Induction of Apoptosis Results in Spontaneous Maturation of Tetravirus Procapsids in Vivo

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 70-dependent -35 and -10 regions are shown in green, putative hyuC 70-1 and hyuC 70-2 -dependent -35 and -10 regions are shown in blue and the putative hyuH 54-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.

1 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) GTTCTCCGGAATCGGCGCTGCGAGGGAACGTATCGAGTTTCG ATTAGA CG B11291(101) GTTCTCCGGAATCGGCGCTGCGAGGGAACGTATCGAGTTTCGATTAGACG I-671 (97) ---CGCCGGATGTGGGGCCTTTGATGAGTGG---GCGTGTCGAGACGTCG RU-OR hyuC1 (1) ------

151 hyuH 70 hyuC 70-2 hyuH 54 200 AE01(151) CGG ---- TTGAAA GCG - AGC G-GTCATTGAA- TA C GG AA CCTC TGCCAA- 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 70-1 350 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