Comparative sequence analysis of diatom silicon transporters

Toward a mechanistic model of silicon transport

Kimberlee Thamatrakoln, Andrew J. Alverson, Mark Hildebrand

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

Silicon is an important element in biology, for organisms ranging from unicellular algae to humans. It acts as a structural material for both plants and animals, but can also function as a metabolite or regulator of gene expression, affecting a wide range of cellular processes. Molecular details of biological interaction with silicon are poorly understood. Diatoms, the largest group of silicifying organisms, are a good model system for studying this interaction. The first proteins shown to directly interact with silicon were diatom silicon transporters (SITs). Because the basis for substrate recognition lies within the primary sequence of a protein, identification of conserved amino acid residues would provide insight into the mechanism of SIT function. Lack of SIT sequences from a diversity of diatoms and high sequence conservation in known SITs has precluded identification of such residues. In this study, PCR was used to amplify partial SIT sequences from eight diverse diatom species. Multiple gene copies were prevalent in each species, and phylogenetic analysis showed that SITs generally group according to species. In addition to partial SIT sequences, full-length SIT genes were identified from the pennate diatom, Nitzschia alba (Lewin and Lewin), and the centric diatom Skeletonema costatum (Greville) Cleve. Comparing these SITs with previously identified SITs showed structural differences between SITs of centrics and pennates, suggesting differences in transport mechanism or regulation. Comparative amino acid analysis identified conserved regions that may be important for silicon transport, including repeats of the motif GXQ. A model for silicon uptake and efflux is presented that is consistent with known aspects of transport.

Original languageEnglish (US)
Pages (from-to)822-834
Number of pages13
JournalJournal of Phycology
Volume42
Issue number4
DOIs
StatePublished - Aug 1 2006

Fingerprint

Bacillariophyceae
mechanistic models
silicon
transporters
diatom
sequence analysis
analysis
algae
amino acid
Skeletonema costatum
amino acids
protein
Nitzschia
gene
organisms
regulator genes

All Science Journal Classification (ASJC) codes

  • Aquatic Science
  • Plant Science

Keywords

  • Diatom
  • Sequence comparison
  • Silicon
  • Silicon transporter

Cite this

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abstract = "Silicon is an important element in biology, for organisms ranging from unicellular algae to humans. It acts as a structural material for both plants and animals, but can also function as a metabolite or regulator of gene expression, affecting a wide range of cellular processes. Molecular details of biological interaction with silicon are poorly understood. Diatoms, the largest group of silicifying organisms, are a good model system for studying this interaction. The first proteins shown to directly interact with silicon were diatom silicon transporters (SITs). Because the basis for substrate recognition lies within the primary sequence of a protein, identification of conserved amino acid residues would provide insight into the mechanism of SIT function. Lack of SIT sequences from a diversity of diatoms and high sequence conservation in known SITs has precluded identification of such residues. In this study, PCR was used to amplify partial SIT sequences from eight diverse diatom species. Multiple gene copies were prevalent in each species, and phylogenetic analysis showed that SITs generally group according to species. In addition to partial SIT sequences, full-length SIT genes were identified from the pennate diatom, Nitzschia alba (Lewin and Lewin), and the centric diatom Skeletonema costatum (Greville) Cleve. Comparing these SITs with previously identified SITs showed structural differences between SITs of centrics and pennates, suggesting differences in transport mechanism or regulation. Comparative amino acid analysis identified conserved regions that may be important for silicon transport, including repeats of the motif GXQ. A model for silicon uptake and efflux is presented that is consistent with known aspects of transport.",
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Comparative sequence analysis of diatom silicon transporters : Toward a mechanistic model of silicon transport. / Thamatrakoln, Kimberlee; Alverson, Andrew J.; Hildebrand, Mark.

In: Journal of Phycology, Vol. 42, No. 4, 01.08.2006, p. 822-834.

Research output: Contribution to journalArticle

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T1 - Comparative sequence analysis of diatom silicon transporters

T2 - Toward a mechanistic model of silicon transport

AU - Thamatrakoln, Kimberlee

AU - Alverson, Andrew J.

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