Infectious Virions of Bombyx Mori Latent Virus Are Incorporated into Bombyx Mori Nucleopolyhedrovirus Occlusion Bodies

Tsukui, Keita; Yagisawa, Chihiro; Fujimoto, Shota; Ogawa, Moe; Kokusho, Ryuhei; Nozawa, Masahiro; Kawasaki, Hideki; Katsuma, Susumu; Iwanaga, Masako

doi:10.3390/v11040316

Cited by 5 publications

(6 citation statements)

References 23 publications

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“…3 b). Within the gradient, fraction series [ 1 – 9 ] are similar to each other, while fraction 10 is most different from all others. This is consistent with fraction 10 constituting an acetone precipitation of all proteins that were not separated in the previous fractionation steps.…”

Section: Resultsmentioning

confidence: 99%

“…Hence, it has been long recognized as an excellent system for drug screening and safety assessment [5,6]. Furthermore, the BmN4 cell line of Bombyx mori [7] has been intensely used in studying many different biological aspects in the laboratory, including virus infection [8,9] and germline piRNA biology [10]. Despite the widespread usage of this ovary-derived cell line, its exact genomic sequence and a tested gene structure model is still missing.…”

Section: Introductionmentioning

confidence: 99%

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Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

2020

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Background The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise. Results Combining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage. Conclusions We show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

2020

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show abstract

“…Fractionation replicates correlate very well (average Pearson correlation coe cient >0.97) ( Fig 3A) and cluster together in the rst two PCA dimensions ( Fig 3B). Within the gradient, fraction series [1][2][3], [4][5][6][7] and [8][9] are similar to each other, while fraction 10 is most different from all others. This is consistent with fraction 10 constituting an acetone precipitation of all proteins that were not separated in the previous fractionation steps.…”

Section: Subcellular Localization Of Proteins Determined By Lopit-dcmentioning

confidence: 92%

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Levin¹,

Scheibe²,

Butter³

2020

Preprint

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BackgroundThe process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-Seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise. ResultsCombining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6,200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage. ConclusionsWe show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.

show abstract

“…Within the gradient, fraction series [1][2][3], [4][5][6][7] and [8][9] are similar to each other, while fraction 10 is most different from all others. This is consistent with fraction 10 constituting an acetone precipitation of all proteins that were not separated in the previous fractionation steps.…”

Section: Subcellular Localization Of Proteins Determined By Lopit-dcmentioning

confidence: 92%

“…Hence, it has been long recognized as an excellent system for drug screening and safety assessment [5], [6]. Furthermore, the BmN4 cell line of Bombyx mori [7] has been intensely used in studying many different biological aspects in the laboratory, including virus infection [8], [9] and germline piRNA biology [10]. Despite the widespread usage of this ovary-derived cell line, its exact genomic sequence and a tested gene structure model is still missing as this cell line does not originate from the genome sequenced Bombyx mori strains.…”

Section: Introductionmentioning

confidence: 99%

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Levin¹,

Scheibe²,

Butter³

2020

Preprint

View full text Add to dashboard Cite

Background The process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-Seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise. Results Combining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6,200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage. Conclusions We show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information.

show abstract

Infectious Virions of Bombyx Mori Latent Virus Are Incorporated into Bombyx Mori Nucleopolyhedrovirus Occlusion Bodies

Cited by 5 publications

References 23 publications

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

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Infectious Virions of Bombyx Mori Latent Virus Are Incorporated into Bombyx Mori Nucleopolyhedrovirus Occlusion Bodies

Cited by 5 publications

References 23 publications

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori&nbsp;BmN4 cell line

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

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Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line