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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 March 2022) | Viewed by 46579

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Prof. Dr. Jen-Tsung Chen

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Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
Interests: bioactive compounds; chromatography techniques; medicinal plants; phytochemicals; plant biotechnology; plant growth regulators; plant secondary metabolites
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Dear Colleagues,

This Special Issue is the continuation of our previous special issue "Orchid Biochemistry".

Orchidaceae is one of the largest families among the angiosperms and is represented by approximately 25,000–28,000 species worldwide across a wide range of habitats. Orchids are well known for their attractive flowers and have high economical value in the global horticultural market. What often receives less attention is the fact that some orchids are edible or scented, and more than this, many species have long been used in preparations as traditional medicine. In the past two decades, extensive studies have been carried out on genetic and functional genomic analysis to achieve progress in biotechnology and breeding programs for orchids. However, in-depth research on the bioactive compounds of orchids is still limited to several species.

In order to address the lack of phytochemical knowledge, this Special Issue aims to integrate recent innovative approaches and attempts to make significant progress in orchid biochemistry by expanding knowledge on a wide range of topics, including biosynthetic machinery, pharmacognosy, biotechnology, and high-throughput technologies, including bioinformatics and other related topics.

Dr. Jen-Tsung Chen
Guest Editor

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Keywords

Biochemistry
Bioinformatics
Biosynthetic machinery
Flower scent
Gene expression
Genomics
High-throughput technologies
Metabolomics
Orchid
Pharmacognosy
Pharmacology
Proteomics
Traditional medicine
Transcriptomics

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Orchid Biochemistry in International Journal of Molecular Sciences (33 articles)

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

3 pages, 176 KiB

Open AccessEditorial

Orchid Biochemistry 2.0

by Jen-Tsung Chen

Int. J. Mol. Sci. 2022, 23(12), 6823; https://doi.org/10.3390/ijms23126823 - 19 Jun 2022

Cited by 1 | Viewed by 2052

Abstract

In the Special Issue entitled “Orchid Biochemistry”, researchers explored the biochemistry and molecular mechanisms of pigment formation, flower scent, bioactive compounds, plant–microbial interaction, as well as aspects of biotechnology, and these studies have greatly enriched the understanding in the field of orchid biology [...] Read more.

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

Research

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29 pages, 3068 KiB

Open AccessArticle

Nectar Chemistry or Flower Morphology—What Is More Important for the Reproductive Success of Generalist Orchid Epipactis palustris in Natural and Anthropogenic Populations?

by Emilia Brzosko, Andrzej Bajguz, Justyna Burzyńska and Magdalena Chmur

Int. J. Mol. Sci. 2021, 22(22), 12164; https://doi.org/10.3390/ijms222212164 - 10 Nov 2021

Cited by 4 | Viewed by 2404

Abstract

The aim of this study was to determine the level of reproductive success (RS) in natural and anthropogenic populations of generalist orchid Epipactis palustris and its dependence on flower structure and nectar composition, i.e., amino acids and sugars. We found that both pollinaria removal and female reproductive success were high and similar in all populations, despite differences in flower traits and nectar chemistry. Flower structures were weakly correlated with parameters of RS. Nectar traits were more important in shaping RS; although, we noted differentiated selection on nectar components in distinct populations. Individuals in natural populations produced nectar with a larger amount of sugars and amino acids. The sucrose to (fructose and glucose) ratio in natural populations was close to 1, while in anthropogenic ones, a clear domination of fructose and glucose was noted. Our results indicate that the flower traits and nectar composition of E. palustris reflect its generalist character and meet the requirements of a wide range of pollinators, differing according to body sizes, mouth apparatus, and dietary needs. Simultaneously, differentiation of nectar chemistry suggests a variation of pollinator assemblages in particular populations or domination of their some groups. To our knowledge, a comparison of nectar chemistry between natural and anthropogenic populations of orchids is reported for the first time in this paper. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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18 pages, 3333 KiB

Open AccessArticle

Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development

by Francesca Lucibelli, Maria Carmen Valoroso, Günter Theißen, Susanne Nolden, Mariana Mondragon-Palomino and Serena Aceto

Int. J. Mol. Sci. 2021, 22(13), 7025; https://doi.org/10.3390/ijms22137025 - 29 Jun 2021

Cited by 11 | Viewed by 6130

Abstract

The molecular basis of orchid flower development is accomplished through a specific regulatory program in which the class B MADS-box AP3/DEF genes play a central role. In particular, the differential expression of four class B AP3/DEF genes is responsible for specification of organ identities in the orchid perianth. Other MADS-box genes (AGL6 and SEP-like) enrich the molecular program underpinning the orchid perianth development, resulting in the expansion of the original “orchid code” in an even more complex gene regulatory network. To identify candidates that could interact with the AP3/DEF genes in orchids, we conducted an in silico differential expression analysis in wild-type and peloric Phalaenopsis. The results suggest that a YABBY DL-like gene could be involved in the molecular program leading to the development of the orchid perianth, particularly the labellum. Two YABBY DL/CRC homologs are present in the genome of Phalaenopsis equestris, PeDL1 and PeDL2, and both express two alternative isoforms. Quantitative real-time PCR analyses revealed that both genes are expressed in column and ovary. In addition, PeDL2 is more strongly expressed the labellum than in the other tepals of wild-type flowers. This pattern is similar to that of the AP3/DEF genes PeMADS3/4 and opposite to that of PeMADS2/5. In peloric mutant Phalaenopsis, where labellum-like structures substitute the lateral inner tepals, PeDL2 is expressed at similar levels of the PeMADS2-5 genes, suggesting the involvement of PeDL2 in the development of the labellum, together with the PeMADS2-PeMADS5 genes. Although the yeast two-hybrid analysis did not reveal the ability of PeDL2 to bind the PeMADS2-PeMADS5 proteins directly, the existence of regulatory interactions is suggested by the presence of CArG-boxes and other MADS-box transcription factor binding sites within the putative promoter of the orchid DL2 gene. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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21 pages, 3575 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of the APETALA2 (AP2) Transcription Factor in Dendrobium officinale

by Danqi Zeng, Jaime A. Teixeira da Silva, Mingze Zhang, Zhenming Yu, Can Si, Conghui Zhao, Guangyi Dai, Chunmei He and Jun Duan

Int. J. Mol. Sci. 2021, 22(10), 5221; https://doi.org/10.3390/ijms22105221 - 14 May 2021

Cited by 16 | Viewed by 3422

Abstract

The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 DoAP2 TFs that were identified from the D. officinale genome and named DoAP2-1 to DoAP2-14 were divided into three clades: euAP2, euANT, and basalANT. The promoters of all DoAP2 genes contained cis-regulatory elements related to plant development and also responsive to plant hormones and stress. qRT-PCR analysis showed the abundant expression of DoAP2-2, DoAP2-5, DoAP2-7, DoAP2-8 and DoAP2-12 genes in protocorm-like bodies (PLBs), while DoAP2-3, DoAP2-4, DoAP2-6, DoAP2-9, DoAP2-10 and DoAP2-11 expression was strong in plantlets. In addition, the expression of some DoAP2 genes was down-regulated during flower development. These results suggest that DoAP2 genes may play roles in plant regeneration and flower development in D. officinale. Four DoAP2 genes (DoAP2-1 from euAP2, DoAP2-2 from euANT, and DoAP2-6 and DoAP2-11 from basal ANT) were selected for further analyses. The transcriptional activation of DoAP2-1, DoAP2-2, DoAP2-6 and DoAP2-11 proteins, which were localized in the nucleus of Arabidopsis thaliana mesophyll protoplasts, was further analyzed by a dual-luciferase reporter gene system in Nicotiana benthamiana leaves. Our data showed that pBD-DoAP2-1, pBD-DoAP2-2, pBD-DoAP2-6 and pBD-DoAP2-11 significantly repressed the expression of the LUC reporter compared with the negative control (pBD), suggesting that these DoAP2 proteins may act as transcriptional repressors in the nucleus of plant cells. Our findings on AP2 genes in D. officinale shed light on the function of AP2 genes in this orchid and other plant species. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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27 pages, 1792 KiB

Open AccessArticle

How Are the Flower Structure and Nectar Composition of the Generalistic Orchid Neottia ovata Adapted to a Wide Range of Pollinators?

by Emilia Brzosko, Andrzej Bajguz, Magdalena Chmur, Justyna Burzyńska, Edyta Jermakowicz, Paweł Mirski and Piotr Zieliński

Int. J. Mol. Sci. 2021, 22(4), 2214; https://doi.org/10.3390/ijms22042214 - 23 Feb 2021

Cited by 12 | Viewed by 3593

Abstract

Plant-pollinator interactions significantly influence reproductive success (RS) and drive the evolution of pollination syndromes. In the context of RS, mainly the role of flower morphology is touched. The importance of nectar properties is less studied, despite its significance in pollination effectiveness. Therefore, the aim of this study was to test selection on flower morphology and nectar chemistry in the generalistic orchid Neottia ovata. In 2019–2020, we measured three floral displays and six flower traits, pollinaria removal (PR), female reproductive success (FRS), and determined the soil properties. The sugars and amino acids (AAs) were analyzed using the HPLC method. Data were analyzed using multiple statistical methods (boxplots, ternary plot, one-way ANOVA, Kruskal-Wallis test, and PCA). Variation of flower structure and nectar chemistry and their weak correlation with RS confirms the generalistic character of N. ovata. In particular populations, different traits were under selection. PR was high and similar in all populations in both years, while FRS was lower and varied among populations. Nectar was dominated by glucose, fructose, and included 28 AAs (Ala and Glu have the highest content). Sugars and AAs influenced mainly FRS. Among soil parameters, carbon and carbon:nitrogen ratio seems to be the most important in shaping flower structure and nectar chemistry. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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15 pages, 2914 KiB

Open AccessArticle

Functional Characterization of a Dendrobium officinale Geraniol Synthase DoGES1 Involved in Floral Scent Formation

by Conghui Zhao, Zhenming Yu, Jaime A. Teixeira da Silva, Chunmei He, Haobin Wang, Can Si, Mingze Zhang, Danqi Zeng and Jun Duan

Int. J. Mol. Sci. 2020, 21(19), 7005; https://doi.org/10.3390/ijms21197005 - 23 Sep 2020

Cited by 27 | Viewed by 4720

Abstract

Floral scent is a key ornamental trait that determines the quality and commercial value of orchids. Geraniol, an important volatile monoterpene in orchids that attracts pollinators, is also involved in responses to stresses but the geraniol synthase (GES) responsible for its synthesis in the medicinal orchid Dendrobium officinale has not yet been identified. In this study, three potential geraniol synthases were mined from the D. officinale genome. DoGES1, which was localized in chloroplasts, was characterized as a geraniol synthase. DoGES1 was highly expressed in flowers, especially in petals. DoGES1 transcript levels were high in the budding stage of D. officinale flowers at 11:00 a.m. DoGES1 catalyzed geraniol in vitro, and transient expression of DoGES1 in Nicotiana benthamiana leaves resulted in the accumulation of geraniol in vivo. These findings on DoGES1 advance our understanding of geraniol biosynthesis in orchids, and lay the basis for genetic modification of floral scent in D. officinale or in other ornamental orchids. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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17 pages, 3861 KiB

Open AccessArticle

DoRWA3 from Dendrobium officinale Plays an Essential Role in Acetylation of Polysaccharides

by Can Si, Jaime A. Teixeira da Silva, Chunmei He, Zhenming Yu, Conghui Zhao, Haobin Wang, Mingze Zhang and Jun Duan

Int. J. Mol. Sci. 2020, 21(17), 6250; https://doi.org/10.3390/ijms21176250 - 28 Aug 2020

Cited by 13 | Viewed by 3843

Abstract

The acetylation or deacetylation of polysaccharides can influence their physical properties and biological activities. One main constituent of the edible medicinal orchid, Dendrobium officinale, is water-soluble polysaccharides (WSPs) with substituted O-acetyl groups. Both O-acetyl groups and WSPs show a similar trend in different organs, but the genes coding for enzymes that transfer acetyl groups to WSPs have not been identified. In this study, we report that REDUCED WALL ACETYLATION (RWA) proteins may act as acetyltransferases. Three DoRWA genes were identified, cloned, and sequenced. They were sensitive to abscisic acid (ABA), but there were no differences in germination rate and root length between wild type and 35S::DoRWA3 transgenic lines under ABA stress. Three DoRWA proteins were localized in the endoplasmic reticulum. DoRWA3 had relatively stronger transcript levels in organs where acetyl groups accumulated than DoRWA1 and DoRWA2, was co-expressed with polysaccharides synthetic genes, so it was considered as a candidate acetyltransferase gene. The level of acetylation of polysaccharides increased significantly in the seeds, leaves and stems of three 35S::DoRWA3 transgenic lines compared to wild type plants. These results indicate that DoRWA3 can transfer acetyl groups to polysaccharides and is a candidate protein to improve the biological activity of other edible and medicinal plants. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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23 pages, 3676 KiB

Open AccessArticle

Symbiotic and Asymbiotic Germination of Dendrobium officinale (Orchidaceae) Respond Differently to Exogenous Gibberellins

by Juan Chen, Bo Yan, Yanjing Tang, Yongmei Xing, Yang Li, Dongyu Zhou and Shunxing Guo

Int. J. Mol. Sci. 2020, 21(17), 6104; https://doi.org/10.3390/ijms21176104 - 25 Aug 2020

Cited by 18 | Viewed by 4020

Abstract

Seeds of almost all orchids depend on mycorrhizal fungi to induce their germination in the wild. The regulation of this symbiotic germination of orchid seeds involves complex crosstalk interactions between mycorrhizal establishment and the germination process. The aim of this study was to investigate the effect of gibberellins (GAs) on the symbiotic germination of Dendrobium officinale seeds and its functioning in the mutualistic interaction between orchid species and their mycobionts. To do this, we used liquid chromatograph-mass spectrometer to quantify endogenous hormones across different development stages between symbiotic and asymbiotic germination of D. officinale, as well as real-time quantitative PCR to investigate gene expression levels during seed germination under the different treatment concentrations of exogenous gibberellic acids (GA₃). Our results showed that the level of endogenous GA₃ was not significantly different between the asymbiotic and symbiotic germination groups, but the ratio of GA₃ and abscisic acids (ABA) was significantly higher during symbiotic germination than asymbiotic germination. Exogenous GA₃ treatment showed that a high concentration of GA₃ could inhibit fungal colonization in the embryo cell and decrease the seed germination rate, but did not significantly affect asymbiotic germination or the growth of the free-living fungal mycelium. The expression of genes involved in the common symbiotic pathway (e.g., calcium-binding protein and calcium-dependent protein kinase) responded to the changed concentrations of exogenous GA₃. Taken together, our results demonstrate that GA₃ is probably a key signal molecule for crosstalk between the seed germination pathway and mycorrhiza symbiosis during the orchid seed symbiotic germination. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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17 pages, 3530 KiB

Open AccessArticle

Upregulation of the MYB2 Transcription Factor is Associated with Increased Accumulation of Anthocyanin in the Leaves of Dendrobium bigibbum

by Gah-Hyun Lim, Se Won Kim, Jaihyunk Ryu, Si-Yong Kang, Jin-Baek Kim and Sang Hoon Kim

Int. J. Mol. Sci. 2020, 21(16), 5653; https://doi.org/10.3390/ijms21165653 - 6 Aug 2020

Cited by 14 | Viewed by 3391

Abstract

Orchids with colorful leaves and flowers have significant ornamental value. Here, we used γ-irradiation-based mutagenesis to produce a Dendrobium bigibbum mutant that developed purple instead of the normal green leaves. RNA sequencing of the mutant plant identified 2513 differentially expressed genes, including 1870 up- and 706 downregulated genes. The purple leaf color of mutant leaves was associated with increased expression of genes that encoded key biosynthetic enzymes in the anthocyanin biosynthetic pathway. In addition, the mutant leaves also showed increased expression of several families of transcription factors including the MYB2 gene. Transient overexpression of D. biggibumMYB2 in Nicotiana benthamiana was associated with increased expression of endogenous anthocyanin biosynthesis genes. Interestingly, transient overexpression of orthologous MYB2 genes from other orchids did not upregulate expression of endogenous anthocyanin biosynthesis genes. Together, these results suggest that the purple coloration of D. biggibum leaves is at least associated with increased expression of the MYB2 gene, and the MYB2 orthologs from orchids likely function differently, regardless of their high level of similarity. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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22 pages, 13695 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profile of TPS Gene Family in Dendrobium officinale and the Role of DoTPS10 in Linalool Biosynthesis

by Zhenming Yu, Conghui Zhao, Guihua Zhang, Jaime A. Teixeira da Silva and Jun Duan

Int. J. Mol. Sci. 2020, 21(15), 5419; https://doi.org/10.3390/ijms21155419 - 30 Jul 2020

Cited by 64 | Viewed by 6560

Abstract

Terpene synthase (TPS) is a critical enzyme responsible for the biosynthesis of terpenes, which possess diverse roles in plant growth and development. Although many terpenes have been reported in orchids, limited information is available regarding the genome-wide identification and characterization of the TPS family in the orchid, Dendrobium officinale. By integrating the D. officinale genome and transcriptional data, 34 TPS genes were found in D. officinale. These were divided into four subfamilies (TPS-a, TPS-b, TPS-c, and TPS-e/f). Distinct tempospatial expression profiles of DoTPS genes were observed in 10 organs of D. officinale. Most DoTPS genes were predominantly expressed in flowers, followed by roots and stems. Expression of the majority of DoTPS genes was enhanced following exposure to cold and osmotic stresses. Recombinant DoTPS10 protein, located in chloroplasts, uniquely converted geranyl diphosphate to linalool in vitro. The DoTPS10 gene, which resulted in linalool formation, was highly expressed during all flower developmental stages. Methyl jasmonate significantly up-regulated DoTPS10 expression and linalool accumulation. These results simultaneously provide valuable insight into understanding the roles of the TPS family and lay a basis for further studies on the regulation of terpenoid biosynthesis by DoTPS in D. officinale. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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Review

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19 pages, 7512 KiB

Open AccessReview

Evolution of Terpene Synthases in Orchidaceae

by Li-Min Huang, Hsin Huang, Yu-Chen Chuang, Wen-Huei Chen, Chun-Neng Wang and Hong-Hwa Chen

Int. J. Mol. Sci. 2021, 22(13), 6947; https://doi.org/10.3390/ijms22136947 - 28 Jun 2021

Cited by 23 | Viewed by 4686

Abstract

Terpenoids are the largest class of plant secondary metabolites and are one of the major emitted volatile compounds released to the atmosphere. They have functions of attracting pollinators or defense function, insecticidal properties, and are even used as pharmaceutical agents. Because of the importance of terpenoids, an increasing number of plants are required to investigate the function and evolution of terpene synthases (TPSs) that are the key enzymes in terpenoids biosynthesis. Orchidacea, containing more than 800 genera and 28,000 species, is one of the largest and most diverse families of flowering plants, and is widely distributed. Here, the diversification of the TPSs evolution in Orchidaceae is revealed. A characterization and phylogeny of TPSs from four different species with whole genome sequences is available. Phylogenetic analysis of orchid TPSs indicates these genes are divided into TPS-a, -b, -e/f, and g subfamilies, and their duplicated copies are increased in derived orchid species compared to that in the early divergence orchid, A. shenzhenica. The large increase of both TPS-a and TPS-b copies can probably be attributed to the pro-duction of different volatile compounds for attracting pollinators or generating chemical defenses in derived orchid lineages; while the duplications of TPS-g and TPS-e/f copies occurred in a species-dependent manner. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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