5.4 Molecular biological methods
5.4.1 Oligonucleotides and plasmids
in liquid nitrogen and stored at -80°C.
E. coli strains were supplemented with 200 µL of 50% glycerol (10% final concentration) and stored at -80°C.
5.3.5 Motility assay of M. xanthus
Motility assays were performed on different agar plates favoring either A- or S-motility (Table 5-8). Cells were grown to OD550 0.5 to 0.9, harvested, and resuspended in CTT medium to a calculated density of 5.0 ×109 cells/ml. 5µl of cell suspension were placed on the two different motility plates and incubated at 32°C. After 24 h, colony morphology and colony edges were observed visually in a Leica MZ8 stereomicroscope and a Leica IMB/E inverted microscope and visualized using a Leica DFC280 CCD camera (Leica Microsystems).
Check in frame deletion
Generation of MXAN3112 in frame deletion
KA-295 Primer A forward ccgGAATTCGGTTAGAAGGGCCTCCAT
KA-296 Primer B reverse GCCGTTGGCCTTGTCGAGCGGAGTGATTTTCAT KA-297 Primer C forward CCGCTCGACAAGGCCAACGGCGACTCC KA-298 Primer D reverse gcgGGATCCCCGGAAGAGGGCGGAGTAGTG KA-323 Primer E forward
Check insertion
TTCATCGAACCTTGCTCCC
KA-324 Primer F reverse Check insertion
TGCTCGAAGTGGAACACGC
KA-333 Primer G forward Check in frame deletion
ATCCGGCAGAAGCGGTTCG
KA-334 Primer H reverse Check in frame deletion
CTTCTTCTGGGACAGATACGC
Generation of MXAN0634 in frame deletion
KA-371 Primer A forward ccgGAATTCCGACGAGCAGTTGAGCACCAG KA-372 Primer B reverse gcgTCTAGACACGCGGCGCGGCCTGCG KA-373 Primer C forward gcgTCTAGAGTCACCCCAAGCCATTCC KA-374 Primer D reverse gccAAGCTTCCTTGAAGTTCAGGAAGAGC KA-375 Primer E forward
Check insertion
GGGTCTCCGCTGTATCGC
KA-376 Primer F reverse Check insertion
GGCAGCGAGGACTTCTGG
KA-377 Primer G forward Check in frame deletion
GGAACCAGATGATGGACAAGC
KA-378 Primer H reverse Check in frame deletion
TCGTGGATGGCTTCCTCG
Generation of MXAN0635 insertion mutant
KA-224 Forward gcgGGATCCTCCACGTCCTACGCCTGG KA-225 Reverse gccAAGCTTCGGATAGTGCGTCTGGAG Generation of MXAN0636 insertion mutant
KA-250 Forward ccgGAATTCGAGGCGTTGCTCGACACC KA-251 Reverse gcgGGATCCGGCCAGCAGCTTCACCCG KA-284 Forward
Check insertion
GCTCCAGACGCACTATCCG
KA-285 Reverse Check insertion
AGGACGGGAAGTAGCCAGG
Table 5-12. PCR primers used for generation of complementation under native and pilA promoter
Name Description Sequence
agmE under native promoter
KA-314 Forward gcgGGATCCGTCACCCCAAGCCATTCC
KA-207 Reverse gccAAGCTTTCATCAGCCGGCCTGCTGGGT KA-288 Forward gcgTCTAGAATGGAAGCGCCGACGTAC MXAN0636 under native promoter
KA-347 Forward gcgGGATCCGCTCGCGGACTTCCTGTCC KA-348 Reverse gccAAGCTTTCAGCGCACCGTGGCCTG MXAN0636 under pilA promoter
KA-349 Forward gcgTCTAGAATGAAGAAAGCCTTTGAACAGAACG KA-348 Reverse gccAAGCTTTCAGCGCACCGTGGCCTG
MXAN3112 under pilA promoter
KA-337 Forward gcgTCTAGAATGAAAATCACTCCGCTCG KA-338 Reverse gccAAGCTTTCAGGAGTCGCCGTTGGC
Table 5-13. PCR primers used for generation of fusion proteins Name Description Sequence
agmE-GFP at native site
KA-289 Forward ccgGAATTCATGGAAGCGCCGACGTAC
KA-219 Reverse gcgGGATCCGGCGGAGCCGCCGGCCTGCTGGGTGCC agmE-mCherry under native promoter for attB and carS
KA-327 Forward ccgGGTACCGTCACCCCAAGCCATTCC
KA-219 Reverse gcgGGATCCGGCGGAGCCGCCGGCCTGCTGGGTGCC agmE-mCherry under pilA promoter for attB
KA-219 Reverse GCGGGATCCGGCGGAGCCGCCGGCCTGCTGGGTGCC KA-288 Forward GCGTCTAGAATGGAAGCGCCGACGTAC
ftsZ-GFP and ftsZ-mCherry under native promoter for attB
KA-335 Forward ATCGCTCATATGGAACAACCGCCGCGTGGG KA-336 Reverse CGGGGTACCCGGCAGTTCCGTCTGGCC divIVA-mCherry at native site
KA-299 Forward attgcgCCCGGGATGAAAATCACTCCGCTCGAC KA-300 Reverse gcgGGATCCGGCGGAGCCGGAGTCGCCGTTGGCCTT
Table 5-14. PCR primers used for overexpression of protein constructs in pET45b+ unless indicated. For AgmE point mutants, primers binding the desired amino acid substitution are shown here. These same AgmE primers were used to generate amino acid substitution for in vivo complementation.
Name Description Sequence Overexpression construct agmE
KA-206 Forward gcgGGATCCCATGGAAGCGCCGACGTAC KA-207 Reverse gccAAGCTTTCATCAGCCGGCCTGCTGGGT Overexpression construct agmED90A
KA-236 Forward GACCTCGCCAGCCAGGGC
KA-237 Reverse GCCCTGGCTGGCGAGGTC
Overexpression construct agmED170A
KA-238 Forward GAGGCCCAGTACGCCGTC
KA-239 Reverse GACGGCGTACTGGGCCTC
Overexpression construct agmED175A
KA-240 Forward GTCTTCGCCGCGCCGCCG
KA-241 Reverse CGGCGGCGCGGCGAAGAC
Overexpression construct agmEK66Q
KA-242 Forward ACCGGCCAGACGTCGCTG
KA-243 Reverse CAGCGACGTCTGGCCGGT
Overexpression construct ftsZ
KA-342 Forward gcgGGATCCCATGGACCAGTTCGATCAGAACAAG KA-343 Reverse gccAAGCTTTCATTACGGCAGTTCCGTCTGGC Overexpression construct MXAN0636
KA-344 Forward gcgGGATCCCATGAAGAAAGCCTTTGAACAGAACG KA-345 Reverse gccAAGCTTTCATCAGCGCACCGTGGCCTG Overexpression of MXAN3112
KA-318 Forward gcgGGATCCgATGAAAATCACTCCGCTCGACATC KA-319 Reverse for pET24b+ gccAAGCTTGGAGTCGCCGTTGGCCTT
KA-320 Reverse gccAAGCTTTCATCAGGAGTCGCCGTTGGC Table 5-15. Primers used to verify integration at attB locus
Name Description Sequence
attB rechts Genome specific attB forward primer
GGAATGATCGGACCAGCTGAA
attB links Genome specific attB downstream primer
CGGCACACTGAGGCCACATA
attP rechts Plasmid specific attP forward primer
GCTTTCGCGACATGGAGGA
attP links Plasmid specific attP reverse primer
GGGAAGCTCTGGGTACGAA
Table 5-16. Primers used to verify integration at carS locus for constructs containing mCherry fusions
Name Description Sequence KA-403 Primer binding pCT2
plasmid forward
TCGGCTGCAACTTTGTCATGCTTGACAC
KA-316 mCherry internal primer reverse
CTTGAAGCCCTCGGGGAAGGA
KA-404 Forward primer binding the
kanamycin cassette
TTTTTTTTCATATGAGCCATATTCAACGGGAAACGTC
KA-405 Reverse primer binding the
kanamycin cassette
ATAAGCTTTTAGAAAAACTCATCGAGCATCAAATGAAAC
M13 fwd General sequencing primer forward CGCCAGGGTTTTCCCAGTCACGAC M13 rv General sequencing primer reverse ATGCTCACTCATTAGGCACCCCAG
KA-231 Sequencing pSWU30 forward GGATGTGCTGCAAGGCGATTAAGTTGG KA-232 Sequencing pSWU30 reverse GCTTTACACTTTATGCTTCCGGCTCG
KA-233 GFP forward CACATGGTCCTGCTGGAGTTCG
KA-234 GFP reverse TGTGGCCGTTTACGTCGCCGTCCAGCTC KA-254 PilA promoter seq reverse GTGCGCACCTGGGTTGGCATGCG
KA-255 PilA promoter seq forward TGAGGGAGCCACGGTTGATGAG KA-276 pET45b+ forward TGGCGCCGGTGATGCCGGCC KA-277 pET45b+ reverse ATCCGGATATAGTTCCTCCT KA-308 pCT2 seq forward CGCGTTCAATCGGACCAGCGGAGG KA-309 pCT2 seq reverse CGCGGATGCCGTCGCGCTCACCCG KA-316 mCherry reverse CTTGAAGCCCTCGGGGAAGGA KA-317 mCherry forward CCTCCCTGCAGGACGGCGAGT KA-406 Internal primer of FtsZ for
sequencing forward
CGTGCAGGGCATCAGCGACC
KA-407 Internal primer of FtsZ for sequencing reverse
GGTCGCTGATGCCCTGCACG
Table 5-18. Primers used to map agmE locus
Name Description Sequence
KA-278 Intergenic region agmE and MXAN0636 forward GCTCCAGACGCACTATCCG KA-279 Intergenic region agmE and MXAN0636 reverse CTCGGTGTCGAGCAACGC
KA-280 Intergenic region agmE and MXAN0634 forward GTGGAATCCCTCTGCTCG
KA-281 Intergenic region agmE and MXAN0634 reverse CTTCTCGAAGTCCTCGCC KA-282 Internal region of agmE forward TCCCACGTCCTACGCCTGG
KA-283 Internal region of agmEreverse CGGATAGTGCGTCTGGAG
Table 5-19. List of plasmid used in this study.
Plasmids Genotype Reference
pBluescript II SK-
Vector for cloning, blue/white selection, AmpR Fermentas (St. Leon-Rot)
pBGS18 Vector for insertion mutants, KmR (Spratt et al., 1986) pBJ114 Vector for in frame deletion, KmR (Julien et al., 2000) pSWU30 Vector for inserting at attB (Wu et al., 1997) pSW105 Vector for inserting at attB containing pilA
promoter
S. Weiss (MPI-Marburg)
pFGBJ frzS-GFP, KmR (Mignot et al.,
2005)
pCT2 Vector for inserting at carS locus (Mignot et al., 2007a)
pGFy148 aglZ-GFP, KmR G. Freymark
(MPI-Marburg) pET45b+ Expression vector , T7 promoter, N-term His6
-tag, AmpR
Novagen/Merck (Darmstadt) pET24b+ Expression vector , T7 promoter, N-term His6
-tag, KmR
Novagen/Merck (Darmstadt) pMT935 Derivative of pCT2 containing mCherry fusion
protein
M. Thanbichler (MPI-Marburg)
pFCrGFP GFP fusion protein from Chlamydomonas Biocat (Heilderberg) pKA1 pBJ114-agmE in-frame deletion, KmR This study pKA2 pBGS18-agmE insertion fragment, KmR This study pKA3 pET45b+ - agmE with extra stop codon, AmpR This study pKA10 pBJ114- agmE-GFP fusion This study pKA12 pET45b+ - agmED90A with extra stop codon,
AmpR
This study
pKA13 pET45b+ - agmED170A with extra stop codon, AmpR
This study
pKA14 pET45b+ - agmED175A with extra stop codon, AmpR
This study
pKA15 pET45b+ - agmEK66Q with extra stop codon, AmpR
This study
pKA16 pBJ114- C-term GFP with linker, KmR This study pKA18 pBGS18- MXAN0636 insertion, KmR This study
pKA19 pSW105-PpilA agmE (start-stop),Mx8 attP, KmR
This study
pKA20 pSW105-PpilA agmE-GFP, Mx8 attP, KmR This study pKA21 pBJ114- MXAN0636-mCherry, KmR This study
pKA22 pBJ114-mCherry This study
pKA23 pBJ114-mCherry with linker This study pKA24 pBJ114- MXAN3112 in frame deletion, KmR This study
pKA25 pBJ114-MXAN3112-mCherry, KmR This study pKA26 pSWU30- Pnat agmE+, Mx8 attP ,TcR This study pKA28 pSWU30- Pnat agmE-mCherry, Mx8 attP ,TcR This study
pKA30 pMT935-Pnat ftsZ-mCherry, carS ,KmR This study pKA32 pSWU30-Pnat ftsZ-mCherry, Mx8 attP ,TcR This study pKA36 pSWU30-Pnat agmED90A, Mx8 attP ,TcR This study pKA37 pSWU30-Pnat agmED175A, Mx8 attP ,TcR This study pKA38 pSWU30-Pnat agmEK66Q, Mx8 attP ,TcR This study pKA41 pSW105- PpilA MXAN0636 (start-stop), Mx8
attP ,KmR
This study
,TcR
pKA44 pBJ114-MXAN0634 in frame deletion This study pKA45 pSW105- PpilA agmE-mCherry, Mx8 attP ,KmR This study pKA46 pSWU30- Pnat mCherry-MXAN0636 Mx8 attP
,TcR
This study
pKA47 pSWU30- N-term mCherry with linker, Mx8 attP ,TcR
This study
pKA48 pSW105- ftsZ (start-stop) Mx8 attP ,KmR This study pKA49 pBJ114- C-term mCherry with linker This study
pKA51 pSWU30- Pnat ftsZ-GFP, Mx8 attP ,TcR This study pKA53 pCT2- Pnat agmE-mCherry, carS, KmR This study pMM1 pET45b+ - ftsZ with extra stop codon, AmpR Marlen Mock
(MPI-Marburg) pMM2 pET45b+ - MXAN0636 with extra stop codon,
AmpR
Marlen Mock (MPI-Marburg)