Download msb4100181-sup-0001 - Molecular Systems Biology

sRNAs and their targets
sRNA
RyhB*
RyhB
Target
fur
sodB
RyhB
sdhC
RyhB
sdhD
RyhB
bfr
RyhB
ftnA
RyhB
fumA
RyhB
acnA
RyhB
MicA
shiA
ompA
RseX
RseX
MicC
ompA
ompC
ompC
RybB
RybB
RybB
ompC
ompW
rpoE
IpeX
ompC
IpeX
ompF
MicF
ompF
OmrA*
fepA
Reference
(Vecerek et al., 2007)
(Masse and
Gottesman, 2002;
Urban and Vogel,
2007)
(Masse and
Gottesman, 2002)
(Masse and
Gottesman, 2002)
(Masse and
Gottesman, 2002)
(Masse and
Gottesman, 2002)
(Masse and
Gottesman, 2002)
(Masse and
Gottesman, 2002)
(Prevost et al., 2007)
(Rasmussen et al.,
2005; Udekwu et al.,
2005; Urban and
Vogel, 2007)
(Douchin et al., 2006)
(Douchin et al., 2006)
(Chen et al., 2004;
Urban and Vogel,
2007)
(Johansen et al., 2006)
(Johansen et al., 2006)
(Thompson et al.,
2007)
(Castillo-Keller et al.,
2006)
(Castillo-Keller et al.,
2006)
(Aiba et al., 1987;
Andersen and Delihas,
1990; Mizuno et al.,
1984; Ramani et al.,
1994; Urban and
Vogel, 2007)
(Guillier and
Gottesman, 2006)
OmrA
fecA
OmrA
cirA
OmrA
ompT
OmrB*
fecA
OmrB
cirA
OmrB
ompT
OmrB
OmrA
OxyS
gntP
gntP
fhlA
OxyS
rpoS
OxyS
OxyS
OxyS
RprA
yobF
wrbA
ybaY
rpoS
DsrA
rpoS
DsrA
hns
Sok
mok-hok
GcvB
oppA
(Guillier and
Gottesman, 2006)
(Guillier and
Gottesman, 2006)
(Guillier and
Gottesman, 2006)
(Guillier and
Gottesman, 2006)
(Guillier and
Gottesman, 2006)
(Guillier and
Gottesman, 2006)
(Tjaden et al., 2006)
(Tjaden et al., 2006)
(Altuvia et al., 1998;
Argaman and Altuvia,
2000)
(Altuvia et al., 1997;
Zhang et al., 1997;
Zhang et al., 1998)
(Tjaden et al., 2006)
(Tjaden et al., 2006)
(Tjaden et al., 2006)
(Majdalani et al.,
2001; Majdalani et al.,
2002)
(Lease et al., 1998;
Majdalani et al., 1998;
Majdalani et al., 2002;
Sledjeski et al., 1996)
(Lease et al., 1998;
Sledjeski and
Gottesman, 1995;
Urban and Vogel,
2007)
(Franch et al., 1997;
Franch et al., 1999;
Gerdes et al., 1992;
Gerdes et al., 1990;
Pedersen and Gerdes,
1999; Thisted and
Gerdes, 1992; Thisted
et al., 1994)
(Tjaden et al., 2006;
Urbanowski et al.,
2000)
GcvB
dppA
Istr1
SgrS
tisAB
ptsG
Spot42
galK
RdlD
SymR
DicF
ldrD
symE
ftsZ
GadY
gadX
RydC
yejABEF
(Tjaden et al., 2006;
Urban and Vogel,
2007; Urbanowski et
al., 2000)
(Vogel et al., 2004)
(Kawamoto et al.,
2006; Kawamoto et
al., 2005; Kimata et
al., 2001; Morita et al.,
2005; Urban and
Vogel, 2007;
Vanderpool and
Gottesman, 2004)
(Moller et al., 2002;
Urban and Vogel,
2007)
(Kawano et al., 2002)
(Kawano et al., 2007)
(Tetart et al., 1992;
Tetart and Bouche,
1992)
Positive! (Opdyke et
al., 2004)
(Antal et al., 2005)
*Additional targets based on microarray data were suggested for RyhB (Masse et al.,
2005) and for OmrA and OmrB (Guillier and Gottesman, 2006).
References
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coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding.
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Andersen, J., and Delihas, N. (1990) micF RNA binds to the 5' end of ompF mRNA and
to a protein from Escherichia coli. Biochemistry 29: 9249-9256
Antal, M., Bordeau, V., Douchin, V., and Felden, B. (2005) A small bacterial RNA
regulates a putative ABC transporter. J Biol Chem 280: 7901-7908
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Castillo-Keller, M., Vuong, P., and Misra, R. (2006) Novel mechanism of Escherichia
coli porin regulation. J Bacteriol 188: 576-586
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bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in
Escherichia coli. J Biol Chem 281: 12253-12259
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Franch, T., Gultyaev, A. P., and Gerdes, K. (1997) Programmed cell death by hok/sok of
plasmid R1: processing at the hok mRNA 3'-end triggers structural rearrangements that
allow translation and antisense RNA binding. J Mol Biol 273: 38-51
Franch, T., Thisted, T., and Gerdes, K. (1999) Ribonuclease III processing of coaxially
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gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of
the stable hok, srnB and pndA effector messenger RNAs. J Mol Biol 226: 637-649
Gerdes, K., Thisted, T., and Martinussen, J. (1990) Mechanism of post-segregational
killing by the hok/sok system of plasmid R1: sok antisense RNA regulates formation of a
hok mRNA species correlated with killing of plasmid-free cells. Mol Microbiol 4: 18071818
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membrane by two small regulatory RNAs. Mol Microbiol 59: 231-247
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Kawamoto, H., Koide, Y., Morita, T., and Aiba, H. (2006) Base-pairing requirement for
RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq.
Mol Microbiol 61: 1013-1022
Kawamoto, H., Morita, T., Shimizu, A., Inada, T., and Aiba, H. (2005) Implication of
membrane localization of target mRNA in the action of a small RNA: mechanism of
post-transcriptional regulation of glucose transporter in Escherichia coli. Genes Dev 19:
328-338
Kawano, M., Aravind, L., and Storz, G. (2007) An antisense RNA controls synthesis of
an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 64: 738-754
Kawano, M., Oshima, T., Kasai, H., and Mori, H. (2002) Molecular characterization of
long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-aminoacid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Mol
Microbiol 45: 333-349
Kimata, K., Tanaka, Y., Inada, T., and Aiba, H. (2001) Expression of the glucose
transporter gene, ptsG, is regulated at the mRNA degradation step in response to
glycolytic flux in Escherichia coli. Embo J 20: 3587-3595
Lease, R. A., Cusick, M. E., and Belfort, M. (1998) Riboregulation in Escherichia coli:
DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc Natl Acad Sci U S A 95:
12456-12461
Liu, M. Y., Gui, G., Wei, B., Preston, J. F., 3rd, Oakford, L., Yuksel, U., Giedroc, D. P.,
and Romeo, T. (1997) The RNA molecule CsrB binds to the global regulatory protein
CsrA and antagonizes its activity in Escherichia coli. J Biol Chem 272: 17502-17510
Majdalani, N., Chen, S., Murrow, J., St John, K., and Gottesman, S. (2001) Regulation of
RpoS by a novel small RNA: the characterization of RprA. Mol Microbiol 39: 1382-1394
Majdalani, N., Cunning, C., Sledjeski, D., Elliott, T., and Gottesman, S. (1998) DsrA
RNA regulates translation of RpoS message by an anti-antisense mechanism,
independent of its action as an antisilencer of transcription. Proc Natl Acad Sci U S A 95:
12462-12467
Majdalani, N., Hernandez, D., and Gottesman, S. (2002) Regulation and mode of action
of the second small RNA activator of RpoS translation, RprA. Mol Microbiol 46: 813826
Masse, E., and Gottesman, S. (2002) A small RNA regulates the expression of genes
involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A 99: 4620-4625
Mizuno, T., Chou, M. Y., and Inouye, M. (1984) A unique mechanism regulating gene
expression: translational inhibition by a complementary RNA transcript (micRNA). Proc
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RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev 16:
1696-1706
Morita, T., Maki, K., and Aiba, H. (2005) RNase E-based ribonucleoprotein complexes:
mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs.
Genes Dev 19: 2176-2186
Opdyke, J. A., Kang, J. G., and Storz, G. (2004) GadY, a small-RNA regulator of acid
response genes in Escherichia coli. J Bacteriol 186: 6698-6705
Pedersen, K., and Gerdes, K. (1999) Multiple hok genes on the chromosome of
Escherichia coli. Mol Microbiol 32: 1090-1102
Prevost, K., Salvail, H., Desnoyers, G., Jacques, J. F., Phaneuf, E., and Masse, E. (2007)
The small RNA RyhB activates the translation of shiA mRNA encoding a permease of
shikimate, a compound involved in siderophore synthesis. Mol Microbiol 64: 1260-1273
Ramani, N., Hedeshian, M., and Freundlich, M. (1994) micF antisense RNA has a major
role in osmoregulation of OmpF in Escherichia coli. J Bacteriol 176: 5005-5010
Rasmussen, A. A., Eriksen, M., Gilany, K., Udesen, C., Franch, T., Petersen, C., and
Valentin-Hansen, P. (2005) Regulation of ompA mRNA stability: the role of a small
regulatory RNA in growth phase-dependent control. Mol Microbiol 58: 1421-1429
Sledjeski, D., and Gottesman, S. (1995) A small RNA acts as an antisilencer of the HNS-silenced rcsA gene of Escherichia coli. Proc Natl Acad Sci U S A 92: 2003-2007
Sledjeski, D. D., Gupta, A., and Gottesman, S. (1996) The small RNA, DsrA, is essential
for the low temperature expression of RpoS during exponential growth in Escherichia
coli. Embo J 15: 3993-4000
Tetart, F., Albigot, R., Conter, A., Mulder, E., and Bouche, J. P. (1992) Involvement of
FtsZ in coupling of nucleoid separation with septation. Mol Microbiol 6: 621-627
Tetart, F., and Bouche, J. P. (1992) Regulation of the expression of the cell-cycle gene
ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ
molecules. Mol Microbiol 6: 615-620
Thisted, T., and Gerdes, K. (1992) Mechanism of post-segregational killing by the
hok/sok system of plasmid R1. Sok antisense RNA regulates hok gene expression
indirectly through the overlapping mok gene. J Mol Biol 223: 41-54
Thisted, T., Sorensen, N. S., Wagner, E. G., and Gerdes, K. (1994) Mechanism of postsegregational killing: Sok antisense RNA interacts with Hok mRNA via its 5'-end singlestranded leader and competes with the 3'-end of Hok mRNA for binding to the mok
translational initiation region. Embo J 13: 1960-1968
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regulated by a small RNA in Escherichia coli. J Bacteriol
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Storz, G. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids
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(2005) Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA.
Genes Dev 19: 2355-2366
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RNA MicA. Nucleic Acids Res 35: 1279-1288
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Escherichia coli small RNAs in vivo. Nucleic Acids Res 35: 1018-1037
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small untranslated RNA involved in expression of the dipeptide and oligopeptide
transport systems in Escherichia coli. Mol Microbiol 37: 856-868
Vanderpool, C. K., and Gottesman, S. (2004) Involvement of a novel transcriptional
activator and small RNA in post-transcriptional regulation of the glucose
phosphoenolpyruvate phosphotransferase system. Mol Microbiol 54: 1076-1089
Vecerek, B., Moll, I., and Blasi, U. (2007) Control of Fur synthesis by the non-coding
RNA RyhB and iron-responsive decoding. Embo J 26: 965-975
Vogel, J., Argaman, L., Wagner, E. G., and Altuvia, S. (2004) The small RNA IstR
inhibits synthesis of an SOS-induced toxic peptide. Curr Biol 14: 2271-2276
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C. S., Georgellis, D., Babitzke, P., and Romeo, T. (2003) A novel sRNA component of
the carbon storage regulatory system of Escherichia coli. Mol Microbiol 48: 657-670
Zhang, A., Altuvia, S., and Storz, G. (1997) The novel oxyS RNA regulates expression of
the sigma s subunit of Escherichia coli RNA polymerase. Nucleic Acids Symp Ser 27-28
Zhang, A., Altuvia, S., Tiwari, A., Argaman, L., Hengge-Aronis, R., and Storz, G. (1998)
The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein.
Embo J 17: 6061-6068