TABLE 3.
qRT-PCR analysis of gene expressiona
| Schu4 ORF no. | Putative function | Fold differenceb
|
qRT-PCR primer pair (5′-3′)d | |
|---|---|---|---|---|
| Microarray | qRT-PCR | |||
| 26c | Hypothetical protein (FigD) | 14.8 | 13.4 | F: AAGCCTAATGGTAGCTGGTGAATC |
| R: TTTTGGTGAGACTCCGTAAGTTTTT | ||||
| 29c | Hypothetical protein (FigA) | 19.7 | 24.7 | F: GGCTACTAAAGACAAAACACTAATGCC |
| R: CAGACTCAGGCGATACTGTTCTTG | ||||
| 27c | Diaminopimelate decarboxylase (FigC) | 15.1 | 13.0 | F: GGTTTAGCAGGAATAAGCCCTACTC |
| R: TTGTCGCGGCATATAGTTCTAAATC | ||||
| 28c | Hypothetical protein (FigB) | 9.9 | 19.1 | F: GAGTTTTTTAGCTCAGACCCGATAATC |
| R: ATCGGCGCTGAAAATAGCA | ||||
| 651c | Proton-dependent oligopeptide family protein | 2.4 | 0.6 | F: CTCGCAAAAAAGACATTAGTATAAAATTAAAT |
| R: AAGTTGCAAATTGTCCCCAAA | ||||
| 1712c | Intracellular growth locus, subunit c (IglC) | 3.0 | 2.6 | F: AAAAAGGAGAATGATTATGAGTGAGATG |
| R: TGCAGTAGGATCAGTTCTCACATG | ||||
| 403 | Peptide deformylase | 2.8 | 3.2 | F: CAGCTATAATATTTCAGCATGAATTTAATCA |
| R: AGCAAATTTAGCTTGTAGTTCTTCGTT | ||||
| 1699 | Conserved hypothetical protein (PdpA) | 2.6 | 2.6 | F: TGAGTTAATTTCAAACTCTGCCATATC |
| R: GTTTGGGTATATGCCATTTCACAG | ||||
| 1780 | Putative transposase | 1.5 | 1.1 | F: AAGAACCGGAGATTATAGTTCAAAGC |
| R: AAATACTGTTCAATCAATGTTTTATCGG | ||||
| 651c | Proton-dependent oligopeptide family protein | 1.3 | 0.7 | F: CGTTGATAGTAAAACTATTGGTTTTGCA |
| R: GGAAGAGCAACCACTTGATTTAATAGA | ||||
| 664c | Histidine decarboxylase | 1.0 | 1.1 | F: CATTTGATGGTGCTTTTCTACCG |
| R: ATATTCCTGAAGGCATCGGATTAC | ||||
| 583 | Outer membrane-associated protein | 0.9 | 1.0 | F: CAAATCTAGCAGGTCAAGCAACAG |
| R: AACACTTGCTTGAACATTTCTAGATAGTTC | ||||
| 700 | Conserved hypothetical protein | 0.8 | 0.6 | F: AAAATGGTGTTCGCCTTTTGG |
| R: CCTTCGACATCATCTTTGTAGTCAAC | ||||
| 445 | ABC transporter, ATP-binding, pseudogene | 0.9 | 1.2 | F: TTAGAAGAGTTTGTTGGAGGATATGATG |
| R: ATTTTTCGACAACTCACTGTTATTTTTAGT | ||||
| 881c | Amino acid permease | 0.4 | 0.6 | F: CCAAGGTTCAGAAATTATCGGACTA |
| R: GTGCTTAGCGATTCTTGGCAT | ||||
| 50 | Translation initiation factor IF2 | 0.6 | 0.8 | F: TTGGCGCGTATTCTGTTAAGAC |
| R: GCTCGCATTGAAGTAAAAGCCT | ||||
| 140 | 50S ribosomal protein L11 | 0.5 | 0.8 | F: ACGCCACCTGCTTCTTACTTAATT |
| R: CGCACGAGTTATAGTTCCAACAA | ||||
| 350 | DNA-directed RNA polymerase, alpha subunit | 0.7 | 0.7 | F: TTGACAAACCAAAGAGCATTTAGC |
| R: TCTCAAGCTCGGTTGGTATCG | ||||
| 1695 | Chaperone protein, GroES | 0.4 | 0.5 | F: GCTCAAGAGAAACCTAGCCAAGG |
| R: ACATCCATAGGTAGCGTAGTGCC | ||||
| 326 | 50S ribosomal protein L4 | 0.5 | 0.7 | F: AGTTTCTGGTGGCGGTGC |
| R: GGTGAACGGATAGTACCCGCT | ||||
| 1696 | Chaperone protein, GroEL | 0.4 | 0.7 | F: TTCAAAGACAGCGGATGTTGC |
| R: GCGACAGCTTTTAGACCCTCTG | ||||
a
qRT-PCR for each gene was performed with two individually prepared RNA samples, each in triplicate.
b
The fold difference indicates the gene expression level under iron-restricted conditions relative to that obtained under iron-replete conditions.
c
ORF 651 in the F. tularensis Schu4 genome was found to be fragmented into two separate ORFs in the F. tularensis LVS genome by the deletion of a single nucleotide.
d
F, forward; R, reverse.