A TALE-inspired computational screen for proteins that contain approximate tandem repeats

PLoS One. 2017 Jun 15;12(6):e0179173. doi: 10.1371/journal.pone.0179173. eCollection 2017.

Abstract

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

MeSH terms

  • Bacteria / genetics*
  • Bacterial Proteins / genetics*
  • Computer Simulation
  • Fungal Proteins / genetics*
  • Fungi / genetics*
  • Sequence Analysis, Protein / methods*
  • Tandem Repeat Sequences / genetics*

Substances

  • Bacterial Proteins
  • Fungal Proteins

Grants and funding

The research was supported by National Science Centre funds (grant No. UMO-2011/02/A/NZ1/00052) issued to MB [https://www.ncn.gov.pl/]. Work of JK was partially supported by the grant (Pol-Nor/207085/65/2013) from Norway Grant through the Polish-Norwegian Research Programme operated by the National Centre for Research and Development (NCBR) [http://www.ncbr.gov.pl/]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.