Evolutionary and Functional Analysis of Membrane-Bound NAC Transcription Factor Genes in Soybean

Abstract

Functional divergence is thought to be an important evolutionary driving force for the retention of duplicate genes. We reconstructed the evolutionary history of soybean (Glycine max) membrane-bound NAC transcription factor (NTL) genes. NTLs are thought to be components of stress signaling and unique in their requirement for proteolytic cleavage to free them from the membrane. Most of the 15 GmNTL genes appear to have evolved under strong purifying selection. By analyzing the phylogenetic tree and gene synteny, we identified seven duplicate gene pairs generated by the latest whole-genome duplication. The members of each pair were shown to have variously diverged at the transcriptional (organ specificity and responsiveness to stress), posttranscriptional (alternative splicing), and protein (proteolysis-mediated membrane release and transactivation activity) levels. The dormant (full-length protein) and active (protein without a transmembrane motif) forms of one pair of duplicated gene products (GmNTL1/GmNLT11) were each separately constitutively expressed in Arabidopsis (Arabidopsis thaliana). The heteroexpression of active but not dormant forms of these proteins caused improved tolerance to abiotic stresses, suggesting that membrane release was required for their functionality. Arabidopsis carrying the dormant form of GmNTL1 was more tolerant to hydrogen peroxide, which induces its membrane release. Tolerance was not increased in the line carrying dormant GmNTL11, which was not released by hydrogen peroxide treatment. Thus, NTL-release pattern changes may cause phenotypic divergence. It was concluded that a variety of functional divergences contributed to the retention of these GmNTL duplicates.

A GmSIN1/GmNCED3s/GmRbohBs Feed-Forward Loop Acts as a Signal Amplifier That Regulates Root Growth in Soybean Exposed to Salt Stress

“…The cDNA synthesis, RT-qPCR, and data analysis were conducted as described previously by Li et al (2016). Gene-specific primers (sequences given in Supplemental Table 4) were designed using Beacon Designer v7.…”

“…This generated the p35S pro :GmSIN1-GFP construct. The Arabidopsis protoplast transformation and GFP signal observation were conducted as described previously (Li et al, 2016). The p35S pro :GFP (Li et al, 2011) transgenic protoplasts were used as localization controls for expression in the cytoplasm/nucleus.…”

NTL8 Regulates Trichome Formation in Arabidopsis by Directly Activating R3 MYB Genes TRY and TCL1

“…3E). However, these three NTLs are more closely related to two membrane-associated NAC transcription factors from soybean (Li et al, 2016) and two from tomato, rather than NTL2 (Fig. 3E).…”

Peer Review #1 of "Genome-wide characterization and expression analysis of soybean trihelix gene family (v0.1)"

“…The calculation of gene expression levels followed the 2 -ΔΔCT method described by Livak and Schmittgen (2001). GmActin (Glyma.18G290800) was used as the internal reference gene for the submergence, JA, SA and ACC treatment (Song et al, 2018), and GmELF1b (Glyma.02G276600) was used as the internal reference gene for the salinity and ABA treatments (Yim et al, 2015;Li et al, 2016). The primers of the selected trihelix genes used for qRT-PCR are listed in Table S9.…”