Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses

Abstract

Background The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. Results Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. Conclusions Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.

Hypometabolism to survive the long polar night in the diatomFragilariopsis cylindrus

“…Here the maintenance of expression of the cryptochromes CPF2 and 3, CPD photolyase DNA repair and RAD family DNA repair genes in prolonged darkness ( Figure 5 ) may contribute to the resistance of diatoms to extreme environmental conditions. Similarly, many genes encoding chitinase are upregulated in darkness, reinforcing the hypothesis of a role for this gene family in responses to environmental changes in diatoms ( 55 ). The persistence of the diatom-specific cyclins dsCYC2 and 3 in the dark may be involved in cell division arrest signaling driven by interaction with photoreceptors such as aureochromes, although the latter do not appear to be regulated at the transcriptomic level ( 17 , 56 ) ( Table S5 ).…”

“…Similarly, many genes encoding chitinase are upregulated in darkness, reinforcing the hypothesis of a role for this gene family in responses to environmental changes in diatoms (55). The persistence of the diatom-specific cyclins dsCYC2 and 3 in the dark may be involved in cell division arrest signaling driven by interaction with photoreceptors such as aureochromes, although the latter do not appear to be regulated at the transcriptomic level (17,56) (Table S5).…”

Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes

“…Traller et al (2016) compiled chitin metabolism pathway genes in Cyclotella cryptica [14]. Cheng et al (2021) characterised a gene family of 24 members encoding chitinases in T. pseudonana [43]. In contrast, the identification of these classes of genes in T. weissflogii at the whole-genome or -transcriptome level has been lacking.…”

Modulating chitin synthesis in marine algae with iminosugars obtained by SmI2 and FeCl3-mediated diastereoselective carbonyl ene reaction

“…There are structural data of the active site of some glycosidases available in the presence of substrate or substrate analogues 25–30 but there seems to be no general mechanism of action. 24 Iminosugars have also been reported to interfere with glycosyltransferases 31–33 including chitin synthases (CHS) (EC 2.4.1.16).…”

“…21 On the other hand, transition state mimetics are not a prerequisite for highly efficient targeting of glycosidases, as clinical treatments have shown, and structure/ function predictions can hardly be made. 23,24 There are structural data of the active site of some glycosidases available in the presence of substrate or substrate analogues [25][26][27][28][29][30] but there seems to be no general mechanism of action. 24 Iminosugars have also been reported to interfere with glycosyltransferases [31][32][33] including chitin synthases (CHS) (EC 2.4.…”