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