Phylogeny and Molecular Evolution Analysis of PIN-FORMED 1 in Angiosperm

PLOS ONE, Dec 2019

PIN-FORMED 1 (PIN1) is an important secondary transporter and determines the direction of intercellular auxin flow. As PIN1 performs the conserved function of auxin transport, it is expected that the sequence and structure of PIN1 is conserved. Therefore, we hypothesized that PIN1 evolve under pervasive purifying selection in the protein-coding sequences in angiosperm. To test this hypothesis, we performed detailed evolutionary analyses of 67 PIN1 sequences from 35 angiosperm species. We found that the PIN1 sequences are highly conserved within their transmembrane regions, part of their hydrophilic regions. We also found that there are two or more PIN1 copies in some of these angiosperm species. PIN1 sequences from Poaceae and Brassicaceae are representative of the modern clade. We identified 12 highly conserved motifs and a significant number of family-specific sites within these motifs. One family-specific site within Motif 11 shows a different residue between monocots and dicots, and is functionally critical for the polarity of PIN1. Likewise, the function of PIN1 appears to be different between monocots and dicots since the phenotype associated with PIN1 overexpression is opposite between Arabidopsis and rice. The evolution of angiosperm PIN1 protein-coding sequences appears to have been primarily driven by purifying selection, but traces of positive selection associated with sequences from certain families also seem to be present. We verified this observation by calculating the numbers of non-synonymous and synonymous changes on each branch of a phylogenetic tree. Our results indicate that the evolution of angiosperm PIN1 sequences involve strong purifying selection. In addition, our results suggest that the conserved sequences of PIN1 derive from a combination of the family-specific site variations and conserved motifs during their unique evolutionary processes, which is critical for the functional integrity and stability of these auxin transporters, especially in new species. Finally, functional difference of PIN1 is likely to be present in angiosperm because the positive selection is occurred in one branch of Poaceae.

A PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089289&type=printable

Phylogeny and Molecular Evolution Analysis of PIN-FORMED 1 in Angiosperm

Citation: Wang P, Cheng T, Wu S, Zhao F, Wang G, et al. ( Phylogeny and Molecular Evolution Analysis of PIN- FORMED 1 in Angiosperm Pengkai Wang 0 Tielong Cheng 0 Shuang Wu 0 Fangfang Zhao 0 Guangping Wang 0 Liming Yang 0 Mengzhu Lu 0 Jinhui Chen 0 Jisen Shi 0 Zhang Zhang, Beijing Institute of Genomics, Chinese Academy of Sciences, China 0 1 Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University , Nanjing , China , 2 Division of Research Management, Chinese Academy of Forestry , Beijing , China , 3 School of Life Sciences, Huaiyin Normal University , Huaian, Jiangsu , China , 4 State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry , Beijing , China PIN-FORMED 1 (PIN1) is an important secondary transporter and determines the direction of intercellular auxin flow. As PIN1 performs the conserved function of auxin transport, it is expected that the sequence and structure of PIN1 is conserved. Therefore, we hypothesized that PIN1 evolve under pervasive purifying selection in the protein-coding sequences in angiosperm. To test this hypothesis, we performed detailed evolutionary analyses of 67 PIN1 sequences from 35 angiosperm species. We found that the PIN1 sequences are highly conserved within their transmembrane regions, part of their hydrophilic regions. We also found that there are two or more PIN1 copies in some of these angiosperm species. PIN1 sequences from Poaceae and Brassicaceae are representative of the modern clade. We identified 12 highly conserved motifs and a significant number of family-specific sites within these motifs. One family-specific site within Motif 11 shows a different residue between monocots and dicots, and is functionally critical for the polarity of PIN1. Likewise, the function of PIN1 appears to be different between monocots and dicots since the phenotype associated with PIN1 overexpression is opposite between Arabidopsis and rice. The evolution of angiosperm PIN1 protein-coding sequences appears to have been primarily driven by purifying selection, but traces of positive selection associated with sequences from certain families also seem to be present. We verified this observation by calculating the numbers of non-synonymous and synonymous changes on each branch of a phylogenetic tree. Our results indicate that the evolution of angiosperm PIN1 sequences involve strong purifying selection. In addition, our results suggest that the conserved sequences of PIN1 derive from a combination of the family-specific site variations and conserved motifs during their unique evolutionary processes, which is critical for the functional integrity and stability of these auxin transporters, especially in new species. Finally, functional difference of PIN1 is likely to be present in angiosperm because the positive selection is occurred in one branch of Poaceae. - Funding: This work was supported by grants from the National High Technology Research and Development Program of China (863 Program, 2013AA102705), the National Science Foundation of China to Jinhui Chen (No. 31170619), to Jisen Shi (No. 30930077), To Tielong Cheng (No. 31270707), the Program for New Century Excellent Talents by the Ministry of Education and The priority Academic Program Development of Jiangsu Higher Education Institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. The plant hormone auxin is involved in many aspects of plant growth and development, including embryogenesis, organogenesis, tissue differentiation and gravitropism[1,2]. At the same time, auxin is required for the division, enlargement and differentiation of individual plant cells. Auxin as signal molecule between cells, tissues and organs contributes to the coordination and integration of growth and development in the whole plant and to physiological responses of plants to environmental signal[3,4]. There is evidence that auxin plays a central role in the majority of plant hormonal functions, as various hormones interact with auxin[5]. Indole-3acetic acid (IAA) is considered as the primary naturally occurring auxin in plants[6]. Recently, some experimental evidence demonstrates the positive feedback loop consisting of auxin and its efflux carrier PIN-FORMED1 (PIN1) plays an important role in the spatiotemporal regulation of organ formation[7]. For PIN1 transport auxin, they regulate a number of developmental processes, including morphogenesis, organogenesis, and stress responses[5,8,9]. They are oriented in the plasma membrane such that they mediate the directional flux of auxin within tissues and generate auxin gradients that influence development[10,11]. A number of studies have shown that some amino acids and motifs in AtPIN1 deter (...truncated)


This is a preview of a remote PDF: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089289&type=printable

Pengkai Wang, Tielong Cheng, Shuang Wu, Fangfang Zhao, Guangping Wang, Liming Yang, Mengzhu Lu, Jinhui Chen, Jisen Shi. Phylogeny and Molecular Evolution Analysis of PIN-FORMED 1 in Angiosperm, PLOS ONE, 2014, 2, DOI: 10.1371/journal.pone.0089289