Sitting-duck (????)промоторы

Литические и лизогенные

  • Transcriptional interference between convergent promoters caused by elongation over the promoter.[Mol Cell. 2004]

Callen BP, Shearwin KE, Egan JB

Mol Cell. 2004 Jun 4; 14(5):647-56.

 

2.4. Сигналы внешней среды и опосредованные асРНК регуляторные функции

  • The challenge of regulation in a minimal photoautotroph: non-coding RNAs in Prochlorococcus.[PLoS Genet. 2008]

Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR

PLoS Genet. 2008 Aug 29; 4(8):e1000173.

  • Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis.[J Bacteriol. 2006]

Silvaggi JM, Perkins JB, Losick R

J Bacteriol. 2006 Jan; 188(2):532-41.

  • The Listeria transcriptional landscape from saprophytism to virulence.[Nature. 2009]

Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P

Nature. 2009 Jun 18; 459(7249):950-6.

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.

Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, Voss B, Steglich C, Wilde A, Vogel J, Hess WR

Proc Natl Acad Sci U S A. 2011 Feb 1; 108(5):2124-9.

 

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

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

Mol Syst Biol. 2009; 5():305.

 

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

Dühring U, Axmann IM, Hess WR, Wilde A

Proc Natl Acad Sci U S A. 2006 May 2; 103(18):7054-8.

 

---уровень асРНК реагирует на изменение в потребности СО2, условий освещения и доступности железа.

2.4.1 Гомеостаз минералов и патогенность

  • S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum.[Nucleic Acids Res. 2008]

André G, Even S, Putzer H, Burguière P, Croux C, Danchin A, Martin-Verstraete I, Soutourina O

Nucleic Acids Res. 2008 Oct; 36(18):5955-69.

  • An antisense RNA that governs the expression kinetics of a multifunctional virulence gene.[Mol Microbiol. 2010]

Lee EJ, Groisman EA

Mol Microbiol. 2010 May; 76(4):1020-33.

  • A cis-encoded antisense small RNA regulated by the HP0165-HP0166 two-component system controls expression of ureB in Helicobacter pylori.[J Bacteriol. 2011]

Wen Y, Feng J, Scott DR, Marcus EA, Sachs G

J Bacteriol. 2011 Jan; 193(1):40-51.

2.5 Роль РНК-РНК взаимодействий для регуляции с помощью асРНК

Токсин-антитоксин энтеробактерий

  • Repression of small toxic protein synthesis by the Sib and OhsC small RNAs.[Mol Microbiol. 2008]

Fozo EM, Kawano M, Fontaine F, Kaya Y, Mendieta KS, Jones KL, Ocampo A, Rudd KE, Storz G

Mol Microbiol. 2008 Dec; 70(5):1076-93.

  • Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family.[Nucleic Acids Res. 2010]

Han K, Kim KS, Bak G, Park H, Lee Y

Nucleic Acids Res. 2010 Sep; 38(17):5851-66.

Домены высоковариабельны, определяют специфичность

Физхимия взаимодействий

  • Thermodynamics of RNA-RNA binding.[Bioinformatics. 2006]

Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL

Bioinformatics. 2006 May 15; 22(10):1177-82.

Вторичные структуры

  • The role of site accessibility in microRNA target recognition.[Nat Genet. 2007]

Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E

Nat Genet. 2007 Oct; 39(10):1278-84.

  • IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.[Bioinformatics. 2008]

Busch A, Richter AS, Backofen R

Bioinformatics. 2008 Dec 15; 24(24):2849-56.

дсДНК подвергается обработке эндонуклеазой 3

  • The continuing story of endoribonuclease III.[J Mol Microbiol Biotechnol. 2004]

Drider D, Condon C

J Mol Microbiol Biotechnol. 2004; 8(4):195-200.

Не обязательно полный гетеродуплекс

  • Four-way junctions in antisense RNA-mRNA complexes involved in plasmid replication control: a common theme?[J Mol Biol. 2001]

Kolb FA, Westhof E, Ehresmann B, Ehresmann C, Wagner EG, Romby P

J Mol Biol. 2001 Jun 8; 309(3):605-14.

 

Но не всегда 3, может быть Е

  • RNase E is required for induction of the glutamate-dependent acid resistance system in Escherichia coli.[Biosci Biotechnol Biochem. 2007]

Takada A, Umitsuki G, Nagai K, Wachi M

Biosci Biotechnol Biochem. 2007 Jan; 71(1):158-64.

SymR: An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin.

Kawano M, Aravind L, Storz G

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

 

AmgR: An antisense RNA that governs the expression kinetics of a multifunctional virulence gene.

Lee EJ, Groisman EA

Mol Microbiol. 2010 May; 76(4):1020-33.

 

2.6 Биологическое значение бактериальных асРНК

2.6.1 Эффективность регуляторных асРНК

 

 

IsrR/isiA система (An internal antisense RNA regulates expression of the photosynthesis gene isiA.[Proc Natl Acad Sci U S A. 2006]

Dühring U, Axmann IM, Hess WR, Wilde A

Proc Natl Acad Sci U S A. 2006 May 2; 103(18):7054-8.)

Модель

  • Quantitative characteristics of gene regulation by small RNA.[PLoS Biol. 2007]

Levine E, Zhang Z, Kuhlman T, Hwa T

PLoS Biol. 2007 Sep; 5(9):e229.

  • Small RNAs establish delays and temporal thresholds in gene expression.[Biophys J. 2008]

Legewie S, Dienst D, Wilde A, Herzel H, Axmann IM

Biophys J. 2008 Oct; 95(7):3232-8.

 

Стохастический взгляд на асРНК-регуляцию (случайности в отдельных клетках)

Транскрипционные всплески

  • Real-time kinetics of gene activity in individual bacteria.[Cell. 2005]

Golding I, Paulsson J, Zawilski SM, Cox EC

Cell. 2005 Dec 16; 123(6):1025-36.

Регуляторные РНК подавляют «шум» сильнее, чем просто подавленная транскрипция (важно для isiA (An internal antisense RNA regulates expression of the photosynthesis gene isiA.

Dühring U, Axmann IM, Hess WR, Wilde A

Proc Natl Acad Sci U S A. 2006 May 2; 103(18):7054-8.) и symE (An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin.

Kawano M, Aravind L, Storz G. Mol Microbiol. 2007 May; 64(3):738-54.) еще токсин-антитоксин (Small toxic proteins and the antisense RNAs that repress them.[Microbiol Mol Biol Rev. 2008] Fozo EM, Hemm MR, Storz G. Microbiol Mol Biol Rev. 2008 Dec; 72(4):579-89, Table of Contents.) или транспозоны

  • Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions.[PLoS One. 2010]

Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, Gaspin C, Romby P, Schrenzel J, Francois P

PLoS One. 2010 May 20; 5(5):e10725.

  • Regulation of transposition in bacteria.[Res Microbiol. 2004]

Nagy Z, Chandler M

Res Microbiol. 2004 Jun; 155(5):387-98.

  • Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.[PLoS Genet. 2008]

Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J

PLoS Genet. 2008 Aug 22; 4(8):e1000163.

Количества

 

 

  • A quantitative comparison of sRNA-based and protein-based gene regulation.[Mol Syst Biol. 2008]

Mehta P, Goyal S, Wingreen NS

Mol Syst Biol. 2008; 4():221.

  • Small RNAs establish gene expression thresholds.[Curr Opin Microbiol. 2008]

Levine E, Hwa T

Curr Opin Microbiol. 2008 Dec; 11(6):574-9.

Если концентрации мРНК и асРНК одинаковы и близки к порогу, то шума много, не так эффективно подавляет, как белки

  • Antisense expression increases gene expression variability and locus interdependency.[Mol Syst Biol. 2011]

Xu Z, Wei W, Gagneur J, Clauder-Münster S, Smolik M, Huber W, Steinmetz LM

Mol Syst Biol. 2011 Feb 15; 7():468.

 

Но это мб полезно, повышает фенотипическую гетерогенность популяции при генетической однородности