Advanced Bacterial Genetics [Methods in Enzymology No 421] (AP, Bio Med 1
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METHODS IN ENZYMOLOGY
EDITORS-IN-CHIEF
John N. Abelson Melvin I. Simon
DIVISION OF BIOLOGY
CALIFORNIA INSTITUTE OF TECHNOLOGY
PASADENA, CALIFORNIA
FOUNDING EDITORS
Sidney P. Colowick and Nathan O. Kaplan
Table of Contents
C
ONTRIBUTORS TO
V
OLUME
421................. vi
P
REFACE
........................
ix
V
OLUMES IN
S
ERIES
.....................
xi
Section I. Strain Collections and Genetic Nomenclature
1. Strain Collections and Genetic Nomenclature
S
TANLEY
R. M
ALOY AND
K
ELLY
T. H
UGHES
3
Section II. Transposons
2. Use of Antibiotic-Resistant Transposons
for Mutagenesis
S
TANLEY
R. M
ALOY
11
3.
In Vivo
Mutagenesis Using EZ-Tn
5
TM
17
J
OHN
R. K
IRBY
4. Identification of Essential Genes in Bacteria
D
AVID
R. H
ILLYARD AND
M
ICHAEL
J. R
EDD
21
35
5. Isolation of Transposon Insertions
S
TANLEY
R. M
ALOY
42
6. Localized Mutagenesis
S
TANLEY
R. M
ALOY
51
7. Generation of Deletions and Duplications
Using Transposons as Portable Regions
of Homology with Emphasis on Mud and
Tn
10
Transposons
K
ELLY
T. H
UGHES
8. Target-Directed Proteolysis
In Vivo
M
ARKUS
E
SER
,
T
ANJA
H
ENRICHS
,
D
ANA
B
OYD
,
AND
M
ICHAEL
E
HRMANN
68
9. Sets of Transposon-Generated Sequence-
Tagged Mutants for Structure–Function
Analysis and Engineering
B
ETH
T
RAXLER AND
E
LIORA
G
ACHELET
83
10. Using Genomic Microarrays to Study
Insertional/Transposon Mutant Libraries
D
AVID
N. B
ALDWIN AND
N
INA
R. S
ALAMA
90
v
vi
TABLE OF CONTENTS
11. Screening Transposon Mutant Libraries Using
Full-Genome Oligonucleotide Microarrays
K
ELLY
M. W
INTERBERG AND
W
ILLIAM
S. R
EZNIKOFF
110
12. Creating Recombination-Activated Genes
and Sequence-Defined Mutant Libraries
Using Transposons
L
ARRY
G
ALLAGHER
,
C
HERI
T
URNER
,
E
LIZABETH
R
AMAGE
,
AND
C
OLIN
M
ANOIL
126
13. Use of Operon and Gene Fusions to Study
Gene Regulation in
Salmonella
K
ELLY
T. H
UGHES AND
S
TANLEY
R. M
ALOY
140
14. Genomic Screening for Regulatory Genes
Using the T-POP Transposon
C
HANGHAN
L
EE
,
C
HRISTOPHER
W
OZNIAK
,
J
OYCE
E. K
ARLINSEY
,
AND
K
ELLY
T. H
UGHES
159
Section III. Phage
15. Recombineering:
In Vivo
Genetic Engineering
in
E. coli, S. enterica
, and Beyond
J
AMES
A. S
AWITZKE
,
L
YNN
C. T
HOMASON
,
N
INA
C
OSTANTINO
,
M
IKHAIL
B
UBUNENKO
,
S
IMANTI
D
ATTA
,
AND
D
ONALD
L. C
OURT
171
199
16.
l
-Red Genetic Engineering in
Salmonella
enterica
serovar Typhimurium
J
OYCE
E. K
ARLINSEY
17. Probing Nucleoid Structure in Bacteria Using
Phage Lambda Integrase-Mediated
Chromosome Rearrangements
N
ATHALIE
G
ARCIA
-R
USSELL
,
S
AMANTHA
S. O
RCHARD
,
AND
A
NCA
M. S
EGALL
209
18. Dissecting Nucleic Acid–Protein Interactions
Using Challenge Phage
S
TANLEY
R. M
ALOY AND
J
EFFREY
G
ARDNER
227
19. Mu
d
-P22
J
ENNY
A. C
RAIN AND
S
TANLEY
R. M
ALOY
249
20. Phage Metagenomics
V
ERONICA
C
ASAS AND
F
OREST
R
OHWER
259
A
UTHOR
I
NDEX.
269
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.
.
.
.
.
.
S
UBJECT
I
NDEX.
279
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.
Contributors to Volume 421
Article numbers are in parentheses following the names of contributors.
Affiliations listed are current.
D
AVID
N. B
ALDWIN
(10),
Human Biology
Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington
D
ANA
B
OYD
(8),
Department of Microbio-
logy and Molecular Genetics, Harvard
Medical School, Boston, Massachusetts
M
IKHAIL
B
UBUNENKO
(15),
Molecular Con-
trol and Genetics, National Cancer
Institute at Frederick, Frederick, Maryland
V
ERONICA
C
ASAS
(20),
Center for Micro-
bial Sciences, SanDiego State University,
San Diego, California
N
INA
C
OSTANTINO
(15),
Molecular Control
and Genetics, National Cancer Institute
at Frederick, Frederick, Maryland
D
ONALD
L. C
OURT
(15),
Molecular Con-
trol and Genetics, National Cancer
Institute at Frederick, Frederick, Maryland
J
ENNY
A. C
RAIN
(19),
Department of
Biology, Center for Microbial Sciences,
San Diego State University, San Diego,
California
S
IMANTI
D
ATTA
(15),
Molecular Control
and Genetics, National Cancer Institute
at Frederick, Frederick, Maryland
M
ICHAEL
E
HRMANN
(8),
Centre for Medical
Biotechnology, University Duisburg-
Essen, Essen, Germany
M
ARKUS
E
SER
(8),
School of Biosciences,
Cardiff University, Cardiff, United
Kingdom
E
LIORA
G
ACHELET
(9),
Department of
Microbiology, University of Washington,
Seattle, Washington
L
ARRY
G
ALLAGHER
(12),
Department
of Genome Sciences, University of
Washington, Seattle, Washington
N
ATHALIE
G
ARCIA
-R
USSELL
(17),
Depart-
ment of Biology, San Diego State
University, San Diego, California
J
EFFREY
G
ARDNER
(18),
Department of
Microbiology, University of
Illinois,
Urbana, Illinois
T
ANJA
H
ENRICHS
(8),
School of Biosciences,
Cardiff University, Cardiff, United
Kingdom
D
AVID
R. H
ILLYARD
(4),
Department of
Pathology, University of Utah, Salt Lake
City, Utah
K
ELLY
T. H
UGHES
(1, 7, 13, 14),
Depart-
ment of Biology, University of Utah, Salt
Lake City, Utah
J
OYCE
E. K
ARLINSEY
(14, 16),
Department of
Microbiology, University of Washington,
Seattle, Washington
J
OHN
R. K
IRBY
(3),
School of Biology,
Georgia Institute of Technology, Atlanta,
Georgia
C
HANGHAN
L
EE
(14),
Department of
Microbiology, University of Washing-
ton, Seattle, Washington
S
TANLEY
R. M
ALOY
(1, 2, 5, 6, 13, 18, 19),
Department of Biology, Center forMicro-
bial Sciences, San Diego State University,
San Diego, California
C
OLIN
M
ANOIL
(12),
Department of Gen-
ome Sciences, University of Washington,
Seattle, Washington
vii
viii
CONTRIBUTORS TO VOLUME
421
S
AMANTHA
S. O
RCHARD
(17),
Department
of Biology, San Diego State University,
San Diego, California
E
LIZABETH
R
AMAGE
(12),
Department
of Genome Sciences, University of
Washington, Seattle, Washington
A
NCA
M. S
EGALL
(17),
Center for Micro-
bial Sciences, SanDiego State University,
San Diego, California
L
YNN
C. T
HOMASON
(15),
Molecular Control
and Genetics, National Cancer Institute
at Frederick, Frederick, Maryland
B
ETH
T
RAXLER
(9),
Department of Micro-
biology, University of Washington,
Seattle, Washington
M
ICHAEL
J. R
EDD
(4),
Department of
Oncological Science, Huntsman Cancer
Institute, University of Utah, Salt Lake
City, Utah
W
ILLIAM
S. R
EZNIKOFF
(11),
Department of
Biochemistry, University of Wisconsin-
Madison, Madison, Wisconsin
F
OREST
R
OHWER
(20),
Center for Microbial
Sciences, San Diego State University,
San Diego, California
N
INA
R. S
ALAMA
(10),
Human Biology
Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington
J
AMES
A. S
AWITZKE
(15),
Molecular Control
and Genetics, National Cancer Institute at
Frederick, Frederick, Maryland
C
HERI
T
URNER
(12),
Department of Gen-
ome Sciences, University of Washington,
Seattle, Washington
K
ELLY
M. W
INTERBERG
(11),
Department
of Biology, University of Utah, Salt
Lake City, Utah
C
HRISTOPHER
W
OZNIAK
(14),
Department
of Microbiology,
University
of
Washington, Seattle, Washington
P
HILIP
Y
OUDERIAN
(18),
Department of
Biology, Texas A&M University, Col-
lege Station, Texas
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