Next Article in Journal
Molecular Research in Pancreatic Cancer: Small Molecule Inhibitors, Their Mechanistic Pathways and Beyond
Next Article in Special Issue
Early Fruit Development Regulation-Related Genes Concordantly Expressed with TCP Transcription Factors in Tomato (Solanum lycopersicum)
Previous Article in Journal
Ductal Hyperkeratinization and Acinar Renewal Abnormality: New Concepts on Pathogenesis of Meibomian Gland Dysfunction
Previous Article in Special Issue
Genetic Diversity Analysis of Banana Cultivars (Musa sp.) in Saudi Arabia Based on AFLP Marker
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
CIMB
Volume 45
Issue 3
10.3390/cimb45030123
cimb-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Cloning of Three Cytokinin Oxidase/Dehydrogenase Genes in Bambusa oldhamii

by
Chun-Yen Hsieh
1 and
Lu-Sheng Hsieh
2,*
1
Department of Pathology and Laboratory Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei City 11101, Taiwan
2
Department of Food Science, College of Agriculture, Tunghai University, Taichung 40704, Taiwan
*
Author to whom correspondence should be addressed.
Curr. Issues Mol. Biol. 2023, 45(3), 1902-1913; https://doi.org/10.3390/cimb45030123
Submission received: 4 February 2023 / Revised: 23 February 2023 / Accepted: 24 February 2023 / Published: 27 February 2023
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)
Browse Figures
Versions Notes

Abstract

:
Cytokinin oxidase/dehydrogenase (CKX) catalyzes the irreversible breakdown of active cytokinins, which are a class of plant hormones that regulate cell division. According to conserved sequences of CKX genes from monocotyledons, PCR primers were designed to synthesize a probe for screening a bamboo genomic library. Cloned results of three genes encoding cytokinin oxidase were named as follows: BoCKX1, BoCKX2, and BoCKX3. In comparing the exon-intron structures among the above three genes, there are three exons and two introns in BoCKX1 and BoCKX3 genes, whereas BoCKX2 contains four exons and three introns. The amino acid sequence of BoCKX2 protein shares 78% and 79% identity with BoCKX1 and BoCKX3 proteins, respectively. BoCKX1 and BoCKX3 genes are particularly closely related given that the amino acid and nucleotide sequence identities are more than 90%. These three BoCKX proteins carried putative signal peptide sequences typical of secretion pathway, and a GHS-motif was found at N-terminal flavin adenine dinucleotide (FAD) binding domain, suggesting that BoCKX proteins might covalently conjugate with an FAD cofactor through a predicted histidine residue.

1. Introduction

Cytokinin is a phytohormone of plant growth regulators, playing an important role in the control of plant division. Many developmental events, such as shoot and root branching, leaf development, delay of senescence, and chloroplast ripening are directly regulated by the physiological functions of cytokinins [1,2,3,4,5]. In plants, the homeostasis of cytokinins is balanced in many aspects [6], including rate of de novo synthesis by isopentenyl transferase enzyme [7], rate of interconversion and transport [8], and rate of cytokinin turnover, mainly by cytokinin oxidase/dehydrogenase [9].
The CKX gene-encoded cytokinin oxidase/dehydrogenase enzyme (CKX, EC 1.5.99.12) catalyzes the turnover of the cytokinins, isopentenyl-adenine, zeatin, and their ribosides by a unique enzymatic reaction by cleaving and oxidizing its side chain for converting isopentenyladenine to unsaturated 3-methyl-2-butenal and adenine [2,10]. CKX enzyme activity was initially identified by Pačes and coworkers in 1971 [11] and named by Whitty and Hall in 1974 [12]. After nearly three decades, ZmCKX1 was the first CKX gene independently cloned by two research groups in maize Zea mays [13,14]. CKX proteins are usually encoded by homologous genes in plants, such as Arabidopsis thaliana [15,16], Hordeum vulgare [17,18], Jatropha curcas [19], Oryza sativa [9,20,21], Zea mays [22,23], and so on. Recently, 23 BnCKX genes were identified in Brassica napus [24]. Therefore, CKX enzyme activity largely governs the utilization of cytokinins in plant cells.
Elevated cytokinin levels were linked with increased cytokinin degradation by CKX enzyme in many plants, such as Zea mays [25], Triticum aestivum [26], and Brassica napus [24,27], suggesting that CKX gene expression is manipulated by endogenous cytokinin extents [5]. Overexpression of the AtCKX3 [28] and OsCKX2 [9] are associated with reduced flower numbers and grain numbers, respectively. Expression of the AtCKX1 in Nicotiana tabacum enhances drought and heat stress tolerance, indicating that cytokinin levels may have a positive effect on plant stress responses [29,30,31]. Under salinity condition, rice yield penalty is reduced by knockdown of the OsCKX2 gene as well as increased inflorescence meristem cytokinin extent [32].
Alternation in CKX enzymatic activity changes cytokinin concentrations in cells and tissues. CKX enzymes play key roles in contributing to the regulation of cytokinin-dependent processes and in controlling local cytokinin level [33]. Functions of CKX proteins can be regulated by several post-translational modifications, e.g., glycosylation, and contain FAD as a cofactor [21,34]. CKX proteins are widely detected in various subcellular compartments, such as chloroplast, mitochondria, and so on [35]. Most CKX enzymes are localized in the apoplast, e.g., ZmCKX1 [23], or vacuole, e.g., AtCKX1 and AtCKX3 [36]. Some CKX proteins are shown to be cytosolic enzymes, such as AtCKX7 [37] and ZmCKX10 [23]. AtCKX1 protein is recently reported to be an endoplasmic reticulum (ER) membrane protein [16].
Bambusa oldhamii, green bamboo, is a perennial plant in the tropics and subtropics, and bamboo shoot is an economic vegetable in far-eastern Asia [38,39,40,41,42,43,44]. Bamboo is one of the fast-growth timber plants, which are controlled by plant hormones, especially cytokinins [45]. Bamboo cytokinin biosynthesis by the BoAIPT1 isopentenyltransferase enzyme [7] and cytokinin degradation by the BoCKX enzymes may play equally important roles for fine-tuning cytokinin levels in the rapid-dividing tissues. In this study, we cloned and reported three completely sequenced CKX genes, including all exon-intron conformations and partial upstream promoter regions. Sequence analysis of the BoCKX1–3 predicts multiple asparagine residues as putative target sites of glycosylation. In addition, several cis-acting elements were discovered from the promoters regions of three BoCKX genes.

2. Materials and Methods

2.1. Plant Material

Edible fresh green bamboo shoot mainly harvested between April and September from Mucha mountain areas, Taipei City, Taiwan. Samples were divided into inedible shell and edible shoot and were frozen and stored at −80 °C freezer.

2.2. Reagents

DNA ladders and iProof DNA polymerase were obtained from Bio-Rad, Hercules, CA, USA. PrimeStar DNA polymerase mixture was purchased from Takara, Kusatsu, Shiga, Japan. T4 DNA ligase and restriction endonucleases were purchased from New England Biolabs, Ipswich, MA, USA. SeaKem® LE Agarose was obtained from Lonza, Basel, Switzerland. Gel extraction/PCR cleanup kit was purchased from Biotools, New Taipei City, Taiwan. Plasmid mini-prep kit was obtained from Geneaid, New Taipei City, Taiwan. Oligonucleotides synthesis and DNA sequencing services were provided by Tri-I Biotech, New Taipei City, Taiwan.

2.3. Total RNA Extraction, cDNA Synthesis, and DIG Labeled Probe Preparation

TRIZOL reagents (Invitrogen, Waltham, MA, USA) were used to extract total RNA from bamboo etiolated shoots and utilized as materials for complementary DNA (cDNA) synthesis using MMLV reverse transcriptase (Invitrogen, Waltham, MA, USA), and used as PCR template. Degenerate primers CKX-F (5′-GGGAGATGGTGACGTGCTCCAA-3′) and CKX-R (5′-CAGCGACACSRMGTAGAACAC-3′) were designed according to the conserved regions of the OsCKX1 and OsCKX2 genes from Oryza sativa [4]. PCR reaction was carried out at 94 °C for 30 s, 60 °C for 30 s, and 72 °C for 1 min, and then repeated for 30 cycle-reaction. The 900 bp BoCKX fragment (Figure S1) was confirmed by DNA sequencing (Tri-I Biotech, New Taipei City, Taiwan). DIG-labeled probe was synthesized by PCR reaction using DIG DNA labeling kit supplied by Roche, Basel, Switzerland.

2.4. Genomic Library Screening, Phage DNA Preparation, and DNA Sequencing by Chromosome Walking

A genomic library of green bamboo was previously constructed by Lambda FIX® II/XhoI Partial Fill-In Vector Kit (Strategene, San Diego, CA, USA) [7]. Nine to twenty-three kb bamboo genomic DNA fragments were conjugated with a 41.9 kb Lambda FIX® II vector, and the overall phage DNA constructed were between 50 and 65 kb [7]. The DIG-labeled BoCKX probe was used to screen the bamboo genomic DNA library. Plaques of phages were transferred onto a Hybond-H+ hybridization membrane (MilliporeSigma, Burlington, MA, USA). The processes of hybridization and detection were based on the instructions of the manufacturer (Roche, Basel, Switzerland). Phage DNA was purified from E. coli XL1-Blue MRA (P2) by traditional method [46] and digested by NotI restriction endonuclease. Phage DNA isolated from positive clones (Lambda midi kit, Qiagene, Hilden, Germany) were further confirmed by DNA sequencing (Tri-I Biotech, New Taipei City, Taiwan), and chromosome walking method was used to obtain complete genomic sequences of the three BoCKX genes.

2.5. Bioinformatics and Promoter Analysis

Protein sequence alignment was analyzed by Vector NTI Suite 10 Sequence Software (Invitrogen, Waltham, MA, USA). Phosphorylation and glycosylation sites were predicted by NetNGly (http://www.cbs.dtu.dk/servies/NetNGly/, accessed on 15 March 2020) [47] and NetPhos (http://www.cbs.dtu.dk/services/NetPhos/, accessed on 15 March 2020) [48], respectively. The putative cis-acting elements and the transcriptional start site were predicted by PlantPAN (retrieved from: http://PlantPAN.itps.ncku.edu.tw, accessed on 25 May 2020) [49] and PlantProm (retrieved from: http://mendel.cs.rhul.ac.uk, accessed on 25 May 2020) [50].

3. Results

3.1. Cloning of Three BoCKXs Genes by Screening a Bamboo Genomic DNA Library

A Lambda FIX® II genomic library constructed genomic DNA was hybridized and screened by a DIG labeled BoCKX probe (Figure S1) [38]. Sequence alignment results showed a high similarity of 64% between the deduced amino acid sequence of the BoCKX probe and ZmCKX1 proteins (Figure S1). Phage DNAs were isolated from positive clones and digested by NotI restriction enzyme (Figure 1), followed by DNA sequencing. Three different digestion patterns from four positive clones were observed, indicating that three different BoCKX genes were identified. Chromosome walking methodology was performed to obtain the total sequence information of these positive clones. Luckily, three full-length BoCKX genes with partial promoter regions were obtained, namely BoCKX1 (Figure 1A, lane 1), BoCKX2 (Figure 1B, lanes 1 and 2), and BoCKX3 (Figure 1A, lane 2). Gene names, BoCKX1–3, were designated in the order of DNA sequencing accomplished. These genomic DNA sequences had been deposited at GenBank (Bethesda, MD, USA) with accession numbers, GU263785, GU263786, and GU263787, respectively.

3.2. Genomic Organization of the Three BoCKXs Genes

Phage DNA containing bamboo CKX genes were completely sequenced by chromosome walking method, and exon-intron structures of the three BoCKX genes were plotted in Figure 2A. The intron-exon organizations of various CKX genes in plants were compared and shown in Figure 2B. BoCKX1 contained a 1578 bp open-reading frame (ORF) and encoded a 525 amino acid polypeptide or a 57.0 kDa protein (Figure 2A). BoCKX2 contained a 1572 bp ORF and encoded a 523 amino acid polypeptide or a 57.4 kDa protein (Figure 2A). BoCKX3 contained a 1569 bp ORF and encoded a 522 amino acid polypeptide or a 56.6 kDa protein (Figure 2A).
BoCKX1 and BoCKX3 were composed of three exons and two introns (Figure 2A,B), as also observed in other CKX genes, such as OsCKX1 [4] and ZmCKX1 [13,14]. Unlike BoCKX1 and BoCKX3, the exon 2 of BoCKX2 was divided into exons 2a and 2b (Figure 2A,B). As a result, BoCKX2 possessed four exons and three introns, similar to Dendrobium sonia DsCKX1 [51] and OsCKX2 (Figure 2B) [4]. AtCKX1–6 genes all consisted of four introns and five exons (Figure 2B) [15].

3.3. Protein Similarity of CKXs Proteins

Protein sequence alignment research revealed that BoCKX proteins had 71–92% identities, with BoCKX1 protein being the most similar to BoCKX3 protein (92% identity; Figure 3 and Table 1).
The deduced amino acid sequences of CKXs from several plant species underwent phylogenetic analysis (Figure 4). All CKX protein sequences contained a conserved GHS motif as the FAD-binding site and the histidine residue within the GHS motif may be responsible for covalently conjugated with FAD cofactor [34]. OsCKX1 and ZmCKX1 proteins were the closest homolog to BoCKX1 (78% identity) and BoCKX3 (76% identity) proteins, and these genes contained similar exon-intron organization (Figure 2B, Figure 4). Although BoCKX2 and OsCKX2 shared identical genomic organization (Figure 2B, Figure 4), the amino acid similarity was only 52% identity.

3.4. Analysis of the cis-Acting Elements in BoCKX1

To better understand the potential transcriptional regulations, the upstream sequence of the BoCKX1 was completely sequenced and limited promoter region (−262) was obtained (Figure 5). PlantProm [50] predicted the probable transcriptional start site (+1) of BoCKX1, which was situated 83 base pairs from the translational start codon (ATG, Figure 5). Promoter sequence analysis was obtained from PlantPAN [49], and a putative TATA box and an NGATT motif [52] were addressed at −27 and −235 positions, respectively (Figure 5).

3.5. Analysis of the cis-Acting Elements in BoCKX2

To better understand the potential transcriptional regulations, the upstream sequence of the BoCKX2 was completely sequenced and over 1.4 kb promoter region was obtained (Figure 6). PlantProm [50] predicted the probable transcriptional start site (+1) of BoCKX2, which was situated 44 base pairs from the translational start codon (ATG, Figure 6). Promoter sequence analysis was performed by PlantPAN [49], and a putative TATA box and CAAT box were addressed at −27 and −40 positions, respectively (Figure 6). Among the promoter region, nine NGATT motifs [52] and one as-1 like conserved site (−1289) [53] were identified (Figure 6).

3.6. Analysis of the cis-Acting Elements in BoCKX3

To better understand the potential transcriptional regulations, the upstream sequence of the BoCKX3 was completely sequenced and ~1.2 kb promoter region was obtained (Figure 7). PlantProm [50] predicted the probable transcriptional start site (+1) of BoCKX2, which was situated 79 base pairs from the translational start codon (ATG, Figure 7). Promoter sequence analysis was obtained by PlantPAN [49], a putative TATA box was addressed at −24 position, and five NGATT conserved regions [52] were boxed (Figure 7).

3.7. Comparison of Features in Plant CKX Proteins

CKX proteins had been reported to localize at different compartments [16,23,36,37], and some of them were secreted proteins [23]. All three BoCKX proteins were predicted to carry putative signal peptide sequences typical of secretion pathway (Table 2). Cytosolic and vacuolar forms of CKX were identified in other species [16,36], suggesting that there still may be some unknown BoCKX genes in B. oldhamii.
CKX functions are regulated by post-translational modifications, e.g., glycosylation. All CKX proteins were predicted to be glycoproteins (Table 2), and maize CKXs had been shown to be glycoproteins [14]. By using the NetNGly algorithms, BoCKX1, BoCKX2, and BoCKX3 had seven, five, and six putative glycosylation sites and at least five of them were more than 50% probability (Table 2), implying that BoCKX1–3 may be glycoproteins. In addition to glycosylation, many phosphorylation sites were predicted in BoCKX1–3 (Table 3); however, substantial results are needed.

4. Discussion

A multi-gene family of CKX in plants has been reported previously [17,36]. In this study, we identified three cytokinin oxidase/dehydrogenase genes from green bamboo by screening a bamboo genomic DNA library (Figure 1). In the genomic DNA library construction, 9–23 kb bamboo genomic fragments were ligated with a phage vector [7]. Fortunately, four positive clones isolated contained three full coding regions as well as different sizes promoter regions (Figure 1). BoCKX1 and BoCKX3 genes had identical exon-intron structures (Figure 2A) as well as 92% amino acid sequence identity (Table 1). The exon-intron structure of the BoCKX2 was slightly different in comparison with the above two genes (Figure 2A). All three BoCKX genes showed similar exon-intron organizations between other CKX genes (Figure 2B). In theory, cytoplasmic, ER-membrane, or vascular-localized CKX should exist in green bamboo, and more screening of bamboo genomic DNA can be performed.
Several putative cis-acting elements were predicted from promoter regions of the BoCKX1–3 genes (Figure 5, Figure 6, and Figure 7), and the functions of the motifs were listed in Table 3. All three BoCKX genes contained a conserved TATA box and a typical CAAT box was identified in the upstream site of TATA box of the BoCKX2 [50]. CKX gene expression is induced by abiotic stress and plant hormones, such as abscisic acid and cytokinins [25]. As-1 box [53,56,57] and NGATT motif [52,58,59] were present in the 5′-flanking regions of BoCKX genes, suggesting that the BoCKX gene expressions may be affected by different plant hormones and cytokinin response regulator proteins.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cimb45030123/s1, Figure S1: Alignment of the deduced amino acid sequences of BoCKX-specific probe and ZmCKX1.

Author Contributions

Methodology, C.-Y.H. and L.-S.H.; validation, L.-S.H.; investigation, C.-Y.H. and L.-S.H.; resources, C.-Y.H. and L.-S.H.; data curation, L.-S.H.; writing—original draft preparation, C.-Y.H. and L.-S.H.; writing—review and editing, L.-S.H.; supervision, L.-S.H.; project administration, L.-S.H.; funding acquisition, C.-Y.H. and L.-S.H. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by research grants from the Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan (2020SKHAND006 to C.-Y.H.) and from the National Science and Technology Council, Taiwan (NSTC 110-2313-B-029-001-MY3 to L.-S.H.).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data are contained in the main article.

Acknowledgments

The authors appreciate Ai-Yu Wang for providing the bamboo genomic DNA library and GiGi Chin Wen Lim for critically amending this manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Gan, S.; Amasino, R.M. Inhibition of leaf senescence by autoregulated production of cytokinin. Science 1995, 270, 1986–1988. [Google Scholar] [CrossRef]
  2. Mok, D.W.S.; Mok, M.C. Cytokinin metabolism and action. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2001, 52, 89–118. [Google Scholar] [CrossRef] [PubMed]
  3. Werner, T.; Schmülling, T. Cytokinin action in plant development. Curr. Opin. Plant Biol. 2009, 12, 527–538. [Google Scholar] [CrossRef] [PubMed]
  4. Tsai, Y.C.; Weir, N.R.; Hill, K.; Zhang, W.; Kim, H.J.; Shiu, S.H.; Schaller, G.E.; Kieber, J.J. Characterization of genes involved in cytokinin signaling and metabolism from rice. Plant Physiol. 2012, 158, 1666–1684. [Google Scholar] [CrossRef] [Green Version]
  5. Jameson, P.E.; Song, J. Cytokinin: A key driver of seed yield. J. Exp. Bot. 2016, 67, 593–606. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  6. Chen, L.; Zhao, J.; Song, J.; Jameson, P.E. Cytokinin glucosyl transferases, key regulators of cytokinin homeostasis, have potential value for wheat improvement. Plant Biotechnol. J. 2021, 19, 878–896. [Google Scholar] [CrossRef] [PubMed]
  7. Yeh, C.S.; Hsieh, L.S.; Yang, C.C.; Lee, P.D. Molecular characterization of isopentenyltransferase (BoAIPT1) from Bambusa oldhamii expressed in Escherichia coli. Bot. Stud. 2011, 52, 249–256. [Google Scholar]
  8. Sakakibara, H. Cytokinins: Activity, biosynthesis, and translocation. Annu. Rev. Plant Biol. 2006, 57, 431–449. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  9. Ashikari, M.; Sakakibara, H.; Lin, S.; Yamamoto, T.; Takashi, T.; Nishimura, A.; Angeles, E.R.; Qian, Q.; Kitano, H.; Matsuoka, M. Cytokinin oxidase regulates rice grain production. Science 2005, 309, 741–745. [Google Scholar] [CrossRef]
  10. Werner, T.; Köllmer, I.; Bartrina, I.; Holst, K.; Schmülling, T. New insights into the biology of cytokinin degradation. Plant Biol. 2006, 8, 371–381. [Google Scholar] [CrossRef]
  11. Pačes, V.; Werstiuk, E.; Hall, R.H. Conversion of N6-(D2-isopentenyl) adenosine to adenosine by enzyme activity in tobacco tissue. Plant Physiol. 1971, 48, 775–778. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  12. Whitty, C.D.; Hall, R.H. A cytokinin oxidase in Zea mays. Can. J. Biochem. 1974, 52, 787–799. [Google Scholar] [CrossRef] [PubMed]
  13. Houba-Hérin, N.; Pethe, C.; d’Alayer, J.; Laloue, M. Cytokinin oxidase from Zea mays: Purification, cDNA cloning and expression in moss protoplasts. Plant J. 1999, 17, 615–626. [Google Scholar] [CrossRef] [PubMed]
  14. Morris, R.O.; Bilyeu, K.D.; Laskey, J.G.; Cheikh, N.N. Isolation of a gene encoding a glycosylated cytokinin oxidase from maize. Biochem. Biophys. Res. Commun. 1999, 255, 328–333. [Google Scholar] [CrossRef]
  15. Vision, T.J.; Brown, D.G.; Tanksley, S.D. The origins of genomic duplications in Arabidopsis. Science 2000, 290, 2114–2117. [Google Scholar] [CrossRef] [Green Version]
  16. Niemann, M.C.E.; Weber, H.; Hluska, T.; Leonte, G.; Anderson, S.M.; Novák, O.; Senes, A.; Werner, T. The cytokinin oxidase/dehydrogenase CKX1 is a membrane-bound protein requiring homooligomerization in the endoplasmic reticulum for its cellular activity. Plant Physiol. 2018, 176, 2024–2039. [Google Scholar] [CrossRef]
  17. Galuszka, P.; Frébortová, J.; Werner, T.; Yamada, M.; Strnad, M.; Schmülling, T.; Frébort, I. Cytokinin oxidase/dehydrogenase genes in barley and wheat: Cloning and heterologous expression. Eur. J. Biochem. 2004, 271, 3990–4002. [Google Scholar] [CrossRef]
  18. Gasparis, S.; Przyborowski, M.; Kała, M.; Nadolska-Orczyk, A. Knockout of the HvCKX1 or HvCKX3 gene in barley (Hordeum vulgare L.) by RNA-guided cas9 nuclease affects the regulation of cytokinin metabolism and root morphology. Cells 2019, 8, 782. [Google Scholar] [CrossRef] [Green Version]
  19. Cai, L.; Zhang, L.; Fu, Q.; Xu, Z.F. Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas. PeerJ 2018, 6, e4812. [Google Scholar] [CrossRef] [Green Version]
  20. Gao, S.; Fang, J.; Xu, F.; Wang, W.; Sun, X.; Chu, J.; Cai, B.; Feng, Y.; Chu, C. Cytokinin oxidase/dehydrogenase 4 integrates cytokinin and auxin signaling to control rice crown root formation. Plant Physiol. 2014, 165, 1035–1046. [Google Scholar] [CrossRef] [Green Version]
  21. Yeh, S.Y.; Chen, H.W.; Ng, C.Y.; Lin, C.Y.; Tseng, T.H.; Li, W.H.; Ku, M. Down-regulation of cytokinin oxidase 2 expression increases tiller number and improves rice yield. Rice 2015, 8, 36. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Massonneau, A.; Houba-Hérin, N.; Pethe, C.; Madzak, C.; Falque, M.; Mercy, M.; Kopecny, D.; Majira, A.; Rogowsky, P.; Laloue, M. Maize cytokinin oxidase genes: Differential expression and cloning of two new cDNAs. J. Exp. Bot. 2004, 55, 2549–2557. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Smehilová, M.; Galuszka, P.; Bilyeu, K.D.; Jaworek, P.; Kowalska, M.; Sebela, M.; Sedlárová, M.; English, J.T.; Frébort, I. Subcellular localization and biochemical comparison of cytosolic and secreted cytokinin dehydrogenase enzymes from maize. J. Exp. Bot. 2009, 60, 2701–2712. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Liu, P.; Zhang, C.; Ma, J.Q.; Zhang, L.Y.; Yang, B.; Tang, X.Y.; Huang, L.; Zhou, X.T.; Lu, K.; Li, J.N. Genome-wide identification and expression profiling of cytokinin oxidase/dehydrogenase (CKX) genes reveal likely roles in pod development and stress responses in oilseed rape (Brassica napus L.). Genes 2018, 9, 168. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Brugière, N.; Jiao, S.; Hantke, S.; Zinselmeier, C.; Roessler, J.A.; Niu, X.; Jones, R.J.; Habben, J.E. Cytokinin oxidase gene expression in maize is localized to the vasculature, and is induced by cytokinins, abscisic acid, and abiotic stress. Plant Physiol. 2003, 132, 1228–1240. [Google Scholar] [CrossRef] [Green Version]
  26. Song, J.; Jiang, L.; Jameson, P.E. Co-ordinate regulation of cytokinin gene family members during flag leaf and reproductive development in wheat. BMC Plant Biol. 2012, 12, 78. [Google Scholar] [CrossRef] [Green Version]
  27. Song, J.; Jiang, L.; Jameson, P.E. Expression patterns of Brassica napus genes implicate IPT, CKX, sucrose transporter, cell wall invertase and amino acid permease gene family members in leaf, flower, silique and seed development. J. Exp. Bot. 2015, 66, 5067–5082. [Google Scholar] [CrossRef] [Green Version]
  28. Werner, T.; Motyka, V.; Laucou, V.; Smets, R.; Van Onckelen, H.; Schmülling, T. Cytokinin-deficient transgenic Arabidopsis plants show multiple developmental alterations indicating opposite functions of cytokinins in the regulation of shoot and root meristem activity. Plant Cell 2003, 15, 2532–2550. [Google Scholar] [CrossRef] [Green Version]
  29. Nishiyama, R.; Watanabe, Y.; Fujita, Y.; Le, D.T.; Kojima, M.; Werner, T.; Vankova, R.; Yamaguchi-Shinozaki, K.; Shinozaki, K.; Kakimoto, T.; et al. Analysis of cytokinin mutants and regulation of cytokinin metabolic genes reveals important regulatory roles of cytokinins in drought, salt and abscisic acid responses, and abscisic acid biosynthesis. Plant Cell 2011, 23, 2169–2183. [Google Scholar] [CrossRef] [Green Version]
  30. Macková, H.; Hronková, M.; Dobrá, J.; Turečková, V.; Novák, O.; Lubovská, Z.; Motyka, V.; Haisel, D.; Hájek, T.; Prášil, I.T.; et al. Enhanced drought and heat stress tolerance of tobacco plants with ectopically enhanced cytokinin oxidase/dehydrogenase gene expression. J. Exp. Bot. 2013, 64, 2805–2815. [Google Scholar] [CrossRef]
  31. Lubovská, Z.; Dobrá, J.; Storchová, H.; Wilhelmová, N.; Vanková, R. Cytokinin oxidase/dehydrogenase overexpression modifies antioxidant defense against heat, drought and their combination in Nicotiana tabacum plants. J. Plant Physiol. 2014, 171, 1625–1633. [Google Scholar] [CrossRef] [PubMed]
  32. Joshi, R.; Sahoo, K.K.; Tripathi, A.K.; Kumar, R.; Gupta, B.K.; Pareek, A.; Singla-Pareek, S.L. Knockdown of an inflorescence meristem-specific cytokinin oxidase—OsCKX2 in rice reduces yield penalty under salinity stress condition. Plant Cell Environ. 2018, 41, 936–946. [Google Scholar] [CrossRef]
  33. Rinaldi, A.C.; Comandini, O. Cytokinin oxidase strikes again. Trends Plant Sci. 1999, 4, 300. [Google Scholar] [CrossRef] [PubMed]
  34. Bilyeu, K.D.; Cole, J.L.; Laskey, J.G.; Riekhof, W.R.; Esparza, T.J.; Kramer, M.D.; Morris, R.O. Molecular and biochemical characterization of a cytokinin oxidase from maize. Plant Physiol. 2001, 125, 378–386. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  35. Schmülling, T.; Werner, T.; Riefler, M.; Krupková, E.; Bartrina y Manns, I. Structure and function of cytokinin oxidase/dehydrogenase genes of maize, rice, Arabidopsis and other species. J. Plant Res. 2003, 116, 241–252. [Google Scholar] [CrossRef]
  36. Bilyeu, K.D.; Frébort, I. Vacuolar and cytosolic cytokinin dehydrogenases of Arabidopsis thaliana: Heterologous expression, purification and properties. Phytochemistry 2010, 71, 1970–1978. [Google Scholar] [CrossRef]
  37. Köllmer, I.; Novák, O.; Strnad, M.; Schmülling, T.; Werner, T. Overexpression of the cytosolic cytokinin oxidase/dehydrogenase (CKX7) from Arabidopsis causes specific changes in root growth and xylem differentiation. Plant J. 2014, 78, 359–371. [Google Scholar] [CrossRef] [PubMed]
  38. Hsieh, L.S.; Ma, G.J.; Yang, C.C.; Lee, P.D. Cloning, expression, site-directed mutagenesis and immunolocalization of phenylalanine ammonia-lyase in Bambusa oldhamii. Phytochemistry 2010, 71, 1999–2009. [Google Scholar] [CrossRef]
  39. Hsieh, L.S.; Hsieh, Y.L.; Yeh, C.S.; Cheng, C.Y.; Yang, C.C.; Lee, P.D. Molecular characterization of a phenylalanine ammonia-lyase gene (BoPAL1) from Bambusa oldhamii. Mol. Biol. Rep. 2011, 38, 283–290. [Google Scholar] [CrossRef]
  40. Hsieh, C.Y.; Huang, Y.H.; Lin, Z.Y.; Hsieh, L.S. Insights into the substrate selectivity of Bambusa oldhamii phenylalanine ammonia-lyase 1 and 2 through mutational analysis. Phytochem. Lett. 2020, 38, 140–143. [Google Scholar] [CrossRef]
  41. Hsiao, C.J.; Hsieh, C.Y.; Hsieh, L.S. Cloning and characterization of the Bambusa oldhamii BoMDH-encoded malate dehydrogenase. Protein Expr. Purif. 2020, 174, 105665. [Google Scholar] [CrossRef]
  42. Hong, P.Y.; Huang, Y.H.; Lim, G.G.C.W.; Chen, Y.P.; Hsiao, C.J.; Chen, L.H.; Ciou, J.Y.; Hsieh, L.S. Production of trans-cinnamic acid by immobilization of the Bambusa oldhamii BoPAL1 and BoPAL2 phenylalanine ammonia-lyases on electrospun nanofibers. Int. J. Mol. Sci. 2021, 22, 11184. [Google Scholar] [CrossRef]
  43. Hsieh, C.Y.; Huang, Y.H.; Yeh, H.H.; Hong, P.Y.; Hsiao, C.J.; Hsieh, L.S. Phenylalanine, tyrosine, and DOPA are bona fide substrates for Bambusa oldhamii BoPAL4. Catalysts 2021, 11, 1263. [Google Scholar] [CrossRef]
  44. Huang, Y.H.; You, W.C.; Hong, P.Y.; Chang, Y.T.; Ciou, J.Y.; Hsieh, L.S. Molecular characterization of the Bambusa oldhamii BoPAL3-encoded phenylalanine ammonia-lyase. Phytochem. Lett. 2022, 48, 15–18. [Google Scholar] [CrossRef]
  45. Gamuyao, R.; Nagai, K.; Ayano, M.; Mori, Y.; Minami, A.; Kojima, M.; Suzuki, T.; Sakakibara, H.; Higashiyama, T.; Ashikari, M.; et al. Hormone distribution and transcriptome profiles in bamboo shoots provide insights on bamboo stem emergence and growth. Plant Cell Physiol. 2017, 58, 702–716. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  46. Jakočiūnė, D.; Moodley, A. A rapid bacteriophage DNA extraction method. Methods Protoc. 2018, 1, 27. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  47. Gupta, R.; Jung, E.; Brunak, S. Prediction of N-glycosylation Sites in Human Proteins. 2004. Available online: https://www.cbs.dtu.dk/services/NetNGlyc/ (accessed on 15 March 2020).
  48. Blom, N.; Sicheritz-Pontén, T.; Gupta, R.; Gammeltoft, S.; Brunak, S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004, 4, 1633–1649. [Google Scholar] [CrossRef] [PubMed]
  49. Chang, W.C.; Lee, T.Y.; Huang, H.D.; Huang, H.Y.; Pan, R.L. PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group. BMC Genom. 2008, 9, 561. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  50. Shahmuradov, I.A.; Gammerman, A.J.; Hancock, J.M.; Bramley, P.M.; Solovyev, V.V. PlantProm: A database of plant promoter sequences. Nucleic Acids Res. 2003, 31, 114–117. [Google Scholar] [CrossRef] [Green Version]
  51. Yang, S.H.; Yu, H.; Goh, C.J. Functional characterisation of a cytokinin oxidase gene DsCKX1 in Dendrobium orchid. Plant Mol. Biol. 2003, 51, 237–248. [Google Scholar] [CrossRef] [PubMed]
  52. He, L.; Xu, J.; Wang, Y.; Yang, K. Transcription factor ANACo74 binds to NRS1, NRS2, or MybSt1 element in addition to the NACRS to regulate gene expression. Int. J. Mol. Sci. 2018, 19, 3271. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  53. Kaur, A.; Pati, P.K.; Pati, A.M.; Nagpal, A.K. In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PLoS ONE 2017, 12, e0184523. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  54. Wilkins, M.R.; Lindskog, I.; Gasteiger, E.; Bairoch, A.; Sanchez, J.C.; Hochstrasser, D.F.; Appel, R.D. Detailed peptide characterization using PEPTIDEMASS: A World-Wide Web accessible tool. Electrophoresis 1997, 18, 403–408. [Google Scholar] [CrossRef] [PubMed]
  55. Nakai, K.; Horton, P. PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 1999, 24, 34–36. [Google Scholar] [CrossRef]
  56. Lam, E.; Cha, N.H. ASF-2: A factor that binds to the cauliflower mosaic virus 35S promoter and a conserved GATA motif in cab promoter. Plant Cell 1989, 1, 1147–1156. [Google Scholar] [CrossRef]
  57. Benfey, P.N.; Cha, N.H. The cauliflower mosaic virus 35S promoter: Combinatorial regulation of transcription in plants. Science 1990, 250, 959–966. [Google Scholar] [CrossRef] [Green Version]
  58. Sakai, H.; Aoyama, T.; Oka, A. Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Plant J. 2000, 24, 703–711. [Google Scholar] [CrossRef] [PubMed]
  59. Sakai, H.; Honma, T.; Sato, S.; Kato, T.; Tabata, S.; Oka, A. ARR1, a transcription factor for genes immediately responsive to cytokinins. Science 2001, 294, 1519–1521. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Cimb 45 00123 g001 550
Figure 1. Three CKX genes were isolated by screening a bamboo genomic DNA Library. BoCKX1 (A, lane 1), BoCKX2 (B, lanes 1 and 2), and BoCKX3 (A, lane 2) phagemids were purified and then digested by NotI. The size of the Lambda FIX II vector (41.9 kb) was indicated.
Figure 1. Three CKX genes were isolated by screening a bamboo genomic DNA Library. BoCKX1 (A, lane 1), BoCKX2 (B, lanes 1 and 2), and BoCKX3 (A, lane 2) phagemids were purified and then digested by NotI. The size of the Lambda FIX II vector (41.9 kb) was indicated.
Cimb 45 00123 g001
Cimb 45 00123 g002 550
Figure 2. Exon-intron organization of Bamboo CKX genes. Introns (lines) and exons (rectangles) were graphed to scale, along with the number of base pairs (bp). Sequences compared (A) were isolated from Bambusa oldhamii (BoCKX1, GU263785; BoCKX2, GU263786; and BoCKX3, GU263787). Exon-intron structures of the CKX genes were compared among different species (B).
Figure 2. Exon-intron organization of Bamboo CKX genes. Introns (lines) and exons (rectangles) were graphed to scale, along with the number of base pairs (bp). Sequences compared (A) were isolated from Bambusa oldhamii (BoCKX1, GU263785; BoCKX2, GU263786; and BoCKX3, GU263787). Exon-intron structures of the CKX genes were compared among different species (B).
Cimb 45 00123 g002
Cimb 45 00123 g003 550
Figure 3. Sequence alignment of the primary structure of BoCKX proteins with CKXs proteins from other species. The sequences shown here were from Arabidopsis thaliana (AtCKX1), Bambusa oldhamii (BoCKX1–3), Dendrobium sonia (DsCKX1), Hordeum vulgare (HvCKX2), Oryza sativa (OsCKX1–3), and Zea mays (ZmCKX1). The conserved FAD-binding site, GHS motif, was indicated.
Figure 3. Sequence alignment of the primary structure of BoCKX proteins with CKXs proteins from other species. The sequences shown here were from Arabidopsis thaliana (AtCKX1), Bambusa oldhamii (BoCKX1–3), Dendrobium sonia (DsCKX1), Hordeum vulgare (HvCKX2), Oryza sativa (OsCKX1–3), and Zea mays (ZmCKX1). The conserved FAD-binding site, GHS motif, was indicated.
Cimb 45 00123 g003
Cimb 45 00123 g004 550
Figure 4. Phylogenetic analysis of CKXs from other plant species by Vector NTI Suite 10 Sequence Software (Invitrogen, Waltham, MA, USA).
Figure 4. Phylogenetic analysis of CKXs from other plant species by Vector NTI Suite 10 Sequence Software (Invitrogen, Waltham, MA, USA).
Cimb 45 00123 g004
Cimb 45 00123 g005 550
Figure 5. Promoter sequence analysis of the BoCKX1 gene. The start codon of translation (ATG) was shaded. The predicted transcriptional start site was indicated as “+1”. The putative functional TATA box and one NGATT element were indicated.
Figure 5. Promoter sequence analysis of the BoCKX1 gene. The start codon of translation (ATG) was shaded. The predicted transcriptional start site was indicated as “+1”. The putative functional TATA box and one NGATT element were indicated.
Cimb 45 00123 g005
Cimb 45 00123 g006 550
Figure 6. Promoter sequence analysis of the BoCKX2 gene. The start codon of translation was shaded. The predicted transcriptional start site was indicated as “+1”. The putative functional TATA box, CAAT box, as-1 like motif and ten NGATT elements were designated.
Figure 6. Promoter sequence analysis of the BoCKX2 gene. The start codon of translation was shaded. The predicted transcriptional start site was indicated as “+1”. The putative functional TATA box, CAAT box, as-1 like motif and ten NGATT elements were designated.
Cimb 45 00123 g006
Cimb 45 00123 g007 550
Figure 7. Promoter sequence analysis of the BoCKX3 gene. The start codon of translation was shaded. The predicted transcriptional start site was indicated as “+1”. The putative functional TATA box and five NGATT elements were designated.
Figure 7. Promoter sequence analysis of the BoCKX3 gene. The start codon of translation was shaded. The predicted transcriptional start site was indicated as “+1”. The putative functional TATA box and five NGATT elements were designated.
Cimb 45 00123 g007
Table
Table 1. Amino acids identities (%) among the coding regions of the BoCKX1, BoCKX2, and BoCKX3 proteins.
Table 1. Amino acids identities (%) among the coding regions of the BoCKX1, BoCKX2, and BoCKX3 proteins.
BoCKX1BoCKX2BoCKX3
BoCKX11007892
BoCKX2 10079
BoCKX3 100
Table
Table 2. Features of different CKX proteins from various plants.
Table 2. Features of different CKX proteins from various plants.
Gene Name aNo. of ExonsLength
(aa)		Mass
(kDa) b		Subcellular Localization (PSORT) cGlycosylation Sites dPhosphorylation Sites e
Ser Thr Tyr		Reference
BoCKX1352557.0S f7/611/84/16/3This study
BoCKX2452357.4S5/514/85/38/3This study
BoCKX3352256.6S6/511/83/18/4This study
DsCKX1453660.4S2/2h ---[51]
OsCKX1355859.1S2/1---[35]
OsCKX2453256.0M g6/5---[35]
OsCKX3552558.0S3/3---[35]
ZmCKX1353457.2S8/5---[22]
a Bo, Bambusa oldhamii; Ds, Dendrobium sonia; Os, Oryza sativa; Zm, Zea mays. b Molecular mass calculated with peptide-mass tool (http://ca.expasy.org/tool/peptide-mass.html accessed on 15 March 2020) [54]. c Subcellular localization predicted with PSORT (http://psort.nibb.ac.jp/ accessed on 15 March 2020) [55]. d All predicted N-glycosylation sites/predicted glycosylation sites with 50% probability were analyzed by NetNGly (http://www.cbs.dtu.dk/servies/NetNGly/ accessed on 15 March 2020) [47]. e Phosphorylation site with 50% probability/predicted phosphorylation site with 90% probability was analyzed by NetPhos (http://www.cbs.dtu.dk/services/NetPhos/ accessed on 15 March 2020) [48]. f S: secretory pathway. g M: mitochondria. h -: non-determined.
Table
Table 3. Predicted cis-acting elements of the BoCKX genes and its functions.
Table 3. Predicted cis-acting elements of the BoCKX genes and its functions.
Cis-ElementConsensus SequenceFunctionReferences
TATA boxTATAATCore promoter cis-element of genes in eukaryotes[50]
CAAT boxCAATThe CAAT box is a conserved consensus sequence as the binding site of the RNA transcriptional factor[50]
As-1 boxTGACGActivation sequence 1 (as-1) is a salicylic acid (SA)- and auxin-responsive element[53,56,57]
NGATTN=G/A/C/T GATTArabidopsis cytokinin response regulators ARR1 binding element[52,58,59]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Hsieh, C.-Y.; Hsieh, L.-S. Cloning of Three Cytokinin Oxidase/Dehydrogenase Genes in Bambusa oldhamii. Curr. Issues Mol. Biol. 2023, 45, 1902-1913. https://doi.org/10.3390/cimb45030123

AMA Style

Hsieh C-Y, Hsieh L-S. Cloning of Three Cytokinin Oxidase/Dehydrogenase Genes in Bambusa oldhamii. Current Issues in Molecular Biology. 2023; 45(3):1902-1913. https://doi.org/10.3390/cimb45030123

Chicago/Turabian Style

Hsieh, Chun-Yen, and Lu-Sheng Hsieh. 2023. "Cloning of Three Cytokinin Oxidase/Dehydrogenase Genes in Bambusa oldhamii" Current Issues in Molecular Biology 45, no. 3: 1902-1913. https://doi.org/10.3390/cimb45030123

Article Metrics

Back to TopTop