Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana

Abstract

BackgroundSilicon plays important biological roles, but the mechanisms of cellular responses to silicon are poorly understood. We report the first analysis of cell cycle arrest and recovery from silicon starvation in the diatom Thalassiosira pseudonana using whole genome microarrays.ResultsThree known responses to silicon were examined, 1) silicified cell wall synthesis, 2) recovery from silicon starvation, and 3) co-regulation with silicon transporter (SIT) genes. In terms of diatom cell wall formation, thus far only cell surface proteins and proteins tightly associated with silica have been characterized. Our analysis has identified new genes potentially involved in silica formation, and other genes potentially involved in signaling, trafficking, protein degradation, glycosylation and transport, which provides a larger-scale picture of the processes involved. During silicon starvation, an overrepresentation of transcription and translation related genes were up-regulated, indicating that T. pseudonana is poised to rapidly recover from silicon starvation and resume cell cycle progression upon silicon replenishment. This is in contrast to other types of limitation, and provides the first molecular data explaining the well-established environmental response of diatoms to grow as blooms and to out-compete other classes of microalgae for growth. Comparison of our data with a previous diatom cell cycle analysis indicates that assignment of the cell cycle specific stage of particular cyclins and cyclin dependent kinases should be re-evaluated. Finally, genes co-varying in expression with the SITs enabled identification of a new class of diatom-specific proteins containing a unique domain, and a putative silicon efflux protein.ConclusionsAnalysis of the T. pseudonana microarray data has provided a wealth of new genes to investigate previously uncharacterized cellular phenomenon related to silicon metabolism, silicon’s interaction with cellular components, and environmental responses to silicon.

Transcript level coordination of carbon pathways during silicon starvation‐induced lipid accumulation in the diatom Thalassiosira pseudonana

“…Studies aimed at elucidating changes in transcript abundance during nutrient‐limited lipid accumulation often use nitrogen as the limiting nutrient, which is a stressful condition and induces massive cellular changes such as chlorosis and an associated down‐regulation of photosynthesis (Sun et al ., 2013; Abida et al ., 2015; Levitan et al ., 2015). In contrast, short‐term (24 h) silicon starvation has been used as a method to synchronize diatom cultures, and is not generally considered a stressful condition (Coombs et al ., 1967; Hildebrand et al ., 2007; Shrestha et al ., 2012). Silicon starvation‐induced changes in transcript abundance are more likely to reflect the cellular processes that occur as T. pseudonana arrests growth, rather than a response to stress.…”

“…Parameters investigated were genome‐wide transcript abundance (using both microarrays and RNA‐Seq), cell cycle progression and growth, lipid content (lipophilic dyes and fatty acid methyl ester analysis), pigment concentrations, shifts in photophysiology (photosynthesis–irradiance ( P – I ) curves and fast repetition rate fluorometry), and chloroplast features using imaging flow cytometry. Details of these methods in addition to which biochemical and physiological parameters were evaluated for a given experiment can be found in the supporting information (Supporting Information Methods S1; Table S1; Folch et al ., 1957; Platt et al ., 1975; Lewis & Smith, 1983; Benjamini & Hochberg, 1995; Kolber et al ., 1998; Arrigo et al ., 1999; Hildebrand & Dahlin, 2000; Zapata et al ., 2000; Dodds et al ., 2005; Shrestha et al ., 2012; Kim et al ., 2013; Love et al ., 2014). …”

“…Advances in high‐throughput sequencing have facilitated culture‐based transcriptomic studies in diatoms, providing insight into the adaptive response of these organisms to environmental change, such as high light (Park et al ., 2010), carbon dioxide (Hennon et al ., 2015), phosphorus stress (Dyhrman et al ., 2012), nitrogen and silicon limitation and release (Mock et al ., 2008; Sapriel et al ., 2009; Hockin et al ., 2012; Shrestha et al ., 2012; Bender et al ., 2014), iron starvation (Allen et al ., 2008), and other stressors (Maheswari et al ., 2010). A more complete understanding of the significance of transcriptional control of cellular processes is important for an improved understanding of the basic biology of diatoms and other microalgae, and has implications for environmental and biotechnological studies.…”

“…Alternatively, recent functional genomics studies in diatoms and other microalgae have shown that transcription of large suites of genes is coordinated with growth‐related processes such as chloroplast division, release from nitrogen and silicon starvation, cell wall synthesis, onset of cell division, and circadian shifts, suggesting that many genes may be under the control of master regulators (i.e. redox state, transcription factors) that choreograph genome‐wide transcription (Gillard et al ., 2008; Monnier et al ., 2010; Allen et al ., 2011; Shrestha et al ., 2012; Ashworth et al ., 2013). Consequently, changes in transcript abundance can be interpreted as an adaptive response to specific environmental conditions, as a part of a coordinated regulatory program associated with growth, or a combination of both factors.…”

Assessment of sequence variation from SIT1 gene on diatom (Bacillariophyceae) using in silico PCR

“…Nevertheless, the frustule formation and ornamentation can be influenced by external and internal condition of diatoms. An internal factor which can drive the frustule form is transporter protein, sensor interaction, vesicle, protein expression and cell communication [2]. These internal factors are originated from genes expressing specific proteins.…”