The inner ear proteome of fish

Thomas, Oliver R. B.; Swearer, Stephen E.; Kapp, Eugene A.; Peng, P.; Tonkin‐Hill, Gerry; Papenfuss, Anthony T.; Roberts, Anne M.; Bernard, Pascal; Roberts, Blaine R

doi:10.1111/febs.14715

Cited by 51 publications

(50 citation statements)

References 79 publications

(129 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While we show here that we can successfully sequence several known modern skeletal proteins in fossil coral specimens, future method refinement may consider inclusion of other, non-enzymatic, peptide cleavage methods; this could include the use of cyanogen bromide (e.g. 73 ), although significant accumulation of methionine oxidation in fossil specimens would minimize its effectiveness 74 .…”

Section: Discussionmentioning

confidence: 96%

First sequencing of ancient coral skeletal proteins

Drake

Whitelegge

Jacobs

2020

Sci Rep

View full text Add to dashboard Cite

Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC–MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.

show abstract

Section: Discussionmentioning

confidence: 96%

First sequencing of ancient coral skeletal proteins

Drake

Whitelegge

Jacobs

2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The absence of pks1 does not visibly appear to affect hair cell development that are required for otolith nucleation either [ 9 ]. It has been previously suggested that apolipoprotein could potentially bind polyketide synthase [ 4 , 25 ]. Given our RNA-seq analysis of nco , we see no significant change in any apolipoprotein expression.…”

Section: Discussionmentioning

confidence: 99%

“…These genes are all part of a regulatory network during hypergravity-mediated bone formation [ 52 ]. Furthermore, the presence of osteoblast-associated proteins within teleost otoliths suggest a common mechanism between bone mineralization and otolith biomineralization [ 4 ]. Future studies will attempt to clarify the roles of Endothelin-1 and eNOS signaling pathways during biomineralization events.…”

Section: Discussionmentioning

confidence: 99%

“…Zebrafish otoliths are primarily composed of calcium carbonate (CaCO 3 ), in the form of aragonite, which accounts for ~99% of the total otolithic mass with the remainder consisting of proteins called otoconins [ 2 , 3 ]. Further analysis of teleost otoliths has identified more than 380 protein components [ 4 ]. Based on the level of protein expression or changes in the rate of otolith growth, the polymorph of calcium carbonate crystals can change [ 1 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Zebrafish otolith biomineralization requires polyketide synthase

Thiessen

Grzegorski

Chin

et al. 2019

Mechanisms of Development

View full text Add to dashboard Cite

Deflecting biomineralized crystals attached to vestibular hair cells are necessary for maintaining balance. Zebrafish ( Danio rerio ) are useful organisms to study these biomineralized crystals called otoliths, as many required genes are homologous to human otoconial development. We sought to identify and characterize the causative gene in a trio of homozygous recessive mutants, no content ( nco ) and corkscrew ( csr ), and vanished ( vns ), which fail to develop otoliths during early ear development. We show that nco , csr , and vns have potentially deleterious mutations in polyketide synthase ( pks1 ), a multi-modular protein that has been previously implicated in biomineralization events in chordates and echinoderms. We found that Otoconin-90 (Oc90) expression within the otocyst is diffuse in nco and csr ; therefore, it is not sufficient for otolith biomineralization in zebrafish. Similarly, normal localization of Otogelin, a protein required for otolith tethering in the otolithic membrane, is not sufficient for Oc90 attachment. Furthermore, eNOS signaling and Endothelin-1 signaling were the most up- and down-regulated pathways during otolith agenesis in nco , respectively. Our results demonstrate distinct processes for otolith nucleation and biomineralization in vertebrates and will be a starting point for models that are independent of Oc90-mediated seeding. This study will serve as a basis for investigating the role of eNOS signaling and Endothelin-1 signaling during otolith formation.

show abstract

“…Interestingly, a lot of proteins involved in the biomineralization of calcium phosphate and calcium carbonate are IDPs . These include, for example, mammalian proteins: osteopontin (OPN), bone sialoprotein (BSP), dentin sialophosphoprotein (DSPP), as well as a zebrafish otolith matrix protein Starmaker (Stm), and its homologs from other fish species . However, more ordered proteins are also involved, for example: otoconin‐90 (OC90), amorphous calcium carbonate‐binding protein (ACCBP), otolin‐1 …”

Section: Introductionmentioning

confidence: 99%

Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals

et al. 2020

View full text Add to dashboard Cite

Dentin matrix protein 1 (DMP1) is an acidic, extracellular matrix protein essential for biomineralization of calcium phosphate, in bone and dentin. It is proteolytically processed into two fragments, 44K and 56K. Recently, the presence of DMP1 was noticed in inner ear, specifically in otoconia, which are calcium carbonate biominerals involved in sensing of balance. In this study, the solution structure and biomineralization activity of otoconial 44K and 56K fragments toward calcium carbonate were investigated. The results of analytical ultracentrifugation, circular dichroism, and gel filtration indicated that DMP1 fragments are disordered in solution. Notably, 56K formed oligomers in the presence of calcium ions. It was also observed that both fragments influenced the crystal growth by in vitro biomineralization assay and scanning electron microscopy. In addition, they sequester the calcium ions during the calcite formation. Calcium carbonate crystals precipitated in vitro changed their size and shape in the presence of DMP1 fragments. Oligomerization propensity of 56K may significantly enhance this function. Our study indicates that intrinsically disordered DMP1 has a previously unknown regulatory function for biomineralization of otoconia.

show abstract

The inner ear proteome of fish

Cited by 51 publications

References 79 publications

First sequencing of ancient coral skeletal proteins

First sequencing of ancient coral skeletal proteins

Zebrafish otolith biomineralization requires polyketide synthase

Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals

Contact Info

Product

Resources

About