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Chapter 3 : RNases and Helicases in Gram-Positive Bacteria

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Abstract:

Posttranscriptional regulation is a key modulator of gene expression in bacteria and allows their rapid adaptation to the environment. This regulation can be performed by proteins and/or RNA, by modifying either mRNA stability and/or translation. RNases are key enzymes in these processes. There are two main classes of RNases: endoribonucleases, which cleave directly in the “body” of the RNA; and exoribonucleases, which attack RNA from either its 5′ or 3′ end. Although RNases play a central role in RNA metabolism, these enzymes are not identical in Gram-negative and Gram-positive bacteria. For example, endoribonuclease E (RNase E) initiates bulk mRNA degradation and is essential in , but this RNase is absent in many , such as .

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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Figures

Image of Figure 1
Figure 1

A schematic view of the pathways involved in RNA degradation in Gram-positive bacteria. (A) Primary mRNA transcripts in bacteria are protected at their 5′ end by a triphosphate group. Initiation of mRNA degradation can involve an endoribonuclease cut (RNase Y or RNase III), which is the limiting step. This step generates a downstream product with a 5′ monophosphate extremity, which can be attacked by the 5′-to-3′ exoribonuclease RNase J (in blue). The 3′ end of the upstream cleavage product is degraded by 3′-to-5′ exoribonucleases (in green), principally PNPase in . (B) In the alternative degradation pathway, the 5′ triphosphate of the mRNA can be converted to a 5′ monophosphate by an RNA pyrophosphohydrolase (e.g., RppH [yellow square]). After removal of the triphosphate, the mRNA can be degraded by the 5′-to-3′ exoribonuclease RNase J or by RNase Y in cases where initial cleavage by RNase Y is sensitive to the 5′ status of the mRNA.

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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Figure 2

Comparison of the domain structure of RNases described in this review. All structures are based on RNases found in except RNase E (structure from ). Abbreviations: H, RNase H domain; CCD, coiled-coil domain; TMD, transmembrane domain; β-Lact., β-lactamase domain. RNA binding domains: S1, S1 domain; KH, KH domain; AR2, AR2 domain; RBD, RNA binding domain; dsRBD, double-stranded RNA binding omain.

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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Figure 3

(A) Role of RNase Y in the regulation of expression by the -encoded sRNA VR-RNA. VR-RNA binds the 5′ UTR of the mRNA, encoding a collagenase, and triggers cleavage of the mRNA by RNase Y. This cleavage in turn stabilizes the mRNA by creating a stem-loop structure at the 5′ end of the mRNA. The binding of the sRNA also stimulates translation by releasing the SD sequence ( ). (B) The RoxS sRNA binds to the SD sequence of mRNA, inhibiting its translation. The reduction of the ribosome trafficking on the mRNA uncovers RNase Y cleavage sites. The sRNA is in blue, the mRNA target is colored in black, the SD sequence is in gray, ribosomes are in blue, and RNase Y is represented by red scissors.

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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Figure 4

Regulation of the expression of the operon. When tryptophan is not limiting, the TRAP protein binds to the 5′ UTR of the operon and facilitates transcriptional termination at the terminator. The aborted transcript is probably cleaved by either RNase Y or J1 followed by the attack of the new 3′ end by PNPase. This degradation allows release of the TRAP protein for further regulation (left). When tryptophan is limiting, TRAP complex does not bind to the operon and an antiterminator structure can be formed to allow transcription of the mRNA (right). The mRNA is colored in black, the SD sequence is in gray, Ter is for terminator and anti-Ter for antiterminator, TRAP proteins are colored in green, PNPase is represented by a light green Pacman symbol, and RNase Y/J1 by red scissors.

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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Figure 5

Role of RNase III in the regulation of gene expression by antisense and -encoded sRNA. (A) type I TA system TxpA/RatA. The 3′ end of the RatA sRNA forms a large duplex with the mRNA, which is then cleaved by RNase III. (B) The excludon in . One of the transcripts of the operon starts with the Lmo0677 open reading frame on the opposite strand. The long 5′ UTR of the operon (Anti0677) is antisense to the operon. The duplex RNA is probably cleaved by RNase III, although this has not been shown directly. (C) RNAIII represses translation of the mRNA by sequestering the SD sequence ( ). The sRNA is in blue, the mRNA target is colored in black, the SD sequence is in gray, and RNase III represented by red scissors.

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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Figure 6

Role of RNase J in the regulation of gene expression by antisense and -encoded sRNA. (A) RoxS sRNA forms base-pairing interactions with the first 7 nucleotides of the mRNA to create a stable RNA helix at the 5′ end of the mRNA and protect it from degradation by RNase J1 (left) ( ). RoxS binding also stimulates translation by rendering the SD sequence more accessible. This increase of translation protects the mRNA from degradation by RNase Y (left). In contrast, when RoxS does not bind to , the 5′ end of this mRNA is free and can be attacked by RNase J1. The SD sequence of mRNA also stays embedded in a stem-loop structure that reduces its translation efficiency and promotes degradation by RNase Y (right). Exoribonucleolytic activity of RNase J1 is represented by a light blue Pacman symbol. The sRNA is in blue, the mRNA target is colored in black, the SD sequence is in gray, and ribosomes are in blue. (B) The 5′ UTR of the mRNA base-pairs with the coding sequence of the mRNA to block endoribonucleolytic cleavage by RNase J2 ( ). The inhibition of the endoribonucleolytic activity of RNase J2 is represented by red scissors.

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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Figure 7

Schematic representation of the DLN. RNase Y is anchored at the membrane and can transiently interact with metabolic enzymes (enolase and phosphofructokinase) and the 3′-to-5′ exoribonuclease PNPase. Domains of interaction between RNase Y and each partner are not characterized. Transient interactions are represented by two-headed arrows. RNase Y domains are indicated (TMD, transmembrane domain; CCD, coiled-coil domain; KH, KH domain; HD, HD domain with the catalytic site represented by red scissors).

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017
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References

/content/book/10.1128/9781683670247.chap3
1. Sala A,, Bordes P,, Genevaux P . 2014. Multiple toxin-antitoxin systems in Mycobacterium tuberculosis. Toxins (Basel) 6 : 1002 1020.[PubMed]
2. Lehnik-Habrink M,, Newman J,, Rothe FM,, Solovyova AS,, Rodrigues C,, Herzberg C,, Commichau FM,, Lewis RJ,, Stülke J . 2011. RNase Y in Bacillus subtilis: a natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. J Bacteriol 193 : 5431 5441.[PubMed]
3. Gilet L,, DiChiara JM,, Figaro S,, Bechhofer DH,, Condon C . 2015. Small stable RNA maturation and turnover in Bacillus subtilis. Mol Microbiol 95 : 270 282.[PubMed]
4. Durand S,, Gilet L,, Bessières P,, Nicolas P,, Condon C . 2012. Three essential ribonucleases—RNase Y, J1, and III—control the abundance of a majority of Bacillus subtilis mRNAs. PLoS Genet 8 : e1002520.[CrossRef][PubMed]
5. Laalami S,, Bessières P,, Rocca A,, Zig L,, Nicolas P,, Putzer H . 2013. Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays. PLoS One 8 : e54062.[CrossRef][PubMed]
6. Obana N,, Nakamura K,, Nomura N . 2016. Role of RNase Y in Clostridium perfringens mRNA decay and processing. J Bacteriol 199 : e00703-16.[CrossRef][PubMed]
7. Deloughery A,, Dengler V,, Chai Y,, Losick R . 2011. A multiprotein complex required for biofilm formation by Bacillus subtilis. Mol Microbiol 99 : 425 437.[PubMed]
8. Figaro S,, Durand S,, Gilet L,, Cayet N,, Sachse M,, Condon C . 2013. Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence. J Bacteriol 195 : 2340 2348.[PubMed]
9. Chen Z,, Itzek A,, Malke H,, Ferretti JJ,, Kreth J . 2013. Multiple roles of RNase Y in Streptococcus pyogenes mRNA processing and degradation. J Bacteriol 195 : 2585 2594.[PubMed]
10. Marincola G,, Schäfer T,, Behler J,, Bernhardt J,, Ohlsen K,, Goerke C,, Wolz C . 2012. RNase Y of Staphylococcus aureus and its role in the activation of virulence genes. Mol Microbiol 85 : 817 832.[PubMed]
11. Khemici V,, Prados J,, Linder P,, Redder P . 2015. Decay-initiating endoribonucleolytic cleavage by RNase Y is kept under tight control via sequence preference and sub-cellular localisation. PLoS Genet 11 : e1005577.[CrossRef][PubMed]
12. Shahbabian K,, Jamalli A,, Zig L,, Putzer H . 2009. RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J 28 : 3523 3533.[PubMed]
13. Marincola G,, Wolz C . 2017. Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus. Nucleic Acids Res 45 : 5980 5994.[PubMed]
14. Durand S,, Braun F,, Lioliou E,, Romilly C,, Helfer AC,, Kuhn L,, Quittot N,, Nicolas P,, Romby P,, Condon C . 2015. A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis. PLoS Genet 11 : e1004957.[CrossRef][PubMed]
15. Deikus G,, Babitzke P,, Bechhofer DH . 2004. Recycling of a regulatory protein by degradation of the RNA to which it binds. Proc Natl Acad Sci U S A 101 : 2747 2751.[PubMed]
16. Deikus G,, Bechhofer DH . 2009. Bacillus subtilis trp Leader RNA: RNase J1 endonuclease cleavage specificity and PNPase processing. J Biol Chem 284 : 26394 26401.[PubMed]
17. Deikus G,, Bechhofer DH . 2011. 5′ end-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA. J Biol Chem 286 : 34932 34940.[PubMed]
18. Panganiban AT,, Whiteley HR . 1983. Purification and properties of a new Bacillus subtilis RNA processing enzyme. Cleavage of phage SP82 mRNA and Bacillus subtilis precursor rRNA. J Biol Chem 258 : 12487 12493.[PubMed]
19. Oguro A,, Kakeshita H,, Nakamura K,, Yamane K,, Wang W,, Bechhofer DH . 1998. Bacillus subtilis RNase III cleaves both 5′- and 3′-sites of the small cytoplasmic RNA precursor. J Biol Chem 273 : 19542 19547.[PubMed]
20. Lioliou E,, Sharma CM,, Caldelari I,, Helfer AC,, Fechter P,, Vandenesch F,, Vogel J,, Romby P . 2012. Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet 8 : e1002782.[CrossRef][PubMed]
21. Stead MB,, Marshburn S,, Mohanty BK,, Mitra J,, Pena Castillo L,, Ray D,, van Bakel H,, Hughes TR,, Kushner SR . 2011. Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res 39 : 3188 3203.[PubMed]
22. 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 . 2009. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459 : 950 956.[PubMed]
23. Lasa I,, Toledo-Arana A,, Dobin A,, Villanueva M,, de los Mozos IR,, Vergara-Irigaray M,, Segura V,, Fagegaltier D,, Penadés JR,, Valle J,, Solano C,, Gingeras TR . 2011. Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A 108 : 20172 20177.[PubMed]
24. Novick RP,, Ross HF,, Projan SJ,, Kornblum J,, Kreiswirth B,, Moghazeh S . 1993. Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J 12 : 3967 3975.[PubMed]
25. Kaito C,, Saito Y,, Ikuo M,, Omae Y,, Mao H,, Nagano G,, Fujiyuki T,, Numata S,, Han X,, Obata K,, Hasegawa S,, Yamaguchi H,, Inokuchi K,, Ito T,, Hiramatsu K,, Sekimizu K . 2013. Mobile genetic element SCC mec-encoded psm-mec RNA suppresses translation of agrA and attenuates MRSA virulence. PLoS Pathog 9 : e1003269.[CrossRef][PubMed]
26. Deltcheva E,, Chylinski K,, Sharma CM,, Gonzales K,, Chao Y,, Pirzada ZA,, Eckert MR,, Vogel J,, Charpentier E . 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471 : 602 607.[PubMed]
27. Redko Y,, Bechhofer DH,, Condon C . 2008. Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis. Mol Microbiol 68 : 1096 1106.[PubMed]
28. Olmedo G,, Guzmán P . 2008. Mini-III, a fourth class of RNase III catalyses maturation of the Bacillus subtilis 23S ribosomal RNA. Mol Microbiol 68 : 1073 1076.[PubMed]
29. Hotto AM,, Castandet B,, Gilet L,, Higdon A,, Condon C,, Stern DB . 2015. Arabidopsis chloroplast mini-ribonuclease III participates in rRNA maturation and intron recycling. Plant Cell 27 : 724 740.[PubMed]
30. Aït-Bara S,, Carpousis AJ . 2015. RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs. Mol Microbiol 97 : 1021 1135.[PubMed]
31. Zeller ME,, Csanadi A,, Miczak A,, Rose T,, Bizebard T,, Kaberdin VR . 2007. Quaternary structure and biochemical properties of mycobacterial RNase E/G. Biochem J 403 : 207 215.[PubMed]
32. Taverniti V,, Forti F,, Ghisotti D,, Putzer H . 2011. Mycobacterium smegmatis RNase J is a 5′-3′ exo-/endoribonuclease and both RNase J and RNase E are involved in ribosomal RNA maturation. Mol Microbiol 82 : 1260 1276.[PubMed]
33. Kovacs L,, Csanadi A,, Megyeri K,, Kaberdin VR,, Miczak A . 2005. Mycobacterial RNase E-associated proteins. Microbiol Immunol 49 : 1003 1007.[PubMed]
34. Pfeiffer V,, Papenfort K,, Lucchini S,, Hinton JC,, Vogel J . 2009. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16 : 840 846.[PubMed]
35. Bandyra KJ,, Said N,, Pfeiffer V,, Górna MW,, Vogel J,, Luisi BF . 2012. The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell 47 : 943 953.[PubMed]
36. Wen T,, Oussenko IA,, Pellegrini O,, Bechhofer DH,, Condon C . 2005. Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis. Nucleic Acids Res 33 : 3636 3643.[PubMed]
37. Oussenko IA,, Abe T,, Ujiie H,, Muto A,, Bechhofer DH . 2005. Participation of 3′-to-5′ exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol 187 : 2758 2767.[PubMed]
38. Even S,, Pellegrini O,, Zig L,, Labas V,, Vinh J,, Bréchemmier-Baey D,, Putzer H . 2005. Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E. Nucleic Acids Res 33 : 2141 2152.[PubMed]
39. Dorléans A,, Li de la Sierra-Gallay I,, Piton J,, Zig L,, Gilet L,, Putzer H,, Condon C . 2011. Molecular basis for the recognition and cleavage of RNA by the bifunctional 5′-3′ exo/endoribonuclease RNase J. Structure 19 : 1252 1261.[PubMed]
40. Newman JA,, Hewitt L,, Rodrigues C,, Solovyova A,, Harwood CR,, Lewis RJ . 2011. Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1. Structure 19 : 1241 1251.[PubMed]
41. Mathy N,, Hébert A,, Mervelet P,, Bénard L,, Dorléans A,, Li de la Sierra-Gallay I,, Noirot P,, Putzer H,, Condon C . 2010. Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol Microbiol 75 : 489 498.[PubMed]
42. Commichau FM,, Rothe FM,, Herzberg C,, Wagner E,, Hellwig D,, Lehnik-Habrink M,, Hammer E,, Völker U,, Stülke J,, Volker U,, Stulke J . 2009. Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 8 : 1350 1360.[PubMed]
43. Mathy N,, Bénard L,, Pellegrini O,, Daou R,, Wen T,, Condon C . 2007. 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129 : 681 692.[PubMed]
44. Li de la Sierra-Gallay I,, Zig L,, Jamalli A,, Putzer H,, de la Sierra-Gallay IL . 2008. Structural insights into the dual activity of RNase J. Nat Struct Mol Biol 15 : 206 212.[PubMed]
45. Linder P,, Lemeille S,, Redder P . 2014. Transcriptome-wide analyses of 5′-ends in RNase J mutants of a Gram-positive pathogen reveal a role in RNA maturation, regulation and degradation. PLoS Genet 10 : e1004207.[CrossRef][PubMed]
46. Hausmann S,, Guimarães VA,, Garcin D,, Baumann N,, Linder P,, Redder P,, Redder P . 2017. Both exo- and endo-nucleolytic activities of RNase J1 from Staphylococcus aureus are manganese dependent and active on triphosphorylated 5′-ends. RNA Biol 14 : 1431 1443.[PubMed]
47. Bugrysheva JV,, Scott JR . 2010. The ribonucleases J1 and J2 are essential for growth and have independent roles in mRNA decay in Streptococcus pyogenes. Mol Microbiol 75 : 731 743.[PubMed]
48. Chen X,, Liu N,, Khajotia S,, Qi F,, Merritt J,, Merritt J . 2015. RNases J1 and J2 are critical pleiotropic regulators in Streptococcus mutans. Microbiology 161 : 797 806.[PubMed]
49. Gao P,, Pinkston KL,, Bourgogne A,, Murray BE,, van Hoof A,, Harvey BR . 2017. Functional studies of E. faecalis RNase J2 and its role in virulence and fitness. PLoS One 12 : e0175212.[CrossRef][PubMed]
50. Luttinger A,, Hahn J,, Dubnau D . 1996. Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol Microbiol 19 : 343 356.[PubMed]
51. Durand S,, Braun F,, Helfer AC,, Romby P,, Condon C . 2017. sRNA-mediated activation of gene expression by inhibition of 5′-3′ exonucleolytic mRNA degradation. eLife 6 : e23602.[CrossRef][PubMed]
52. Liu N,, Niu G,, Xie Z,, Chen Z,, Itzek A,, Kreth J,, Gillaspy A,, Zeng L,, Burne R,, Qi F,, Merritt J . 2015. The Streptococcus mutans irvA gene encodes a trans-acting riboregulatory mRNA. Mol Cell 57 : 179 190.[PubMed]
53. Deutscher MP,, Reuven NB . 1991. Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A 88 : 3277 3280.[PubMed]
54. Wang ZF,, Whitfield ML,, Ingledue TC III,, Dominski Z,, Marzluff WF . 1996. The protein that binds the 3′ end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. Genes Dev 10 : 3028 3040.[PubMed]
55. Liu B,, Deikus G,, Bree A,, Durand S,, Kearns DB,, Bechhofer DH . 2014. Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains. Mol Microbiol 94 : 41 55.[PubMed]
56. Wang W,, Bechhofer DH . 1996. Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain. J Bacteriol 178 : 2375 2382.[PubMed]
57. Deikus G,, Bechhofer DH . 2007. Initiation of decay of Bacillus subtilis trp leader RNA. J Biol Chem 282 : 20238 20244.[PubMed]
58. De Lay N,, Gottesman S . 2011. Role of polynucleotide phosphorylase in sRNA function in Escherichia coli. RNA 17 : 1172 1189.[PubMed]
59. Bandyra KJ,, Sinha D,, Syrjanen J,, Luisi BF,, De Lay NR . 2016. The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes. RNA 22 : 360 372.[PubMed]
60. Khemici V,, Linder P . 2016. RNA helicases in bacteria. Curr Opin Microbiol 30 : 58 66.[PubMed]
61. Fairman-Williams ME,, Guenther UP,, Jankowsky E . 2010. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 20 : 313 324.[PubMed]
62. Koo JT,, Choe J,, Moseley SL . 2004. HrpA, a DEAH-box RNA helicase, is involved in mRNA processing of a fimbrial operon in Escherichia coli. Mol Microbiol 52 : 1813 1826.[PubMed]
63. Salman-Dilgimen A,, Hardy PO,, Radolf JD,, Caimano MJ,, Chaconas G . 2013. HrpA, an RNA helicase involved in RNA processing, is required for mouse infectivity and tick transmission of the Lyme disease spirochete. PLoS Pathog 9 : e1003841.[CrossRef][PubMed]
64. Granato LM,, Picchi SC,, Andrade MO,, Takita MA,, de Souza AA,, Wang N,, Machado MA . 2016. The ATP-dependent RNA helicase HrpB plays an important role in motility and biofilm formation in Xanthomonas citri subsp. citri. BMC Microbiol 16 : 55.[CrossRef][PubMed]
65. Uson ML,, Ordonez H,, Shuman S . 2015. Mycobacterium smegmatis HelY is an RNA-activated ATPase/dATPase and 3′-to-5′ helicase that unwinds 3′-tailed RNA duplexes and RNA:DNA hybrids. J Bacteriol 197 : 3057 3065.[PubMed]
66. Giraud C,, Hausmann S,, Lemeille S,, Prados J,, Redder P,, Linder P . 2015. The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus. RNA Biol 12 : 658 674.[PubMed]
67. Pandiani F,, Brillard J,, Bornard I,, Michaud C,, Chamot S,, Nguyen-the C,, Broussolle V . 2010. Differential involvement of the five RNA helicases in adaptation of Bacillus cereus ATCC 14579 to low growth temperatures. Appl Environ Microbiol 76 : 6692 6697.[PubMed]
68. Lehnik-Habrink M,, Rempeters L,, Kovács ÁT,, Wrede C,, Baierlein C,, Krebber H,, Kuipers OP,, Stülke J . 2013. DEAD-box RNA helicases in Bacillus subtilis have multiple functions and act independently from each other. J Bacteriol 195 : 534 544.[PubMed]
69. Bäreclev C,, Vaitkevicius K,, Netterling S,, Johansson J . 2014. DExD-box RNA-helicases in Listeria monocytogenes are important for growth, ribosomal maturation, rRNA processing and virulence factor expression. RNA Biol 11 : 1457 1466.[PubMed]
70. Redder P,, Hausmann S,, Khemici V,, Yasrebi H,, Linder P . 2015. Bacterial versatility requires DEAD-box RNA helicases. FEMS Microbiol Rev 39 : 392 412.[PubMed]
71. Lehnik-Habrink M,, Pförtner H,, Rempeters L,, Pietack N,, Herzberg C,, Stülke J . 2010. The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex. Mol Microbiol 77 : 958 971.
72. Roux CM,, DeMuth JP,, Dunman PM . 2011. Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. J Bacteriol 193 : 5520 5526.[PubMed]
73. Oun S,, Redder P,, Didier JP,, François P,, Corvaglia AR,, Buttazzoni E,, Giraud C,, Girard M,, Schrenzel J,, Linder P . 2013. The CshA DEAD-box RNA helicase is important for quorum sensing control in Staphylococcus aureus. RNA Biol 10 : 157 165.[PubMed]
74. Newman JA,, Hewitt L,, Rodrigues C,, Solovyova AS,, Harwood CR,, Lewis RJ . 2012. Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome. J Mol Biol 416 : 121 136.[PubMed]
75. Salvo E,, Alabi S,, Liu B,, Schlessinger A,, Bechhofer DH . 2016. Interaction of Bacillus subtilis polynucleotide phosphorylase and RNase Y: structural mapping and effect on mRNA turnover. J Biol Chem 291 : 6655 6663.[PubMed]
76. Cascante-Estepa N,, Gunka K,, Stülke J . 2016. Localization of components of the RNA-degrading machine in Bacillus subtilis. Front Microbiol 7 : 1492.[CrossRef][PubMed]
77. Jamalli A,, Hébert A,, Zig L,, Putzer H . 2014. Control of expression of the RNases J1 and J2 in Bacillus subtilis. J Bacteriol 196 : 318 324.[PubMed]
78. DiChiara JM,, Liu B,, Figaro S,, Condon C,, Bechhofer DH . 2016. Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains. Nucleic Acids Res 44 : 3373 3389.[PubMed]
79. Zhang X,, Zhu Q,, Tian T,, Zhao C,, Zang J,, Xue T,, Sun B . 2015. Identification of RNAIII-binding proteins in Staphylococcus aureus using tethered RNAs and streptavidin aptamers based pull-down assay. BMC Microbiol 15 : 102.[CrossRef][PubMed]
80. Condon C,, Putzer H . 2002. The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res 30 : 5339 5346.[PubMed]
81. Kaberdin VR,, Singh D,, Lin-Chao S . 2011. Composition and conservation of the mRNA-degrading machinery in bacteria. J Biomed Sci 18 : 23.[CrossRef][PubMed]
82. Bronesky D,, Wu Z,, Marzi S,, Walter P,, Geissmann T,, Moreau K,, Vandenesch F,, Caldelari I,, Romby P . 2016. Staphylococcus aureus RNAIII and its regulon link quorum sensing, stress responses, metabolic adaptation, and regulation of virulence gene expression. Annu Rev Microbiol 70 : 299 316.[PubMed]
83. Obana N,, Shirahama Y,, Abe K,, Nakamura K . 2010. Stabilization of Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5′ leader sequence. Mol Microbiol 77 : 1416 1428.[PubMed]
84. Boisset S,, Geissmann T,, Huntzinger E,, Fechter P,, Bendridi N,, Possedko M,, Chevalier C,, Helfer AC,, Benito Y,, Jacquier A,, Gaspin C,, Vandenesch F,, Romby P . 2007. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 21 : 1353 1366.[PubMed]

Tables

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Table 1

RNases and their functions

Citation: Durand S, Condon C. 2019. RNases and Helicases in Gram-Positive Bacteria, p 37-53. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0003-2017

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