Genome Mining of Plant NPFs Reveals Varying Conservation of Signature Motifs Associated With the Mechanism of Transport

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This article focuses on four structural features of nitrate peptide families/proton-coupled oligopeptide transporters/peptide transporters that have been shown by structural and functional studies to be essential to proton-coupled symport transport.

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17 p.

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Longo, Antonella; Miles, Nicholas W. & Dickstein, Rebecca December 4, 2018.

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This article focuses on four structural features of nitrate peptide families/proton-coupled oligopeptide transporters/peptide transporters that have been shown by structural and functional studies to be essential to proton-coupled symport transport.

Physical Description

17 p.

Notes

Abstract: Nitrogen is essential for all living species and may be taken up from the environment
in different forms like nitrate or peptides. In plants, members of a transporter family
named NPFs transport nitrate and peptides across biological membranes. NPFs are
phylogenetically related to a family of peptide transporters (PTRs) or proton-coupled
oligopeptide transporters (POTs) that are evolutionarily conserved in all organisms
except in Archaea. POTs are present in low numbers in bacteria, algae and animals.
NPFs have expanded in plants and evolved to transport a wide range of substrates
including phytohormones and glucosinolates. Functional studies have shown that most
NPFs, like POTs, operate as symporters with simultaneous inwardly directed movement
of protons. Here we focus on four structural features of NPFs/POTs/PTRs that have
been shown by structural and functional studies to be essential to proton-coupled
symport transport. The first two features are implicated in proton binding and transport:
a conserved motif named ExxER/K, located in the first transmembrane helix (TMH1)
and a D/E residue in TMH7 that has been observed in some bacterial and algal
transporters. The third and fourth features are two inter-helical salt bridges between
residues on TMH1 and TMH7 or TMH4 and TMH10. To understand if the mechanism of
transport is conserved in NPFs with the expansion to novel substrates, we collected
NPFs sequences from 42 plant genomes. Sequence alignment revealed that the
ExxER/K motif is not strictly conserved and its conservation level is different in the NPF
subfamilies. The proton binding site on TMH7 is missing in all NPFs with the exception
of two NPFs from moss. The two moss NPFs also have a positively charged amino acid
on TMH1 that can form the salt bridge with the TMH7 negative residue. None of the
other NPFs we examined harbor residues that can form the TMH1–TMH7 salt bridge.
In contrast, the amino acids required to form the TMH4–TMH10 salt bridge are highly
conserved in NPFs, with some exceptions. These results support the need for further
biochemical and structural studies of individual NPFs for a better understanding of the
transport mechanism in this family of transporters.

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  • Frontiers in Plant Science, 2018. Lausanne, Switzerland: Frontiers Research Foundation

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  • Publication Title: Frontiers in Plant Science
  • Volume: 9
  • Page Start: 1
  • Page End: 17
  • Peer Reviewed: Yes

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  • December 4, 2018

Submitted Date

  • July 12, 2018

Accepted Date

  • October 26, 2018

Added to The UNT Digital Library

  • Dec. 19, 2018, 12:07 p.m.

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Longo, Antonella; Miles, Nicholas W. & Dickstein, Rebecca. Genome Mining of Plant NPFs Reveals Varying Conservation of Signature Motifs Associated With the Mechanism of Transport, article, December 4, 2018; Lausanne, Switzerland. (digital.library.unt.edu/ark:/67531/metadc1393831/: accessed January 24, 2019), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT College of Arts and Sciences.