D a Genome Sequence o he Ty amine P oduce En e ococcus
du ans S ain IPLA 655
Vic o Lade o, Daniel M. Lina es, Bea iz del Rio, Ma ia Fe nandez, M. C uz Ma in, Miguel A. Al a ez
Ins i u o de P oduc os Lác eos de As u ias, IPLA-CSIC, Paseo Rio Lina es s/n, Villa iciosa, As u ias, Spain
We he e epo a 3.059-Mbp d a assembly o he genome o En e ococcus du ans s ain IPLA 655. This dai y isola e p o ides a
model o s udying he egula ion o he biosyn hesis o y amine (a oxic compound). These esul s should aid ou unde s and-
ing o y amine p oduc ion and allow y amine accumula ion in ood o be educed.
Recei ed 3 Ap il 2013 Accep ed 4 Ap il 2013 Published 16 May 2013
Ci a ion Lade o V, Lina es DM, del Rio B, Fe nandez M, Ma in MC, Al a ez MA. 2013. D a genome sequence o he y amine p oduce En e ococcus du ans s ain IPLA 655.
Genome Announc. 1(3):e00265-13. doi:10.1128/genomeA.00265-13.
Copy igh © 2013 Lade o 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 3.0 Unpo ed license.
Add ess co espondence o Miguel A. Al a ez, [email p o ec ed].
En e ococcus du ans is a mino componen o he in es inal mi-
c obio a o humans and domes ic animals (1). I is commonly
ound in animal-de i ed ood p oduc s, especially milk and
cheese (2). This bac e ium p oduces y amine—a biogenic amine
(BA) equen ly p esen in e men ed oods—by deca boxyla ing
y osine. The inges ion o ood wi h high y amine concen a ions
causes an in oxica ion, known as he cheese eac ion, cha ac e -
ized by mig aine, hype ension, e c. (3). Ty amine p oduc ion in
bac e ia has been ela ed o ene gy p oduc ion and he acidic
s ess esponse (4).
E.du ans s ain IPLA 655, which was isola ed om a adi-
ional cheese (5), p o ides a model o esea ch in o y amine
p oduc ion (6–9). A genomic lib a y o 0.5 kbp was cons uc ed
and subjec ed o pai ed-end sequencing (p o iding app oxi-
ma ely 150- old co e age) using a HiSeq 1000 Sys em sequence
(Illumina) a he Beijing Genomics Ins i u e (China). Quali y-
il e ed eads we e assembled in o con igs using Vel e so wa e
(h p://www.ebi.ac.uk/~ze bino/ el e /). Anno a ion was pe -
o med using he P oka yo ic Genomes Anno a ion Pipeline
(PGAAP) a he NCBI (h p://www.ncbi.nlm.nih.go /genomes
/s a ic/Pipeline.h ml), and imp o ed wi h esul s ob ained om
BLAST analysis (h p://blas .ncbi.nlm.nih.go ). The d a genome
sequence o E. du ans IPLA 655 in ol es 3,059,052 bp, a GC con en
o 37.7%, and 141 con igs anging om 201 o 203,388 bp. I encodes
2,853 p edic ed coding sequences. Single p edic ed copies o 16S, 23S,
and 5S RNA genes we e ound, as well as 51 genes o RNAs.
In ag eemen wi h i s dai y o igin, E. du ans IPLA 655 may
me abolize lac ose; a lac ose phospho ans e ase ope on
(lacXGEFDCBAR) was iden i ied in i s genome. Howe e , no ex a-
cellula caseinoly ic p o ease genes we e ound. The genome con ains
he y amine p oduc ion clus e , bu no o he BA clus e s.
BA p oduc ion clus e s gene ally include a gene simila o
hose encoding he co esponding aminoacyl- RNA syn he ase,
bu wi h unp o en unc ion. Su p isingly, analysis o he E. du ans
IPLA 655 genome showed no o he y osyl- RNA syn he ase gene
besides he y osyl- RNA syn he ase-like gene ( y S) in he y-
amine clus e . This con i ms ha y S encodes a y osyl- RNA
syn he ase. Up egula ed a a low pH (9), when y osine is deca -
boxyla ed o coun e ac acidic s ess, he inc eased p oduc would
ensu e he supply o y osine o p o ein biosyn hesis.
No e idence o i ulence- ela ed genes o an ibio ic esis ance
genes was seen. A leas h ee p ophages we e de ec ed; hese we e
mos homologouswi hp ophageso E. aecium.Somegenesin ol ed
in plasmid mobiliza ion o eplica ion we e de ec ed, along wi h wo
pu a i e oxin/an i- oxin plasmid s abiliza ion sys ems, in ag eemen
wi h he p esence o a leas h ee plasmids (da a no shown).
The genome sequence o E. du ans IPLA 655 should aid ou
unde s anding o he gene ic egula ion and physiological signi -
icance o y amine biosyn hesis, and pe haps sugges ways o e-
ducing y amine accumula ion in ood.
Nucleo ide sequence accession numbe s. The esul s o his
whole-genome sho gun p ojec we e deposi ed in he DDBJ/
EMBL/GenBankda abaseunde accession numbe AOSM00000000.
The e sion o he genome desc ibed he e has he accession num-
be AOSM01000000.
ACKNOWLEDGMENTS
This wo k was unded by he Spanish Minis y o Economy and Compe -
i i eness (AGL2010-18430) and CSIC (201270E144). B.D.R. and D.M.L.
a e bene icia ies o JAE-DOC con ac s (CSIC).
REFERENCES
1.De iese LA, Vancanney M, Descheemaeke P, Baele M, Van Landuy
HW, Go d s B, Bu aye P, Swings J, Haeseb ouck F. 2002. Di e en ia ion
and iden i ica ion o En e ococcus du ans,E.hi ae and E. illo um. J. Appl.
Mic obiol. 92:821–827.
2.Ogie JC, Se o P. 2008. Sa e y assessmen o dai y mic oo ganisms: he
En e ococcus genus. In . J. Food Mic obiol. 126:291–301.
3.Lade o V, Calles-En íquez M, Fe nández M, Al a ez MA. 2010. Toxico-
logical e ec s o die a y biogenic amines. Cu . Nu . Food Sci. 6:145–156.
4.Molenaa D, Bossche JS, en B ink B, D iessen AJ, Konings WN. 1993.
Gene a ion o a p o on mo i e o ce by his idine deca boxyla ion and elec-
ogenic his idine/his amine an ipo in Lac obacillus buchne i. J. Bac e iol.
175:2864–2870.
5.Fe nández M, Lina es DM, Al a ez MA. 2004. Sequencing o he y osine
deca boxylase clus e o Lac ococcus lac is IPLA 655 and he de elopmen o
a PCR me hod o de ec ing y osine deca boxyla ing lac ic acid bac e ia. J.
Food P o ec . 67:2521–2529.
6.Fe nández M, Lina es DM, Rod íguez A, Al a ez MA. 2007. Fac o s
Genome Announcemen sMay/June 2013 Volume 1 Issue 3 e00265-13 genomea.asm.o g 1
a ec ing y amine p oduc ion in En e ococcus du ans IPLA 655. Appl. Mi-
c obiol. Bio echnol. 73:1400–1406.
7.Lina es DM, Fe nández M, Ma ín MC, Al a ez MA. 2009. Ty amine
biosyn hesis in En e ococcus du ans is ansc ip ionally egula ed by he
ex acellula pH and y osine concen a ion. Mic ob. Bio echnol.
2:625–633.
8.Fe nández de Palencia P, Fe nández M, Mohedano ML, Lade o V,
Que edo C, Al a ez MA, López P. 2011. Role o y amine syn hesis by
ood-bo ne En e ococcus du ans in adap a ion o he gas oin es inal ac
en i onmen . Appl. En i on. Mic obiol. 77:699–702.
9.Lina es DM, Fe nández M, del Río B, Lade o V, Ma in MC, Al a ez
MA. 2012. The y osyl- RNA syn he ase like gene loca ed in he y amine
biosyn hesis clus e o En e ococcus du ans is ansc ip ionally egula ed by
y osine concen a ion and ex acellula pH. BMC Mic obiol. 12:23.
Lade o e al.
Genome Announcemen s2genomea.asm.o g May/June 2013 Volume 1 Issue 3 e00265-13