Evolution
- Viral taxonomyThe effect of metagenomics on understanding the diversity and evolution of viruses
The effect of metagenomics on understanding the diversity and evolution of viruses
- Philip Hunter, Freelance journalist (ph{at}philiphunter.com)1
The advent of next‐generation sequencing and metagenomics is challenging viral taxonomy to define and characterize viruses along with providing novel insights into the vast diversity of viruses and their evolution.
- © 2017 The Author
- The greatest kinetochore show on earth
Coordinated chromosome duplication and segregation is key to the existence of every organism on our planet. In eukaryotes, sophisticated protein assemblies called kinetochores are universally required for chromosome segregation, but their protein composition can diverge across the eukaryotic tree of life. In this issue of EMBO Reports, van Hooff et al [1] shed light on kinetochore evolution with a comprehensive study of kinetochore composition across 90 phylogenetically diverse eukaryotes. They show that certain kinetochore complexes have taken distinct evolutionary paths to arrive at a strikingly broad compositional array in present‐day eukaryotes, providing exciting new insights into the origins, function, and flexibility of eukaryotic kinetochores.
See also: JJE van Hooff et al (September 2017)
A study in this issue provides a comprehensive evolutionary analysis of kinetochore composition across phylogenetically diverse eukaryotes using comparative genomics, providing new insights into the origins, function, and flexibility of eukaryotic kinetochores.
- © 2017 The Authors
- Loss of the canonical spindle orientation function in the Pins/LGN homolog AGS3
- Mehdi Saadaoui (mehdi.saadaoui{at}pasteur.fr)*,1,5,
- Daijiro Konno2,
- Karine Loulier3,
- Rosette Goiame1,
- Vaibhav Jadhav4,
- Marina Mapelli4,
- Fumio Matsuzaki2 and
- Xavier Morin (xavier.morin{at}ens.fr)*,1
- 1Cell Division and Neurogenesis Group, Ecole Normale Supérieure, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), PSL Research University, Paris, France
- 2Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, Chuo‐ku, Kobe, Japan
- 3UPMC Université Paris 06, Sorbonne Universités, CNRS, Inserm, Institut de la Vision, Paris, France
- 4Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- 5Present Address: Morphogenesis in Higher Vertebrates, Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- ↵*
Corresponding author. Tel: +33 1 45 68 81 54; E‐mail: mehdi.saadaoui{at}pasteur.fr
Corresponding author. Tel: +33 1 44 32 37 29; E‐mail: xavier.morin{at}ens.fr
Using planar divisions in the vertebrate neuroepithelium as a model, the authors uncover multiple differences that contribute to the functional divergence of AGS3 and LGN, the two vertebrate homologs of Drosophila Pins.
Synopsis
Using planar divisions in the vertebrate neuroepithelium as a model, the authors explore the proposed conservation of a “spindle orientation” function between LGN and AGS3, two homologs of the Drosophila G‐protein regulator Pins. The study uncovers multiple differences that contribute to the functional divergence of AGS3.
LGN localizes at the cell cortex in different cell types where spindle orientation relies on its function, while AGS3 remains cytoplasmic.
A systematic dissection shows that despite extensive sequence and structure conservation, each of the three TPR, Linker and GPR modules has diverged functionally between LGN and AGS3.
Despite their shared role in spindle orientation in fly and vertebrates, Pins and LGN are not functionally interchangeable in vivo.
EMBO Reports (2017) 18: 1509–1520
- Received July 12, 2016.
- Revision received May 14, 2017.
- Accepted May 19, 2017.
- © 2017 The Authors
- Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics
- Jolien JE van Hooff1,2,3,
- Eelco Tromer1,2,
- Leny M van Wijk2,
- Berend Snel (b.snel{at}uu.nl)*,2,† and
- Geert JPL Kops (g.kops{at}hubrecht.eu)*,1,3,4,†
- 1Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- 2Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands
- 3Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- 4Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht, The Netherlands
- ↵*
Corresponding author. Tel: +31 302538102; E‐mail: b.snel{at}uu.nl
Corresponding author. Tel: +31 302121907; E‐mail: g.kops{at}hubrecht.eu
↵† These authors contributed equally to this work as senior authors
During cell division, the kinetochore connects centromeric DNA to spindle microtubules, which is essential for eukaryotic chromosome segregation. This study uncovers and describes the evolution and diversity of eukaryotic kinetochores by comparative genomics.
Synopsis
During cell division, the kinetochore connects centromeric DNA to spindle microtubules, which is essential for eukaryotic chromosome segregation. This study uncovers and describes the evolution and diversity of eukaryotic kinetochores by comparative genomics.
The majority of kinetochore proteins were present in the last eukaryotic common ancestor (LECA).
Divergent kinetochores emerged post‐LECA through gene loss, duplication, displacement, sequence divergence and innovations.
The diverse functions of various kinetochore proteins is elucidated by examining their co‐evolution.
EMBO Reports (2017) 18: 1559–1571
- Received February 18, 2017.
- Revision received May 12, 2017.
- Accepted May 17, 2017.
- © 2017 The Authors. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
- Enzyme sub‐functionalization driven by regulation
The emergence of functional novelties during protein evolution has puzzled scientists for many years. Most proposed models focus on repeated duplication‐divergence cycles, but the entanglement of selection pressures acting on the control of transcriptional and enzymatic activity, for example, by metabolites, has not been addressed so far. In this issue of EMBO Reports, Noda‐Garcia et al [1] describe two glutamate dehydrogenase paralogs from Bacillus subtilis with very similar sequences and under two distinct modes of activity control. The functional divergence of these two enzymes during evolution is driven by an interlinked combination of differences between their enzymatic properties and their transcriptional regulation. This article thus illuminates another level of complexity in molecular evolution that may help understand the hitherto unexplained co‐existence of paralogous genes that at first sight appear to be functionally redundant.
See also: L Noda‐Garcia et al (July 2017)
A study in this issue shows how the co‐evolution of transcriptional and enzyme activity regulation contributes to the functional divergence of two Bacilli glutamate dehydrogenase paralogs.
- © 2017 The Authors
- Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation
- Lianet Noda‐Garcia1,
- Maria Luisa Romero Romero1,
- Liam M Longo1,
- Ilana Kolodkin‐Gal2 and
- Dan S Tawfik (dan.tawfik{at}weizmann.ac.il)*,1
- 1Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- ↵*Corresponding author. Tel: +972 8 934 3637; E‐mail: dan.tawfik{at}weizmann.ac.il
Bacilli have two glutamate dehydrogenase paralogues. Regulation has diverged from transcriptional control in one paralogue (RocG) to enzyme control in the other (GudB), thus creating incompatibility upon swaps of enzymes and regulatory regions.
Synopsis
Bacilli have two glutamate dehydrogenase paralogues. Regulation has diverged from transcriptional control in one paralogue (RocG) to enzyme control in the other (GudB), thus creating incompatibility upon swaps of enzymes and regulatory regions (promoter/terminator).
Swapping enzymes and regulatory regions of the Bacilli glutamate dehydrogenase paralogues reveals coevolution of transcription and enzyme regulation.
Coevolution of transcriptional and enzymatic regulation underlies paralogue‐specific spatio‐temporal control.
The Bacilli glutamate dehydrogenases are regulated via oligomer assembly.
EMBO Reports (2017) 18: 1139–1149
- Received January 25, 2017.
- Revision received March 23, 2017.
- Accepted March 27, 2017.
- © 2017 The Authors
- Feel the beatMusic exploits our brain's ability to predict and the dopamine‐reward system to instill pleasure
Music exploits our brain's ability to predict and the dopamine‐reward system to instill pleasure
- Katrin Weigmann, Freelance journalist (mail{at}k-weigmann.de)1
Music unfolds over time and music perception has much to do with making temporal predictions. But how does the brain interpret upcoming auditory events, and why are humans better at it than most other animals?
- © 2017 The Author
- An incoherent feed‐forward loop mediates robustness and tunability in a plant immune network
- Akira Mine1,2,
- Tatsuya Nobori1,†,
- Maria C Salazar‐Rondon1,†,
- Thomas M Winkelmüller1,
- Shajahan Anver1,
- Dieter Becker1 and
- Kenichi Tsuda (tsuda{at}mpipz.mpg.de)*,1
- 1Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- 2Center for Gene Research, Nagoya University, Chikusa‐Ku Nagoya, Japan
- ↵*Corresponding author. Tel: +49 221 5062 302; E‐mail: tsuda{at}mpipz.mpg.de
↵† These authors contributed equally to this work
This study identifies an incoherent type‐4 feed‐forward loop (I4‐FFL) consisting of jasmonate, PAD4, and EDS5 in Arabidopsis. This I4‐FFL ensures robust and tunable accumulation of salicylic acid during immune activation through flagellin sensing.
Synopsis
This study identifies an incoherent type‐4 feed‐forward loop (I4‐FFL) consisting of jasmonate, PAD4, and EDS5 in Arabidopsis. This I4‐FFL ensures robust and tunable accumulation of salicylic acid during immune activation through flagellin sensing.
Jasmonate (JA) induces EDS5 expression while repressing the positive EDS5 regulator PAD4.
MYC transcription factors mediate gene regulation by JA.
JA mitigates salicylic acid (SA) accumulation and bacterial resistance through PAD4 inhibition.
Upon perturbation of PAD4, JA supports SA accumulation and bacterial resistance via the regulation of EDS5.
EMBO Reports (2017) 18: 464–476
- Received July 13, 2016.
- Revision received November 9, 2016.
- Accepted December 8, 2016.
- © 2017 The Authors
- When nuclear‐encoded proteins and mitochondrial RNAs do not get along, species split apart
The emergence of barriers to reproduction between two populations is one of the most important features of speciation. Among the mechanisms of reproductive isolation are incompatible interactions between gene products of the parental species that reduce the fitness of hybrid individuals. The accumulation of such incompatibilities is described by the Bateson–Dobzhansky–Muller model (BDM) [1] that provides a framework for understanding how genes can coevolve to stay compatible within populations and become incompatible between populations. Only a handful of such loci have been identified and characterized at the molecular level. In this issue of EMBO Reports, Jhuang and colleagues [2] show that BDM incompatibilities have accumulated between a nuclear‐encoded gene and a mitochondrial ribosomal RNA between two yeast species.
See also: H‐Y Jhuang et al (January 2017)
Mitochondrial and nuclear genomes coevolve in eukaryotes. Jhuang and collaborators found a mismatched pair of mitochondrial and nuclear genes between two yeast species that strongly impairs mitochondrial function and contributes to reproductive isolation.
- © 2016 The Authors
- Mitochondrial–nuclear co‐evolution leads to hybrid incompatibility through pentatricopeptide repeat proteins
- 1Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- 2Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- 3Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- ↵*Corresponding author. Tel: +886 2 26519574; E‐mail: jleu{at}imb.sinica.edu.tw
Mitochondrial–nuclear incompatibility can cause reproductive isolation between species. This study shows that fast co‐evolution between flexible PPR proteins and their mitochondrial RNA targets represents a common driving force in the development of hybrid incompatibility.
Synopsis
Mitochondrial–nuclear incompatibility can cause reproductive isolation between species. This study shows that fast co‐evolution between flexible PPR proteins and their mitochondrial RNA targets represents a common driving force in the development of hybrid incompatibility.
Fast evolution of a PPR protein Ccm1 leads to symmetric incompatibility between two closely related yeast species.
The CCM1 incompatibility causes reduced levels of mitochondrial 15S rRNA and protein translation.
The CCM1 incompatibility can be rescued by mutations in the PPR motifs or mitochondrial DNA.
Two‐thirds of yeast PPR proteins have evolved mitochondrial–nuclear incompatibility among the Saccharomyces sensu stricto species.
EMBO Reports (2017) 18: 87–101
- Received September 7, 2016.
- Revision received October 9, 2016.
- Accepted October 21, 2016.
- © 2016 The Authors
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