An internal antisense RNA regulates expression of the photosynthesis gene isiA

Evidence for a major role of antisense RNAs in cyanobacterial gene regulation.

Georg J, Voss B, Scholz I, Mitschke J, Wilde A, Hess WR.

Author information

• Faculty of Biology and Freiburg Initiative in Systems Biology, University of Freiburg, Freiburg 79104, Germany.

Abstract

Information on the numbers and functions of naturally occurring antisense RNAs (asRNAs) in eubacteria has thus far remained incomplete. Here, we screened the model cyanobacterium Synechocystis sp. PCC 6803 for asRNAs using four different methods. In the final data set, the number of known noncoding RNAs rose from 6 earlier identified to 60 and of asRNAs from 1 to 73 (28 were verified using at least three methods). Among these, there are many asRNAs to housekeeping, regulatory or metabolic genes, as well as to genes encoding electron transport proteins. Transferring cultures to high light, carbon-limited conditions or darkness influenced the expression levels of several asRNAs, suggesting their functional relevance. Examples include the asRNA to rpl1, which accumulates in a light-dependent manner and may be required for processing the L11 r-operon and the SyR7 noncoding RNA, which is antisense to the murF 5' UTR, possibly modulating murein biosynthesis. Extrapolated to the whole genome, approximately 10% of all genes in Synechocystis are influenced by asRNAs. Thus, chromosomally encoded asRNAs may have an important function in eubacterial regulatory networks.

Evidence for a major role of antisense RNAs in cyanobacterial gene regulation.

Georg J, Voss B, Scholz I, Mitschke J, Wilde A, Hess WR.

Author information

• Faculty of Biology and Freiburg Initiative in Systems Biology, University of Freiburg, Freiburg 79104, Germany.

Abstract

Information on the numbers and functions of naturally occurring antisense RNAs (asRNAs) in eubacteria has thus far remained incomplete. Here, we screened the model cyanobacterium Synechocystis sp. PCC 6803 for asRNAs using four different methods. In the final data set, the number of known noncoding RNAs rose from 6 earlier identified to 60 and of asRNAs from 1 to 73 (28 were verified using at least three methods). Among these, there are many asRNAs to housekeeping, regulatory or metabolic genes, as well as to genes encoding electron transport proteins. Transferring cultures to high light, carbon-limited conditions or darkness influenced the expression levels of several asRNAs, suggesting their functional relevance. Examples include the asRNA to rpl1, which accumulates in a light-dependent manner and may be required for processing the L11 r-operon and the SyR7 noncoding RNA, which is antisense to the murF 5' UTR, possibly modulating murein biosynthesis. Extrapolated to the whole genome, approximately 10% of all genes in Synechocystis are influenced by asRNAs. Thus, chromosomally encoded asRNAs may have an important function in eubacterial regulatory networks.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758717/

2.2 Типы антисмысловых РНК

Бактериальные асРНК разнообразны, не имеют общих черт, кроме того факта, что считываются с противоположной цепи транскрипционной единицы. Тем не менее, они могут быть примерно классифицированы в зависимости от их расположения, как 5'-перекрывающиеся (расходящийся, голова к голове), 3'-перекрывающиеся (сходящийся, хвост к хвосту), или находящиеся внутри асРНК. Транскрипты от белок-кодирующих генов с длинными 5 'или 3' нетранслирующими областями, которые существенно перекрываются с мРНК, происходящих из других генов, представляют собой эффективный способ для сохранения регуляторных связей между генами. (анабена Identification of a furA cis antisense RNA in the cyanobacterium Anabaena sp. PCC 7120.[J Mol Biol. 2006] Hernández JA, Muro-Pastor AM, Flores E, Bes MT, Peleato ML, Fillat MF)

2.3 Механизм действия асРНК у бактерий

2.3.1. Изменение стабильности целевой РНК

IsiA/IsrR

An internal antisense RNA regulates expression of the photosynthesis gene isiA.

Dühring U, Axmann IM, Hess WR, Wilde A.

Author information

• Department of Plant Biochemistry, Institute of Biology, Humboldt-University Berlin, Chausseestrasse 117, D-10115 Berlin, Germany.

Abstract

Small regulatory noncoding RNAs exist in both eukaryotic and prokaryotic organisms. Most of these RNA transcripts are trans-encoded RNAs with short and only partial antisense complementarity to their target RNAs, which regulate gene expression by modifying mRNA stability and translation. In contrast, reports on the function of cis-encoded, perfectly complementary antisense RNAs in eubacteria are rare. Cyanobacteria respond to iron deficiency by expressing IsiA (iron stress-induced protein A), which forms a giant ring structure around photosystem I. Here, we show that this process is controlled by IsrR (iron stress-repressed RNA), a cis-encoded antisense RNA transcribed from the isiA noncoding strand. Artificial overexpression of IsrR under iron stress causes a strongly diminished number of IsiA-photosystem I supercomplexes, whereas IsrR depletion results in premature expression of IsiA. The coupled degradation of IsrR/isiA mRNA duplexes appears to be a reversible switch that can respond to environmental changes. IsrR is the only RNA known so far to regulate a photosynthesis component.

http://www.ncbi.nlm.nih.gov/pubmed/16636284/

An internal antisense RNA regulates expression of the photosynthesis gene isiA

Ulf Dühring,^*† Ilka M. Axmann,^†‡ Wolfgang R. Hess,^§¶ and Annegret Wilde^*

у кишечной палочки GadY, a small-RNA regulator of acid response genes in Escherichia coli.[J Bacteriol. 2004]

Opdyke JA, Kang JG, Storz G

J Bacteriol. 2004 Oct; 186(20):6698-705.

Роль РНКаз

• Ribonuclease E is a 5'-end-dependent endonuclease.[Nature. 1998]

Mackie GA

Nature. 1998 Oct 15; 395(6703):720-3.

• Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection.[Nucleic Acids Res. 2011]

Stazic D, Lindell D, Steglich C

Nucleic Acids Res. 2011 Jun; 39(11):4890-9.

2.3.2 Изменение трансляции

symR/SymE пара у энтеробактерий

• An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin.[Mol Microbiol. 2007]

Kawano M, Aravind L, Storz G

Mol Microbiol. 2007 May; 64(3):738-54.

Роль сайта связывания рибосом

• Small RNA binding to 5' mRNA coding region inhibits translational initiation.[Mol Cell. 2008]

Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J

Mol Cell. 2008 Dec 26; 32(6):827-37.

-Связывание выключает

• An antisense RNA inhibits translation by competing with standby ribosomes.[Mol Cell. 2007]

Darfeuille F, Unoson C, Vogel J, Wagner EG

Mol Cell. 2007 May 11; 26(3):381-92.

Или повышает

• 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. 1998]

Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S

Proc Natl Acad Sci U S A. 1998 Oct 13; 95(21):12462-7.

2.3.3 Терминация транскрипции

Оперон транспорта и биосинтеза железа у Vibrio anguillarum

• Antisense RNA, fur, iron, and the regulation of iron transport genes in Vibrio anguillarum.[J Biol Chem. 1996]

Chen Q, Crosa JH

J Biol Chem. 1996 Aug 2; 271(31):18885-91.

• Regulation of the expression of bacterial iron transport genes: possible role of an antisense RNA as a repressor.[Gene. 1993]

Salinas PC, Waldbeser LS, Crosa JH

Gene. 1993 Jan 15; 123(1):33-8.

Механизм тут Transcription termination within the iron transport-biosynthesis operon of Vibrio anguillarum requires an antisense RNA.[J Bacteriol. 2007]

Stork M, Di Lorenzo M, Welch TJ, Crosa JH

J Bacteriol. 2007 May; 189(9):3479-88.

Контроль гена вирулентности icsA у Shigella flexneri