alteromonas macleodii altde 4,412,285 bp 1 pb 0.5 mpb 1.1 mpb 1.6 mpb 2.2 mpb 2.7 mpb 3.3 mpb 3.8...
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Alteromonas macleodii AltDE
4,412,285 bp
1 pb
0.5 Mpb
1.1 Mpb
1.6 Mpb
2.2 Mpb
2.7 Mpb
3.3 Mpb
3.8 Mpb
Figure S1 Representation of AltDE genome (center in black) indicating their closest bacterial homologues. From the inner to the outer circles, first circle shows percentage G+C plot; second, third and fourth circles show, respectively, orthologous genes in Pychromonas ingrahamii 37, Alteromonadales bacterium TW7 and Pseudoalteromas atlantica T6c. The fifth circle represents orthologous genes in other species.
E-Value
Others
Pseudoalteromonas atlantica T6c
Alteromonadales bacterium Tw7Pychromonas ingrahamii 37
-5>E
>-25
-26>
E>-5
0
-51>
E>-7
5
-76>
E
GC% fluctuation
Alteromonas macleodii AltDE
Figure S2 (a) Regions of co-linearity shared by assembled contigs of the A. macleodii ATCC 27216 (larger than 30 Kbp) and the genome of A. maclodii AltDE. Syntenic regions are represented in red and inversions in blue. (b) Sinteny of A. macleodii AltDE with Pseudoalteromonas atlantica T6c.
550
518
340
51460
74
75
51567048351
712
539
524900 1049800 1574700 2099600 2624500 3149400 3674300 4199200
A. macleodii AltDE genome
a
b
A. macleodii AltDE genome
Psedudoalteromonas atlantica T6c genome
%ID scale
74 76 78 80 82 84 86 88 90 92 94 96 98
A. macleodii ATCC 21256 contigs > 30 Kbp
A. macleodii AltDE genome
Pseudoalteromonas atlantica T6c genome
Figure S3 Genomic islands of A. macleodii AltDE with putative phage origin. Schematic representations of ORFs and their functional assignment are shown for (a) Genomic island 3; (b) Genomic island 10; (c) Genomic island 11; and (d) Genomic island 13.
2200 bp
GI 3
GI 11
GI 13
GI 10
834088
Phage related DNA polymerase
Phage Stx2-82-gp25
891155
DNA directed DNA polymerase I
Enterobacterial phague gp25
Phage related p.Enterobacterial phague gp24 Phague PBC5
PKD domain Endodeoxyribonuclease
PhagueBcep22 gp55
Phage related p. Phague PBC5
Phague, PaP3
Phage Stx2-82-gp25
Phage phi018p
Membrane anchor virus p.
3882928 3914088
2200 bp
FunZ
Type I restriction modification system
deoxyribonucleasemethyltransferase
Plasmid maintenance system antidote p.
Ubal thif-type NAD /fad binding fold
Transposase
Integrase, IS element
Phage related
Hypothetical p.Outside of the island
2200 bp
4039705 4062499
Reverse transcriptase integrase domains ISS
Transposase IS911
Transcriptional regulator XRE family
TransposaseISCps1
Transposase ISCps1
4359069 4387945
2200 bp
DNA or RNA helicase superfamily II
HipA
Transcriptional regulator, XRE
Helix-turn-helix DEAD/DEAH box helicase
methyltransferase
Inner membrane p.
Restriction subunit
VrlI Phage transcriptional regulator AlpA
Transcriptional regulator
SAM dependent methyltransferase
HipA
transcriptional regulator
Filamentation p.
Type I restriction modification system
a
b
c
d
ATPase AAA superfamily
GI 12
Figure S4 Genomic islands of A. macleodii AltDE containing genes for alternative catabolic pathways. Schematic representations of ORFs and their functional assignment are shown for (a) Genomic island 1; (b) Genomic island 6; and (c) Genomic island 12.
Transposase
Integrase, IS element
Phage relatedHypothetical p.Nitrate reductase
Outside of the islandHeavy-metal related p.
GI 6
1577210 1606929
GntR regulatory p.
Keto-deoxyglucono-
kinase
Alginate lyase precursor
ISSod6
Chain II cytochrome oxidase
Chain I cytochrome oxidase
Dioxygenase (ferredoxin reductase)
Vitamine K epoxide reductase
Toxin/Antitoxin system MazE/MazF
ISSod6
Keto-deosyglucono-kinase
4-hidroxy-2-oxoglutarate aldolase
Sensory box/GGDEF
2200 bp
4138524
2200 bp
CBS domain pair
Parvulin peptidyl-prolyl-
isomerase
Nitrate reductase chaperone NarJ
His-Kin. Nitrate / nitrite specific Nitrate
transporter
Nitrate/nitrite response regulator
CheY
MoeA
Mo converting
factor sub.1
Molybdopterin guanine dinucleotide synthase
Molybdopterin cofactor biosynthesis
4184769MoeB
Lipid carrier p.
Thiamine pyrophosphate binding domain
proteases
Acyl-CoA dehydrogenase
Oxoisovalerate dehydrogenase
and sub.
NO signalling NorA
Anaerobic nitric oxide reductase transcription regulator
Invasion gene expression up-regulator SirB
Heme/copper membrane p.
Nitratetransporter
Nitrate transporter
Serine-threonine p. kinase
Hemerythrin cation binding p.
ABC transporter ATPase
Anaerobic ribonucleoside tri-phosphate reductase
Radical enzyme
activating protein
Molibdenum ABC transporter system
nitrate reductase
and sub.)
ABCE
Molibdopterin cofactor biosynthesis
Other Nitrogen metabolism related p.
GI 1
84100
2200 bp
YdhE (NsrE)
Metallo--lactamase
FAD dependent pyridine nucleotide disulphide
Outer membrane
receptor
ATP cytochrome related transport
mdlB sub. II
Cytochrome D ubiquinol oxidase
Rhodanesa related
sulfurtransferase
Zn- dependent glyoxylase
Alkyl hydroperoxide reductase
Thiol-disulfide interchange p.
Transcriptional regulator, LuxR family
Outer membrane p.
Cation efflux system CzcA
*
ATPase- DNA repair
Type III restricition
enzyme
ATP binding protein
Cystein desulfurase
Transcriptional regulator
Methyltranferase type II
Membrane fusion HlyD secretion p.
ABC multidrug transporter system
FhuE receptor
RelA /SpoT
Choline-glycine betain transporter
sub. I
Cytochrome BD-II oxidase
*
a
b
c
142154
Figure S5 Genomic islands of A. macleodii AltDE containing genes coding for cell surface components. Schematic representations of ORFs and their functional assignment are shown for (a) the region between MADE_00965 and MADE_00985; (b) Genomic island 7; and (c) Genomic Island 8.
GI 5
1003524 1035257
2200 pb
flagellin
phosphomanomutase
Manose-1-phosphate-guanylyltransferase
G II
Iduronate sulfatase
ISDet2-transposase
Lipopolysaccharide-A p.
Glycosyltransferase II
Transposase
Hypothetical p.
Polysaccharide / Carbohydrate related p.
Outside of the island
Glycosyl-transferase
1374175
1418585
Lipopolysaccharide modification
acyltransferase
Secreted polysaccharide
polymerase
Polysaccharide biosynthesis
Asparagine synthase
Dolichyl-phosphate mannose synthase
TPR domain p.
Hpr Kinase
FAD binding p.
G II G II
2200 bp
a
c
2436218 2464633
Giant-protein (VCBS repeats)
Type I secretion ATPase, PrtD
HlyD secretion p.
Thiopurine S-methyl transferase
d GI 7
2200 bp
GI 8e
2200 bp
3146590 NeuA, CMP-N-acetylneuraminic acid synthase
Methionyl-tRNA-formyltransferase
NeuB, sialic acid synthetase
Methionyl-tRNA formyl transferase
LmbE Maf-1
Flagellar chaperone
FliS
Flagellar capping p. FliD
FlaG
Flagellin FliC-like
Flagellin FliC-like
Flagellar synthesisFlgL
3169706
Integrase, IS element
G II
b
2805984 2814735
1000 bp
Polysaccharide biosynthesis p.
O-acetyltransferase
Capsule polysaccharide
biosynthesis
G II
Figure S6 Growth curves of AltDE and ATCC 27126 at different Zinc concentrations.
0,010,1
1,0C +
Concentration ofZn(O2CCH3)2 mM 5,00
Time (h)
0
0,2
0,4
0,6
0,8
1
1,2
1,4
1,6
0 10 20 30 40 50 60
ATCC 27126
AltDE
D.O
(59
5 n
m)
Figure S7 AltDE tetranucleotide skew and codon use. (a) AltDE genome tetranucleotide frequency skew (calculated in sliding windows of 25 Kbp). (b) Differences in the frequency use of a given codon between AltDE islands and the complete genome. The usage fraction of a codon was calculated as its proportion (0 to 1) referred to the most common codon. Each codon use value in an island was subtracted from that calculated for the complete genome, thus values closer to zero indicate more similar codon use.
a
microaerobic respiration
metal resistance / hydrogenase
putative phage
CRISPR /urease
alternative LPS O-chain giant protein
flagellin
mercury resistance
putative phages
nitrate respiration
lysogenic phage
Tetr
anuc
leot
ide
freq
uenc
y
Alteromonas macleodii AltDE genome
1Genomic
Islands 2 3 4 5 6 7 8 9 10 11 12 13
b
GC
A
GC
C
GC
G
GC
T
GT
A
GT
C
GT
G
GT
T
CT
A
CT
C
CT
G
CT
T
TT
A
TT
G
AT
A
AT
C
AT
T
GG
A
GG
C
GG
G
GG
T
CC
A
CC
C
CC
G
CC
T
TT
C
TT
T
CA
C
CA
T
TG
G
TA
C
TA
T
TG
C
TG
T
AT
G
AA
A
AA
G
AG
A
AG
G
CG
A
CG
C
CG
G
CG
T
GA
C
GA
T
GA
A
GA
G
AA
C
AA
T
CA
A
CA
G
AG
C
AG
T
TC
A
TC
C
TC
G
TC
T
AC
A
AC
C
AC
G
AC
T
Ala Val Leu Ile Gly Pro Phe His Trp Tyr Lys ArgCys Met Asp AsnGlu SerGlu Thr
-0,8
-0,4
0
0,4
0,8
0,8
-0,8
-0,4
0
0,4
GI3 GI10 GI11 GI13
GI4 GI9
-0,8
-0,4
0
0,4
0,8
GI5 GI6 GI7 GI8
-0,8
-0,4
0
0,4
0,8
GI1 GI2 GI12
0.0
0.1
Freq
uenc
y co
don
usag
e
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