Cloning of a cDNA encoding DNA topoisomerase I in Daucus carota and expression analysis in relation to cell proliferation

Genes, proteins and other networks regulating somatic embryogenesis in plants

Background

Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUS-LIKE 15 (AGL15) are very important and are part of molecular network.

Main text (observation)

This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation.

Conclusions

The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.

Structural insight of DNA topoisomerases I from camptothecin-producing plants revealed by molecular dynamics simulations

DNA topoisomerase I (Top1) catalyzes changes in DNA topology by cleaving and rejoining one strand of the double stranded (ds)DNA. Eukaryotic Top1s are the cellular target of the plant-derived anticancer indole alkaloid camptothecin (CPT), which reversibly stabilizes the Top1-dsDNA complex. However, CPT-producing plants, including Camptotheca acuminata, Ophiorrhiza pumila and Ophiorrhiza liukiuensis, are highly resistant to CPT because they possess point-mutated Top1. Here, the adaptive convergent evolution is reported between CPT production ability and mutations in their Top1, as a universal resistance mechanism found in all tested CPT-producing plants. This includes Nothapodytes nimmoniana, one of the major sources of CPT. To obtain a structural insight of the resistance mechanism, molecular dynamics simulations of CPT- resistant and -sensitive plant Top1s complexed with dsDNA and topotecan (a CPT derivative) were performed, these being compared to that for the CPT-sensitive human Top1. As a result, two mutations, Val617Gly and Asp710Gly, were identified in O. pumila Top1 and C. acuminata Top1, respectively. The substitutions at these two positions, surprisingly, are the same as those found in a CPT derivative-resistant human colon adenocarcinoma cell line. The results also demonstrated an increased linker flexibility of the CPT-resistant Top1, providing an additional explanation for the resistance mechanism found in CPT-producing plants. These mutations could reflect the long evolutionary adaptation of CPT-producing plant Top1s to confer a higher degree of resistance.

Abscisic acid and sucrose increase the protein content in date palm somatic embryos, causing changes in 2-DE profile

Various supplements (abscisic acid (ABA) or sucrose) were added to the initial embryo culture medium (M3) with the aim of improving the vigour of vitroplants deriving from date palm somatic embryogenesis. ABA (20 and 40 microM) and sucrose (90 g/l) applied for 4 and 2 weeks respectively increased embryo thickness, with no apparent difference in length. ABA (5-40 microM) increased embryo proliferation rate. Somatic embryos maintained in modified M3 (M3 supplemented with ABA and an increased sucrose concentration) contained a higher amount of protein than those maintained in initial M3 (no ABA, 30 g/l of sucrose), with a 1.5-1.7-fold increase depending on the compound and concentration assayed. The 1-D and 2-DE protein profiles showed qualitative and quantitative differences between the somatic embryos cultured in initial M3 (control) and in modified M3. Statistical analysis of spot intensity was performed by principal component analysis, yielding two accurate groups of samples and determining the most discriminating spots. Samples were also clustered using Euclidean distance with an average linkage algorithm. Thirty-four variable spots were identified using mass spectrometry analysis. Identified proteins were classified into the following functional categories: energy metabolism (five proteins); protein translation, folding and degradation (9); redox maintenance (5); cytoskeleton (3); storage protein (2); and with no assigned function as (10). While "up-regulation" of stress-related proteins and "down-regulation" of energy metabolism proteins were observed in somatic embryos matured in M3 supplemented with ABA, storage proteins (legumin) were "up-regulated" in somatic embryos matured in M3 supplemented with increased sucrose.

Response to UV-C radiation in topo I-deficient carrot cells with low ascorbate levels

In animal cells, recent studies have emphasized the role played by DNA topoisomerase I (topo I) both as a cofactor of DNA repair complexes and/or as a damage sensor. All these functions are still unexplored in plant cells, where information concerning the relationships between DNA damage, PCD induction, and topo I are also limited. The main goal of this study was to investigate the possible responses activated in topo I-depleted plant cells under oxidative stress conditions which induce DNA damage. The carrot (Daucus carota L.) AT1-beta/22 cell line analysed in this study (characterized by an antisense-mediated reduction of top1beta gene expression of approximately 46% in association with a low ascorbate content) was more sensitive to UV-C radiation than the control line, showing consistent cell death and high levels of 8-oxo-dG accumulation. The topo I-depleted cells were also highly susceptible to the cross-linking agent mitomycin C. The death response was associated with a lack of oxidative burst and there were no changes in ascorbate metabolism in response to UV-C treatment. Electron and fluorescence microscopy suggested the presence of three forms of cell death in the UV-C-treated AT1-beta/22 population: necrosis, apoptotic-like PCD, and autophagy. Taken together, the data reported here support a reduced DNA repair capability in carrot topo I-deficient cells while the putative relationship between topo I-depletion and ascorbate impairment is also discussed.

A draft gene regulatory network for cellular totipotency reprogramming during plant somatic embryogenesis

The complexity of the somatic embryogenesis (SE) transcriptome suggests that numerous molecules are involved. To understand better the functional genomics of complex molecular systems during this important reprogramming process, we used bioinformatics and a pathway database to construct a draft network based on transcriptionally regulated SE-related genes, from functional genomics assays readout to high-level biological data interpretation. Here, a complex molecular system was unraveled by this network. This draft network is a potential reservoir for hundreds of testable predictions about cellular processes in early SE. This work could provide a useful test for modeling of a systems network and may have merit as a study presenting an advanced technology application due to its biological and economical importance. The approach presented here is scalable and can be extended to include additional data types. In particular, this effective system approach will be applied to various targeted gene networks in the future.

Pea DNA topoisomerase I is phosphorylated and stimulated by casein kinase 2 and protein kinase C

DNA topoisomerase I catalyzes the relaxation of superhelical DNA tension and is vital for DNA metabolism; therefore, it is essential for growth and development of plants. Here, we have studied the phosphorylation-dependent regulation of topoisomerase I from pea (Pisum sativum). The purified enzyme did not show autophosphorylation but was phosphorylated in an Mg(2+)-dependent manner by endogenous protein kinases present in pea nuclear extracts. This phosphorylation was abolished with calf intestinal alkaline phosphatase and lambda phosphatase. It was also phosphorylated by exogenous casein kinase 2 (CK2), protein kinase C (PKC; from animal sources), and an endogenous pea protein, which was purified using a novel phorbol myristate acetate affinity chromatography method. All of these phosphorylations were inhibited by heparin (inhibitor of CK2) and calphostin (inhibitor of PKC), suggesting that pea topoisomerase I is a bona fide substrate for these kinases. Spermine and spermidine had no effect on the CK2-mediated phosphorylation, suggesting that it is polyamine independent. Phospho-amino acid analysis showed that only serine residues were phosphorylated, which was further confirmed using antiphosphoserine antibody. The topoisomerase I activity increased after phosphorylation with exogenous CK2 and PKC. This study shows that these kinases may contribute to the physiological regulation of DNA topoisomerase I activity and overall DNA metabolism in plants.

Isolation and functional analysis of the 5'-flanking region of carrot top1beta gene coding for the beta isoform of DNA topoisomerase I

We have isolated and functionally characterized the promoter region of the top1beta gene encoding carrot (Daucus carota) DNA topoisomerase Ibeta. The major transcription start site was mapped by primer extension analysis 164 nt upstream the ATG translation start codon. Sequence analysis of the 5'-upstream region of the gene revealed the presence of a canonical TATA-like box at position -35 bp and several cis-acting sequences, including a (CT)n element in the leader region of the gene, a myb-related motif and the Dof element NtBBF-1, which correlate with the inducible expression pattern of this gene. Functional reporter analysis of the top1beta 5'-flanking region was performed in both carrot and Arabidopsis thaliana transfected protoplasts. The region at -719 to +161 was sufficient to confer high expression level in both species. The transient expression assay in protoplasts induced to stop dividing confirmed that the promoter, whose activity is low in quiescent cells, is activated when protoplasts are induced to proliferate by exogenous application of growth factors.

Carrot cells contain two top1 genes having the coding capacity for two distinct DNA topoisomerases I

Five DNA topoisomerase I cDNA clones were isolated from a carrot (Daucus carota) cDNA library and two classes of nucleotide sequences were found. One component of the first class, pTop9, perfectly matches the open reading frame of pTop28, a truncated top1 cDNA previously described, and extended it by 594 nucleotides (top1alpha). A member of the second class, pTop11, contains an open reading frame 2727 bp long (top1ss) with a coding capacity for a second putative DNA topoisomerase I of 101 kDa. Both pTop9 and pTop11 clones are full length cDNAs. The two deduced amino acid sequences share a relevant similarity (89%) only at the C-terminal domain, whereas the similarity is reduced to 32% in the N-terminal region. Southern blot analysis and PCR amplification of genomic DNAs from carrot pure lines suggested the presence of two distinct loci. Northern blot analysis revealed the presence of two distinct transcripts of 3.0 and 3.2 kb in both cycling and starved cell populations. Three fusion peptides corresponding to the N-terminal domain of the alpha and ss forms and from the common C-terminal domain of carrot topoisomerases I were overexpressed in E. coli cells and used to raise antibodies in rabbit. Immunolocalization seems to suggest the presence of two topoisomerases I in carrot nuclei.

cDNA cloning of Physarum polycephalum DNA topoisomerase I and expression analysis in plasmodia treated with cAMP

cDNA encoding DNA topoisomerase I from Physarum polycephalum was isolated from a poly(A)+ -primed library (3'-region) and by PCR (5'-region). The coding region of cDNA was 3045 bp, encoding a polypeptide of molecular mass of 112 kDa. Identity between predicted amino acids sequences of conserved domains and corresponding domains from another eukaryotic type I DNA topoisomerases varied from 33.2 to 53.5% for the core domain and from 33.8 to 57.4% for the C-terminal domain. A peculiar feature of Physarum DNA topoisomerase I was a stretch of repeated KPAX...X motifs in the N-terminal domain of the polypeptide. Although treatment of the plasmodia with db-cAMP increased relaxing activity of the DNA topoisomerase I several-fold, there was only a slight increase in the mRNA level.

Alternative splicing in the Caenorhabditis elegans DNA topoisomerase I gene

5'-end cDNA fragments of the Caenorhabditis elegans DNA topoisomerase I gene were obtained by rapid amplification of the cDNA ends from C. elegans mRNAs. The presence of a SL1 sequence at the 5'-terminus of the cDNA sequence suggested trans-splicing of the pre-mRNA. By comparing the complete cDNA sequence with the genomic lambda DNA clones, the gene structure composed of five exons was established. Alternative splicing deleting the second exon was observed in the cDNA fragments obtained by a gene-specific reverse transcription followed by polymerase chain reactions. The shorter mRNA missing the second exon was expressed at all the developmental stages, while the full-length mRNA was present only in embryos.