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Citation for Study 11394

Citation title: "Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification".

Study name: "Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification".

This study is part of submission 11384 (Status: Published).

Citation

Mcdonald T.R., Dietrich F., & Lutzoni F. 2011. Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification. Molecular Biology and Evolution, .

Authors

• Mcdonald T.R.
• Dietrich F.
• Lutzoni F.

Abstract

The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rhesus factor proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: the AMT family as defined here exhibits vertical gene transfer (i.e. standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers. These ancient horizontal gene transfer events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This re-circumscription of the AMTP family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule, because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with ammonium transporters and ammonia permeases forming two distinct and possibly monophyletic groups.

Keywords

ammonium transporter, fungal and plant evolution, horizontal gene transfer, lichen symbiosis, methylammonium permease

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S11394
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref19617,
  	 author = {Tami R McDonald and Fred  Dietrich and Francois  Lutzoni},
  	 title = {Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification},
  	 year = {2011},
  	 keywords = {ammonium transporter, fungal and plant evolution, horizontal gene transfer, lichen symbiosis, methylammonium permease},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Biology and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane.  Although it has been established that the Rhesus factor proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear.  Here we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family.  Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP and Rh).  We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: the AMT family as defined here exhibits vertical gene transfer (i.e. standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers.  These ancient horizontal gene transfer events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi.  This re-circumscription of the AMTP family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule, because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade.  The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with ammonium transporters and ammonia permeases forming two distinct and possibly monophyletic groups. }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 19617
  AU  - McDonald,Tami R
  AU  - Dietrich,Fred 
  AU  - Lutzoni,Francois 
  T1  - Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification
  PY  - 2011
  KW  - ammonium transporter
  KW  - fungal and plant evolution
  KW  - horizontal gene transfer
  KW  - lichen symbiosis
  KW  - methylammonium permease
  UR  - http://dx.doi.org/
  N2  - The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane.  Although it has been established that the Rhesus factor proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear.  Here we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family.  Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP and Rh).  We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: the AMT family as defined here exhibits vertical gene transfer (i.e. standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers.  These ancient horizontal gene transfer events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi.  This re-circumscription of the AMTP family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule, because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade.  The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with ammonium transporters and ammonia permeases forming two distinct and possibly monophyletic groups. 
  L3  - 
  JF  - Molecular Biology and Evolution
  VL  - 
  IS  - 
  ER  -