DOI: 10.5281/zenodo.11086255
title: An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host

description: Only a few bacteria are able to colonize the nuclei of eukaryotes and nearly all of these are known from protists. One bacterial clade, however, “Candidatus Endonucleobacter”, infects the nuclei of deep-sea mussels, where it replicates to ≥ 80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate so massively and avoid apoptosis is not known. Dual RNA-seq transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that in contrast to previous assumptions, “Ca. Endonucleobacter” does not gain most of its nutrition from nuclear DNA or RNA. Instead, “Ca. Endonucleobacter” upregulated genes for importing sugars, lipids, amino acids and possibly mucin from its host, and digested these nutrients. “Ca. Endonucleobacter” likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis (IAPs), proteins previously only known from animals and a few invertebrate viruses. Comparative phylogenetic analyses revealed that “Ca. Endonucleobacter” acquired IAPs repeatedly through horizontal gene transfer (HGT) from their hosts in convergent acquisition. HGT from eukaryotes to bacteria, although assumed to be rare, may be more common than currently recognized, particularly in bacteria that live in intimate associations with eukaryotic hosts.
description: Bioinformatics

Ca.E.childressi.gbk = Ca. Endonucleobacter childressi RAST-annotated genome in gbk format

Ca.E.childressi.gff = Ca. Endonucleobacter childressi RAST-annotated genome in GFF3 format

Ca.E.puteoserpentis.gbk = Ca. Endonucleobacter puteoserpentis RAST-annotated genome in gbk format

Ca.E.puteoserpentis.gff = Ca. Endonucleobacter puteoserpentis RAST-annotated genome in GFF3 format

3963.N6.bbnorm.Trinity.cent97.MEGANclean.fasta = Gigantidas childressi de novo transcriptome3963.N6.bbnorm.Trinity.cent97.MEGANclean.Trinotate.1e-3.pep.trans.xls = Trinotate annotation table for Gigantidas childressi de novo transcriptome

3885_3802_Bput_GillFoot_norm_Trinity.cent97.MEGANclean.fasta = Bathymodiolus puteoserpentis de novo transcriptome3885_3802_Bput_GillFoot_norm_Trinity.cent97.MEGANclean.Trinotate.1e-3.pep.trans.xls = Trinotate annotation table for Bathymodiolus puteoserpentis de novo transcriptomeIAP_hmm_profile.rar = folder containing the IAPs hmm profiles used in this study for the identification of inhibitors of apoptosis in "Ca. Endonucleobacter" genomes.
description: Microscopy data source

2018-02-09_B.put_ROV499-1-2(504)_IrinaII_SOX_NIX_MOX_DAPI_MAGP_63x_Pic006_early-infection-stage.lsm = Figure 1, fluorescent image of early infection stage

2018-02-09_B.put_ROV499-1-2(504)_IrinaII_SOX_NIX_MOX_DAPI_MAGP_63x_Pic003_mid-infection-stage.lsm = Figure 1, fluorescent image of mid infection stage2018-02-09_B.put_ROV499-1-2(504)_IrinaII_SOX_NIX_MOX_DAPI_MAGP_63x_Pic004_late-infection-stage.lsm = Figure 1, fluorescent image of late infection stageB_childressi_M071_G3_056.tif = Figure 1, TEM image of early infection stageB_childressi_M832_A1_004 = Figure 1, TEM image of mid infection stageB_childressi_NIX_closeup_M071_high_res = Figure 1, TEM image of late infection stage; Extended Data Figure 3Bchi_N9_EUB_NIX_DAPI_SlideI_002.vsi = Extended Data Figure 1, Gigantidas childressi filament overview

Bput_ROV499-1-1_EUB_NIX_DAPI_20X_001.vsi = Extended Data Figure 1, Bathymodiolus puteoserpentis filament overviewGchi_N9_GoM_MAGP_EUBI-III_NIX64_DAPI_adhesion-patch_stitched_40X_001.lsm = Extended Data Figure 1, Gigantidas childressi adhesion patch

Bput_504_Sl1_IrinaII_MAGP_EUBI-III_Kist_NIX64_DAPI_003_Stitched.lsm = Extended Data Figure 1, Bathymodiolus puteoserpentis adhesion patchGchi_N9_GoM_MAGP_EUBI-III_NIX64_DAPI_snapshot_airyscan_processed_shifted_100X_003.czi = Extended Data Figure 1, Gigantidas childressi Airyscan snapshotBput_ROV499-1-1_IrinaII_MAGP_EUBI-III_NIX64_DAPI_snapshot_airyscan_processed_shifted_100X_004.czi = Extended Data Figure 1, Bathymodiolus puteoserpentis Airyscan snapshotBchi_N5_GoM_MAGP_EUK(647)_NileRed_NIX(488)_DAPI_snapshot_airyscan_processed_63X_001.czi = Extended Data Figure 4, Gigantidas childressi 18S rRNA quantification - Non-infected & Early infection stageBchi_N5_GoM_MAGP_EUK(647)_NileRed_NIX(488)_DAPI_snapshot_airyscan_processed_63X_002.czi = Extended Data Figure 4, Gigantidas childressi 18S rRNA quantification - Mid infection stageBchi_N5_GoM_MAGP_EUK(647)_NileRed_NIX(488)_DAPI_snapshot_airyscan_processed_63X_003.czi = Extended Data Figure 4, Gigantidas childressi 18S rRNA quantification - Late infection stageB_C_M071_L9_056.tif = Extended Data Figure 6, Viral infection Ca. E. childressi general viewB_C_M071_L9_057.tif = Extended Data Figure 6, Viral infection Ca. E. childressi closeup