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Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays.

Cao J, Li X, Lv Y, Ding L - Front Plant Sci (2015)

Bottom Line: We found an expansion process of this gene family in evolution.ZmUC16 was strongly expressed after drought treatment.This study will provide a basis for future understanding the characterization of this family.

View Article: PubMed Central - PubMed

Affiliation: Institute of Life Sciences, Jiangsu University Zhenjiang, China.

ABSTRACT
Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.

No MeSH data available.


Quantitative RT-PCR analysis of nine selected ZmPC genes under the salt and drought treatments. The relative expression level of each transcript was shown here. Error bars indicate standard deviation (SD) of independent biological replicates. Asterisk indicates a significant difference from the control (∗p < 0.05; ∗∗p < 0.01).
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Figure 6: Quantitative RT-PCR analysis of nine selected ZmPC genes under the salt and drought treatments. The relative expression level of each transcript was shown here. Error bars indicate standard deviation (SD) of independent biological replicates. Asterisk indicates a significant difference from the control (∗p < 0.05; ∗∗p < 0.01).

Mentions: We first used publicly available microarray data to detect the spatiotemporal expression patterns of the maize PC genes. Expression profiles of the PC genes were mined at 34 different tissues. Only 54 probes were detected standing for the 54 ZmPC transcripts. The remaining six transcripts with no detectable expression signal are GRMZM2G463441, GRMZM2G136879, GRMZM2G148624, GRMZM2G047208, GRMZM2G085504, and AC209987.4_FGT010. The results indicated that these genes are expressed variously in different tissues, implying that they may be involved in many growth and developmental processes (Figure 5). Such as, most ZmPC genes of clade A showed high expression levels in the root, leaf and internodes, but low expression levels in the endosperm and embryo. In contrast, ZmPC genes in clade B presented the oppositive results compared with clade A. That is, most members of clade B displayed high expression levels in the embryo and endosperm, but showed low level expression in the leaf, root and internodes. This suggested that ZmPC genes in different clades may be involved in various biological processes. Some ZmPCs were also found to be highly expressed in some specific organs, such as, ZmSC5 in anthers, ZmUC3 and ZmUC23 in embryo, suggesting that they might be involved in the growth and development of these organs in maize. Similar results have also been observed in their homologs in Arabidopsis (AtENODL1/5/6/7/11/12/16, AtAGP6/11, and FLA3; Yu et al., 2005; Levitin et al., 2008; Li et al., 2010; Ma et al., 2011), rice (OsENODL9/14/16/17; Ma et al., 2011), and B. rapa (BrENODL22/27 and BrSCL8/9; Li et al., 2013), which were highly expressed in reproductive organs. The functions of some PC genes have been investigated in several studies. For example, a sieve element-specific expressed gene (AtENODL9) may be involved in determining reproductive potential in Arabidopsis (Khan et al., 2007); AtAGP6 and AtAGP11 are involved in pollen tube growth (Levitin et al., 2008); Over expression of the FLA3 led to short siliques with low seed set due to the reduced stamen filament, suggesting that the FLA3 gene is involved in microspore development and pollen intine formation (Li et al., 2010). Next, we also investigated the expression patterns of nine ZmPCs detected in maize seedlings subjected to salt and drought treatments by qRT-PCR. The primers were listed in Table 3. The analysis revealed that these genes are differently expressed under salt and drought conditions (Figure 6). Among the nine detected ZmPC genes, all members were down-regulated under salt treatment. And five members (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. Some rice PC genes (OsENODL19, OsENODL12, OsUCL17, OsUCL20, OsUCL7, OsUCL8, and OsUCL18) have been investigated to be down-regulated by drought and/or salt stresses (Ma et al., 2011). Interestingly, we also found that ZmUC16/21 were significantly up-regulated after drought treatment, suggesting that these ZmPCs are more likely to play key roles in maize drought response. An increasing number of evidence has suggested that PCs may also function in stress responses. Previous studies reported that some PCs, such as, OsUCL23/26/27 (Ma et al., 2011), BrUCL6/16 (Li et al., 2013), were up-regulated under drought or salt stresses. Moreover, over-expression of AtBCB/AtSC3 could confer aluminum resistance in Arabidopsis (Ezaki et al., 2001, 2005). And BcBCP1 can enhance tolerance to osmotic stress when over-expressed in tobacco (Wu et al., 2011). The differential expression profiles of different PC family genes may imply diverse roles of plant response to stress. On the other hand, PC genes which are up-regulated during several abiotic stresses are likely to be required for enhancing resistance to stress. Therefore, PCs can function in developmental processes and stress responses.


Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays.

Cao J, Li X, Lv Y, Ding L - Front Plant Sci (2015)

Quantitative RT-PCR analysis of nine selected ZmPC genes under the salt and drought treatments. The relative expression level of each transcript was shown here. Error bars indicate standard deviation (SD) of independent biological replicates. Asterisk indicates a significant difference from the control (∗p < 0.05; ∗∗p < 0.01).
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Related In: Results  -  Collection

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Figure 6: Quantitative RT-PCR analysis of nine selected ZmPC genes under the salt and drought treatments. The relative expression level of each transcript was shown here. Error bars indicate standard deviation (SD) of independent biological replicates. Asterisk indicates a significant difference from the control (∗p < 0.05; ∗∗p < 0.01).
Mentions: We first used publicly available microarray data to detect the spatiotemporal expression patterns of the maize PC genes. Expression profiles of the PC genes were mined at 34 different tissues. Only 54 probes were detected standing for the 54 ZmPC transcripts. The remaining six transcripts with no detectable expression signal are GRMZM2G463441, GRMZM2G136879, GRMZM2G148624, GRMZM2G047208, GRMZM2G085504, and AC209987.4_FGT010. The results indicated that these genes are expressed variously in different tissues, implying that they may be involved in many growth and developmental processes (Figure 5). Such as, most ZmPC genes of clade A showed high expression levels in the root, leaf and internodes, but low expression levels in the endosperm and embryo. In contrast, ZmPC genes in clade B presented the oppositive results compared with clade A. That is, most members of clade B displayed high expression levels in the embryo and endosperm, but showed low level expression in the leaf, root and internodes. This suggested that ZmPC genes in different clades may be involved in various biological processes. Some ZmPCs were also found to be highly expressed in some specific organs, such as, ZmSC5 in anthers, ZmUC3 and ZmUC23 in embryo, suggesting that they might be involved in the growth and development of these organs in maize. Similar results have also been observed in their homologs in Arabidopsis (AtENODL1/5/6/7/11/12/16, AtAGP6/11, and FLA3; Yu et al., 2005; Levitin et al., 2008; Li et al., 2010; Ma et al., 2011), rice (OsENODL9/14/16/17; Ma et al., 2011), and B. rapa (BrENODL22/27 and BrSCL8/9; Li et al., 2013), which were highly expressed in reproductive organs. The functions of some PC genes have been investigated in several studies. For example, a sieve element-specific expressed gene (AtENODL9) may be involved in determining reproductive potential in Arabidopsis (Khan et al., 2007); AtAGP6 and AtAGP11 are involved in pollen tube growth (Levitin et al., 2008); Over expression of the FLA3 led to short siliques with low seed set due to the reduced stamen filament, suggesting that the FLA3 gene is involved in microspore development and pollen intine formation (Li et al., 2010). Next, we also investigated the expression patterns of nine ZmPCs detected in maize seedlings subjected to salt and drought treatments by qRT-PCR. The primers were listed in Table 3. The analysis revealed that these genes are differently expressed under salt and drought conditions (Figure 6). Among the nine detected ZmPC genes, all members were down-regulated under salt treatment. And five members (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. Some rice PC genes (OsENODL19, OsENODL12, OsUCL17, OsUCL20, OsUCL7, OsUCL8, and OsUCL18) have been investigated to be down-regulated by drought and/or salt stresses (Ma et al., 2011). Interestingly, we also found that ZmUC16/21 were significantly up-regulated after drought treatment, suggesting that these ZmPCs are more likely to play key roles in maize drought response. An increasing number of evidence has suggested that PCs may also function in stress responses. Previous studies reported that some PCs, such as, OsUCL23/26/27 (Ma et al., 2011), BrUCL6/16 (Li et al., 2013), were up-regulated under drought or salt stresses. Moreover, over-expression of AtBCB/AtSC3 could confer aluminum resistance in Arabidopsis (Ezaki et al., 2001, 2005). And BcBCP1 can enhance tolerance to osmotic stress when over-expressed in tobacco (Wu et al., 2011). The differential expression profiles of different PC family genes may imply diverse roles of plant response to stress. On the other hand, PC genes which are up-regulated during several abiotic stresses are likely to be required for enhancing resistance to stress. Therefore, PCs can function in developmental processes and stress responses.

Bottom Line: We found an expansion process of this gene family in evolution.ZmUC16 was strongly expressed after drought treatment.This study will provide a basis for future understanding the characterization of this family.

View Article: PubMed Central - PubMed

Affiliation: Institute of Life Sciences, Jiangsu University Zhenjiang, China.

ABSTRACT
Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.

No MeSH data available.