Regulation of hydantoin-hydrolyzing enzyme expression in Agrobacterium tumefaciens strain RU-AE01
M Jiwaji, RA Dorrington
Supplementary data
Fig. S1
Alignment of the promoter regions of the hyu genes from Agrobacterium strains RU-AE01 (NCBI Accession Number FJ360446), RU-OR (Hartley 2001), IP 1-671 (NCBI Accession Number AF335479) and NRRL B11291 (NCBI Accession Number X91070). Sequences start at the nucleotide directly upstream the A of the ATG start codon for both the hyuH and the hyuC genes. Exact matches are shown by the grey shading. §: denotes the last nucleotide of the intergenic sequence in NRRL B11291 (nt 220 on the RU-AE01 sequence); *: denotes the position at which the A of the ATG start codon for the HyuC in NRRL B11291 is positioned (nt 221 on the RU-AE01 sequence); ·: denotes the position at which the available nucleotide sequence for RU-OR hyuC1 begins (320 nt on the RU-AE01 sequence). Gaps were introduced to generate optimal alignments. The sequences boxed by a bold line represent the conserved sequences. Putative hyuH s70-dependent -35 and -10 regions are shown in green, putative hyuC s70-1 and hyuC s70-2 -dependent -35 and -10 regions are shown in blue and the putative hyuH s54-dependent promoter is shown in pink. Transcriptional start sites are indicated by the boxed nucleotides. Dotted lines under the sequence show the nucleotides that were altered using site-directed mutagenesis.
HyuH 1 50
AE01(1)CAT AAAGCAGCTCTCAGGGTTGATAGATAAATTCTATATGCGGTATGATGTT
B11291(1) AAAGCAGCTCTCAGGGTTGATGGATAAATTCTATATGCGGTATGATGTT
I-671(1) GATGCAGCTCTACGGTCGGAGACA-AAATTCTATATAAAGAACTATATT
RU-OR hyuC1(1) ------
51 100
AE01(51) CTTTATATAAAGTTTTCATGTTGCCTTGTATCTGTCAAGCGGGAAGGGAA
B11291(51) CTTTATATAAAGTTTTCATGTTGCCTTGTATCTGTCAAGCGGGAAGGGAA
I-671(50) CTTTATAGAAAGCTTGCATGATGCTTTAAAACTGTCAAGCGGACTTAG--
RU-OR hyuC1 (1) ------
101 150
AE01(101) GTTCTCCGGAATCGGCGCTGCGAGGGAACGTATCGAGTTTCGATTAGACG
B11291(101) GTTCTCCGGAATCGGCGCTGCGAGGGAACGTATCGAGTTTCGATTAGACG
I-671 (97) ---CGCCGGATGTGGGGCCTTTGATGAGTGG---GCGTGTCGAGACGTCG
RU-OR hyuC1 (1) ------
151 hyuH s70 hyuC s70-2 hyuH s54 200
AE01(151) CGG----TTGAAAGCG-AGCG-GTCATTGAA-TACGGAACCTCTGCCAA-
B11291(151) CGG----TTGAAAGCGCAGCGAGTCATTGAACTACGGAACCTCTGCCAAA
I-671(142) CGGACAATTTCAGGCG-CGCG-G--ATCGAA-TGCTCG-CATTTGCTAAA
RU-OR hyuC1 (1) ------
201 §* 250
AE01(192) –CCCTATTCGGCGAGCTGGATTTTT TCTTCTCGTTCGCGAGCTCCTA---
B11291(196) -CCCTATTCGGCGAGCTGGA------
I-671(186) AAGATAGACAGATTGCGTGATTTTT CAGCAGTTATCGCGATTGCCTCGCC
RU-OR hyuC1 (1) ------
251 300
AE01(239) AAACGGCGCCGTTCAATCCGGGTGAAAAAGTTCAACCATCG-GAAATTTT
B11291(215) ------
I-671(236) AAGGGGTCGTGTTGCTGTTTCACGACGGAATCCTTTCATGGCGTAATTTT
RU-OR hyuC1(1) ------
301 · hyuC s70-1 350
AE01(288) GAC--CCTGGTCCT--TG ACAGATCAAAAGTTTTACGCCTGTAGTATGAG
B11291(215) ------
I-671(286) TACATCCGCGACCTGTTG ACAGATCCGCAGTTTTAGTCCCGTTATCTTCG
RU-OR hyuC1 (1) ------ACAGATCAAAAGTTTTACGCCTGTAGTATGAG
351 400
AE01(334) TACTGCATGTGGCATTTA-TCCTTTTTGTAGAACAATCATTGGCGTGCCA
B11291(215) ------
I-671(336) TGCTGCATGCAATATCAAATTCTTTATGCAGAATAACGATTGACAAAT--
RU-OR hyuC1(134) TACTGCATGTGGCATTTA-TCCTTTTTGTAGAACAATCATTGGCGTGCCA
401 450
AE01(383) AGCTGAGACGTGTGTTCCTGAAATGTGCATAGCAGCGTTCTCCCGGCCGC
B11291(215) ------
I-671(384) AGCCGCCACGCGGGTTCCGGGAAAGAGCACCGCAGCATTCTCCCGGCCGC
RU-OR hyuC1(83) AGCTGAGACGTGTGTTCCTGAAATGTGCATAGCAGCGTTCTCCCGGCCGC
451 487 HyuC
AE01(433) GAGGCCGGATTAA---CTATCGAAGGAGCAAAGGTTC ATG
B11291(215) ------
I-671(434) TGAGCCGGACATCGCGCATTTGAAGGAGCATAGGTTC
RU-OR hyuC1(133) GAGGCCGGATTAA---CTATCGAAGGAGCAAAGGTTC
2