista V, Esclapez J, Bonete MJ. Novel Glutamate-Putrescine Ligase Activity in Haloferax mediterranei: A New Function for glnA-2 Gene. Biomolecules 2021; 11:biom11081156. [PMID: 34439822 PMCID: PMC8394153 DOI: 10.3390/biom11081156] [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: 06/30/2021] [Revised: 07/25/2021] [Accepted: 07/31/2021] [Indexed: 02/06/2023] Open
Abstract
The genome of the halophilic archaea Haloferax mediterranei contains three ORFs that show homology with glutamine synthetase (GS) (glnA-1, glnA-2, and glnA-3). Previous studies have focused on the role of GlnA-1, suggesting that proteins GlnA-2 and GlnA-3 could play a different role to that of GS. Glutamine synthetase (EC 6.3.1.2) belongs to the class of ligases, including 20 subclasses of other different enzymes, such as aspartate–ammonia ligase (EC 6.3.1.1), glutamate–ethylamine ligase (EC 6.3.1.6), and glutamate–putrescine ligase (EC 6.3.1.11). The reaction catalyzed by glutamate–putrescine ligase is comparable to the reaction catalyzed by glutamine synthetase (GS). Both enzymes can bind a glutamate molecule to an amino group: ammonium (GS) or putrescine (glutamate–putrescine ligase). In addition, they present the characteristic catalytic domain of GS, showing significant similarities in their structure. Although these proteins are annotated as GS, the bioinformatics and experimental results obtained in this work indicate that the GlnA-2 protein (HFX_1688) is a glutamate–putrescine ligase, involved in polyamine catabolism. The most significant results are those related to glutamate–putrescine ligase’s activity and the analysis of the transcriptional and translational expression of the glnA-2 gene in the presence of different nitrogen sources. This work confirms a new metabolic pathway in the Archaea domain which extends the knowledge regarding the utilization of alternative nitrogen sources in this domain.
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Affiliation(s)
- Verónica Rodríguez-Herrero
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Arnau Peris
- Institute for Integrative Systems Biology, I2SysBio, Campus Burjassot, University of Valencia-CSIC, 46908 Valencia, Spain;
| | - Mónica Camacho
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Vanesa Bautista
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Julia Esclapez
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
- Correspondence: (J.E.); (M.-J.B.); Tel.: +34-965-903-880 (J.E. & M.-J.B.)
| | - María-José Bonete
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
- Correspondence: (J.E.); (M.-J.B.); Tel.: +34-965-903-880 (J.E. & M.-J.B.)
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3
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Krysenko S, Matthews A, Busche T, Bera A, Wohlleben W. Poly- and Monoamine Metabolism in Streptomyces coelicolor: The New Role of Glutamine Synthetase-Like Enzymes in the Survival under Environmental Stress. Microb Physiol 2021; 31:233-247. [PMID: 34044403 DOI: 10.1159/000516644] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/17/2021] [Indexed: 11/19/2022]
Abstract
Soil bacteria from the genus Streptomyces, phylum Actinobacteria, feature a complex metabolism and diverse adaptations to environmental stress. These characteristics are consequences of variable nutrition availability in the soil and allow survival under changing nitrogen conditions. Streptomyces coelicolor is a model organism for Actinobacteria and is able to use nitrogen from a variety of sources including unusual compounds originating from the decomposition of dead plant and animal material, such as polyamines or monoamines (like ethanolamine). Assimilation of nitrogen from these sources in S. coelicolor remains largely unstudied. Using microbiological, biochemical and in silico approaches, it was recently possible to postulate polyamine and monoamine (ethanolamine) utilization pathways in S. coelicolor. Glutamine synthetase-like enzymes (GS-like) play a central role in these pathways. Extensive studies have revealed that these enzymes are able to detoxify polyamines or monoamines and allow the survival of S. coelicolor in soil containing an excess of these compounds. On the other hand, at low concentrations, polyamines and monoamines can be utilized as nitrogen and carbon sources. It has been demonstrated that the first step in poly-/monoamine assimilation is catalyzed by GlnA3 (a γ-glutamylpolyamine synthetase) and GlnA4 (a γ-glutamylethanolamide synthetase), respectively. First insights into the regulation of polyamine and ethanolamine metabolism have revealed that the expression of the glnA3 and the glnA4 gene are controlled on the transcriptional level.
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Affiliation(s)
- Sergii Krysenko
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Arne Matthews
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Agnieszka Bera
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
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4
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Dutilh BE, Huynen MA, Bruno WJ, Snel B. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 2004; 58:527-39. [PMID: 15170256 DOI: 10.1007/s00239-003-2575-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2003] [Accepted: 11/12/2003] [Indexed: 11/25/2022]
Abstract
Phylogenetic trees based on gene repertoires are remarkably similar to the current consensus of life history. Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss. Here we test this argument, by filtering out as noise those orthologous groups that have an inconsistent phylogenetic distribution, using two independent methods. The resulting phylogenies do indeed contain small but significant improvements. More importantly, we find that the majority of orthologous groups contain some phylogenetic signal and that the resulting phylogeny is the only detectable signal present in the gene distribution across genomes. Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.
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Affiliation(s)
- Bas E Dutilh
- Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, University of Nijmegen, Nijmegen, The Netherlands.
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Doolittle WF, Boucher Y, Nesbø CL, Douady CJ, Andersson JO, Roger AJ. How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos Trans R Soc Lond B Biol Sci 2003; 358:39-57; discussion 57-8. [PMID: 12594917 PMCID: PMC1693099 DOI: 10.1098/rstb.2002.1185] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.
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Affiliation(s)
- W F Doolittle
- Genome Atlantic, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada.
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Gupta RS, Bustard K, Falah M, Singh D. Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes. J Bacteriol 1997; 179:345-57. [PMID: 8990285 PMCID: PMC178703 DOI: 10.1128/jb.179.2.345-357.1997] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The 70-kDa heat shock protein (hsp70) sequences define one of the most conserved proteins known to date. The hsp70 genes from Deinococcus proteolyticus and Thermomicrobium roseum, which were chosen as representatives of two of the most deeply branching divisions in the 16S rRNA trees, were cloned and sequenced. hsp70 from both these species as well as Thermus aquaticus contained a large insert in the N-terminal quadrant, which has been observed before as a unique characteristic of gram-negative eubacteria and eukaryotes and is not found in any gram-positive bacteria or archaebacteria. Phylogenetic analysis of hsp70 sequences shows that all of the gram-negative eubacterial species examined to date (which includes members from the genera Deinococcus and Thermus, green nonsulfur bacteria, cyanobacteria, chlamydiae, spirochetes, and alpha-, beta-, and gamma-subdivisions of proteobacteria) form a monophyletic group (excluding eukaryotic homologs which are derived from this group via endosybitic means) strongly supported by the bootstrap scores. A closer affinity of the Deinococcus and Thermus species to the cyanobacteria than to the other available gram-negative sequences is also observed in the present work. In the hsp7O trees, D. proteolyticus and T. aquaticus were found to be the most deeply branching species within the gram-negative eubacteria. The hsp70 homologs from gram-positive bacteria branched separately from gram-negative bacteria and exhibited a closer relationship to and shared sequence signatures with the archaebacteria. A polyphyletic branching of archaebacteria within gram-positive bacteria is strongly favored by different phylogenetic methods. These observations differ from the rRNA-based phylogenies where both gram-negative and gram-positive species are indicated to be polyphyletic. While it remains unclear whether parts of the genome may have variant evolutionary histories, these results call into question the general validity of the currently favored three-domain dogma.
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Affiliation(s)
- R S Gupta
- Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
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