genomic analysis of the novel mycobacteriophage bromden
TRANSCRIPT
Hope CollegeDigital Commons @ Hope College17th Annual Celebration of UndergraduateResearch and Creative Performance (2018)
Celebration of Undergraduate Research andCreative Performance
4-13-2018
Genomic Analysis of the NovelMycobacteriophage BromdenKaitlyn Lein
Kimberly Paquette
Timbree Pederson
Matthew Switalski
Carter Smiley
See next page for additional authors
Follow this and additional works at: https://digitalcommons.hope.edu/curcp_17
Part of the Biology Commons
This Poster is brought to you for free and open access by the Celebration of Undergraduate Research and Creative Performance at Digital Commons @Hope College. It has been accepted for inclusion in 17th Annual Celebration of Undergraduate Research and Creative Performance (2018) by anauthorized administrator of Digital Commons @ Hope College. For more information, please contact [email protected].
Recommended CitationRepository citation: Lein, Kaitlyn; Paquette, Kimberly; Pederson, Timbree; Switalski, Matthew; Smiley, Carter; Oonk, Emma; Baird,Darby; Van Wyk, Brooke; Hemesath, Lilly; Meder, Abigail; Orndorff, Madelyn; and Grimes, Megan, "Genomic Analysis of the NovelMycobacteriophage Bromden" (2018). 17th Annual Celebration of Undergraduate Research and Creative Performance (2018). Paper 20.https://digitalcommons.hope.edu/curcp_17/20April 13, 2018. Copyright © 2018 Hope College, Holland, Michigan.
Student Author(s)Kaitlyn Lein, Kimberly Paquette, Timbree Pederson, Matthew Switalski, Carter Smiley, Emma Oonk, DarbyBaird, Brooke Van Wyk, Lilly Hemesath, Abigail Meder, Madelyn Orndorff, and Megan Grimes
This poster is available at Digital Commons @ Hope College: https://digitalcommons.hope.edu/curcp_17/20
Gen
omic
Ana
lysi
s of
Nov
el M
ycob
acte
rioph
age
Bro
mde
nK
aitly
n Le
in, K
imbe
rly P
aque
tte, T
imbr
ee P
eder
son,
Mat
thew
Sw
itals
ki, C
arte
r Sm
iley,
Em
ma
Oon
k, D
arby
Bai
rd, B
rook
e V
an W
yk, L
illy
Hem
esat
h, A
biga
il M
eder
, Mad
elyn
Orn
dorff
, Meg
an G
rimes
. M
ento
rs: D
r. Jo
seph
Stu
key
Dep
artm
ent o
f Bio
logy
, Hop
e C
olle
ge, H
olla
nd, M
I
I.A
bstr
act
Twen
ty n
ew m
ycob
acte
rioph
ages
wer
e is
olat
ed fr
om s
oil s
ampl
es
colle
cted
aro
und
the
stat
e of
Mic
higa
n an
d ot
her p
arts
of t
he U
nite
d S
tate
s. A
ll ph
ages
wer
e ca
pabl
e of
infe
ctin
g M
ycob
acte
rium
sm
egm
atis
and
wer
e is
olat
ed th
roug
h ei
ther
enr
ichm
ent o
r dire
ct
plat
ing
at 3
2℃. A
var
iety
of p
laqu
e m
orph
olog
ies
wer
e pr
oduc
ed
base
d on
siz
e, s
hape
, and
cla
rity;
bot
h ly
tic a
nd te
mpe
rate
pha
ges
are
repr
esen
ted
in th
is c
olle
ctio
n. T
he m
ycob
acte
rioph
age,
B
rom
den,
was
cho
sen
as o
ne o
f tw
o ph
ages
for c
ompl
ete
geno
me
sequ
enci
ng a
nd c
ompa
rativ
e ge
nom
ic a
naly
ses.
The
pre
dom
inan
t pl
aque
pro
duce
d by
Bro
mde
n af
ter 4
8 ho
urs
at 3
2℃ is
0.5
mm
in
diam
eter
, circ
ular
, and
cle
ar. T
he g
enom
e of
Bro
mde
n is
70.
2 K
b,
58.2
% G
C, a
nd c
onta
ins
119
gene
s. B
rom
den’
s co
mpl
ete
geno
me
sequ
ence
indi
cate
s a
rela
tions
hip
to m
ycob
acte
rioph
ages
of c
lust
er
L, a
nd s
trong
est s
imila
rity
to m
ycob
acte
rioph
age
Dyo
Eda
fos
of
subc
lust
er L
4, w
hich
is th
e on
ly o
ther
mem
ber o
f the
L4
subc
lust
er o
f m
ycob
acte
rioph
ages
. The
two
geno
mes
alig
n at
onl
y 85
% id
entit
y ov
er 8
7% o
f the
sho
rter B
rom
den,
with
the
larg
est d
iffer
ence
bei
ng
an 8
.5 k
b se
ctio
n fo
und
in D
yoE
dafo
s bu
t mis
sing
in B
rom
den.
Thi
s ac
coun
ts fo
r the
diff
eren
ce in
thei
r gen
e nu
mbe
rs, a
s D
yoE
dafo
s ha
s 33
mor
e ge
nes
than
Bro
mde
n. A
uto-
anno
tatio
n in
dica
ted
ther
e ar
e 13
pos
sibl
e tR
NA
gen
es in
Bro
mde
n. T
he G
C c
onte
nt o
f Bro
mde
n (5
8.2%
) is
low
com
pare
d to
mos
t oth
er c
lust
ers
of
myc
obac
terio
phag
es a
s w
ell a
s th
eir c
omm
on h
ost,
M. s
meg
mat
is
(67.
4%).
The
othe
r clu
ster
s w
ith re
lativ
ely
low
GC
con
tent
als
o ha
ve
few
mem
bers
, sug
gest
ing
that
thes
e ph
ages
may
mor
e re
adily
infe
ct
othe
r bac
teria
l hos
ts w
ith lo
wer
GC
con
tent
. A d
etai
led
anal
ysis
of
the
com
plet
e ge
nom
e se
quen
ces
and
com
paris
on w
ith s
eque
nced
m
ycob
acte
rioph
ages
is th
e su
bjec
t of t
he s
econ
d se
mes
ter o
f the
ye
arlo
ng c
ours
e an
d is
pre
sent
ed.
II.In
trod
uctio
nM
ycob
acte
rioph
age
Bio
logy
and
Gen
omic
s-
Nea
rly 9
,700
myc
obac
terio
phag
es h
ave
been
isol
ated
, of
whi
ch 1
,577
hav
e be
en s
eque
nced
and
cha
ract
eriz
ed-
Pha
ges
allo
w fo
r stu
dy o
f myc
obac
teria
thro
ugh
enha
nced
ge
netic
s, u
nder
stan
ding
of h
ow p
hage
con
tribu
te to
bac
teria
l bi
olog
ical
pro
cess
es-
Full
geno
me
sequ
ence
s of
pha
ges
reve
al n
ovel
func
tions
, ge
nes,
and
evo
lutio
n of
myc
obac
teria
l pha
ge a
nd h
osts
Dr.
Jose
ph S
tuke
yD
epar
tmen
t of B
iolo
gyst
ukey
@ho
pe.e
du
III.P
hage
Gen
omic
s R
esea
rch
2017
-201
8
2017
-201
8 Ph
age
Gen
omic
s R
esea
rch
Stud
ents
(Bro
mde
n gr
oup)
and
Pha
ge N
ames
Ack
now
ledg
emen
tsU
nive
rsity
of P
ittsb
urgh
Hat
full
Lab
How
ard
Hug
hes
Med
ical
In
stitu
te
SE
A-P
HA
GE
S P
rogr
am
Hop
e C
olle
ge D
epar
tmen
t of
Bio
logy
TA’s
: Meg
an G
rimes
and
M
adel
yn O
rndo
rff
IV.P
hysi
cal a
nd G
enom
ic C
hara
cter
istic
s
Figu
re 6
- Fr
eque
ncy
of G
C c
onte
nt
in B
rom
den
gene
s (L
eft)
Cal
cula
ting
the
GC
con
tent
for e
ach
gene
in B
rom
den
reve
aled
that
ther
e ar
e no
influ
entia
l out
liers
, but
ther
e ar
e si
x st
atis
tical
ly s
igni
fican
t gen
es.
Gen
es 6
1(50
.12)
, 105
(48.
33),
and
109(
49.7
5) a
re b
elow
2 s
tand
ard
devi
atio
ns fo
r the
GC
con
tent
. G
enes
22
(64.
73),
68(6
7.09
), an
d 10
1(66
.67)
ar
e ab
ove
two
stan
dard
dev
iatio
ns fr
om
the
mea
n.
95%
CI:
[50.
3, 6
4.78
5]. M
ean:
57.
5Fa
ndom
Imag
e
Abb
y M
eder
Boo
gey1
Han
nah
DeV
ore
Dee
rs
Julia
Wils
onP
hout
teA
mel
ia W
aalk
esS
elco
uth
Sar
ah O
len
Laet
aH
anna
h C
izau
skas
Bro
mde
n
Kai
tlyn
Lein
Ladi
ana
Ced
ric P
orte
rP
hutb
ol
Ana
Per
ecki
Sat
urnu
sM
atth
ew S
wita
lski
Mas
todo
n
Lydi
a D
ough
tyTh
yatir
aC
arte
r Sm
iley
Nep
hario
us
Tim
brer
e P
eder
son
Zuri
Bro
oke
Van
Wyk
Oni
sm
Lilly
Hem
esat
hLo
nder
Dar
by B
aird
M
alel
dil
Adr
iana
Mira
belli
Gra
ves
Kim
Paq
uette
P
upil
Zach
Wyl
ie
John
nyC
ache
Que
stio
n: W
hat M
ycob
acte
rium
spe
cies
doe
s B
rom
den
com
mon
ly in
fect
?M
etho
d: L
ook
at th
e ge
ne B
LAS
T, u
nusu
al g
enes
in p
hage
s, c
odon
usa
ge b
ias,
and
GC
con
tent
to fi
nd g
enes
that
hav
e be
en s
tole
n fro
m
host
s.R
esul
ts:
V.Po
tent
ial p
rimar
y ho
sts
Bro
mde
n C
hara
cter
istic
sIs
olat
ed v
ia d
irect
pla
ting
proc
edur
e fro
m m
oist
soi
l sam
ple,
col
lect
ed
by H
anna
h C
izau
skas
in W
estla
nd, M
ichi
gan
from
a p
umpk
in p
atch
that
w
as c
ompo
sted
with
gra
ss c
lippi
ngs
Circ
ular
cle
ar p
laqu
es, 0
.5m
m d
iam
eter
at 4
8 ho
urs
on M
. sm
egm
atis
ho
st a
t 32°
C
Sip
hovi
ridae
Stru
ctur
e
70,1
83 b
ase
pairs
, Lin
ear G
enom
e w
ith 1
0 bp
3’ o
verh
ang,
TC
GA
TCA
GC
C
58.2
% G
C,1
19 p
rote
in c
odin
g ge
nes,
13
tRN
A g
enes
Pia
tt
Dev
era
Cas
eJul
es
Jarv
iP
hara
oh
Arm
adill
o
Figu
re 1
- Tr
ansm
issi
on E
lect
ron
Mic
rosc
opy
Imag
es (D
isco
vere
d 20
15-2
016)
Figu
re 2
- A
ligne
d G
enom
e M
aps
of
Rep
rese
ntat
ive
Phag
es D
epic
ting
Leve
l of
Sim
ilarit
y be
twee
n G
enom
es U
sing
Ph
amer
ator
(Lef
t and
bot
tom
)
Top:
Pha
ge G
uuel
aD fr
om c
lust
er L
2 M
iddl
e: B
rom
den
draf
t fro
m c
lust
er L
4 B
otto
m: D
yoE
dafo
s dr
aft f
rom
clu
ster
L4
Bro
mde
n is
clo
sely
alig
ned
with
bot
h ph
ages
. Pur
ple
colo
r ind
icat
es c
lose
al
ignm
ent.
Bro
mde
n ha
s a
shor
ter g
enom
e th
an b
oth
Guu
elaD
and
Dyo
Eda
fos
(left)
. B
rom
den
has
a sh
orte
r gen
ome
com
pare
d to
the
aver
age
geno
me
leng
th o
f L p
hage
s.
Bro
mde
n’s
com
plet
e ge
nom
e is
sho
wn
belo
w.
Hol
in P
rote
in in
Bro
mde
n A
hol
in is
a p
rote
in th
at fu
nctio
ns to
cre
ate
a “h
ole”
in th
e m
embr
ane
of th
e ho
st c
ell.
This
allo
ws
the
new
ly p
rodu
ced
phag
e to
be
rele
ased
at t
he e
nd o
f the
lytic
cyc
le. O
ne c
ompo
nent
cod
ed fo
r by
a ho
lin g
ene
is a
tran
smem
bran
e do
mai
n, w
hich
allo
ws
the
holin
to a
ttach
to a
spe
cific
are
a in
the
mem
bran
e an
d is
nee
ded
for a
hol
in to
func
tion.
The
re a
re tw
o ge
nes
in B
rom
den
that
cou
ld h
ave
a po
tent
ial h
olin
func
tion,
gp2
8 an
d gp
29, a
ccor
ding
to th
eir l
ocat
ion
and
com
paris
on to
oth
er p
hage
gen
es.
How
ever
, it i
s ha
rd to
det
erm
ine
whi
ch g
ene
is a
hol
in o
r if b
oth
gene
s w
ork
toge
ther
, with
out s
peci
fic la
b da
ta.
Gp2
8:
●15
1 am
ino
acid
s ●
Pha
mily
193
0●
App
letre
e2_2
7, G
uuel
aD_2
9, M
iley1
6_29
, Nic
hola
sp3_
29, W
inky
_29
are
in P
ham
illy
1930
and
hav
e a
holin
func
tion
●0
trans
mem
bran
e do
mai
ns (h
ttp://
ww
w.e
nzim
.hu/
hmm
top/
serv
er/h
mm
top)
G
p29:
●
109
amin
o ac
ids
●P
ham
ily 3
7230
●R
umpe
lstil
tski
n_30
, Joe
Dirt
_28,
Loa
drie
_30
are
in P
ham
ily 3
7230
and
hav
e a
holin
func
tion
●3
trans
mem
bran
e do
mai
ns (h
ttp://
ww
w.e
nzim
.hu/
hmm
top/
serv
er/h
mm
top)
VI.S
peci
fic P
rote
in F
unct
ions
Tape
Mea
sure
Pro
tein
(TM
P) in
Bro
mde
n ●
Pro
tein
that
pro
vide
s in
form
atio
n an
d al
low
s m
ycob
acte
rioph
ages
to tr
ansp
ort
info
rmat
ion
into
the
host
cel
l dur
ing
an in
fect
ion
phas
e●
The
stud
y of
dom
ains
requ
ired
for t
he p
rote
in’s
func
tion
can
lead
to n
ew
disc
over
ies
in th
e ev
olut
ion
of m
ycob
acte
rioph
ages
●
Bro
mde
n’s
TMP
has
two
dom
ains
- see
figu
re 7
to th
e rig
ht fo
r an
exam
ple
●A
naly
zing
the
dom
ains
can
lead
to a
bet
ter u
nder
stan
ding
of t
he ta
pe
mea
sure
pro
tein
of B
rom
den
●Is
the
long
est g
ene
reco
rded
in B
rom
den
at 1
697
amin
o ac
ids
●S
urro
unde
d by
tail
asse
mbl
y ch
aper
ones
and
min
or ta
il pr
otei
ns
Figu
re 4
- Pl
aque
M
orph
olog
yA
fter c
ontin
uing
to p
ick
plaq
ues
from
dire
ct
plat
ing
tech
niqu
es,
Bro
mde
n’s
plaq
ues
wer
e co
nsis
tent
ly
circ
ular
, cle
ar a
nd
0.5m
m in
dia
met
er.
Con
sist
ent m
orph
olog
y pr
oves
it w
as a
pur
e st
ock.
Figu
re 5
- C
odon
Usa
ge B
ias
Com
paris
on (L
eft)
Whe
n co
mpa
ring
the
codo
n us
age
bias
of M
. sm
egm
atis
to th
e co
don
usag
e bi
as o
f Bro
mde
n as
soci
ated
w
ith e
ncod
ed tR
NA
s, w
e fo
und
that
m
any
tRN
A e
ncod
ed c
odon
s w
ere
mor
e fre
quen
tly u
sed
in B
rom
den,
pe
rhap
s ex
plai
ning
the
reas
on fo
r en
code
d tR
NA
s.
Figu
re 3
- Ly
sin
and
Hol
in G
enes
(Top
and
rig
ht)
Bro
mde
n gp
28 a
nd g
p29
(circ
led
in b
lue)
are
lo
cate
d do
wns
tream
of L
ysin
A a
nd L
ysin
B
(bot
h ci
rcle
d in
red)
. The
hol
in g
ene
is
com
mon
ly fo
und
dow
nstre
am b
ecau
se a
ll th
ree
prot
eins
are
use
d in
the
lysi
s m
odul
e.
The
imag
e on
the
right
sho
ws
the
lysi
s pr
oces
s w
ith th
e gr
een
figur
es a
ctin
g as
the
lysi
n pr
otei
ns a
nd t
he b
lue
figur
es a
ctin
g as
th
e ho
lin p
rote
ins.
The
yel
low
and
pur
ple
figur
es re
pres
ent m
embr
anes
of t
he h
ost c
ell.
Th
e ho
lin a
llow
s fo
r the
lysi
n to
pas
s th
roug
h th
e ce
ll m
embr
ane
and
degr
ade
the
oute
r m
embr
ane
in o
rder
to re
leas
e ph
age
prog
eny.
Figu
re 7