# Increased aluminum exposure induces widespread changes in silicon, carbon, and nitrogen metabolism in Entomoneis vertebralis

## TL;DR

Exposure to aluminum increases silica production and alters metabolism in the diatom Entomoneis vertebralis, with potential implications for metabolic engineering.

## Contribution

This study identifies transcriptional responses and potential silicification-associated genes in diatoms exposed to aluminum.

## Key findings

- Aluminum exposure increases biogenic silica content in Entomoneis vertebralis cell walls by approximately twofold.
- Transcription of genes related to carbon fixation and nitrate transport increases despite downregulated nitrogen assimilation pathways.
- Differentially regulated proteins share amino acid motifs and structural features linked to silicification.

## Abstract

Diatoms are a class of algae that play an essential role in global ecology and produce valuable chemicals. They are known for forming intricate nanostructured silica cell walls (frustules). The introduction of non-siliceous elements like aluminum into diatoms induces properties such as a lower dissolution rate of the frustule, increasing the specific surface area of the frustule and enhancing metabolism. Previous studies have focused primarily on characterizing physiological impacts, leaving the genetic response(s) to non-siliceous elements largely unexplored.

This study investigates the transcriptional response of the pennate diatom, Entomoneis vertebralis to dissolved aluminum. Our findings reveal that in the presence of added 10 µM aluminum, biogenic silica content of the cell wall increases approximately twofold along with significant changes to core metabolism. An increase in transcription of genes encoding nitrate transporters has been observed despite the apparent downregulation of nitrogen assimilation pathways. Additionally, increased transcription of genes involved in carbon fixation were noted. Amino acid and protein motif analyses identified proteins that were differentially regulated shared amino acid compositions and motifs characteristic to silicification-associated genes. A unique structure-based analysis pipeline revealed that some of these proteins have a conserved structural core while being diverse in sequence, which could be features associated with biosilicification.

Differential expression transcriptomics has provided insight into diatom metabolism when exposed to aluminum, highlighting potential targets for metabolic engineering. Furthermore, we identified potential silicification-associated genes using tools based on structure and amino acid composition, advancing our understanding of diatom silicification.

The online version contains supplementary material available at 10.1186/s12864-025-12106-7.