Table 1.
Assembly of all available E. superba sequences (454 reads and ESTs).
Figure 1.
Environmental parameters of the Antarctic krill samples.
Antarctic krill (adult specimens) were collected in the Ross Sea (longitude: 167°28′81′′ E – 179°54′68′′ W, latitude 68°40′54′′ S – 77°01′′81′′ S) in January 2004 during the XIX Italian Antarctic Expedition. The global solar irradiance was measured by a pyranometer (CM11, Kipp & Zonen; Delft, Netherlands) installed aboard the RV “Italica”. Time of fishing (local times: 01∶00, 06∶00, 10∶00, 15∶00, and 18∶00), global solar irradiance (W/m2), fishing depth (m), irradiance at fishing depth (W/m2) and local time (h) are reported. A blue color-coded scale provides a rough picture of the underwater irradiance at the fishing depth throughout the 24-hour cycle (actual values are also reported).
Figure 2.
Oscillatory patterns of differentially expressed genes involved in energetic and metabolic processes.
A) Schematic representation of the daily distribution of metabolic processes resulting from the transcriptional signature of several differentially expressed genes throughout the 24-hour cycle. The different metabolic processes are indicated by gradiently colored arrows showing the time of the day corresponding to the higher expression levels of gene groups. The lengths of the arrows and darker colors indicate, respectively, intervals and peaks of expression. Local times are indicated at the bottom of the figure where an indicative representation of light intensity is also shown. The breakdown of energy-yielding nutrients (glycolysis, the Krebs cycle and the electron transport chain) and energy storage pathways (glycogen synthesis and fatty acid synthesis) are specifically activated in the early morning, while glycogen mobilization, gluconeogenesis and fatty acids catabolism are used as a stored energy source in the evening and throughout the night. B) Gene expression profiles of transcripts involved in energetic and metabolic processes are represented. The color of each gene corresponds to the metabolic process in which it is involved. Dashed lines indicate differentially expressed genes identified by a one-way ANOVA test, while solid lines represent differentially expressed genes characterized by a sinusoidal expression patterns detected by CircWaveBatch analysis. Microarray expression values are represented as log2 mean ± standard deviation. Genes are represented with the following abbreviations: fructose 1,6-bisphosphatase (FB), glyceraldehyde-3-phosphate dehydrogenase (GPD), pyruvate kinase (PK), 6-phosphofructokinase (6P), citrate synthase (CS), ATP synthase b (ATP), succinate dehydrogenase type C (SD), isocitrate dehydrogenase [NAD] subunit beta mitochondrial (ID), Acetyl-CoA acetyltransferase (ACA), short-chain specific acyl-CoA dehydrogenase (ACD), Acetyl-CoA carboxylase (ACC), ATP citrate lyase subunit beta (ACL), glycogen debranching enzyme-like (GDE), glycogen synthase (GS), and Glycogenin-1 (G).
Figure 3.
Multiple sequence alignment of the putative E. superba peroxiredoxin active site.
Multiple sequence alignment of a protein region spanning 70 amino acids, including the peroxiredoxin active site (indicated by asterisks), had a high conservation level. Sequences are colored according to the residue type, and the alignment gap is indicated by dash (–). Hs: Homo sapiens, CAH59743; Mm: Mus musculus, AAA69475; Ce: Caenorhabditis elegans, NP_741287; Dm: Drosophila melanogaster, AAG47823; Nc: Neurospora crassa, XP_959621; Sp: Scylla paramamosain, ACJ53746; Er: Eriocheir sinensis, ACF35639.
Figure 4.
Phylogenetic relationships of E.superba opsins.
A) Alignment of the amino acid sequences of E.superba Rh1a and Rh1b opsins obtained by ClustalW. Seven transmembrane domains were predicted using TMPred (http://www.ch.embnet.org/software/TMPRED_form.html), indicated by lines above the sequence and labelled with Roman numerals. Asterisks (*) indicate amino acids functionally related to the long/middle wavelength-sensitive opsins, a colon (:) indicates the attachment site for the retinal Shiff's base linkage to the retinal chromophore. Sequences are colored according to the residue type. An alignment gap is indicated by a dash (–). B) Phylogenetic relationships of the EsRh1 (Rh1a and Rh1b) and opsin orthologs were obtained by neighbor-joining analysis. Bootstrap confidence values are based on 1,000 replicates. Scale bars indicate amino acid substitutions per site. LWS, long-wavelength sensitive; MWS, middle-wavelength sensitive; SWS, short-wavelength sensitive. Accession numbers: Litopenaeus vannamei: ABH00987; Neomysis Americana: ABI48886; Neogonodactylus oerstedii: ACU00212; Archaeomysis grebnitzkii: ABI48867; Euphausia superba LWS: ABI48874; Daphnia pulex: EFX76309; Uca pugilator Rh2: ADQ01810; Hemigrapsus sanguineus: Q25158; Charybdis japonica: AEL33282; Uca vomeris: ACT31580; Uca pugilator Rh1: ADQ01809; Uca pugilator Rh3: E5G6F2; Bos taurus: NP001014890.