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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.


Graphical representation of 10 types of PCs and their comparative analysis among the eight plant species.
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Figure 1: Graphical representation of 10 types of PCs and their comparative analysis among the eight plant species.

Mentions: To further investigate the structural characteristics of PC proteins, we used several bioinformatics websites as described in the materials and methods section to predict the AG glycomodules, SPs, GPI-anchor signals (GASs), and N-glycosylation sites of PCs. Our results (Supplementary Table S1) indicated that 292 PCs were predicted to contain an N-terminal SP required for targeting to the endoplasmic reticulum. In addition, 217 PCs were expected to have GASs responsible for plasma membrane localization. The subcellular localizations of plant PCs have been found to correlate with their specific functions. For example, AtSC3/AtBCB, an Arabidopsis blue copper binding protein, was strongly localized in the plasma membrane and induced by aluminum stress and oxidative stress, suggesting that the plant PCs may participate in some abiotic stress responses (Ezaki et al., 2001, 2005). Additionally, PC proteins accumulated in the sieve element plasma membrane may be involved in determining reproductive potential (Khan et al., 2007). Moreover, 281 PCs had putative AG glycomodules in the (Pro, Ala, Ser, Thr)-rich region. These 281 PCs might be AGPs for the existence of AG glycomodules and SPs. According to the distribution of the SP, PCLD, AGP-like region (ALR) and GAS, these PCs were separated into ten types (Figure 1). Type I PCs had typical properties, including an N-terminal SP, a PCLD, an ALR, and a C-terminal GAS. Type II PCs were short of GAS, while other features were similar to type I. Both GAS and ALR were absent from type VI, VIII, and IX PCs. Interestingly, we also found that type III, IV, VIII, and X PCs possessed two PCLDs, and type V had three PCLDs. The domain repeats are usually thought to evolve through recombination events and intragenic duplication (Björklund et al., 2006). The creation of new multi-domain architectures is an important mechanism that provides opportunities for the organism to expand its repertoire of cellular functions, such as transcriptional regulation, protein transport and assembly (Andrade et al., 2001; D’Andrea and Regan, 2003; Weiner et al., 2006). Furthermore, protein domain repeats may constitute a source of variability. In human genome, duplications are more common in genes containing repeated domains than in non-repeated ones (Björklund et al., 2010). The domain repetition is quite important in evolution, since it provides a path where proteins can evolve through removing or adding functionally similar or distinct blocks (Light et al., 2012). In this study, we identified some multi-PCLD domains in PCs. This presence of PCLD domain repeats contribute to the complexity of this gene family. Its effect on the function of PC proteins remains to be examined. However, our findings suggest that the PCLD repeats may play an important role in PC protein evolution.


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)

Graphical representation of 10 types of PCs and their comparative analysis among the eight plant species.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499708&req=5

Figure 1: Graphical representation of 10 types of PCs and their comparative analysis among the eight plant species.
Mentions: To further investigate the structural characteristics of PC proteins, we used several bioinformatics websites as described in the materials and methods section to predict the AG glycomodules, SPs, GPI-anchor signals (GASs), and N-glycosylation sites of PCs. Our results (Supplementary Table S1) indicated that 292 PCs were predicted to contain an N-terminal SP required for targeting to the endoplasmic reticulum. In addition, 217 PCs were expected to have GASs responsible for plasma membrane localization. The subcellular localizations of plant PCs have been found to correlate with their specific functions. For example, AtSC3/AtBCB, an Arabidopsis blue copper binding protein, was strongly localized in the plasma membrane and induced by aluminum stress and oxidative stress, suggesting that the plant PCs may participate in some abiotic stress responses (Ezaki et al., 2001, 2005). Additionally, PC proteins accumulated in the sieve element plasma membrane may be involved in determining reproductive potential (Khan et al., 2007). Moreover, 281 PCs had putative AG glycomodules in the (Pro, Ala, Ser, Thr)-rich region. These 281 PCs might be AGPs for the existence of AG glycomodules and SPs. According to the distribution of the SP, PCLD, AGP-like region (ALR) and GAS, these PCs were separated into ten types (Figure 1). Type I PCs had typical properties, including an N-terminal SP, a PCLD, an ALR, and a C-terminal GAS. Type II PCs were short of GAS, while other features were similar to type I. Both GAS and ALR were absent from type VI, VIII, and IX PCs. Interestingly, we also found that type III, IV, VIII, and X PCs possessed two PCLDs, and type V had three PCLDs. The domain repeats are usually thought to evolve through recombination events and intragenic duplication (Björklund et al., 2006). The creation of new multi-domain architectures is an important mechanism that provides opportunities for the organism to expand its repertoire of cellular functions, such as transcriptional regulation, protein transport and assembly (Andrade et al., 2001; D’Andrea and Regan, 2003; Weiner et al., 2006). Furthermore, protein domain repeats may constitute a source of variability. In human genome, duplications are more common in genes containing repeated domains than in non-repeated ones (Björklund et al., 2010). The domain repetition is quite important in evolution, since it provides a path where proteins can evolve through removing or adding functionally similar or distinct blocks (Light et al., 2012). In this study, we identified some multi-PCLD domains in PCs. This presence of PCLD domain repeats contribute to the complexity of this gene family. Its effect on the function of PC proteins remains to be examined. However, our findings suggest that the PCLD repeats may play an important role in PC protein evolution.

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.