Actin, actin-related proteins and profilin in diatoms: A comparative genomic analysis

Aumeier, Charlotte; Polinski, Ellen; Menzel, Diedrik

doi:10.1016/j.margen.2015.07.002

Cited by 15 publications

(7 citation statements)

References 96 publications

(112 reference statements)

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“…It is possible that the SAP conserved domain could mediate such interactions. Though the conserved domain does not match any known cytoskeleton interacting domains, a recent paper has shown that diatom actin related and actin binding proteins do not always adhere to the canonical sets, this could explain a novel binding domain 61 . Another possibility is that the conserved domain does not interact directly with cytoskeletal proteins, but with other cytosolic proteins, these multi-protein complexes may then interact with the cytoskeleton.…”

Section: Discussionmentioning

confidence: 95%

Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica

Tesson

Lerch

Hildebrand

2017

Sci Rep

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Diatoms are known for their intricate, silicified cell walls (frustules). Silica polymerization occurs in a compartment called the silica deposition vesicle (SDV) and it was proposed that the cytoskeleton influences silica patterning through the SDV membrane (silicalemma) via interactions with transmembrane proteins. In this work we identify a family of proteins associated with the silicalemma, named SAPs for Silicalemma Associated Proteins. The T. pseudonana SAPs (TpSAPs) are characterized by their motif organization; each contains a transmembrane domain, serine rich region and a conserved cytoplasmic domain. Fluorescent tagging demonstrated that two of the TpSAPs were localized to the silicalemma and that the intralumenal region of TpSAP3 remained embedded in the silica while the cytoplasmic region was cleaved. Knockdown lines of TpSAP1 and 3 displayed malformed valves; which confirmed their roles in frustule morphogenesis. This study provides the first demonstration of altering silica structure through manipulation of a single gene.

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Section: Discussionmentioning

confidence: 95%

Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica

Tesson

Lerch

Hildebrand

2017

Sci Rep

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“…Some research shows that actin and actin‐related genes are highly conservative, and it is an object of comparative research among different diatom species (Aumeier et al. ). Thus, an evolutionary analysis can help us understand the stability of act .…”

Section: Discussionmentioning

confidence: 99%

Carbon fixation gene expression in Skeletonema marinoi in nitrogen‐, phosphate‐, silicate‐starvation, and low‐temperature stress exposure

Liu

Xing²,

et al. 2019

Journal of Phycology

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Diatoms are unicellular algae with a set of extraordinary genes, metabolic pathways, and physiological functions acquired by secondary endosymbiosis, especially for their efficient photosynthetic carbon fixation mechanisms, which can be a reason for their successful environmental adaptation and great contribution to primary production. Based on the available genomic information, the expression patterns of carbon fixation genes were analyzed using transcriptomic sequencing and reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) in Skeletonema marinoi. Meanwhile, suitable reference genes applying to specific experimental treatments were selected. In our results, carbon fixation genes were standardized by actin and TATA box‐binding protein‐coding genes in growth phase samples and stress conditions, respectively. It was found that a series of carbon fixation genes, such as the pyruvate orthophosphate dikinase (PPDK)‐coding gene, had significantly up‐regulated expression in nitrogen‐starvation, phosphate‐starvation, and low‐temperature conditions, but consistently down‐regulated in silicate‐starvation treatment. These carbon fixation genes exhibited variable expression levels in different conditions and will be useful for investigating gene expression mechanisms in S. marinoi and improve our understanding of diatom carbon fixation pathways.

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“…laevis genes used for the functional annotation query. We then picked up the genes that formed orthogroups with actin‐related proteins identified by Aumeier (2014) and Aumeier et al. (2015) and tubulins identified by Khabudaev et al.…”

Section: Methodsmentioning

confidence: 99%

“…We then picked up the genes that formed orthogroups with actin‐related proteins identified by Aumeier (2014) and Aumeier et al. (2015) and tubulins identified by Khabudaev et al. (2022; Table S1 in the Supporting Information).…”

Section: Methodsmentioning

confidence: 99%

“…2.5.2 (Emms & Kelly, 2019) with default parameters along with our protein sequences of P. laevis genes used for the functional annotation query. We then picked up the genes that formed orthogroups with actin-related proteins identified by Aumeier (2014) and Aumeier et al (2015) and tubulins identified by Khabudaev et al (2022;Table S1 in the Supporting Information).…”

Section: Functional Annotationmentioning

confidence: 99%

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Transcriptional responses to salinity‐induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis

Kamakura,

Bilcke,

Sato

2024

Journal of Phycology

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Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up‐regulation of mechanosensitive ion channels and down‐regulation of Ca2+‐ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up‐regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up‐regulation of genes encoding frustule‐related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity‐induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+‐dependent regulation of actin dynamics and frustule‐related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.

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Actin, actin-related proteins and profilin in diatoms: A comparative genomic analysis

Cited by 15 publications

References 96 publications

Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica

Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica

Carbon fixation gene expression in Skeletonema marinoi in nitrogen‐, phosphate‐, silicate‐starvation, and low‐temperature stress exposure

Transcriptional responses to salinity‐induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis

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