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era7 bioinformatics R&D group

Escherichia coli EHEC Germany outbreak preliminary manual functional annotation

Based on the preliminary results of our semi-automated method of annotation we have selected some predicted protein with potential implications in pathogenicity and virulence. There are 33 predicted genes annotated as toxins and we have found three putative hemolysins: Hemolysin E, a putative hemolysin expression modulating protein and a channel protein, hemolysin III family. We have found 31 predicted genes that could be related to specific antibiotic resistance: beta-lactamic, aminoglycoside, macrolide, polymyxin, tetracycline, fosfomycin and deoxycholate, novobiocin, chloramphenicol, bicyclomycin, norfloxacin and enoxacin and 6-mercaptopurine. This strain is rich in adhesion, secretion systems, pathogenicity and virulence related proteins. It seems to have a restriction-modification system, many proteins involved in Fe transport and utilization (siderophores as aerobactin and enterobactin), lysozyme, one inhibitor of pancreatic serine proteases, proteins involved in anaerobic respiration, antimicrobial peptides, proteins involved in quorum-sensing and biofilm formation that could confer competitive advantage to this strain.


**Fast manual annotation **

Based on the preliminary results of our semi-automated method of annotation we have reviewed manually the annotation tagging the principal genes and functions. This preliminary tagging has been carried out analyzing the annotation for each predicted protein following specific interesting points: toxins, hemolysins, antibiotic resistance, pathogenicity, adhesion, plasmid, phage and other features.

We have selected and clustered genes with specific functions especially important from the human health perspective.  The tagged genes are displayed in the following simplified tables. The complete annotation tables are available at:

http://www.era7bioinformatics.com/docs/EHEC_E_COLI_GERMANY_OUTBREAK_Annotation_Era7Bioinformatics_v1562011.xls

**Table 1: Toxins **

In this table we have selected predicted proteins with annotations related with toxin function.

Contig ID

Gen ID

tags

Similar to

Protein names

husec41_c1134

36180

Toxin

Q83Z99

Putative acyltransferase MchD

husec41_c1252

46188

Toxin

D8CGU2

Toxin-antitoxin system, toxin component, PIN family

husec41_c136

40883

Toxin

D7YRT1

Toxin-antitoxin system, antitoxin component, Xre family

husec41_c145

66526

Toxin

C8THQ6

Predicted antitoxin of YafQ-DinJ toxin-antitoxin system

husec41_c145

54284

Toxin

B7LHF6

Toxin of the YafQ-DinJ toxin-antitoxin system

husec41_c1518

5119

Toxin

Q8VSL2

Serine protease sepA autotransporter (EC 3.4.21.-) [Cleaved into: Serine protease sepA; Serine protease sepA translocator]

husec41_c1554

45805

Toxin

C1NDL5

Secreted autotransporter toxin Sat

husec41_c1932

50684

Toxin

B7LBW0

Serine protease pic (ShMu)

husec41_c2009

41962

Toxin

D8ET41

Toxin-antitoxin system protein

husec41_c2132

76041

Toxin

B7MC95

Vacuolating autotransporter toxin

husec41_c291

110361

Toxin

B7LBY5

Serine protease pet (Plasmid-encoded toxin pet) (EC 3.4.21.72)

husec41_c380

110360

Toxin

B7LBY5

Serine protease pet (Plasmid-encoded toxin pet) (EC 3.4.21.72)

husec41_c482

84923

Toxin

C8TUV8

Membrane protein

husec41_c543

42847

Toxin

E6ARB5

Toxin-antitoxin system, antitoxin component, Xre family

husec41_c567

110363

Toxin

B7LBY5

Serine protease pet (Plasmid-encoded toxin pet) (EC 3.4.21.72)

husec41_c581

45751

Toxin

E7J0S6

Putative shET2 enterotoxin

husec41_c59

63485

Toxin

C8TP46

Toxin ChpB of the ChpB-ChpS toxin-antitoxin system

husec41_c672

46347

Toxin

D7X7P6

ShET2 enterotoxin, region

husec41_c69

41563

Toxin

D8BT94

Toxin-antitoxin system, antitoxin component, HicB family

husec41_c74

69806

Toxin

C8TTV0

Toxin of the YoeB-YefM toxin-antitoxin system

husec41_c74

68869

Toxin

A1ACN0

Antitoxin of the YoeB-YefM toxin-antitoxin system

husec41_c746

89468

Toxin

C8TG29

Toxin ChpA

husec41_c782

5124

Toxin

Q8VSL2

Serine protease sepA autotransporter (EC 3.4.21.-) [Cleaved into: Serine protease sepA; Serine protease sepA translocator]

husec41_c797

36434

Toxin

D7ZZI1

Toxin-antitoxin system, antitoxin component, AbrB family

husec41_rep_c2274

50678

Toxin

B7LBW0

Serine protease pic (ShMu)

husec41_rep_c2292

59806

Toxin

B7LBU0

Toxin of the YeeV-YeeU toxin-antitoxin system

husec41_rep_c2292

25611

Toxin

E3PD62

Putative antitoxin

husec41_rep_c2295

19119

Toxin

B3HJU4

Serine proteAse eata (EC 3.4.21.-)

husec41_rep_c2297

108631

Toxin

C6UP08

Shiga toxin II subunit B

husec41_rep_c2297

42022

Toxin

B3BQ93

Shiga toxin subunit A (EC 3.2.2.22)

husec41_rep_c2359

5123

Toxin

Q8VSL2

Serine protease sepA autotransporter (EC 3.4.21.-) [Cleaved into: Serine protease sepA; Serine protease sepA translocator]

husec41_rep_c2607

104486

Toxin

B7MN77

Toxin of the YeeV-YeeU toxin-antitoxin system

husec41_rep_c2848

5126

Toxin

Q8VSL2

Serine protease sepA autotransporter (EC 3.4.21.-) [Cleaved into: Serine protease sepA; Serine protease sepA translocator]

husec41_c1549

66741

Toxin?

D3QPV9

Small toxic membrane polypeptide

husec41_c685

78980

Toxin?

E8YB84

Hok/gef cell toxic protein

husec41_c201

19118

Toxin?

B3HJU4

Serine proteAse eata (EC 3.4.21.-)

Table 2: Hemolysins and heme metabolism related proteins

Contig ID

tags

Similar to

Protein names

husec41_c1375

Hemolysin

B5YXK6

Hemolysin E, chromosomal

husec41_c1786

Hemolysin

Q0TDJ8

Putative hemolysin expression modulating protein

husec41_c604

Hemolysin

D3RHI6

Channel protein, hemolysin III family

husec41_c1103

Heme

C8U6D2

Heme lyase, CcmH subunit

husec41_c1469

Heme

C8U6D2

Heme lyase, CcmH subunit

husec41_c1469

Heme

C8TUD4

Heme lyase, CcmF subunit

husec41_c1914

Heme

C8TUD7

Heme exporter protein C

husec41_c194

Heme

C8TTP2

Sulfoxide reductase heme-binding subunit yedZ (Flavocytochrome yedZ)

husec41_c231

Heme

D3GXL9

Sulfoxide reductase heme-binding subunit yedZ (Flavocytochrome yedZ)

husec41_c458

Heme

C8TIQ7

Siroheme synthase

husec41_c656

Heme

C8TMW6

Heme lyase, NrfG subunit

husec41_c656

Heme

C8TMW5

Heme lyase, NrfF subunit

husec41_c656

Heme

C8TMW4

Heme lyase, NrfE subunit

husec41_c849

Heme

B7LAM4

Heme exporter subunit ; ATP-binding component of ABC superfamily

husec41_c849

Heme

B7LAM3

Heme exporter subunit ; membrane component of ABC superfamily

husec41_c849

Heme

C8TUD7

Heme exporter protein C

**Table 3: Antibiotic resistance. **

In table 3 we have selected genes involved in specific antibiotic resistance and also genes encoding efflux pumps and multidrug resistance proteins that could be involved in some additional antibiotic resistance capabilities of this strain.

Contig ID

tags

Similar to

Protein names

husec41_c1261

Aminoglycoside resistance

C8TVG3

Aminoglycoside/multidrug efflux system protein AcrD

husec41_c177

Aminoglycoside resistance

C8TVG3

Aminoglycoside/multidrug efflux system protein AcrD

husec41_c626

Aminoglycoside resistance

C8TVG3

Aminoglycoside/multidrug efflux system protein AcrD

husec41_c697

Aminoglycoside resistance

C8TVG3

Aminoglycoside/multidrug efflux system protein AcrD

husec41_c738

Aminoglycoside resistance

C8TVG3

Aminoglycoside/multidrug efflux system protein AcrD

husec41_c312

Macrolide resistance

C8TLZ5

Fused macrolide transporter subunits of ABC superfamily: ATP-binding component/membrane component

husec41_c584

Macrolide resistance

C8TLZ5

Fused macrolide transporter subunits of ABC superfamily: ATP-binding component/membrane component

husec41_c312

Macrolide resistance

C8TLZ4

Macrolide transporter subunit, membrane fusion protein component

husec41_c48

Penicillin resistance

B7LBI2

Penicillin-insensitive murein endopeptidase (EC 3.4.24.-) (D-alanyl-D-alanine-endopeptidase) (DD-endopeptidase)

husec41_c1681

Polymyxin resistance

B7LAS5

Polymyxin resistance protein B

husec41_c497

Polymyxin resistance

D6I9J9

Polymyxin resistance protein PmrM

husec41_c2170

beta-lactam resistance

C8UQP5

TEM-1 beta-lactamase

husec41_c642

Tetracycline resistance

D3H382

Tetracycline resistance protein

husec41_c559

beta-lactam resistance

C8TJ28

Regulator of penicillin binding proteins and **beta-lactamase **transcription

husec41_c1436

Tetracycline resistance

C8TNP7

Multidrug resistance protein mdtG

husec41_c55

Fosfomycin and deoxycholate resistance

C8TU05

Multidrug resistance protein mdtA (Multidrug transporter mdtA)

husec41_c1334

Novobiocin and deoxycholate resistance

C6V0N5

Multidrug resistance protein MdtB (Multidrug transporter MdtB)

husec41_c1334

Novobiocin and deoxycholate resistance

C8TU07

Multidrug resistance protein MdtC (Multidrug transporter MdtC)

husec41_c55

Novobiocin and deoxycholate resistance

C8TU07

Multidrug resistance protein MdtC (Multidrug transporter MdtC)

husec41_c1063

chloramphenicol resistance

B7L855

Multidrug resistance protein mdtL

husec41_c654

beta-lactam resistance

C8TNX4

Beta-lactamase/D-alanine carboxypeptidase AmpC

husec41_c229

beta-lactam resistance

C8TIW8

Beta-lactamase/D-alanine carboxypeptidase

husec41_c1120

Beta-lactamic resistance

B7L5H7

Beta-lactam resistance membrane protein

husec41_c30

Beta-lactamic resistance

Q6BBP7

**Beta-lactamase **(Beta-lactamase CTX-M-3) (CTX-M-3 extended-spectrum beta-lactamase) (Extended-spectrum class A beta-lactamase CTX-M-3)

husec41_rep_c2845

Beta-lactamic resistance

B2CD48

**Beta-lactamase **TEM (Fragment)

husec41_c132

Bicyclomycin resistance

B7LAK6

Bicyclomycin/multidrug efflux system

husec41_c720

Bicyclomycin resistance

C6V2S0

Bicyclomycin/multidrug efflux system

husec41_c1017

Polymyxin resistance

C8TUQ2

Bifunctional** polymyxin** resistance protein ArnA

husec41_c497

Polymyxin resistance

C8TUQ2

Bifunctional polymyxin resistance protein ArnA

husec41_c770

norfloxacin and enoxacin resistance

B7LFZ9

Multidrug resistance protein mdtH

husec41_c310

6-mercaptopurine resistance

C8TLE9

Purine ribonucleoside efflux pump nepI

husec41_c212

Antibiotic resistance?

B5Z494

Drug resistance transporter, Bcr/CflA subfamily

husec41_c642

Antibiotic resistance?

D3H381

Tetracycline repressor

husec41_c18

Antibiotic resistance?

C8TME8

Membrane fusion protein (MFP) component of efflux pump, signal anchor

husec41_c348

Antibiotic resistance?

B7LB31

Membrane fusion protein of efflux pump

husec41_c1372

Antibiotic resistance?

D3GVT1

Modulator of drug activity B

husec41_c1352

Antibiotic resistance?

B7LEA2

Multidrug efflux system

husec41_c348

Antibiotic resistance?

B7LB24

Multidrug efflux system component

husec41_c1670

Antibiotic resistance?

B7LHX4

Multidrug efflux system protein

husec41_c684

Antibiotic resistance?

C8TQ83

Multidrug efflux system protein

husec41_c709

Antibiotic resistance?

C8UN45

Multidrug efflux system protein

husec41_c697

Antibiotic resistance?

C8TJ55

Multidrug efflux system protein AcrA

husec41_c1084

Antibiotic resistance?

C8TLV8

Multidrug efflux system protein Cmr

husec41_c75

Antibiotic resistance?

C8TFT3

Multidrug efflux system protein EmrB

husec41_c654

Antibiotic resistance?

C8TNX2

Multidrug efflux system protein SugE

husec41_c214

Antibiotic resistance?

B5YX79

Multidrug resistance protein D

husec41_c212

Antibiotic resistance?

C8TSE0

Multidrug resistance protein mdtK (Multidrug-efflux transporter)

husec41_c288

Antibiotic resistance?

Q3I3P0

ORF3-QacEdelta1 fusion protein

husec41_c656

Antibiotic resistance?

B7LB29

Outer membrane factor of efflux pump

husec41_c407

Antibiotic resistance?

C8TJM6

Predicted antibiotic transporter

husec41_c993

Antibiotic resistance?

C8TTQ9

Predicted multidrug efflux system

husec41_c1456

Antibiotic resistance?

C8TV77

Predicted multidrug efflux system protein Y

husec41_c481

Antibiotic resistance?

C8TV77

Predicted multidrug efflux system protein Y

husec41_c1726

Antibiotic resistance?

C8ULT4

Predicted outer membrane factor of efflux pump

husec41_c1014

Antibiotic resistance?

C8TSY9

Predicted transporter

husec41_c497

Antibiotic resistance?

B7LAS1

Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3)

husec41_c1334

Antibiotic resistance?

D3GZE1

Putative multidrug resistance protein mdtD

husec41_c464

Antibiotic resistance?

C8TU08

Putative multidrug resistance protein mdtD

husec41_c1656

Antibiotic resistance?

B7L8U8

Putative multidrug resistance protein; DLP12 prophage

husec41_c1277

Antibiotic resistance?

B7L7J5

Putative multidrug transporter fused subunits of ABC superfamily transporter: permease component; ATP-binding component

husec41_c225

Antibiotic resistance?

C8TUQ0

UDP-4-amino-4-deoxy-L-arabinose–oxoglutarate aminotransferase (EC 2.6.1.87) (UDP-(beta-L-threo-pentapyranosyl-4’‘-ulose diphosphate) aminotransferase) (UDP-4-amino-4-deoxy-L-arabinose aminotransferase)

husec41_c1017

Antibiotic resistance?

C6V2Y6

Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase (EC 2.7.8.30) (Undecaprenyl-phosphate Ara4FN transferase)

husec41_c225

Antibiotic resistance?

D3H1C1

Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase (EC 2.7.8.30) (Undecaprenyl-phosphate Ara4FN transferase)

husec41_c181

Antibiotic resistance?

B7LAR9

Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase (EC 2.7.8.30) (Undecaprenyl-phosphate Ara4FN transferase) (Ara4FN transferase)

husec41_c908

Antibiotic resistance?

C8TMT4

DNA-damage-inducible SOS response protein DinF

husec41_c481

Antibiotic resistance?

C8TV78

EmrKY-TolC multidrug resistance efflux pump protein K, membrane fusion protein component

husec41_c2258

Antibiotic resistance?

B7LBS1

EmrKY-TolC multidrug resistance efflux pump, membrane fusion protein component

husec41_c2050

Antibiotic resistance?

C8U6F0

Fused predicted multidrug transport subunits of ABC superfamily: membrane component/ATP-binding component

husec41_c931

Antibiotic resistance?

C8TUF0

Fused predicted multidrug transport subunits of ABC superfamily: membrane component/ATP-binding component

husec41_c449

Antibiotic resistance?

C8TJ42

Fused predicted multidrug transporter subunits of ABC superfamily: ATP-binding components

husec41_c449

Antibiotic resistance?

C8TJ41

Fused predicted multidrug transporter subunits of ABC superfamily: ATP-binding components

husec41_c897

Antibiotic resistance?

C8U8G6

Fused predicted multidrug transporter subunits of ABC superfamily: membrane component/ATP-binding component

husec41_c1382

Antibiotic resistance?

B7L9Q8

Wzx

husec41_c2032

Antibiotic resistance?

Q93NP6

Wzx

husec41_c2082

Antibiotic resistance?

Q93NP6

Wzx

husec41_c2085

Antibiotic resistance?

B7L9Q8

Wzx

husec41_c832

Antibiotic resistance?

C8TRP6

DNA-binding transcriptional dual activator MarA of multiple antibiotic resistance

husec41_c832

Antibiotic resistance?

C8TRP5

DNA-binding transcriptional repressor MarR of multiple antibiotic resistance

husec41_c795

Antibiotic resistance?

C8THH6

Fused glycosyl transferase and transpeptidase

husec41_c440

Antibiotic resistance?

C8TJI6

Fused penicillin-binding protein 1a: murein transglycosylase/murein transpeptidase

husec41_c1203

Antibiotic resistance?

C8TJV0

Multidrug resistance efflux transporter MdtE

husec41_c1099

Antibiotic resistance?

D3GR96

Penicillin-binding protein 1B [includes: penicillin-insensitive transglycosylase; penicillin sensitive transpeptidase] (EC 2.4.1.129) (EC 3.4.-.-)

husec41_c1011

Antibiotic resistance?

C6UUQ5

p-hydroxybenzoic acid efflux pump subunit AaeA (pHBA efflux pump protein A)

husec41_c1123

Antibiotic resistance?

C8TIE2

p-hydroxybenzoic acid efflux pump subunit AaeA (pHBA efflux pump protein A)

husec41_c1011

Antibiotic resistance?

C8TIE1

p-hydroxybenzoic acid efflux pump subunit AaeB (pHBA efflux pump protein B)

husec41_c150

Antibiotic resistance?

C8TIE1

p-hydroxybenzoic acid efflux pump subunit AaeB (pHBA efflux pump protein B)

husec41_c228

Antibiotic resistance?

C6UU60

Predicted methyl viologen efflux pump

husec41_c1148

Antibiotic resistance?

C8TL54

Predicted multidrug or homocysteine efflux system protein HsrA

husec41_c124

Antibiotic resistance?

B7L8U8

Putative multidrug resistance protein; DLP12 prophage