Complete Sequence of Succinamopine Ti-Plasmid pTiEU6 Reveals Its Evolutionary Relatedness with Nopaline-Type Ti-Plasmids

Genome Biol Evol. 2019 Sep 1;11(9):2480-2491. doi: 10.1093/gbe/evz173.

Abstract

Agrobacterium tumefaciens is the etiological agent of plant crown gall disease, which is induced by the delivery of a set of oncogenic genes into plant cells from its tumor-inducing (Ti) plasmid. Here we present the first complete sequence of a succinamopine-type Ti-plasmid. Plasmid pTiEU6 is comprised of 176,375 bp with an overall GC content of 56.1% and 195 putative protein-coding sequences could be identified. This Ti-plasmid is most closely related to nopaline-type Ti-plasmids. It contains a single T-region which is somewhat smaller than that of the nopaline-type Ti-plasmids and in which the gene for nopaline synthesis is replaced by a gene (sus) for succinamopine synthesis. Also in pTiEU6 the nopaline catabolic genes are replaced by genes for succinamopine catabolism. In order to trace the evolutionary origin of pTiEU6, we sequenced six nopaline Ti-plasmids to enlarge the scope for comparison to this class of plasmids. Average nucleotide identity analysis revealed that pTiEU6 was most closely related to nopaline Ti-plasmids pTiT37 and pTiSAKURA. In line with this traces of several transposable elements were present in all the nopaline Ti plasmids and in pTiEU6, but one specific transposable element insertion, that of a copy of IS1182, was present at the same site only in pTiEU6, pTiT37, and pTiSAKURA, but not in the other Ti plasmids. This suggests that pTiEU6 evolved after diversification of nopaline Ti-plasmids by DNA recombination between a pTiT37-like nopaline Ti-plasmid and another plasmid, thus introducing amongst others new catabolic genes matching a new opine synthase gene for succinamopine synthesis.

Keywords: Agrobacterium tumefaciens; Ti-plasmid; nopaline; pTiEU6; succinamopine.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agrobacterium tumefaciens / genetics*
  • Agrobacterium tumefaciens / metabolism*
  • Amino Acids / metabolism*
  • Arginine / analogs & derivatives*
  • Arginine / metabolism
  • DNA Transposable Elements
  • DNA, Bacterial
  • Evolution, Molecular
  • Phylogeny
  • Plant Tumor-Inducing Plasmids / genetics*
  • Plant Tumors / microbiology
  • Sequence Analysis, DNA

Substances

  • Amino Acids
  • DNA Transposable Elements
  • DNA, Bacterial
  • T-DNA
  • nopaline
  • succinamopine
  • Arginine