The divergence and positive selection of the plant‐specific <scp>BURP</scp>‐containing protein family

Wang, Lihui; Wu, Ningning; Zhu, Yan; Song, Wanlu; Zhao, Xin; Li, Yaxuan; Hu, Yingkao

doi:10.1002/ece3.1792

Cited by 21 publications

(20 citation statements)

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“…Ka and Ks for corresponding duplicated gene pairs were obtained directly from The Plant Genome Duplication Database ( http://chibba.agtec.uga.edu/duplication/ ) [ 68 ]. Detailed information on the anchor points of duplicated gene pairs and the mean Ks values have been described previously [ 91 , 92 ]. The approximate date of the duplication event was calculated using the mean Ks values from T = Ks/2λ [ 93 ], assuming clocklike rates (λ) of synonymous substitution of 6.5 × 10 −9 for rice [ 66 ] and 1.5 × 10 −8 for Arabidopsis [ 94 ].…”

Section: Methodsmentioning

confidence: 99%

“…Positive selection was identified using a maximum likelihood approach by “codeml” in PAML under the site model and branch-site model [ 76 – 78 ]. The two model analysis of MATE family and subfamilies was performed according to the previously described method [ 92 ].…”

Section: Methodsmentioning

confidence: 99%

“…Functional divergence and the importance of amino acid residues among MATE gene subfamilies were predicted using the DIVERGE v3.0 package [ 72 – 74 , 95 , 96 ], which estimates significant changes in site-specific shifts according to evolutionary rate (Type-I) or amino acid properties (Type-II) after the emergence of two paralogous sequences. Detailed information on the estimation of functional divergence has been described previously [ 92 ].…”

Section: Methodsmentioning

confidence: 99%

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The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

et al. 2016

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BackgroundMultidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection.ResultsForty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies. In both species, the MATE gene family has expanded mainly through tandem and segmental duplications. A transcriptome atlas showed considerable differences in expression among the genes, in terms of transcript abundance and expression patterns under normal growth conditions, indicating wide functional divergence in this family. In both rice and Arabidopsis, the MATE genes showed consistent functional divergence trends, with highly significant Type-I divergence in each subfamily, while Type-II divergence mainly occurred in subfamily III. The Type-II coefficients between rice subfamilies I/III, II/III, and IV/III were all significantly greater than zero, while only the Type-II coefficient between Arabidopsis IV/III subfamilies was significantly greater than zero.A site-specific model analysis indicated that MATE genes have relatively conserved evolutionary trends. A branch-site model suggested that the extent of positive selection on each subfamily of rice and Arabidopsis was different: subfamily II of Arabidopsis showed higher positive selection than other subfamilies, whereas in rice, positive selection was highest in subfamily III. In addition, the analyses identified 18 rice sites and 7 Arabidopsis sites that were responsible for positive selection and for Type-I and Type-II functional divergence; there were no common sites between rice and Arabidopsis. Five coevolving amino acid sites were identified in rice and three in Arabidopsis; these sites might have important roles in maintaining local structural stability and protein functional domains.ConclusionsWe demonstrate that the MATE gene family expanded through tandem and segmental duplication in both rice and Arabidopsis. Overall, the results of our analyses contribute to improved understanding of the molecular evolution and functions of the MATE gene family in plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0895-0) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

et al. 2016

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“…Sutton et al (1992) was the first to show that the LEA gene is rapidly expressed in Hordeum vulgare seedlings at low temperature, and therefore, the seedlings rapidly generated stress proteins. In addition, many studies have shown that oleosin (Shimada et al 2008), plant cytochrome P450 (Divi and Krishna 2010;Yang et al 2014); BURP domain-containing protein (Wang et al 2016), and cysteine proteinase inhibitors (Valdés-Rodríguez et al 2007;Hwang et al 2010;Zhang and Fu 2018) have a mitigation effect on low-temperature stress. Among these, plant cytochrome P450 is involved in the biosynthesis of brassinosteroids (BRs), which play an important role in increasing seedling tolerance and resistance to environmental stress.…”

Section: Transcriptome Analysis At Different Germination Stages Undermentioning

confidence: 99%

Low-temperature tolerance and transcriptome analyses during seed germination of Anabasis aphylla

Peng

Chang

Chu

et al. 2019

Journal of Plant Interactions

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This study aimed to explore differences in the low-temperature tolerance of a desert plant, Anabasis aphylla, at different seed germination stages during the fall using transcriptome sequencing to identify related genes. The survival rate of the seeds decreased with lower temperatures at different germination stages, and the tolerance of the stages in decreasing order was as follows: imbibition (I) ≈ testa rupture (II) > testa removal (III) > elongation (IV). Superoxide dismutase, peroxidase, and catalase activities and the malondialdehyde content showed a downward trend after stage II. Transcriptome sequencing of seeds, including ripe and dry dominant seeds (W1) and seeds during different germination stages [imbibition (W2), testa removal (W3), and elongation (W4)] was performed. Some genes were downregulated during seed germination, which mainly included cytochrome P450, oleosin, ethylene-responsive transcription factor, and low temperature-induced protein. This study suggests that downregulated of some genes may result in a decrease in lowtemperature tolerance.

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“…In Vicia faba L . (broad bean), USP (a non-storage seed protein with unknown function) is expressed during the early stages of both zygotic embryogenesis and in vitro embryogenesis 12 . BURP domain-containing proteins also regulate fruit ripening.…”

Section: Introductionmentioning

confidence: 99%

Drought and exogenous abscisic acid alter hydrogen peroxide accumulation and differentially regulate the expression of two maize RD22-like genes

Phillips

Ludidi

2017

Sci Rep

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Increased biosynthesis of abscisic acid (ABA) occurs in plants in response to water deficit, which is mediated by changes in the levels of reactive oxygen species such as H 2 O 2 . Water deficit and ABA induce expression of some RD22-like proteins. This study aimed to evaluate the effect of water deficit and exogenous ABA (50 µM ABA applied every 24 hours for a total of 72 hours) on H 2 O 2 content in Zea mays (maize) and to characterise genes encoding two putative maize RD22-like proteins (designated ZmRD22A and ZmRD22B). The expression profiles of the two putative maize RD22-like genes in response to water deficit and treatment with ABA were examined in leaves. In silico analyses showed that the maize RD22-like proteins share domain organisation with previously characterized RD22-like proteins. Both water deficit and exogenous ABA resulted in increased H 2 O 2 content in leaves but the increase was more pronounced in response to water deficit than to exogenous ABA. Lignin content was not affected by exogenous ABA, whereas it was decreased by water deficit. Expression of both RD22-like genes was up-regulated by drought but the ZmRD22A gene was not influenced by exogenous ABA, whereas ZmRD22B was highly responsive to exogenous ABA.Abscisic acid (ABA) is a phytohormone involved in the induction of drought-responsive genes in Arabidopsis thaliana 1 , Oryza sativa 2 and Glycine max 3 . The induction of drought-responsive genes by ABA occurs through the binding of specific transcription factors, such as ABA-responsive element binding protein (AREB) and abscisic acid response element-binding factors (ABF), to cis-acting elements in the promoter regions of drought-responsive genes 4, 5 . However, there are several drought-induced genes which are not responsive to ABA. The induction of the expression of these genes involves the binding of specific transcription factors, such as dehydration responsive element binding (DREB) proteins, to cis-acting elements in promoters of these genes 6 .Some of the drought-responsive genes which are responsive to ABA signals are the plant-specific RD22-like proteins, which are members of the BURP domain-containing protein family 7 . RD22-like proteins have been identified in Arabidopsis thaliana 8 , Brassica napus 9 and Glycine max 10 . The BURP domain-containing family of proteins is named after its primary sub-families BNM2, USP, RD22 and PG1β. These proteins have been identified in a variety of plant species where they are expressed under a diverse range of conditions and in various plant organs 7 . BURP domain-containing proteins are expressed during the early stage of microspore embryogenesis in Brassica napus L. (oilseed rape) seeds, as is seen with BNM2 11 . In Vicia faba L. (broad bean), USP (a non-storage seed protein with unknown function) is expressed during the early stages of both zygotic embryogenesis and in vitro embryogenesis 12 . BURP domain-containing proteins also regulate fruit ripening. PG1β, which is the non-catalytic β-subunit of polygalacturonase isozyme (PG), ac...

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The divergence and positive selection of the plant‐specific BURP‐containing protein family

Cited by 21 publications

References 92 publications

The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

Low-temperature tolerance and transcriptome analyses during seed germination of Anabasis aphylla

Drought and exogenous abscisic acid alter hydrogen peroxide accumulation and differentially regulate the expression of two maize RD22-like genes

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