TABLE 2.

Primers used in this study

Primer and purpose	Sequencea
To construct probes for S1 nuclease mapping
agl3E/agl3R Forward	CGCTGCCGCCGCACGCGGTGGTCA
agl3E/agl3R Reverse	TGAGGTCCCCGTTGACGATGAGACC
HrdB Forward	CGGCCGCAAGGTACGAGTTGATGA
HrdB Reverse	CCATGACAGAGACGGACTCGGCG
To amplify the promoter fragment for XylE fusions
agl3E/agl3R Forward	TCGGCGTCCCGGAAGCTTCCGATGTCGCCG (wild-type sequence, AAGCGT)
agl3E/agl3R Reverse	GAGATAGGGGAGAAGCTTGTCGTTGTGCGA (wt sequence, GACCTT)
To construct deletion mutations
SCO7167 Upstream	ATCGCCTATCGATAGAACATAATCGATAGGGAGGGCGACATTCCGGGGATCCGTCGACC
SCO7165 Downstream	TTCGCCCCGGTGGCGGGGATGTCGTGTCGTGCGCTCATGTGTAGGCTGGAGCTGCTTC
SCO7162 Downstream	GCCCTGGTCCTGTGTCCACCTGTGGCCCGGCGCCCGCTGTGTAGGCTGGAGCTGCTTC
SCO7168 Upstream	CCGCGTACACGCTCCGCTCAGCCGTGGCCGTGATCGTGAATTCCGGGGATCCGTCGACC
To confirm deletion mutations
agl3R Forward	CGACCGGCTCACGACCGGCCCGCGA
SCO7165 Reverse	CGCCGGACGGCGGAGTCCCGACGGA
SCO7162 Reverse	AGGGCCAGGGCCAGGGCCAGGACCG
P1	ATTCCGGGGATCCGTCGACCTGCA
P2	TGTAGGCTGGAGCTGCTTCGAAGT
To construct His6-tagged agl3R protein
His6-Agl3R Forward	TTGTTGTAGAAGACGAGGGA
His6-Agl3R Reverse	GGGGCGGCTCAGATCTCTT
For RT-PCR
WhiB Forward	GTCGACGACGCGGACGAGGAA
WhiB Reverse	AGATGCCGAAGCGCTCGTCGT
WhiG Forward	TGTGGCGGTCGTACAAGACGA
WhiG Reverse	ATCGCGTACGTCTCGAACTTG
WhiH Forward	AGCTGGGCCAGATGATCGTCT
WhiH Reverse	AAGGCACGCCATTCGATGATG
WhiE Forward	TCTTCATGTCCGGCAACCGGA
WhiE Reverse	TAGAGCAGCCGCAGCCGTTCC
SigF Forward	GGAGGTGCTGTCCTGCATCGA
SigF Reverse	GGAAACTACGTGCCAGTAGCC
Agl3R Forward	ACTGCTGTCCGACCAGGTGTA
Alg3R Reverse	CCGCGAACTCCTTCGATGATG
Agl3E Forward	AACATCACACCGAACCTGACC
Agl3E Reverse	AGGGGAGGACCTTGTCGTTGT
HrdB Forward	GCCTTCGAAGCTGACCAGATT
HrdB Reverse	CGGTCGCCTTCCTGCTGGTCA

^aUnderlining indicates the HindIII restriction site; boldface indicates altered bases.