AbstractMimivirus bradfordmassiliense (Mimivirus) is a giant virus that infects Acanthamoeba species – opportunistic human pathogens. Long- and short-read sequencing were used to generate a de novo transcriptome of the host and followed the dynamics of both host and virus transcriptomes over the course of infection.

摘要Mimivirus bradfordmassiliense（Mimivirus）是一种巨大的病毒，可感染棘阿米巴物种-机会性人类病原体。长读和短读测序用于产生宿主的从头转录组，并在感染过程中跟踪宿主和病毒转录组的动态。

The assembled transcriptome of the host included 22,604 transcripts and 13,043 genes, with N50 = 2,372 nucleotides. Functional enrichment analysis revealed major changes in the host transcriptome, namely, enrichment in downregulated genes associated with cytoskeleton homeostasis and DNA replication, repair, and nucleotide synthesis.

宿主的组装转录组包括22604个转录本和13043个基因，其中N50=2372个核苷酸。功能富集分析揭示了宿主转录组的主要变化，即与细胞骨架稳态和DNA复制，修复和核苷酸合成相关的下调基因的富集。

These modulations, together with those implicated by other enriched processes, indicate cell cycle arrest, which was demonstrated experimentally. We also observed upregulation of host genes associated with transcription, secretory pathways and, as reported here for the first time, peroxisomes and the ubiquitin-proteasome system.

这些调节以及其他富集过程所涉及的调节表明细胞周期停滞，这已通过实验证明。我们还观察到与转录，分泌途径以及过氧化物酶体和泛素-蛋白酶体系统相关的宿主基因的上调。

In Mimivirus, the early stages of infection were marked by upregulated genes related to DNA replication, transcription, translation, and nucleotide metabolism, and in later stages, enrichment in genes associated with lipid metabolism, carbohydrates, and proteases. Some of the changes observed in the amoebal transcriptome likely point to Mimivirus infection causing dismantling of host cytoskeleton and translocation of endoplasmic reticulum membranes to viral factory areas..

在Mimivirus中，感染的早期阶段以与DNA复制，转录，翻译和核苷酸代谢相关的上调基因为标志，而在后期阶段，与脂质代谢，碳水化合物和蛋白酶相关的基因富集。在变形虫转录组中观察到的一些变化可能指向模拟病毒感染，导致宿主细胞骨架的破坏和内质网膜向病毒工厂区域的移位。。

IntroductionMimivirus bradfordmassiliense (Mimivirus) is a member of the nucleo-cytoplasmatic large DNA viruses (NCLDV) clade, whose infection of Acanthamoeba spp. causes massive lysis in the amoebal population. The first giant DNA virus to be discovered, Mimivirus has a diameter of about 750 nm. Its genome, ~ 1.2 × 106 base-pair (bp) long, encodes approximately 1000 open reading frames (ORFs), many of which are orphan genes, with no detectable homologs in other species1,2,3,4.Mimivirus’s target hosts, Acanthamoeba spp., are free-living amoebae that reside in air, soil, and water environments and are recognized as opportunistic human pathogens5,6,7.

引言Mimivirus bradfordmassiliense（Mimivirus）是核质大DNA病毒（NCLDV）进化枝的成员，其感染棘阿米巴属（Acanthamoeba spp。）会导致变形虫种群大量裂解。Mimivirus是第一个被发现的巨型DNA病毒，其直径约为750纳米。它的基因组长约1.2×106个碱基对（bp），编码大约1000个开放阅读框（ORF），其中许多是孤儿基因，在其他物种中没有可检测到的同源物1,2,3,4。Mimivirus的目标宿主棘阿米巴（Acanthamoeba spp。）是自由生活的变形虫，存在于空气，土壤和水环境中，被认为是机会性人类病原体5,6,7。

Indeed, Acanthamoeba polyphaga (AP) is a causative agent of several human diseases, including granulomatous amoebic encephalitis, a rare brain infection that is generally fatal, a skin ulcer in human immunodeficiency virus (HIV) patients, and Acanthamoeba keratitis—a corneal infection that can lead to loss of vision6.

事实上，棘阿米巴多噬菌体（AP）是几种人类疾病的病原体，包括肉芽肿性阿米巴脑炎，一种通常致命的罕见脑部感染，人类免疫缺陷病毒（HIV）患者的皮肤溃疡，以及棘阿米巴角膜炎-一种可导致视力丧失的角膜感染6。

The latter is becoming more prevalent because of the increased use of contact lenses, which nurture amoebal growth when hygiene is inadequate.Mimivirus enters the amoeba host cell via phagocytosis. In the phagosome, it loses its capsid and fuses with the phagosome membrane, after which the viral core enters the cytoplasm8,9.

由于隐形眼镜的使用增加，后者变得越来越普遍，当卫生不充分时，隐形眼镜会促进变形虫的生长。Mimivirus通过吞噬作用进入阿米巴宿主细胞。在吞噬体中，它失去衣壳并与吞噬体膜融合，然后病毒核心进入细胞质8,9。

Therein, viral factories (VFs) begin to be formed and, at 5 h post infection (HPI), they fuse into a single mature VF8,10,11. Viral production occurs in the VF and, at approximately 12–14 HPI, cell lysis occurs, prompting the release of newly-formed viruses into the surrounding medium8,11.To date, one study has described Mimivirus transcriptome dynamics during the infection cycle in Acanthamoeba castellanii (AC), another member of the Acanthamoeba genus12.

其中，病毒工厂（VFs）开始形成，并且在感染后5小时（HPI），它们融合成单个成熟的VF8,10,11。病毒产生发生在VF中，在大约12-14 HPI时，发生细胞裂解，促使新形成的病毒释放到周围的培养基中8,11。迄今为止，一项研究描述了卡斯特拉尼棘阿米巴（Acanthamoeba castellanii）感染周期中的模拟病毒转录组动力学，Acanthamoeba genus12的另一个成员。

However, the dynamics of the host .

然而，主机的动态。

Uninfected AP cells were plated on 3.5-cm glass-bottomed plates (µ-Slide, 8-well, tissue culture-treated (Ibidi IBD-80826 i)). Cells were infected with Mimivirus at MOI ~ 10 for 1, 3 or 5 h. The plates were then washed and incubated with PFA 4% in PBS for 20 min at room temperature (RT), washed three times with PBS for 5 min each, and incubated for an additional 10 min at RT with triton X100 0.1% in PBS.

。将细胞用MOI 〜10的模拟病毒感染1,3或5小时。然后洗涤平板并在室温（RT）下用PBS中的PFA 4%孵育20分钟，用PBS洗涤三次，每次5分钟，并在室温下用triton X100 0.1%的PBS溶液再孵育10分钟。

Cells were washed three times with PBS for 5 min each and incubated with a 1:1000 dilution of DAPI (5 µg/mL) in PBS for ~ 1 h, and then finally washed three times with PBS. Samples were imaged using an Eclipse TI-E Nikon inverted microscope (Nikon Instruments Inc., Melville, NY) with a Plan Apo 100X/1.4 NA lens.

将细胞用PBS洗涤三次，每次5分钟，并与1:1000稀释的DAPI（5µg/mL）在PBS中孵育约1小时，然后最后用PBS洗涤三次。使用Eclipse TI-E Nikon倒置显微镜（Nikon Instruments Inc.，Melville，NY）和Plan Apo 100X/1.4 NA透镜对样品成像。

Images were acquired with a cooled electron-multiplying charge-coupled device (EMCCD) camera (IXON ULTRA 888; Andor).Amoebal genomic DNA staining by EdU.

使用冷却的电子倍增电荷耦合器件（EMCCD）相机（IXON ULTRA 888；Andor）获取图像。。

We used the Click-iT® EdU Cell Proliferation Kit for Imaging (Thermo Fischer, catalog number: C10337). AP cells (5–10% confluency) were grown in PYG in a 3.5-cm petri dish containing EdU nucleotides (20 μM; 1:500), for 24 h at 30°C. Cells were transferred to 8-well plates (Ibidi 80826), to achieve 50–70% confluency, for 10 min, and then washed thrice with fresh PYG and left in the incubator for 1 h, followed by Mimivirus infection at MOI  ~10 for 4, 5, 6, 8, and 10 h.

我们使用Click-iT®EdU细胞增殖试剂盒进行成像（Thermo Fischer，目录号：C10337）。AP细胞（5-10%汇合）在含有EdU核苷酸（20μM；1:500）的3.5厘米培养皿中于PYG中于30°C生长24小时。将细胞转移到8孔板（Ibidi 80826）中，以达到50-70%的融合度，持续10分钟，然后用新鲜PYG洗涤三次，并在培养箱中放置1小时，然后在MOI  〜10处进行模拟病毒感染，持续4、5、6、8和10小时。

Infection was terminated by washing the cells with PBS and incubating them in formaldehyde (3.7% in PBS) for 15 min, followed by three washes with PBS. Triton® X-100 (300 μL, 0.1% in PBS) was added, and the cells were then incubated for additional 10 min at RT, after which they were washed thrice with PBS.

通过用PBS洗涤细胞并将其在甲醛（PBS中3.7%）中孵育15分钟，然后用PBS洗涤三次来终止感染。加入Triton®X-100（300μL，PBS中0.1%），然后将细胞在室温下再孵育10分钟，然后用PBS洗涤三次。

We then followed the manufacturer’s instructions for using the kit. Briefly, 300 μL of Click-iT® reaction mixture were added to each well and the cells were incubated for 30 min at RT, protected from light. The reaction mixture was then removed, and the cells were washed three times with 3% BSA in PBS and stained with DAPI 1:1000.Time-lapse imaging during Mimivirus infection.

。简而言之，向每个孔中加入300μlClick-iT®反应混合物，并将细胞在室温下孵育30分钟，避光。然后除去反应混合物，用PBS中的3%BSA洗涤细胞三次，并用DAPI 1:1000染色。在模拟病毒感染期间进行延时成像。

AP cells were grown on 35 mm2 glass-bottom plates (Mat‐Tek corp. P35G‐1.5‐14‐C), treated with 1 mg/mL poly-L lysine for 1 h, and then infected with Mimivirus at MOI ~ 50, at 30 °C. Widefield images were acquired using a Deltavision microscope (Applied Precision) equipped with a 60X UPlanSApo NA 1.40 objective and a photometrics coolSNAP HQ2 CCD (Roper Scientific, Tucson, AZ).

AP细胞在35 mm2玻璃底板（Mat-Tek corp.P35G-1.5-14-C）上生长，用1 mg/mL聚L-赖氨酸处理1小时，然后在MOI〜50感染模拟病毒，在30°C。使用配备有60X UPlanSApo NA 1.40物镜和photometrics coolSNAP HQ2 CCD（Roper Scientific，Tucson，AZ）的Deltavision显微镜（Applied Precision）获取宽视野图像。

Images were captured every 60 s from 250 min post-infection onward..

从感染后250分钟开始，每60秒拍摄一次图像。。

Data availability

数据可用性

The data sets supporting the results of this article are available in the Figshare repository, https://figshare.com/s/2e61150ec8bea07a5e13Raw data have been deposited in the NCBI BioProject database, BioProject accession number PRJNA720295 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA720295).

，https://figshare.com/s/2e61150ec8bea07a5e13Raw数据已保存在NCBI生物项目数据库中，生物项目登录号为PRJNA720295(https://dataview.ncbi.nlm.nih.gov/object/PRJNA720295)。

AbbreviationsAC:

缩写AC：

Acanthamoeba castellanii

卡氏棘阿米巴

AP:

Acanthamoeba polyphaga

多食棘阿米巴

bp:

bp公司：

Base pairs

碱基对

DEGs:

学位：

Differentially expressed genes

差异表达基因

DR:

医生：

Downregulated

下调

ER:

急诊室：

Endoplasmic reticulum

内质网

ERAD:

ERAD：

ER-associated degradation

ER相关降解

FDR:

罗斯福：

False discovery rate

错误发现率

GO:

转到：

Gene Ontology

基因本体论

HIV:

艾滋病毒：

Human immunodeficiency virus

人类免疫缺陷病毒

HPV:

HPV：

Human papilloma virus

人乳头瘤病毒

HCMV:

巨细胞病毒：

Human cytomegalovirus

人巨细胞病毒

Mimivirus:

Mimivirus：

Mimivirus bradfordmassiliense

Bradfordmassilines拟病毒

NCLDV:

NCLDV:

Nucleo-cytoplasmatic large DNA virus

NGS:

NGS：

Next-generation sequencing

下一代测序

ORF:

开放阅读框：

Open reading frame

打开阅读框

PCA:

主成分分析：

Principal component analysis

主成分分析

HPI:

HPI：

Hours post infection

感染后数小时

RT:

室温：

Room temperature

室温

SMRT:

SMRT：

Single-molecule, real-time

单分子，实时

SR:

销售代表：

Short reads

短读

URG:

URG：

Upregulated genes

上调基因

VF:

VF：

Viral factory

病毒工厂

ReferencesLa Scola, B. et al. A giant virus in amoebae. Science 299(5615), 2033 (2003).Article

参考文献La Scola，B。等人。变形虫中的巨大病毒。科学299（5615），2033（2003）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Raoult, D. et al. The 12-megabase genome sequence of Mimivirus. Science 306(5700), 1344–1350 (2004).Article

Raoult，D。等人。Mimivirus的12兆碱基基因组序列。科学306（5700），1344-1350（2004）。文章

ADS

广告

PubMed

PubMed

Google Scholar

谷歌学者

Renesto, P. et al. Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. J. Virol. 80(23), 11678–11685 (2006).Article

Renesto，P。等人。Mimivirus巨型颗粒包含大部分匿名和独特的基因产物。J、 。80（23），11678–11685（2006）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Legendre, M. et al. Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. Virol J 8, 99 (2011).Article

Legendre，M.等人使用超深基因组和转录组测序打破了模拟病毒的1000个基因屏障。Virol J 8,99（2011）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Khan, N. A. Acanthamoeba: Biology and Pathogenesis 2nd edn, 334 (Caister Academic Press, 2015).

Khan，N.A。棘阿米巴：生物学和发病机制第二版，334（凯斯特学术出版社，2015）。

Google Scholar

谷歌学者

Lorenzo-Morales, J., Khan, N. A. & Walochnik, J. An update on Acanthamoeba keratitis: Diagnosis, pathogenesis and treatment. Parasite 22, 10 (2015).Article

Lorenzo Morales，J.，Khan，N.A。＆Walochnik，J。棘阿米巴角膜炎的最新进展：诊断，发病机制和治疗。寄生虫22,10（2015）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Marciano-Cabral, F. & Cabral, G. Acanthamoeba spp. as agents of disease in humans. Clin. Microbiol. Rev. 16(2), 273–307 (2003).Article

Marciano Cabral，F。＆Cabral，G.Acanthamoeba spp。作为人类疾病的病原体。临床。微生物。修订版16（2），273–307（2003）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Andrade, A. C. D. S. et al. Filling knowledge gaps for mimivirus entry, uncoating, and morphogenesis. J. Virol.https://doi.org/10.1128/JVI.01335-17 (2017).Article

Andrade，A.C.D.S.等人填补了模拟病毒进入，脱壳和形态发生的知识空白。J、 维罗尔。https://doi.org/10.1128/JVI.01335-17（2017年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Zauberman, N. et al. Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus. PLoS Biol. 6(5), e114 (2008).Article

Zauberman，N。等人。棘阿米巴多食性拟态病毒中不同的DNA出口和包装门户。《公共科学图书馆·生物学》。6（5），e114（2008）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Fridmann-Sirkis, Y. et al. Efficiency in complexity: Composition and dynamic nature of mimivirus replication factories. J. Virol. 90(21), 10039–10047 (2016).Article

Fridmann-Sirkis，Y.等人，《复杂性的效率：模拟病毒复制工厂的组成和动态性质》。J、 。90（21），10039–10047（2016）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Yaakov, L. B. et al. Kinetics of mimivirus infection stages quantified using image flow cytometry. Cytometry A 95(5), 534–548 (2019).Article

Yaakov，L.B。等人。使用图像流式细胞术定量模拟病毒感染阶段的动力学。细胞计数A 95（5），534-548（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Legendre, M. et al. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res. 20(5), 664–674 (2010).Article

Legendre，M。等人。mRNA深度测序揭示了模仿病毒中的75个新基因和复杂的转录景观。基因组研究20（5），664-674（2010）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Mutsafi, Y. et al. Membrane assembly during the infection cycle of the giant Mimivirus. PLoS Pathog. 9(5), e1003367 (2013).Article

Mutsafi，Y。等人。巨型拟态病毒感染周期中的膜组装。PLoS Pathog。9（5），e1003367（2013）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Suárez, C. et al. Open membranes are the precursors for assembly of large DNA viruses. Cell Microbiol. 15(11), 1883–1895 (2013).PubMed

Suárez，C。等人。开放膜是组装大型DNA病毒的前体。细胞微生物学。15（11），1883-1895（2013）。PubMed出版社

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Conesa, A. et al. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18), 3674–3676 (2005).Article

Conesa，A。等人。Blast2GO：功能基因组学研究中注释，可视化和分析的通用工具。生物信息学21（18），3674-3676（2005）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Sedgwick, S. G. & Smerdon, S. J. The ankyrin repeat: A diversity of interactions on a common structural framework. Trends Biochem. Sci. 24(8), 311–316 (1999).Article

Sedgwick，S.G.＆Smerdon，S.J。锚蛋白重复序列：共同结构框架上的多种相互作用。趋势生物化学。科学。24（8），311–316（1999）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Notaro, A. et al. Expanding the occurrence of polysaccharides to the viral world: The case of mimivirus. Angew. Chem. Int. Ed. Engl. 60(36), 19897–19904 (2021).Article

Notaro，A.等人将多糖的出现扩展到病毒世界：mimivirus的案例。安吉。。国际英语。60（36），19897–19904（2021）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Piacente, F. et al. The rare sugar N-acetylated viosamine is a major component of Mimivirus fibers. J. Biol. Chem. 292(18), 7385–7394 (2017).Article

Piacente，F。等人。稀有糖N-乙酰化紫精胺是模拟病毒纤维的主要成分。J、 生物。。292（18），7385–7394（2017）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Piacente, F. et al. The autonomous glycosylation of large DNA viruses. Int. J. Mol. Sci. 16(12), 29315–29328 (2015).Article

Piacente，F。等人。大型DNA病毒的自主糖基化。Int.J.Mol.Sci。16（12），29315–29328（2015）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Parakkottil Chothi, M. et al. Identification of an L-rhamnose synthetic pathway in two nucleocytoplasmic large DNA viruses. J. Virol. 84(17), 8829–8838 (2010).Article

Parakkottil-Chothi，M.等人。两种核质大DNA病毒中L-鼠李糖合成途径的鉴定。J、 。84（17），8829–8838（2010）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Bauer, S. et al. Ontologizer 2.0—A multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24(14), 1650–1651 (2008).Article

Bauer，S.等人，《Ontologizer 2.0——GO术语富集分析和数据探索的多功能工具》。生物信息学24（14），1650-1651（2008）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Mutsafi, Y. et al. Vaccinia-like cytoplasmic replication of the giant Mimivirus. Proc. Natl. Acad. Sci. U.S.A 107(13), 5978–5982 (2010).Article

。程序。纳特尔。阿卡德。科学。U、 《美国法典》107（13），5978–5982（2010）。文章

ADS

广告

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Iyer, L. M., Koonin, E. V. & Aravind, L. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Genome Biol. 3(3), 1. https://doi.org/10.1186/gb-2002-3-3-research0012 (2002).Article

。基因组生物学。3（3），1。https://doi.org/10.1186/gb-2002-3-3-research0012（2002年）。文章

Google Scholar

谷歌学者

Alberts, B. Molecular Biology of the Cell 5th edn. (Garland Science, 2008).

Alberts，B。细胞第5版的分子生物学。（加兰科学，2008）。

Google Scholar

谷歌学者

Nandi, D. et al. The ubiquitin-proteasome system. J. Biosci. 31(1), 137–155 (2006).Article

Nandi，D。等人。泛素-蛋白酶体系统。J、 生物科学。31（1），137-155（2006）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Chelkha, N. et al. A Phylogenomic study of acanthamoeba polyphaga draft genome sequences suggests genetic exchanges with giant viruses. Front. Microbiol. 9, 2098 (2018).Article

Chelkha，N。等人。对棘阿米巴多噬菌体基因组序列草案的系统基因组学研究表明，与巨型病毒发生了基因交换。正面。微生物。92098（2018）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Dornas, F. P. et al. Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa. Front. Microbiol.https://doi.org/10.3389/fmicb.2015.01086 (2015).Article

。正面。微生物。https://doi.org/10.3389/fmicb.2015.01086（2015年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Lane, A. N. & Fan, T. W. Regulation of mammalian nucleotide metabolism and biosynthesis. Nucl. Acids Res. 43(4), 2466–2485 (2015).Article

Lane，A.N。＆Fan，T.W。哺乳动物核苷酸代谢和生物合成的调节。核。《酸决议》43（4），2466–2485（2015）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Desany, B. A. et al. Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathway. Genes Dev. 12(18), 2956–2970 (1998).Article

。基因发展12（18），2956-2970（1998）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Yoshizawa-Sugata, N. & Masai, H. Cell cycle synchronization and flow cytometry analysis of mammalian cells. In Cell Cycle Control. Methods in Molecular Biology (Methods and Protocols) Vol. 1170 (eds Noguchi, E. & Gadaleta, M.) (Humana Press, 2014). https://doi.org/10.1007/978-1-4939-0888-2_13.Chapter .

Yoshizawa Sugata，N。＆Masai，H。哺乳动物细胞的细胞周期同步和流式细胞术分析。。分子生物学方法（方法和方案）第1170卷（eds Noguchi，E。＆Gadaleta，M.）（Humana Press，2014）。https://doi.org/10.1007/978-1-4939-0888-2_13.Chapter。

Google Scholar

谷歌学者

He, Y. et al. Influenza A virus replication induces cell cycle arrest in G0/G1 phase. J. Virol. 84(24), 12832–12840 (2010).Article

He，Y。等人。甲型流感病毒复制诱导G0/G1期细胞周期停滞。J、 。84（24），12832–12840（2010）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Ravindran, M. S. et al. Opportunistic intruders: How viruses orchestrate ER functions to infect cells. Nat. Rev. Microbiol. 14(7), 407–420 (2016).Article

Ravindran，M.S.等人，《机会主义入侵者：病毒如何协调ER功能以感染细胞》。自然修订版微生物学。14（7），407–420（2016）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Inoue, T. & Tsai, B. How viruses use the endoplasmic reticulum for entry, replication, and assembly. Cold Spring Harb. Perspect. Biol. 5(1), a013250 (2013).Article

Inoue，T。＆Tsai，B。病毒如何利用内质网进行进入，复制和组装。冷泉兔。透视图。生物学5（1），a013250（2013）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Randow, F. & Lehner, P. J. Viral avoidance and exploitation of the ubiquitin system. Nat. Cell Biol. 11(5), 527–534 (2009).Article

Randow，F。＆Lehner，P.J。病毒避免和泛素系统的利用。自然细胞生物学。11（5），527-534（2009）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Pizzorno, A. et al. Influenza A viruses alter the stability and antiviral contribution of host E3-ubiquitin ligase Mdm2 during the time-course of infection. Sci. Rep. 8(1), 3746 (2018).Article

Pizzorno，A。等人。甲型流感病毒在感染过程中改变宿主E3泛素连接酶Mdm2的稳定性和抗病毒作用。科学。代表8（1），3746（2018）。文章

ADS

广告

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Cook, K. C. et al. Peroxisome plasticity at the virus-host interface. Trends Microbiol. 27(11), 906–914 (2019).Article

Cook，K.C.等人。病毒-宿主界面的过氧化物酶体可塑性。趋势微生物。27（11），906-914（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Jean Beltran, P. M. et al. Infection-induced peroxisome biogenesis is a metabolic strategy for herpesvirus replication. Cell Host Microbe 24(4), 526-541.e7 (2018).Article

Jean Beltran，P.M.等人。感染诱导的过氧化物酶体生物发生是疱疹病毒复制的代谢策略。细胞宿主微生物24（4），526-541.e7（2018）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9(4), 357–359 (2012).Article

Langmead，B。＆Salzberg，S.L。与Bowtie 2快速间隙读取对齐。自然方法9（4），357-359（2012）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33(3), 290–295 (2015).Article

Pertea，M。等人StringTie能够改进从RNA-seq读数重建转录组。美国国家生物技术公司。33（3），290-295（2015）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Bushmanova, E. et al. rnaSPAdes: A de novo transcriptome assembler and its application to RNA-Seq data. Gigasciencehttps://doi.org/10.1093/gigascience/giz100 (2019).Article

Bushmanova，E。等人。rnaSPAdes：从头转录组组装器及其在RNA-Seq数据中的应用。Gigasci公司encehttps://doi.org/10.1093/gigascience/giz100（2019年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Gilbert, D. Gene-omes built from mRNA seq not genome DNA. In 7th Annual Arthropod Genomics Symposium.Schoch, C.L., et al., NCBI Taxonomy: A Comprehensive Update on Curation, Resources and Tools. Database (Oxford) (2020).Rayamajhee, B. et al. A Systematic review of intracellular microorganisms within acanthamoeba to understand potential impact for infection.

Gilbert，D。基因omes由mRNA-seq而非基因组DNA构建。在第七届节肢动物基因组学年度研讨会上。Schoch，C.L。等人，《NCBI分类学：策展，资源和工具的全面更新》。数据库（牛津）（2020）。Rayamajhee，B。等人。对棘阿米巴内细胞内微生物的系统评价，以了解对感染的潜在影响。

Pathogens 10(2), 225 (2021).Article .

病原体10（2），225（2021）。文章。

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

BUSCO. Version 3 (2019). https://gitlab.com/ezlab/busco.Simão, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19), 3210–3212 (2015).Article

布斯科。版本3（2019）。https://gitlab.com/ezlab/busco.Simão，F.A。等人，BUSCO：使用单拷贝直系同源物评估基因组组装和注释完整性。生物信息学31（19），3210-3212（2015）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Acanthamoeba castellanii str. Neff (GCA_000313135.1) (Acastellanii.strNEFF_v1). https://protists.ensembl.org/Acanthamoeba_castellanii_str_neff_gca_000313135/Info/Index.Koressaar, T. & Remm, M. Enhancements and modifications of primer design program Primer3. Bioinformatics 23(10), 1289–1291 (2007).Article .

castellanii街棘阿米巴Neff（GCA\U 000313135.1）（Acastellanii.strNEFF\U v1）。https://protists.ensembl.org/Acanthamoeba_castellanii_str_neff_gca_000313135/Info/Index.Koressaar，T。＆Remm，M。引物设计程序Primer3的增强和修改。生物信息学23（10），1289-1291（2007）。文章。

PubMed

PubMed

Google Scholar

谷歌学者

Untergasser, A. et al. Primer3–new capabilities and interfaces. Nucl. Acids Res 40(15), e115 (2012).Article

Untergasser，A。等人，Primer3–新功能和接口。核。Acids Res 40（15），e115（2012）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Li, B. & Dewey, C. N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12, 323 (2011).Article

Li，B。＆Dewey，C。N。RSEM：从有或没有参考基因组的RNA-Seq数据进行准确的转录本定量。BMC生物信息。12323（2011）。文章

Google Scholar

谷歌学者

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15(12), 550 (2014).Article

Love，M.I.，Huber，W。＆Anders，S。用DESeq2缓和了RNA-seq数据的倍数变化和分散估计。基因组生物学。15（12），550（2014）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Alexa, A., Rahnenführer, J. & Lengauer, T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22(13), 1600–1607 (2006).Article

Alexa，A.，Rahnenführer，J。＆Lengauer，T。通过解相关GO图结构改进了基因表达数据中功能组的评分。。文章

PubMed

PubMed

Google Scholar

谷歌学者

Supek, F. et al. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6(7), e21800 (2011).Article

Supek，F。等人REVIGO总结并可视化了基因本体术语的长列表。PLoS ONE 6（7），e21800（2011）。文章

ADS

广告

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Download referencesAcknowledgementsWe dedicate this paper to Professor Avi Minsky, who passed away this year. We thank Drs. Merav Kedmi and David Pilzer, for their support in SMRT sequencing sample preparation; Maor Knafo, for his assistance with the SMRT sequencing and data analysis; Dr.

下载参考文献致谢我们将本文献给今年去世的阿维·明斯基教授。我们感谢Merav Kedmi博士和David Pilzer博士在SMRT测序样品制备中的支持；Maor Knafo，感谢他在SMRT测序和数据分析方面的帮助；博士。

Liran Ben Yaakov for establishing the UV protocol; and Drs. Ruti Kapon, Shifra Ben Dor, and Inbal Neta-Sharir, for their helpful advice and for reviewing the manuscript.Author informationAuthors and AffiliationsDepartments of Chemical and Structural Biology and Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, IsraelReut Bickels NuriBioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, IsraelEster FeldmesserProtein Analysis Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, IsraelYael Fridmann-SirkisGenomics unit, Department of Life Sciences Core Facilities- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, 7610001, Rehovot, IsraelHadas Keren-ShaulDepartment of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, IsraelReinat Nevo & Ziv ReichDepartment of Chemical and Structural biology, Weizmann Institute of Science, 7610001, Rehovot, IsraelAbraham MinskyAuthorsReut Bickels NuriView author publicationsYou can also search for this author in.

Liran Ben Yaakov建立紫外线协议；以及Ruti Kapon博士，Shifra Ben Dor博士和Inbal Neta Sharir博士，感谢他们的有益建议和审阅手稿。作者信息作者和附属机构魏茨曼科学研究所化学与结构生物学和生物分子科学系，7610001，Rehovot，IsraelReut-Bickels NuriBioinformatics Unit，生命科学系核心设施，魏茨曼科学研究所，7610001，Rehovot，IsraelEster-FeldmesserProtein Analysis Unit，生命科学系核心设施，7610001，Rehovot，IsraelYael-Fridmann-SirkisGenomics Unit，生命科学系核心设施-Nancy&Stephen Grand Israel National Center for Personal Medicine，魏茨曼科学研究所，7610001，Rehovot，IsraelHadas魏茨曼科学研究所生物分子科学系Keren ShaulDepartment of Biomolecular Sciences，Weizmann Institute of Science，7610001，Rehovot，IsraelReinat Nevo&Ziv ReichDepartment of Chemical and Structural Biology，Weizmann Institute of Science，7610001，Rehovot，IsraelAbraham MinskyAuthorsReut Bickels NuriView Author Publications您也可以在中搜索这位作者。

PubMed Google ScholarEster FeldmesserView author publicationsYou can also search for this author in

PubMed Google ScholarEster FeldmesserView作者出版物您也可以在

PubMed Google ScholarYael Fridmann-SirkisView author publicationsYou can also search for this author in

PubMed Google ScholarYael Fridmann SirkisView作者出版物您也可以在

PubMed Google ScholarHadas Keren-ShaulView author publicationsYou can also search for this author in

PubMed Google ScholarHadas Keren ShaulView作者出版物您也可以在

PubMed Google ScholarReinat NevoView author publicationsYou can also search for this author in

PubMed Google ScholarReinat NevoView作者出版物您也可以在

PubMed Google ScholarAbraham MinskyView author publicationsYou can also search for this author in

PubMed Google ScholarAbraham MinskyView作者出版物您也可以在

PubMed Google ScholarZiv ReichView author publicationsYou can also search for this author in

PubMed Google ScholarZiv ReichView作者出版物您也可以在

PubMed Google ScholarContributionsConception and design of the research -RN, YFS, EF. Experiment execution -RN, YFS. Data analysis and interpretation -RN , EF, YFS, Reinat Nevo, HKS. Writing the manuscript- RN, EF, YFS. Critical revision of the article-RN, ZR, AM, Reinat Nevo, HKS, EF, YFS.

PubMed谷歌学术贡献研究的概念和设计-RN，YFS，EF。实验执行-RN，YFS。数据分析和解释-RN，EF，YFS，Reinat Nevo，HKS。撰写手稿-RN，EF，YFS。。

Visualization- RN, Reinat Nevo. Supervision- AM and ZR. Funding acquisition-AM and ZR.Corresponding authorsCorrespondence to.

可视化-RN，Reinat Nevo。监督-AM和ZR。资助收购AM和ZR。通讯作者通讯。

Reut Bickels Nuri or Ziv Reich.Ethics declarations

罗伊·比克尔·努里或齐夫·赖希。道德宣言

Competing interests

相互竞争的利益

The authors declare no competing interests.

作者声明没有利益冲突。

Additional information

其他信息

Abraham Minsky: Deceased

亚伯拉罕·明斯基：已故

Publisher’s noteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Electronic supplementary materialBelow is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2Supplementary Material 3Supplementary Material 4Supplementary Material 5Supplementary Material 6Supplementary Material 7Supplementary Material 8Supplementary Material 9Supplementary Material 10Supplementary Material 11Supplementary Material 12Supplementary Material 13Supplementary Material 14Supplementary Material 15Supplementary Material 16Supplementary Material 17Supplementary Material 18Rights and permissions.

出版商的noteSpringer Nature在已发布地图和机构隶属关系中的管辖权主张方面保持中立。。补充材料1补充材料2补充材料3补充材料4补充材料5补充材料6补充材料7补充材料8补充材料9补充材料10补充材料11补充材料12补充材料13补充材料14补充材料15补充材料16补充材料17补充材料18权利和权限。

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material.

开放获取本文是根据知识共享署名非商业性NoDerivatives 4.0国际许可证授权的，该许可证允许以任何媒介或格式进行任何非商业性使用，共享，分发和复制，只要您对原始作者和来源给予适当的信任，提供知识共享许可证的链接，并指出您是否修改了许可材料。

You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

根据本许可证，您无权共享源自本文或其部分的改编材料。本文中的图像或其他第三方材料包含在文章的知识共享许可证中，除非该材料的信用额度中另有说明。如果材料未包含在文章的知识共享许可中，并且您的预期用途不受法律法规的许可或超出许可用途，则您需要直接获得版权所有者的许可。

To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/..

要查看此许可证的副本，请访问http://creativecommons.org/licenses/by-nc-nd/4.0/..

Reprints and permissionsAbout this articleCite this articleBickels Nuri, R., Feldmesser, E., Fridmann-Sirkis, Y. et al. Acanthamoeba polyphaga de novo transcriptome and its dynamics during Mimivirus infection.

转载和许可本文引用本文Bickels-Nuri，R.，Feldmesser，E.，Fridmann-Sirkis，Y。等人。棘阿米巴多噬菌体从头转录组及其在模拟病毒感染期间的动态。

Sci Rep 14, 25894 (2024). https://doi.org/10.1038/s41598-024-76078-6Download citationReceived: 03 June 2024Accepted: 10 October 2024Published: 29 October 2024DOI: https://doi.org/10.1038/s41598-024-76078-6Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

Sci Rep 1425894（2024）。https://doi.org/10.1038/s41598-024-76078-6Download引文接收日期：2024年6月3日接受日期：2024年10月10日发布日期：2024年10月29日OI：https://doi.org/10.1038/s41598-024-76078-6Share本文与您共享以下链接的任何人都可以阅读此内容：获取可共享链接对不起，本文目前没有可共享的链接。复制到剪贴板。

Provided by the Springer Nature SharedIt content-sharing initiative

由Springer Nature SharedIt内容共享计划提供