TABLE 2.
Identification of σB-regulated genes in B. cereus ATCC 14579 upon mild heat shocka
| Gene | Expression ratio
|
Annotation | Aliasb | Experimentally defined and/or predicted promoter sequencec | E score by HMMER search | ||
|---|---|---|---|---|---|---|---|
| WT/ΔsigB | WT/ΔrsbY | 42°C/30°C | |||||
| bc0862 | 63.1 | 84.0 | 72.9 | Protease I | yfkM | In operon with bc0863 | |
| bc0863 | 72.1 | 31.5 | 34.0 | Catalase | katE | ATGTTTAC-13 bp-GGGTATC-N47-ATG | 4.7 × 10−5 |
| bc0995 | 1.9 | 2.0 | 2.2 | Hypothetical protein | None identified | ||
| bc0996 | 2.1 | 1.8 | 2.0 | Hypothetical protein | None identified | ||
| bc0998 | 123.6 | 86.0 | 70.9 | General stress protein | yflT | ATGTTTAA-14 bp-GTGTACT-N45-ATG | 6.4 × 10−5 |
| bc0999d | ND | ND | ND | Hypothetical protein | In operon with bc0998 | ||
| bc1000 | 98.1 | 42.4 | 36.3 | Hypothetical protein | In operon with bc0998 | ||
| bc1001 | 106.4 | 29.8 | 35.8 | Hypothetical protein | ATGTTTAA-13 bp-GTGTATG-N37-ATGf | 1.3 × 10−5 | |
| bc1002 | 42.6 | 31.7 | 38.3 | Anti-σB factor antagonist | rsbV | ATGTTTAA-13 bp-GGGTAAT-N33-ATG | 1.4 × 10−5 |
| bc1003 | 51.1 | 38.3 | 52.4 | Anti-σB factor | rsbW | In operon with bc1002 | |
| bc1004 | —e | 24.4 | 28.1 | RNA polymerase sigma factor σB | sigB | In operon with bc1002 | |
| bc1005 | 10.6 | 47.4 | 56.0 | Putative bacterioferritin | orf4 | In operon with bc1002 and under control of own promoter, ATGTTTAA-13 bp-GGGTACT-N20-ATG | 6.3 × 10−6 |
| bc1006 | 4.0 | —e | 5.1 | PP2C phosphatase, regulator of σB activity | rsbY | In operon with bc1002 and bc1005 | |
| bc1007 | 2.4 | 2.3 | 3.6 | Chemotaxis protein methyltransferase | In operon with bc1009 | ||
| bc1008 | 3.3 | 3.1 | 4.4 | Two-Component System Histidine Kinase | In operon with bc1009 | ||
| bc1009 | 188.5 | 110.2 | 87.5 | Hypothetical Protein | ATGTTTAA-13 bp-GGGTATG-N40-ATG | 1.1 × 10−5 | |
| bc1010 | 8.2 | 7.0 | 5.5 | Hypothetical Protein | ACGTTTAG-13 bp-GGGTATA-N285-ATG | 1.9 × 10−4 | |
| bc1011 | 33.9 | 25.8 | 23.7 | Hypothetical Protein | In operon with bc1010 | ||
| bc1012d | ND | ND | ND | Hypothetical Protein | ybjQ | In operon with bc1010 | |
| bc2108 | 2.9 | 2.8 | 3.8 | RNA polymerase ECF-type sigma factor | sigZ | None identified | |
| bc2638 | 4.7 | 4.4 | 4.3 | Spore germination protein LC | None identified | ||
| bc3130 | 20.7 | 29.3 | 10.3 | Hypothetical protein | In operon with bc3132 | ||
| bc3131 | 29.5 | 37.3 | 42.6 | Hypothetical protein | In operon with bc3132 | ||
| bc3132 | 7.6 | 2.0 | 2.0 | General stress protein 17M | AGGTTTAA-14 bp-GTGTATT-N48-ATG | 4.3 × 10−5 | |
| bc4641 | 3.3 | 3.9 | 3.8 | Hypothetical protein | ATGAATAA-13 bp-GGGTACG-N10-ATG | 9.3 × 10−5 | |
| bc5391 | 11.2 | 11.0 | 6.1 | Spore coat protein | gerQ | None identified | |
Genes were identified as being σB dependent by a significant difference in expression between the parental strain and both the sigB and rsbY deletion mutants upon a heat shock from 30°C to 42°C for 10 min. ND, not determined; ECF, extracytoplasmic function.
The aliases for the identified genes were based on the gene names of homologs in B. subtilis and/or B. anthracis.
Experimentally confirmed promoter sites (33, 35) are indicated in boldface type. Other promoters were identified by an HMM as outlined in Materials and Methods.
These genes were not represented on the microarray but were previously identified as being σB dependent (35) and are therefore included in this table.
These genes were disrupted by an erythromycin resistance cassette. Therefore, the expression data for these genes were omitted.
A second σB-dependent promoter site was predicted in the HMMER search upstream of this gene. The E score for this predicted site is higher (3.0 × 10−5) (see Table S3 in the supplemental material) than that for the experimentally confirmed promoter indicated in the table.