Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis

<p>Abstract</p> <p>Background</p> <p>Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom <it>Phaeodactylum tricornutum </it>and the centric diatom <it>Thalassiosira pseudonana </it>have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from <it>P. tricornutum </it>and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from <it>P. tricornutum </it>under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions.</p> <p>Results</p> <p>A total of 13 miRNAs were identified. They were probable <it>P. tricornutum</it>-specific novel miRNAs. These miRNAs were sequenced from <it>P. tricornutum </it>under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on.</p> <p>Conclusions</p> <p>Our results indicated that <it>P. tricornutum </it>contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in <it>P. tricornutum </it>metabolism.</p

Transcriptome analysis of the hepatopancreas from the Litopenaeus vannamei infected with different flagellum types of Vibrio alginolyticus strains

Vibrio alginolyticus, one of the prevalently harmful Vibrio species found in the ocean, causes significant economic damage in the shrimp farming industry. Its flagellum serves as a crucial virulence factor in the invasion of host organisms. However, the processes of bacteria flagella recognition and activation of the downstream immune system in shrimp remain unclear. To enhance comprehension of this, a ΔflhG strain was created by in-frame deletion of the flhG gene in V. alginolyticus strain HN08155. Then we utilized the transcriptome analysis to examine the different immune responses in Litopenaeus vannamei hepatopancreas after being infected with the wild type and the mutant strains. The results showed that the ΔflhG strain, unlike the wild type, lost its ability to regulate flagella numbers negatively and displayed multiple flagella. When infected with the hyperflagella-type strain, the RNA-seq revealed the upregulation of several immune-related genes in the shrimp hepatopancreas. Notably, two C-type lectins (CTLs), namely galactose-specific lectin nattectin and macrophage mannose receptor 1, and the TNF receptor-associated factor (TRAF) 6 gene were upregulated significantly. These findings suggested that C-type lectins were potentially involved in flagella recognition in shrimp and the immune system was activated through the TRAF6 pathway after flagella detection by CTLs

Differential Response of <i>Phaeodactylum</i> <i>tricornutum</i> and <i>Cylindrotheca</i> <i>fusiformis</i> to High Concentrations of Cu²⁺ and Zn²⁺

Diatoms can be used as biosensors to assess aquatic environment quality, because they are widely distributed in almost all aquatic environments and show varied sensitivities toward heavy metal ions. The marine planktonic diatoms Phaeodactylum tricornutum (P. tricornutum) and Cylindrotheca fusiformis (C. fusiformis) are typical representatives of planktonic diatoms and benthic diatoms, respectively. C. fusiformis is very sensitive to changes in the concentration of heavy metal ions, and can be used as an indicator of the quality of the sedimental environment, while P. tricornutum can tolerate higher concentrations of heavy metal ions. To explore the potential difference in responses to heavy metal ions between planktonic and benthic diatoms, we compared the transcriptome of P. tricornutum and C. fusiformis under Cu2+ and Zn2+ treatment. The results indicated that P. tricornutum has several genes involved in ion transmembrane transport and ion homeostasis, which are significantly downregulated under Cu2+ and Zn2+ treatment. However, this enrichment of ion transmembrane transport- and ion homeostasis-related genes was not observed in C. fusiformis under Cu2+ and Zn2+ treatment. Additionally, genes related to heavy metal ion stress response such as peroxiredoxin, peroxidase, catalase, glutathione metabolism, phytochelatin, oxidative stress and disulfide reductase, were upregulated in P. tricornutum under Cu2+ and Zn2+ treatment, whereas most of them were downregulated in C. fusiformis under Cu2+ and Zn2+ treatment. This difference in gene expression may be responsible for the difference in sensitivity to heavy metals between P. tricornutum and C. fusiformis

Analysis of the Antioxidant Composition of Low Molecular Weight Metabolites from the Agarolytic Bacterium <i>Alteromonas macleodii</i> QZ9-9: Possibilities for High-Added Value Utilization of Macroalgae

Agar accounts for ~60% of the dry weight of some red macroalgae, and the breakdown of this kind of polysaccharide releases high-value compounds; therefore, the resource utilization of agar is of great significance to improve the added value of these macroalgae. Herein, Alteromonas macleodii QZ9-9 isolated from tropical Gracilaria hainanensis in Hainan Island was characterized as an agarolytic bacterium, which displayed a high agar-degrading activity. The highest diameters of the degradation zones of the A. macleodii QZ9-9 and its extracellular-agarase (12.16 U/mL) were 41.46 mm and 22.89 mm, respectively, and the first-order degradation rate constants of those were 0.02 h−1 and 0.77 U−1, respectively. Importantly, the fermentation products of A. macleodii QZ9-9 exhibited antioxidant activity, and the peak of DPPH scavenging activity of 50 h fermentation products of this strain was up to 50.79% in the reaction for 1 h; the DPPH scavenging activity of low molecule metabolites (≤3 kDa) in particular was up to ~85.85%. A total of 766 metabolites were detected in the low molecule metabolites by metabolomics. The peptide-like metabolites, such as prolyl–histidine, isoleucyl–histidine, isoleucyl–proline and arginyl–proline, and the antioxidant maculosin were found in the top 20 metabolites with relatively high abundance. Additionally, the antioxidant activity of maculosin was further verified in this work. We concluded that the low molecule metabolites of A. macleodii QZ9-9 with relatively high antioxidant activity are interesting candidates for preparing desirable non-toxic antioxidants, thereby facilitating the high value-added utilization of macroalgae in the fields of cosmetic, food preservation, and pharmaceutical industries

The OD 260/280 ratios of extracted nucleic acid.

<p>The OD 260/280 ratios of extracted nucleic acid.</p

Stability of candidate housekeeping gene expression <i>in P. yezoensis</i> (from smallest to largest difference) determined by difference across all samples.

<p>Results are calculated as maximum/minimum. Difference (RNA) is determined by transcript number normalized to total RNA quantity and Difference (DNA) is determined by transcript number normalized to genomic DNA quantity.</p

The melting curve analysis for <i>18S</i> (A), <i>Act3</i> (B), <i>EF1alpha</i> (C), <i>GAPDH</i> (D), <i>PUB-2</i> (E), <i>RPS8</i> (F), <i>TubB</i> (G).

<p>Melting peaks were examined with standard samples and unkown samples (sporophytes, gametophytes and conchospores). The melting curve for each gene had only one peak.</p

The standard curves constructed for <i>18S</i> (A), <i>Act3</i> (B), <i>EF1alpha</i> (C), <i>GAPDH</i> (D), <i>PUB-2</i> (E), <i>RPS8</i> (F), <i>TubB</i> (G).

<p>The results showed that amplification efficiency was between 96% and 103%, and linear correlation coefficient was >0.99.</p