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Chapter 20 : 6S RNA, a Global Regulator of Transcription

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Abstract:

It is now well established that small RNAs (sRNAs) have diverse and widespread roles in regulating gene expression in all organisms ( ). Mechanisms of action are varied but can be broadly classified into three categories: (i) sRNAs that act by base-pairing to target RNAs; (ii) sRNAs that act to modulate protein activity through direct RNA-protein interaction; and (iii) sRNAs that have intrinsic function (e.g., catalytic). Two well-studied sRNA families that modulate protein activity include sRNAs that regulate CsrA protein and 6S RNA, which regulates RNA polymerase (RNAP) and is the focus here as well as in several other reviews ( ). 6S RNA was first identified in ( ), which remains the best-understood model of 6S RNA function, although identification of 6S RNAs and their roles in diverse bacterial species has been an active area of research in the past decade. Here, information for will be presented first, followed by discussion of similarities and differences known or postulated for 6S RNAs in diverse species.

Citation: Wassarman K. 2019. 6S RNA, a Global Regulator of Transcription, p 355-367. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0019-2018
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Figure 1

6S RNA is shown in a secondary structure observed from the cryo-EM 6S RNA-Eσ structure (upstream stem and central region) or predicted from secondary-structure analysis (downstream stem) ( ). For reference, the upstream stem, central region, and downstream stem are indicated. The template central region is in green; the site of initiation for pRNA synthesis is indicated by a red arrow; the nontemplate central region is in blue. 6S RNAs from (6S-1 and 6S-2), , (6S RNA), , and are shown in secondary structures expected when in complex with RNAP, with sites of pRNA synthesis initiation indicated by arrows ( ). pRNA synthesis has not been examined for 6S RNA. Note, some 6S RNAs have been demonstrated or predicted to have base pairing within the central region in isolated RNA (6S-1 and 6S-2 RNA, 6S RNA) ( ), but binding studies support that the central region is fully single stranded when bound to RNAP ( ). Other alternative structures that contribute to 6S RNA release from RNAP during pRNA synthesis also have been observed ( ).

Citation: Wassarman K. 2019. 6S RNA, a Global Regulator of Transcription, p 355-367. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0019-2018
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Image of Figure 2
Figure 2

Comparison of 6S RNA and promoter DNA interactions with region 4.2 of σ. Holoenzyme structures complexed with RNA (PDB ID: 5VT0) ( ) (A and C) and promoter DNA (PDB ID: 5VI5) ( ) (B and D) are centered on region 4.2 of σ and shown without (A and B) or with (C and D) the nucleic acids visible. The cryo-EM structure with 6S RNA is holoenzyme, and the crystal structure with DNA in an open complex is holoenzyme, and thus there are small variations in structure due to sequence changes, although region 4.2 of σ is very highly conserved. Residues within region 4.2 of σ are labeled ( numbering) with color coding based on impact of alanine substitution on binding to RNA (A) or DNA (B) ( ): red, strong decrease; blue, moderate decrease; green, increase. A592 (dark gray) is a position where substitution of a positive or negative residue strongly influences 6S RNA binding with little effect on DNA binding ( ). Residues labeled in light gray (B and D) are locations where alanine substitution did not influence DNA binding, but are included to assist with comparison of the two structures. Other coloring: 6S RNA, green; promoter DNA, purple; β subunit, cyan; β′ subunit, pink; σ (outside of region 4.2), light orange.

Citation: Wassarman K. 2019. 6S RNA, a Global Regulator of Transcription, p 355-367. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0019-2018
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