Evolution
- 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.
- 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
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.
- 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
- Natural mutations in IFITM3 modulate post‐translational regulation and toggle antiviral specificity
- Alex A Compton (alex.compton{at}pasteur.fr)*,1,
- Nicolas Roy1,
- Françoise Porrot1,
- Anne Billet1,
- Nicoletta Casartelli1,
- Jacob S Yount2,
- Chen Liang3 and
- Olivier Schwartz (schwartz{at}pasteur.fr)*,1,4,5
- 1Virus & Immunity Unit, Institut Pasteur, Paris, France
- 2Department of Microbial Infection & Immunity, The Ohio State University, Columbus, OH, USA
- 3Lady Davis Institute, McGill University, Montreal, QC, Canada
- 4CNRS‐URA 3015, Paris, France
- 5Vaccine Research Institute, Creteil, France
- ↵*
Corresponding author. Tel: +33 1456 88576; E‐mail: alex.compton{at}pasteur.fr
Corresponding author. Tel: +33 1456 88353; E‐mail: schwartz{at}pasteur.fr
By analyzing synthetic and naturally occurring mutations of interferon‐induced transmembrane 3 (IFITM3), this study provides novel insight into the antiviral mechanisms at play during HIV‐1 infection. The authors further show that the diversification of IFITM3 genes during evolution may boost the antiviral coverage of host cells and provides selective functional advantages.
Synopsis
By analyzing synthetic and naturally occurring mutations of interferon‐induced transmembrane 3 (IFITM3), this study provides novel insight into the antiviral mechanisms at play during HIV‐1 infection. The authors further show that the diversification of IFITM3 genes during evolution may boost the antiviral coverage of host cells and provides selective functional advantages.
Amino‐terminal mutations of IFITM3 result in an enhanced incorporation into HIV‐1 virions and promote the inhibition of virus–cell fusion.
Two adjacent regulatory motifs that control ubiquitination and endocytosis of IFITM3 regulate its potency and antiviral specificity.
IFITM3 shows recurrent gene duplication and divergence during primate evolution.
EMBO Reports (2016) 17: 1657–1671
- Received May 24, 2016.
- Revision received August 3, 2016.
- Accepted August 3, 2016.
- © 2016 The Authors
- Life's arrow: the Epistemic Singularity
- Ladislav Kováč, Professor of Biochemistry (kovacl{at}fns.uniba.sk)1
The evolution of the universe follows a one‐way path towards increasing complexity, driven by exploiting energy gradients. With life and knowledge continuously evolving, the universe is headed towards a singularity where knowledge itself will reach its apex.
- © 2016 The Author
- Do you speak chemistry?Small chemical compounds represent the evolutionary oldest form of communication between organisms
Small chemical compounds represent the evolutionary oldest form of communication between organisms
Plants have evolved sophisticated chemical communication to sense and warn each other of predators, and to fight back. Understanding the details of this chemical language could aid the search for natural and sustainable methods to increase yields in agriculture.
- © 2016 The Authors
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