D a Genome Sequence and Anno a ion o he Obliga e
Bac e ial Endosymbion Caedibac e aeniospi alis, Causa i e
Agen o he Kille Pheno ype in Pa amecium e au elia
Nes o Zabu annyi,
d,e
Ka in G osse ,
b
Gilles Gaspa oni,
c
Rol Mülle ,
d,e
Ma ina Sch allhamme ,
b
Ma in Simon
a
a
Molecula Cell Dynamics, Cen e o Human and Molecula Biology, Saa land Uni e si y, Saa b ücken,
Ge many
b
Mic obiology, Ins i u e o Biology II, Albe Ludwig Uni e si y o F eibu g, F eibu g, Ge many
c
Gene ics, Cen e o Human and Molecula Biology, Saa land Uni e si y, Saa b ücken, Ge many
d
Depa men o Mic obial Na u al P oduc s, Helmhol z Cen e o In ec ion Resea ch and Depa men o
Pha macy, Helmhol z Ins i u e o Pha maceu ical Resea ch Saa land (HIPS), Saa land Uni e si y, Saa b ücken,
Ge many
e
Ge man Cen e o In ec ion Resea ch (DZIF), Pa ne Si e Hanno e -B aunschweig, Hanno e , Ge many
ABSTRACT Caedibac e aeniospi alis is an obliga e endosymbion li ing in he cy o-
plasm o Pa amecium e au elia.C. aeniospi alis causes he so-called kille ai ,
elimina ing in aspecific compe i o s o i s hos when eleased in o he medium by
he conce ed ac ion o he unusual p o ein s uc u e R-body ( e ac ile body) in ad-
di ion o an as-ye -unknown oxin.
Caedibac e aeniospi alis (Thio ichales,Gammap o eobac e ia) li es in he cy oplasm
o i s hos , Pa amecium e au elia (Ciliopho a). This unicellula , ela i ely la ge
(150-
␮
m) euka yo e sepa a es ege a i e and sexual unc ions, possesses ge mline and
soma ic nuclei, and is a long-es ablished model in gene ics and epigene ics esea ch
(1). A special ea u e o he Pa amecium-Caedibac e symbiosis is he “kille ai .” A
p opo ion o he endosymbion popula ion p oduces an unusual p o ein s uc u e, he
R-body ( e ac ile body) (2). This s uc u e, mos likely ac ing as a deli e y de ice o an
uniden ified oxin, is esponsible o killing symbion - ee, sensi i e pa amecia a e he
inges ion o bac e ia eleased om in ec ed s ains (3). Caedibac e -ha bo ing cells a e
p o ec ed om he le hal e ec o hei symbion s. Cul i a ion o C. aeniospi alis
ou side i s hos has no been accomplished so a .
To al DNA was isola ed om exponen ially g owing pa amecia. Thei in ec ion s a us
was e ified by fluo escence in si u hyb idiza ion, which enabled de ec ion o in acel-
lula C. aeniospi alis 51
T
, as desc ibed elsewhe e (4). To minimize con amina ion om
ood bac e ia, P. e au elia cul u es (s ain 51K ⫽CCAP 1660/3F) we e ed wi h
␤
-lac am-
hype sensi i e Esche ichia coli Δ olC (5) and ea ed wi h 10
␮
gml
⫺1
ampicillin be o e
DNA isola ion (6). Lib a y p epa a ion o whole-genome sequencing used he agmen-
a ion p ocedu e (7). We gene a ed a lib a y o ~500 o 800 bp o subsequen
sequencing on an Illumina MiSeq ins umen (2 ⫻300 nucleo ides [n ]). A e assembly
using he ABySS-pe p og am (8), 24 con igs we e assigned o he genome o C. ae-
niospi alis. These can be di e en ia ed om he hos genome by hei nea ly iden ical
co e age and by hei GC con en o 41.5%, di e ging o he hos genome’s GC con en
o 28% (9). D a genome sequences had a o al sequence leng h o 1.3 Mb (N
50
,
55.531 bp), including he p e iously known plasmid, pKAP, o 41.7 kb (10). The genome
con ains h ee RNA clus e s in 16S-23S-5S configu a ions.
Gene anno a ion o he d a sequence was ca ied ou using P odigal (11),
RNAscan-SE (12), and RNAmme (13) so wa e ools. Nex o 36 RNA genes, 1,080
Recei ed 16 No embe 2017 Accep ed 5
Decembe 2017 Published 18 Janua y 2018
Ci a ion Zabu annyi N, G osse K, Gaspa oni G,
Mülle R, Sch allhamme M, Simon M. 2018.
D a genome sequence and anno a ion o he
obliga e bac e ial endosymbion Caedibac e
aeniospi alis, causa i e agen o he kille
pheno ype in Pa amecium e au elia. Genome
Announc 6:e01418-17. h ps://doi.o g/10.1128/
genomeA.01418-17.
Copy igh ©2018 Zabu annyi e al. This is an
open-access a icle dis ibu ed unde he e ms
o he C ea i e Commons A ibu ion 4.0
In e na ional license.
Add ess co espondence o Ma ina Sch allhamme ,
[email p o ec ed],
o Ma in Simon, [email p o ec ed].
PROKARYOTES
c ossm
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p o ein coding sequences could be iden ified, o which, 787 could be unc ionally
anno a ed by a simila i y sea ch agains he eggNOG da abase wi h he eggNOG-
mappe so wa e (14).
The genome sequence o C. aeniospi alis s ain 51K will imp o e ou unde s anding
o his o ganism and i s symbio ic in e ac ion wi h P. e au elia, including and in
addi ion o he kille ai . The a ailabili y o his sequence in o ma ion enables phy-
logenomic analyses o he genus Caedibac e and will p o ide a aluable esou ce o
he iden ifica ion and analysis o oxin candida es, which migh ha e unusual biological
p ope ies ha explain he need o he R-body as a deli e y de ice.
Accession numbe (s). This whole-genome sho gun p ojec has been deposi ed
a DDBJ/ENA/GenBank unde he accession numbe PGGB00000000. The e sion
desc ibed in his pape is e sion PGGB01000000.
ACKNOWLEDGMENTS
This wo k was suppo ed by he Ge man Science Founda ion (g an SI1397/3-1) and
he Resea ch Inno a ion Fund o he Albe Ludwig Uni e si y o F eibu g.
We a e g a e ul o Jasmin Ki ch and As id Pe e sen o hei assis ance.
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Zabu annyi e al.
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