Limits...
Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily.

Wu N, Zhu Y, Song W, Li Y, Yan Y, Hu Y - BMC Plant Biol. (2014)

Bottom Line: All of tandem duplicated genes were found in group II except one cluster of rice, indicating that tandem duplication greatly promoted the expansion of group II.These results strongly indicated that these groups were experiencing higher positive selection pressure.In short, the results above provide a solid foundation for further functional dissection of the GRAS gene superfamily.

View Article: PubMed Central - PubMed

ABSTRACT

Background: GRAS proteins belong to a plant transcription factor family that is involved with multifarious roles in plants. Although previous studies of this protein family have been reported for Arabidopsis, rice, Chinese cabbage and other species, investigation of expansion patterns and evolutionary rate on the basis of comparative genomics in different species remains inadequate.

Results: A total of 289 GRAS genes were identified in Arabidopsis, B. distachyon, rice, soybean, S. moellendorffii, and P. patens and were grouped into seven subfamilies, supported by the similarity of their exon-intron patterns and structural motifs. All of tandem duplicated genes were found in group II except one cluster of rice, indicating that tandem duplication greatly promoted the expansion of group II. Furthermore, segment duplications were mainly found in the soybean genome, whereas no single expansion pattern dominated in other plant species indicating that GRAS genes from these five species might be subject to a more complex evolutionary mechanism. Interestingly, branch-site model analyses of positive selection showed that a number of sites were positively selected under foreground branches I and V. These results strongly indicated that these groups were experiencing higher positive selection pressure. Meanwhile, the site-specific model revealed that the GRAS genes were under strong positive selection in P. patens. DIVERGE v2.0 was used to detect critical amino acid sites, and the results showed that the shifted evolutionary rate was mainly attributed to the functional divergence between the GRAS genes in the two groups. In addition, the results also demonstrated the expression divergence of the GRAS duplicated genes in the evolution. In short, the results above provide a solid foundation for further functional dissection of the GRAS gene superfamily.

Conclusions: In this work, differential expression, evolutionary rate, and expansion patterns of the GRAS gene family in the six species were predicted. Especially, tandem duplication events played an important role in expansion of group II. Together, these results contribute to further functional analysis and the molecular evolution of the GRAS gene superfamily.

Show MeSH

Related in: MedlinePlus

Model building of the three-dimensional structure of the GRAS protein. The VHIID, LHRII, PFYRE, and SAW motifs are presented in green, yellow, blue, and pink, respectively. The figure was produced using the CPHmodels program, and amino acids refer to the AT3G54220 sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4279901&req=5

Fig2: Model building of the three-dimensional structure of the GRAS protein. The VHIID, LHRII, PFYRE, and SAW motifs are presented in green, yellow, blue, and pink, respectively. The figure was produced using the CPHmodels program, and amino acids refer to the AT3G54220 sequence.

Mentions: Finally, we observed relationships between amino acid sites under positive selection and functional divergence, 14 critical amino acid sites were under positive selection as well as Type I and Type II functional divergence (Additional file 17). We located them on the three-dimensional GRAS structure and performed multiple sequence alignment to further investigate their function. As the displayed sequence produced incompetence by CPHmodels [38], only 12 sites were labeled on the three-dimensional structure, and other amino acid sites were labeled in multiple sequence alignment (Figure 2 and Additional file 13). Among these, two amino acids (296Q and 368S) was located on the LHRI motif, three amino acids (407D, 415P, and 419H) were located on the VHIID motif, and four amino acids (446 T, 448 K, 453 F, and 456 K) were located on the LHRII motif, and five amino acids (490 W, 511R, 518 T, 527A, and 535 V) were located on the PFYRE motif. In short, most of the amino acids were located on the α - helix. These results revealed that these amino acids may act as a major evolutionary force driving the divergence of GRAS-conserved motifs and may further affect the divergence of GRAS subgroup functions. More experimental evidence is needed to understand the functional importance of the identified CAASs. In addition, Zhang et al. recovered significant hits to several Rossmann fold methyltransferase domains in bacterial GRAS proteins [6]. Surprisingly, we also found the Rossmann fold (βαβαβ) in our protein (AT3G54220). These results also showed that the structure of GRAS proteins was conserved in lower and higher organisms.Figure 2


Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily.

Wu N, Zhu Y, Song W, Li Y, Yan Y, Hu Y - BMC Plant Biol. (2014)

Model building of the three-dimensional structure of the GRAS protein. The VHIID, LHRII, PFYRE, and SAW motifs are presented in green, yellow, blue, and pink, respectively. The figure was produced using the CPHmodels program, and amino acids refer to the AT3G54220 sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4279901&req=5

Fig2: Model building of the three-dimensional structure of the GRAS protein. The VHIID, LHRII, PFYRE, and SAW motifs are presented in green, yellow, blue, and pink, respectively. The figure was produced using the CPHmodels program, and amino acids refer to the AT3G54220 sequence.
Mentions: Finally, we observed relationships between amino acid sites under positive selection and functional divergence, 14 critical amino acid sites were under positive selection as well as Type I and Type II functional divergence (Additional file 17). We located them on the three-dimensional GRAS structure and performed multiple sequence alignment to further investigate their function. As the displayed sequence produced incompetence by CPHmodels [38], only 12 sites were labeled on the three-dimensional structure, and other amino acid sites were labeled in multiple sequence alignment (Figure 2 and Additional file 13). Among these, two amino acids (296Q and 368S) was located on the LHRI motif, three amino acids (407D, 415P, and 419H) were located on the VHIID motif, and four amino acids (446 T, 448 K, 453 F, and 456 K) were located on the LHRII motif, and five amino acids (490 W, 511R, 518 T, 527A, and 535 V) were located on the PFYRE motif. In short, most of the amino acids were located on the α - helix. These results revealed that these amino acids may act as a major evolutionary force driving the divergence of GRAS-conserved motifs and may further affect the divergence of GRAS subgroup functions. More experimental evidence is needed to understand the functional importance of the identified CAASs. In addition, Zhang et al. recovered significant hits to several Rossmann fold methyltransferase domains in bacterial GRAS proteins [6]. Surprisingly, we also found the Rossmann fold (βαβαβ) in our protein (AT3G54220). These results also showed that the structure of GRAS proteins was conserved in lower and higher organisms.Figure 2

Bottom Line: All of tandem duplicated genes were found in group II except one cluster of rice, indicating that tandem duplication greatly promoted the expansion of group II.These results strongly indicated that these groups were experiencing higher positive selection pressure.In short, the results above provide a solid foundation for further functional dissection of the GRAS gene superfamily.

View Article: PubMed Central - PubMed

ABSTRACT

Background: GRAS proteins belong to a plant transcription factor family that is involved with multifarious roles in plants. Although previous studies of this protein family have been reported for Arabidopsis, rice, Chinese cabbage and other species, investigation of expansion patterns and evolutionary rate on the basis of comparative genomics in different species remains inadequate.

Results: A total of 289 GRAS genes were identified in Arabidopsis, B. distachyon, rice, soybean, S. moellendorffii, and P. patens and were grouped into seven subfamilies, supported by the similarity of their exon-intron patterns and structural motifs. All of tandem duplicated genes were found in group II except one cluster of rice, indicating that tandem duplication greatly promoted the expansion of group II. Furthermore, segment duplications were mainly found in the soybean genome, whereas no single expansion pattern dominated in other plant species indicating that GRAS genes from these five species might be subject to a more complex evolutionary mechanism. Interestingly, branch-site model analyses of positive selection showed that a number of sites were positively selected under foreground branches I and V. These results strongly indicated that these groups were experiencing higher positive selection pressure. Meanwhile, the site-specific model revealed that the GRAS genes were under strong positive selection in P. patens. DIVERGE v2.0 was used to detect critical amino acid sites, and the results showed that the shifted evolutionary rate was mainly attributed to the functional divergence between the GRAS genes in the two groups. In addition, the results also demonstrated the expression divergence of the GRAS duplicated genes in the evolution. In short, the results above provide a solid foundation for further functional dissection of the GRAS gene superfamily.

Conclusions: In this work, differential expression, evolutionary rate, and expansion patterns of the GRAS gene family in the six species were predicted. Especially, tandem duplication events played an important role in expansion of group II. Together, these results contribute to further functional analysis and the molecular evolution of the GRAS gene superfamily.

Show MeSH
Related in: MedlinePlus