TABLE 2.
Novel sRNAs.
|
A. Novel sRNAs predicted based on RIL-seq results and recently reported in published papers | ||||||||
| Novel | Hosting gene | Genomic | Genomic | Number of | Prediction score | Comment/ | ||
| sRNA | or operon | region | position | unique targets |
(probability of being a sRNA)a |
References | ||
| Exponential | Stationary | Iron limitation | ||||||
| FlgO | flgL | 3′ UTR | 1,140,986 → 1,141,063 | 4 | 0.073 | 0.087 | 0.152 | Hör et al. (2020)b |
| FliX | FliC | 3′ UTR | 2,001,912 ← 2,002,106 | 17 | 0.859 | 0.272 | 0.672 | Hör et al. (2020)b |
| GadF | gadE | 3′ UTR | 3,658,992 → 3,659,082 | 24 | – | 0.684 | – | Melamed et al. (2016) |
| MalH | malG | 3′ UTR | 4,242,531 ← 4,242,629 or 4,242,531 ← 4,242,633c | 38 | 0.416 | 0.468 | 0.596 | Iosub et al. (2020) |
| MotR | motA | 5′ UTR | 1,977,208 ← 1,977,300 | 19 | 0.562 | 0.158 | 0.444 | Hör et al. (2020) |
| NarS-L | narK | 3′ UTR | 1,279,286 → 1,279,520 | 8 | 0.376 | – | 0.380 | Wang et al. (2020) |
| NarS-S | 1,279,337 → 1,279,520 | |||||||
| PspH | pspG | 3′ UTR | 4,263,139 → 4,263,249 | 1 | 0.003 | 0.002 | 0.001 | Melamed et al. (2016) |
| RaiZ | raiA | 3′ UTR | 2,737,381 → 2,737,542 | 29 | 0.337 | 0.482 | 0.296 | Smirnov et al. (2017) |
| RaiZ-S | 2,737,417 → 2,737,542 | |||||||
| RbsZ | rbsB-rbsK | Intergenic in operon | 3,937,045 → 3,937,278 | 4 | 0.091 | 0.035 | 0.105 | Melamed et al. (2020) |
| SdhX (RybD) | sucD | 3′ UTR | 765,050 → 765,150 | 33 | 0.638 | 0.836 | 0.735 | De Mets et al. (2019); Miyakoshi et al. (2019) |
| UhpU | uhpT | 3′ UTR | 3,845,730 ← 3,845,995 | 111 | 0.751 | 0.347 | 0.786 | Hör et al. (2020)b |
| B. Novel sRNA candidates predicted based on RIL-seq results and verified by northern blot analysis in the current study | ||||||||
| AceK-int | aceK | CDS | 4,218,879 → 4,218,963 | 15 | – | 0.592 | 0.084 | Recently verified also by Adams et al. (2021) |
| AllZ | allR | 3′ UTR | 533,629 → 533,863 | 5 | 0.042 | 0.295 | 0.046 | |
| BhsB | bhsA | 3′ UTR | 1,169,303 → 1,169,402 | 2 | – | 0.099 | – | |
| FadZ | fadA | 3′ UTR | 4,027,232 ← unknown | 12 | 0.031 | 0.202 | 0.081 | |
| KilS | kilR | 5′ UTR | 1,418,405 ← 1,418,502 | 3 | 0.033 | 0.154 | 0.032 | |
| XylZ | xylA-xylB | Intergenic in operon | 3,729,386 ← 3,729,545 | 10 | 0.064 | 0.346 | 0.068 | |
| ZbiJ | ybiJ | 3′ UTR | 837,435 ← 837,531 | 21 | 0.223 | 0.374 | 0.506 | Recently verified also by Han and Lory (2021), who called it “asYbiE” |
aDashed cells mean the RNA was not included in the data of the corresponding experiment.
bReferring to unpublished results from Storz’s lab.
cMapping of the 5′ end is according to Iosub et al. (2020). According to our RNA-seq results the 5′ end is at 4,242,609.