Towards understanding inter-strain attachment variations of Escherichia coli during transport in saturated quartz sand - Transport of Multiple Escherichia Coli Transport in Saturated Porous Media

Biology Reference

In-Depth Information

Chapter 3

Table 3. 1: Genes encoding surface structures involved in initial attachment of Escherichia coli including primers and DNA sequences

Gene name

Description / function

Primer name

DNA sequence (5'-> 3')

Amplified

product (bp)

Amplified

product (bp)

Source

Autotransporter proteins:

Adhesin involved in diffuse adherence, consisting of an

Ag43Α and an Ag43Β unit

Autotransporter proteins:

Adhesin involved in diffuse adherence, consisting of an

Ag43Α and an Ag43Β unit

flu (Ag43)

Ag43-550-F

Ag43-550-R

Ag43-2700-F

Ag43-2700-R

UN21

UN22

UN23

UN24

UN19

UN20

Ag43-550-F

Ag43-550-R

Ag43-2700-F

Ag43-2700-R

UN21

UN22

UN23

UN24

UN19

UN20

GTACKRCCAACGGAATGACC

ATCCAGYGCGTRRCCATGTA

GACTATGACCGGATTSTGGC

GGCTGTACCCACCAGTTCAC

TGCAAACATTAAGGGCTCG

CCGGAAACATTGACCATACC

CAGTTTATCAATCAGCTCGGG

CCACCGTTCCGTTATCCTC

CTGGGTGACATTATTGCTTGG

TTTGCTTGTGCGGTAGACTG

GTACKRCCAACGGAATGACC

ATCCAGYGCGTRRCCATGTA

GACTATGACCGGATTSTGGC

GGCTGTACCCACCAGTTCAC

TGCAAACATTAAGGGCTCG

CCGGAAACATTGACCATACC

CAGTTTATCAATCAGCTCGGG

CCACCGTTCCGTTATCCTC

CTGGGTGACATTATTGCTTGG

TTTGCTTGTGCGGTAGACTG

515

This study

719

This study

aidA

Adhesin involved in diffuse adherence (AIDA-I)

450

Chapman et al., 2006

Adhesin involved in diffuse adherence (AIDA-C)

543

Chapman et al., 2006

aah

370

Chapman et al., 2006

Autotransporter adhesin heptosyltransferase encoding

AAH protein which modifies AIDA-I adhesin

Autotransporter adhesin heptosyltransferase encoding

AAH protein which modifies AIDA-I adhesin

Pili/fimbriae:

Central region of Dr antigen-specific fimbrial and

afimbrial adhesin operons (e.g., AFA, Dr, and F1845)

Type IV bundle-forming pili

Pili/fimbriae:

Central region of Dr antigen-specific fimbrial and

afimbrial adhesin operons (e.g., AFA, Dr, and F1845)

Type IV bundle-forming pili

afa/draBC

Afa-F

Afa-R

bfpA-F

bfpA-R

bmaE-F

bmaE-R

faeG-F

faeG-R

fanC-F

fanC-R

fedA-F

fedA-R

FimH-F

FimH-R

focG-F

focG-R

iha-F

iha-R

nfaE-F

nfaE-R

M155-F1

M155-R1

Saa-F

Saa-R

sfa1-F

sfa1-R

sfaS-F

sfaS-R

Afa-F

Afa-R

bfpA-F

bfpA-R

bmaE-F

bmaE-R

faeG-F

faeG-R

fanC-F

fanC-R

fedA-F

fedA-R

FimH-F

FimH-R

focG-F

focG-R

iha-F

iha-R

nfaE-F

nfaE-R

M155-F1

M155-R1

Saa-F

Saa-R

sfa1-F

sfa1-R

sfaS-F

sfaS-R

GGCAGAGGGCCGGCAACAGGC

CCCGTAACGCGCCAGCATCTC

AATGGTGCTTGCGCTTCGTGC

GCCGCTTTATCCAACCTGGTA

ATGGCGCTAACTTGCCATGCTG

AGGGGGACATATAGCCCCCTTC

GGTGATTTCAATGGTTCG

ATTGCTACGTTCAGCGGAGCG

TGGGACTACCAATGCTTCTG

TATCCACCATTAGACGGAGC

GTGAAAAGACTAGTTTATTTC

CTTGTAAGTAACCGCGTAAGC

TGCAGAACGGATAAGCCGTGG

GCAGTCACCTGCCCTCCGGTA

CAGCACGGCAGTGGATACGA

GAATGTCGCCTGCCCATTGCT

CTGGCGGAGGCTCTGAGATCA

TCCTTAAGCTCCCGCGGCTGA

GCTTACTGATTCTGGGATGGA

CGGTGGCCGAGTCATATGCCA

ATGAGGAAACATAATGGCAGG

TCTGGTCAGGTCGTCAATAC

CGTGATGAACAGGCTATTGC

ATGGACATGCCTGTGGCAAC

CTCCGGAGAACTGGGTGCATCTTAC

CGGAGGAGTAATTACAAACCTGGCA

GTGGATACGACGATTACTGTG

CCGCCAGCATTCCCTGTATTC

GGCAGAGGGCCGGCAACAGGC

CCCGTAACGCGCCAGCATCTC

AATGGTGCTTGCGCTTCGTGC

GCCGCTTTATCCAACCTGGTA

ATGGCGCTAACTTGCCATGCTG

AGGGGGACATATAGCCCCCTTC

GGTGATTTCAATGGTTCG

ATTGCTACGTTCAGCGGAGCG

TGGGACTACCAATGCTTCTG

TATCCACCATTAGACGGAGC

GTGAAAAGACTAGTTTATTTC

CTTGTAAGTAACCGCGTAAGC

TGCAGAACGGATAAGCCGTGG

GCAGTCACCTGCCCTCCGGTA

CAGCACGGCAGTGGATACGA

GAATGTCGCCTGCCCATTGCT

CTGGCGGAGGCTCTGAGATCA

TCCTTAAGCTCCCGCGGCTGA

GCTTACTGATTCTGGGATGGA

CGGTGGCCGAGTCATATGCCA

ATGAGGAAACATAATGGCAGG

TCTGGTCAGGTCGTCAATAC

CGTGATGAACAGGCTATTGC

ATGGACATGCCTGTGGCAAC

CTCCGGAGAACTGGGTGCATCTTAC

CGGAGGAGTAATTACAAACCTGGCA

GTGGATACGACGATTACTGTG

CCGCCAGCATTCCCTGTATTC

559

Chapman et al., 2006

bfpA

326

Chapman et al., 2006

bmaE

M-agglutinin subunit

507

Chapman et al., 2006

faeG

F4 fimbrial adhesin

764

Chapman et al., 2006

fanC

F5 fimbrial adhesin

450

Chapman et al., 2006

fedA

F18 fimbrial adhesin

510

Chapman et al., 2006

fimH

D-Mannose-specific adhesin, type 1 fimbriae

508

Chapman et al., 2006

focG

Pilus tip molecule, F1C fimbriae (sialic acid specific)

360

Chapman et al., 2006

iha

Novel nonhemagglutinin adhesin (from O157:H7 and

CFT073)

Nonfimbrial adhesin I assembly and transport

Novel nonhemagglutinin adhesin (from O157:H7 and

CFT073)

Nonfimbrial adhesin I assembly and transport

827

Chapman et al., 2006

nfaE

559

Chapman et al., 2006

paa

Porcine A/E-associated gene

350

Chapman et al., 2006

saa

STEC autoagglutinating adhesin

119

Chapman et al., 2006

sfa/focDE

Central region of sfa (S fimbriae) and foc (F1C

fimbriae) operons

Pilus tip adhesin, S fimbriae (sialic acid specific)

Central region of sfa (S fimbriae) and foc (F1C

fimbriae) operons

Pilus tip adhesin, S fimbriae (sialic acid specific)

410

Chapman et al., 2006

sfaS

240

Chapman et al., 2006

Other:

Forms an outer membrane protein which is involved in

biofilm formation

Forms an outer-membrane lipoprotein induced after

carbon starvation (initial steps in biofilm formation)

Participates in the assembly of outer membrane

proteins

Other:

Forms an outer membrane protein which is involved in

biofilm formation

Forms an outer-membrane lipoprotein induced after

carbon starvation (initial steps in biofilm formation)

Participates in the assembly of outer membrane

proteins

ompC

ompC-F

ompC-R

slp-F

slp-R

surA-F

surA-R

ompC-F

ompC-R

slp-F

slp-R

surA-F

surA-R

CTACATGCGTCTTGGCTTCA

GTTGCGTTRTARGTCTGGGT

GGCATACTGGCAGGTACGTT

GCATAATCACCTGCWGGGTT

TTGCTAACATCGCGAAACAG

CACTCTTGATATCRGCAGCA

CTACATGCGTCTTGGCTTCA

GTTGCGTTRTARGTCTGGGT

GGCATACTGGCAGGTACGTT

GCATAATCACCTGCWGGGTT

TTGCTAACATCGCGAAACAG

CACTCTTGATATCRGCAGCA

633

This study

slp

439

This study

surA

651

This study

Transport of Multiple Escherichia Coli Transport in Saturated Porous Media

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