Proteotranscriptomics – A facilitator in omics research

Levin, Michal; Butter, Falk

doi:10.1016/j.csbj.2022.07.007

Cited by 6 publications

(4 citation statements)

References 94 publications

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“…Previously, most studies exploring the venom composition of sea anemones and other venomous species have only utilised transcriptomics approaches to profile probable toxins in venom. Here, we have provided further evidence to support the assertion that a combined proteomics and transcriptomics approach is essential to accurately profile venom composition [ 24 , 27 , 49 , 50 ], particularly in the context of symbiosis, as anemonefish interact with host sea anemone venom proteins rather than RNA transcripts.…”

Section: Discussionmentioning

confidence: 64%

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Proteotransciptomics of the Most Popular Host Sea Anemone Entacmaea quadricolor Reveals Not All Toxin Genes Expressed by Tentacles Are Recruited into Its Venom Arsenal

Hoepner,

Stewart,

Qiao

et al. 2024

Toxins

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While the unique symbiotic relationship between anemonefishes and sea anemones is iconic, it is still not fully understood how anemonefishes can withstand and thrive within the venomous environment of their host sea anemone. In this study, we used a proteotranscriptomics approach to elucidate the proteinaceous toxin repertoire from the most common host sea anemone, Entacmaea quadricolor. Although 1251 different toxin or toxin-like RNA transcripts were expressed in E. quadricolor tentacles (0.05% of gene clusters, 1.8% of expression) and 5375 proteins were detected in milked venom, only 4% of proteins detected in venom were putative toxins (230), and they only represent on average 14% of the normalised protein expression in the milked venom samples. Thus, most proteins in milked venom do not appear to have a toxin function. This work raises the perils of defining a dominant venom phenotype based on transcriptomics data alone in sea anemones, as we found that the dominant venom phenotype differs between the transcriptome and proteome abundance data. E. quadricolor venom contains a mixture of toxin-like proteins of unknown and known function. A newly identified toxin protein family, Z3, rich in conserved cysteines of unknown function, was the most abundant at the RNA transcript and protein levels. The venom was also rich in toxins from the Protease S1, Kunitz-type and PLA2 toxin protein families and contains toxins from eight venom categories. Exploring the intricate venom toxin components in other host sea anemones will be crucial for improving our understanding of how anemonefish adapt to the venomous environment.

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Section: Discussionmentioning

confidence: 64%

“…The study of sea anemone venom has begun to use a combined transcriptomics and proteomics approach, also known as proteotranscriptomics [ 14 , 24 , 25 , 26 , 27 , 28 ]. Using proteotranscriptomics provides a more holistic overview of venom complexity, enabling the detection of novel proteins [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Proteotransciptomics of the Most Popular Host Sea Anemone Entacmaea quadricolor Reveals Not All Toxin Genes Expressed by Tentacles Are Recruited into Its Venom Arsenal

Hoepner,

Stewart,

Qiao

et al. 2024

Toxins

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show abstract

“…Although the precision of the method was very high, the restrained proteome coverage of the mass spectrometry measurements poses a certain limit to the comprehensiveness of our annotation. In principle, the overall range of detected proteins could be extended by applying technological and methodological adjustments (Levin and Butter 2022). However, even with RNA sequencing, we could detect meaningful counts for only ∼43% of the annotated C. elegans genes (8581 transcripts with at least 10 detected tpm).…”

Section: Discussionmentioning

confidence: 96%

Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis

et al. 2023

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Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to ∼650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics and machine-learning quality control in an approach called proteotranscriptomics, we improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organismCaenorhabditis elegans. Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.

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“…Structure prediction of large genes is still a problem [29]. The best results are obtained by comparing genomic and cDNA sequences or by using proteomic data [30]. Previous identification of P150/ser6 sequences in G. mellonella and E. kuehniella was successfully performed using this approach [13, 14].…”

Section: Discussionmentioning

confidence: 99%

Unravelling the complexity of silk sericins:P150/sericin 6is a new silk gene inBombyx mori

Wu,

Zabelina,

Zurovcova

et al. 2023

Preprint

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Sericins are a small family of highly divergent proteins that serve as adhesives and coatings for silk fibers and are produced in the middle part of the silk gland. So far, five genes encoding sericin proteins have been found in Bombyx mori. Sericins 1 and 3 are responsible for silk adhesion in the cocoon, while sericins 2, 4, and 5 are present in non-cocoon spun silk of younger larvae (including the early last instar). We found a new gene, which we named P150/sericin 6, which appears to be an ortholog of the sericin-like protein previously found in Galleria mellonella. The B. mori sequence of the P150/sericin 6 ORF was previously incorrectly predicted and assigned to two smaller, uncharacterized genes. We present a new P150/sericin 6 gene model and show that it encodes a large protein of 467 kDa. It is characterized by repeats with a high proportion of threonine residues and a short conserved region with a cysteine knot motif (CXCXCX) at the C-terminus. Expression analysis has shown that B. mori P150/ser6 has low transcriptional level in contrast to its G. mellonella homolog. We also discuss the synteny of homologous genes on corresponding chromosomes between moth species and possible phylogenetic relationships between P150/ser6 and cysteine knot mucins. Our results improve our understanding of the evolutionary relationships between adhesion proteins in different lepidopteran species.

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Proteotranscriptomics – A facilitator in omics research

Cited by 6 publications

References 94 publications

Proteotransciptomics of the Most Popular Host Sea Anemone Entacmaea quadricolor Reveals Not All Toxin Genes Expressed by Tentacles Are Recruited into Its Venom Arsenal

Proteotransciptomics of the Most Popular Host Sea Anemone Entacmaea quadricolor Reveals Not All Toxin Genes Expressed by Tentacles Are Recruited into Its Venom Arsenal

Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis

Unravelling the complexity of silk sericins:P150/sericin 6is a new silk gene inBombyx mori

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