Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i>
Auxin plays a central role in growth and plant development. To maintain auxin homeostasis, biological processes such as biosynthesis, transport, degradation, and reversible conjugation are essential. The <i>Gretchen Hagen 3</i> (<i>GH3</i>) family genes codify for the enzymes...
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MDPI AG
2021-09-01
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| author | Hugo A. Méndez-Hernández Ana O. Quintana-Escobar Miguel A. Uc-Chuc Víctor M. Loyola-Vargas |
| author_facet | Hugo A. Méndez-Hernández Ana O. Quintana-Escobar Miguel A. Uc-Chuc Víctor M. Loyola-Vargas |
| author_sort | Hugo A. Méndez-Hernández |
| collection | DOAJ |
| description | Auxin plays a central role in growth and plant development. To maintain auxin homeostasis, biological processes such as biosynthesis, transport, degradation, and reversible conjugation are essential. The <i>Gretchen Hagen 3</i> (<i>GH3</i>) family genes codify for the enzymes that esterify indole-3-acetic acid (IAA) to various amino acids, which is a key process in the induction of somatic embryogenesis (SE). The <i>GH3</i> family is one of the principal families of early response to auxin genes, exhibiting IAA-amido synthetase activity to maintain optimal levels of free auxin in the cell. In this study, we carried out a systematic identification of the <i>GH3</i> gene family in the genome of <i>Coffea canephora</i>, determining a total of 18 <i>CcGH3</i> genes. Analysis of the genetic structures and phylogenetic relationships of <i>CcGH3</i> genes with <i>GH3</i> genes from other plant species revealed that they could be clustered in two major categories with groups 1 and 2 of the <i>GH3</i> family of <i>Arabidopsis</i>. We analyzed the transcriptome expression profiles of the 18 <i>CcGH3</i> genes using RNA-Seq analysis-based data and qRT-PCR during the different points of somatic embryogenesis induction. Furthermore, the endogenous quantification of free and conjugated indole-3-acetic acid (IAA) suggests that the various members of the <i>CcGH3</i> genes play a crucial role during the embryogenic process of <i>C. canephora</i>. Three-dimensional modeling of the selected CcGH3 proteins showed that they consist of two domains: an extensive N-terminal domain and a smaller C-terminal domain. All proteins analyzed in the present study shared a unique conserved structural topology. Additionally, we identified conserved regions that could function to bind nucleotides and specific amino acids for the conjugation of IAA during SE in <i>C. canephora</i>. These results provide a better understanding of the <i>C. canephora GH3</i> gene family for further exploration and possible genetic manipulation. |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T06:15:27Z |
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| spelling | doaj.art-9cf13310317142c499da8324bcccd7f72023-11-22T19:42:46ZengMDPI AGPlants2223-77472021-09-011010203410.3390/plants10102034Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i>Hugo A. Méndez-Hernández0Ana O. Quintana-Escobar1Miguel A. Uc-Chuc2Víctor M. Loyola-Vargas3Plant Biochemistry and Molecular Biology Unit, Yucatan Scientific Research Center, Calle 43, No. 130 x 32 y 34, 97205 Mérida, YUC, MexicoPlant Biochemistry and Molecular Biology Unit, Yucatan Scientific Research Center, Calle 43, No. 130 x 32 y 34, 97205 Mérida, YUC, MexicoPlant Biochemistry and Molecular Biology Unit, Yucatan Scientific Research Center, Calle 43, No. 130 x 32 y 34, 97205 Mérida, YUC, MexicoPlant Biochemistry and Molecular Biology Unit, Yucatan Scientific Research Center, Calle 43, No. 130 x 32 y 34, 97205 Mérida, YUC, MexicoAuxin plays a central role in growth and plant development. To maintain auxin homeostasis, biological processes such as biosynthesis, transport, degradation, and reversible conjugation are essential. The <i>Gretchen Hagen 3</i> (<i>GH3</i>) family genes codify for the enzymes that esterify indole-3-acetic acid (IAA) to various amino acids, which is a key process in the induction of somatic embryogenesis (SE). The <i>GH3</i> family is one of the principal families of early response to auxin genes, exhibiting IAA-amido synthetase activity to maintain optimal levels of free auxin in the cell. In this study, we carried out a systematic identification of the <i>GH3</i> gene family in the genome of <i>Coffea canephora</i>, determining a total of 18 <i>CcGH3</i> genes. Analysis of the genetic structures and phylogenetic relationships of <i>CcGH3</i> genes with <i>GH3</i> genes from other plant species revealed that they could be clustered in two major categories with groups 1 and 2 of the <i>GH3</i> family of <i>Arabidopsis</i>. We analyzed the transcriptome expression profiles of the 18 <i>CcGH3</i> genes using RNA-Seq analysis-based data and qRT-PCR during the different points of somatic embryogenesis induction. Furthermore, the endogenous quantification of free and conjugated indole-3-acetic acid (IAA) suggests that the various members of the <i>CcGH3</i> genes play a crucial role during the embryogenic process of <i>C. canephora</i>. Three-dimensional modeling of the selected CcGH3 proteins showed that they consist of two domains: an extensive N-terminal domain and a smaller C-terminal domain. All proteins analyzed in the present study shared a unique conserved structural topology. Additionally, we identified conserved regions that could function to bind nucleotides and specific amino acids for the conjugation of IAA during SE in <i>C. canephora</i>. These results provide a better understanding of the <i>C. canephora GH3</i> gene family for further exploration and possible genetic manipulation.https://www.mdpi.com/2223-7747/10/10/2034auxinsdocking<i>Coffea canephora</i><i>GH3</i>plant growth regulatorssomatic embryogenesis |
| spellingShingle | Hugo A. Méndez-Hernández Ana O. Quintana-Escobar Miguel A. Uc-Chuc Víctor M. Loyola-Vargas Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i> Plants auxins docking <i>Coffea canephora</i> <i>GH3</i> plant growth regulators somatic embryogenesis |
| title | Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i> |
| title_full | Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i> |
| title_fullStr | Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i> |
| title_full_unstemmed | Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i> |
| title_short | Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of <i>GH3</i> Genes during Somatic Embryogenesis of <i>Coffea canephora</i> |
| title_sort | genome wide analysis modeling and identification of amino acid binding motifs suggest the involvement of i gh3 i genes during somatic embryogenesis of i coffea canephora i |
| topic | auxins docking <i>Coffea canephora</i> <i>GH3</i> plant growth regulators somatic embryogenesis |
| url | https://www.mdpi.com/2223-7747/10/10/2034 |
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