Computational analysis of the effects of nitrogen source and sin1 knockout on biosilica morphology in the model diatom Thalassiosira pseudonana

Abstract

Morphogenesis of the silica based cell walls of diatoms, a large group of microalgae, is a paradigm for the self-assembly of complex 3D nano- and microscale patterned inorganic materials. In recent years, loss-of-function studies using genetic manipulation were successfully applied for the identification of genes that guide silica morphogenesis in diatoms. These studies revealed that the loss of one gene can affect multiple morphological parameters, and the morphological changes can be rather subtle being blurred by natural variations in morphology even within the same clone. Both factors severely hamper the identification of morphological mutants using subjective by-eye inspection of electron micrographs. Here we have developed automated image analysis for objectively quantifying the morphology of ridge networks and pore densities from numerous electron micrographs of diatom biosilica. This study demonstrated differences in ridge network morphology and pore density in diatoms growing on ammonium rather than nitrate as the sole nitrogen source. Furthermore, it revealed shortcomings in previous by-eye evaluation of the biosilica phenotype of the silicanin-1 knockout mutant. We anticipate that the computational methods established in the present work will be invaluable for unraveling genotype–phenotype correlations in diatom biosilica morphogenesis.

The molecular basis for pore pattern morphogenesis in diatom silica

“…However, we noted that sin1KO mutants exhibited a ~35% increase in pore density (Fig. 3B) similar to the dank2KO mutants (49), which would be consistent with Sin1 being part of the dAnk2 complex that destabilizes the nanodroplets. The VSP1.0 provides several more candidates for transmembrane proteins [in addition to SAP1 and SAP3 (14,15)] that might interact with dAnk2 or the other two dAnks (SI Appendix, Table S1).…”

The molecular basis for pore pattern morphogenesis in diatom silica

“…However, we noted that sin1KO mutants exhibited a ~35% increase in pore density ( Fig. 3 B ) similar to the dank2KO mutants ( 49 ), which would be consistent with Sin1 being part of the dAnk2 complex that destabilizes the nanodroplets. The VSP1.0 provides several more candidates for transmembrane proteins [in addition to SAP1 and SAP3 ( 14 , 15 )] that might interact with dAnk2 or the other two dAnks ( SI Appendix , Table S1 ).…”

“…To date, the interaction partners of dAnk1-3 are unknown. We noted that sin1KO mutants exhibited a ~35% increase in cribrum pore density similar to the dank2KO mutants 47 , which would be consistent with Sin1 being part of a dAnk2 promoted cluster of SDV transmembrane proteins that destabilizes the nanodroplets (Fig. 3C).…”

Comparative analysis of organelle genomes provides conflicting evidence between morphological similarity and phylogenetic relationship in diatoms

“…To visualize and compare the morphological characteristics of paraphyletic diatom genera, we redrew the illustrations of several representative diatom species based on their previously reported morphological descriptions and images as follows: Pseudo-nitzschia simulans (Li et al, 2017b;Ajani et al, 2020), Pseudo-nitzschia micropora (Priisholm et al, 2002;Rivera-Vilarelle et al, 2013), Pseudo-nitzschia multiseries (Hasle, 1995;Evans et al, 2004), Pseudonitzschia pungens (Lim et al, 2012;Kim et al, 2015), Pseudo-nitzschia americana (Lundholm et al, 2002a;Rivera-Vilarelle et al, 2013), Fragilariopsis cylindrus (Von Quillfeldt, 2001;Cefarelli et al, 2010), Nitzschia inconspicua (Sonneman et al, 2000;Trobajo et al, 2013), Nitzschia alba (Lewin and Lewin, 1967), Nitzschia palea (Crowell et al, 2019;Wang et al, 2020), Cylindrotheca closterium (Reimann and Lewin, 1964;Ryabushko et al, 2019), Tryblionella apiculata (Gregory, 1857;Yamamoto et al, 2017), Psammodictyon constrictum (Yamamoto et al, 2017), Nitzschia traheaformis (Witkowski et al, 2016), Nitzschia dissipatoides (Archibald, 1982; this study), Bacillaria paxillifer (B. paxillifera; Jahn and Schmid, 2007), Skeletonema marinoi (Jung et al, 2009), Thalassiosira nordenskioeldii (Cleve, 1873;Shevchenko et al, 2020), Discostella pseudostelligera (Houk and Klee, 2004;Guerrero and Echenique, 2006), Minidiscus spinulatus (Li et al, 2020), Cyclotella tecta (Prasad and Nienow, 2006), Thalassiosira pseudonana (Horvat et al, 2021), and Conticribra weissflogii…”