Table 3.
Gene ontology (GO) term assignment and rationale to the different phases of diapause.
| Diapause phase | GO term | Rationale |
|---|---|---|
| Diapause maintenance | Nucleotide-excision repair (4/13) | Known as a repair mechanism in desiccation tolerant stages37. Desiccation/rehydration cycles and prolonged periods in the dry state are associated with remarkable levels of stress to the embryo genome which can result in mutagenesis of the genetic material, inhibition of transcription and replication and delayed growth and development |
| Response to oxidative stress (10/26) | Oxidative stress leads to the accumulation of toxic components called reactive oxygen species (ROS). Therefore, production of antioxidant enzymes is critical for stress resistance during diapause38 and has been shown in a wide range of organisms such as insects39, nematodes40 and rotifers34. The major ROS detoxifying enzymes described in rotifers include peroxidases, thioredoxins, catalases and glutathione-S-transferases34,36 | |
| Oxidoreductase activity (63/147) | A number of proteins with oxidoreductase activity have been described as involved in diapause with a role in detoxification processes and degradation of xenobiotics36. For example, the cytochrome P450 monooxygenase gene has been shown to be overexpressed in insects during diapause3,5. In the case of monogonont rotifers this gene is also related to lipid metabolism (steroidogenesis41) with a potential role in the accumulation of energy reserves for diapause42 | |
| Trehalose biosynthetic process (4/6) | Trehalose is related to dormancy in many prokaryotes and eukaryotes, and is known to be synthesized under dehydration conditions to stabilize other proteins and membranes during drying41,43,44. Trehalose acts as a water replacement molecule and vitrifying agent serving to stabilize cell membranes45. Trehalose is known to accumulate in diapausing cysts of Artemia45,46 and in diapausing rotifer eggs when they enter anhydrobiosis47. Transcripts encoding for trehalose-6-phosphate synthase and for trehalose phosphate synthase enzymes have been detected in diapausing rotifer eggs, suggesting its biosynthesis in rotifers23,25,34 | |
| G protein-coupled receptor signalling pathway (17/206) | G protein-coupled receptors (GPCR) regulate signal transduction pathways and play diverse and pivotal roles in the physiology of insects, especially in resistance to adverse environmental conditions48. Interestingly, a GPCR receptor in the silkworm, B. mori, has been identified as a specific cell surface receptor for the diapause hormone (DH)49. In the nematode, C. elegans, two transcripts for GPCRs have been identified as among the most abundant in the dauer stage50 | |
| Signal transduction (45/544) | Signal transduction pathways (insulin signalling) are known to have a role in the entrance into and maintenance of the dauer state in nematodes51, and diapause in insects52 and killifish53 | |
| Embryo development | Cell–matrix adhesion (3/16) | The interactions of cells with the extracellular matrix play crucial roles during morphogenesis in developing embryos. Interestingly, Clark et al.36 have reported the upregulation of genes involved in cell proliferation and adhesions in the transcription profile of non-diapause embryos in their morphological development into neonate rotifers |
| Potassium ion transport (4/56) | K+ is known to have a role in cell growth through protein synthesis. There is evidence of K+-mediated stimulation of aminoacyl-tRNA (aa-tRNA) synthetase activity in bacteria54 and insects55, with an effect on diapause termination in the latter. Rozema et al.25 have shown high levels of aa-tRNA synthetases in diapausing compared to asexual eggs in Brachionus | |
| Ion transmembrane transport (16/147) | Free ions in the cytosol restart the cell machinery by reactivating cellular enzymes56. Dumont et al.57 showed that cyst hatching in some anostraceans increased after the addition of mobile ion carriers. There is also evidence that increased pH induces diapause termination in Artemia salina26. Interestingly, transmembrane proton transport, and H+-translocating pyrophosphatase activity has been reported in Brachionus diapausing embryos after 30 min of light stimulation for hatching58 | |
| Nucleoside transmembrane transport (1/7) | Nucleosides, precursors of the nucleotides, would provide the material needed to generate new DNA and RNA for cell proliferation in resumed development. In addition, nucleosides (and nucleotides) are key determinants of energy metabolism, ligands for purinergic receptors, and transducers of endocrine signals | |
| Carboxylic acid transport (2/20) | Metabolic depression in diapausing rotifer embryos may be attributed to a putative downregulation of the tricarboxylic acid (TCA) cycle and pyruvate metabolism23,25. Consequently, upregulation of this pathway is expected in diapause termination and development reactivation | |
| Cell motility (1/14) | Cell motility has been related to the resumption of embryonic development after diapause, and changes in the expression of genes encoding for cytoskeletal components (actin and tubulin) have been reported in bdelloid rotifers59 and zebrafish60,61. Clark et al.36 have reported the expression of an actin-binding protein with a role in the regulation of cytoskeletal organization in diapausing Brachionus eggs | |
| Cilium assembly (2/46) and movement (1/10) | Cilium assembly and movement are known to be regulated by the cytoskeleton. Interestingly, one way to recognize the viability of rotifer embryos after diapause is through microscopic observation of the coronal cilia beat (personal observation) | |
| Proteasome mediated ubiquitin dependent protein catabolic process (4/45) | This pathway includes chemical reactions resulting in the breakdown of proteins by hydrolysis of peptide bonds. Whether this is a way to obtain energy for a resource-intensive process such as hatching is yet to be resolved. Genes associated with protease activity are rapidly upregulated in diapausing Brachionus eggs after 30 min of light stimulation for hatching58 | |
| Motor activity (11/131) | Likely related to resumption of morphological development in rotifers and diapausing egg hatching, the function is defined as the generation of force resulting in movement along a microfilament or microtubule coupled to the hydrolysis of a nucleoside triphosphate | |
| Peptidase activities (59/399) | Protein catabolism may constitute a source of amino acids for development after diapause. Several peptidases have been reported to be overexpressed in diapausing Brachionus eggs shortly (30 min-4 h) after receiving a light stimulus for hatching58 |
Numbers in parentheses denote the number of significant differentially expressed genes (p-value < 0.01) out of the total number of genes annotated with that term.