Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa

PLoS One. 2019 Sep 23;14(9):e0222940. doi: 10.1371/journal.pone.0222940. eCollection 2019.

Abstract

Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using RNA-seq data we have analyzed the expression patterns of certain TF families, predicted protein-protein interactions, and analyzed evolutionary trajectories to elucidate their possible roles in salt tolerance. We have detected the top differentially expressed (DE) transcription factor families (MYB, CAMTA, MADS-box and bZIP) that show the most pronounced response to salinity. The majority of DE genes in the four aforementioned TF families cluster together on TF phylogenetic trees, which suggests common evolutionary origins and trajectories. This research represents the first comprehensive TF study of a leaf succulent halophyte including their evolutionary relationships with TFs in other halophyte and salt-senstive plants. These findings provide a foundation for understanding the function of salt-responsive transcription factors in salt tolerance and associated gene regulation in plants.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Chenopodiaceae / genetics*
  • Chenopodiaceae / metabolism
  • Evolution, Molecular
  • Expressed Sequence Tags
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gene Ontology
  • Phylogeny
  • Plant Proteins / classification
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Salt-Tolerant Plants / genetics*
  • Salt-Tolerant Plants / metabolism
  • Sequence Homology, Amino Acid
  • Transcription Factors / classification
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • Plant Proteins
  • Transcription Factors

Grants and funding

This research has been supported by a grant from the Pakistan-US Science and Technology Cooperation Program (http://sites.nationalacademies.org/PGA/Pakistan/index.htm; Phase 4 project jointly funded by the US Department of State, National Academy of Sciences, and Higher Education Commission of Pakistan to BLN, BG and MAK), by the Department of Microbiology and Molecular Biology at Brigham Young University (to BLN), Brigham Young University (grant number 2014 to JDA), and by the Office of Research and Creative Activities, Brigham Young University (grant number 2016 to BLN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.