Structural basis for transcription initiation by bacterial ECF σ factors

Li, Lingting; Fang, Chengli; Zhuang, Ningning; Wang, Tiantian; Zhang, Yu

doi:10.1038/s41467-019-09096-y

Cited by 59 publications

(54 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The "DPE" motif is located on the "specificity loop" of σ S 2 , an essential structural element responsible for recognizing and stabilizing the unwound nucleotide at the most conserved position of promoter DNA (i.e. position -11 of σ S and σ 70 ) in all bacterial transcription initiation complexes (Campagne et al, 2014;Li et al, 2019;Lin et al, 2019;Liu et al, 2016;Zhang et al, 2012). In our structure, the "specificity loop" encloses the NT-11A nucleotide as reported ( Fig.…”

Section: Crl Interacts With σ S and Rnap Core Enzymesupporting

confidence: 57%

Crl activates transcription by stabilizing the active conformation of the master stress factor σ^S

Cui

Shen

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

σ S is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses and antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σ S -mediated transcription requires a σ S -specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an E. coli transcription activation complex (E. coli Crl-TAC) comprising E. coli σ S -RNAP holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with the domain 2 of σ S (σ S 2 ), sharing no interaction with promoter DNA. Subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) results indicate that Crl stabilizes key structural motifs of σ S 2 to promote the assembly of σ S -RNAP holoenzyme and also to facilitate formation of the RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.

show abstract

Section: Crl Interacts With σ S and Rnap Core Enzymesupporting

confidence: 57%

Crl activates transcription by stabilizing the active conformation of the master stress factor σ^S

Cui

Shen

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Thus, it is likely that binding of ASDI’s helix 4 to this area prevents ECF binding to the RNAP core, hampering ECF-dependent transcription when the anti-σ factor in present. Instead, predictions #10 and #11 involve ECF helices 4.2 and 4.4, in two residues involved in the contact with the −35 element of the promoter (33, 36). Taken together, the presence of these strong co-evolutionary signals suggests that the majority of the 10,860 ASDI proteins establish contact to the ECF via these two binding interfaces, connecting the ASDI with both the σ 2 and σ 4 domains.…”

Section: Resultsmentioning

confidence: 99%

“…3E). In the first case, the predicted contact area includes ECF regions 2.1 and 2.2, whose main function is binding to the clamp helices of the β’ subunit of the RNAP (33–35). Thus, it is likely that binding of ASDI’s helix 4 to this area prevents ECF binding to the RNAP core, hampering ECF-dependent transcription when the anti-σ factor in present.…”

Section: Resultsmentioning

confidence: 99%

Co-evolutionary analysis reveals a conserved dual binding interface between extracytoplasmic function (ECF) σ factors and class I anti-σ factors

Casas-Pastor

Diehl

Fritz

2020

Preprint

View full text Add to dashboard Cite

9Extracytoplasmic function σ factors (ECFs) belong to the most abundant signal transduction 10 mechanisms in bacteria. Amongst the diverse regulators of ECF activity, class I anti-σ factors are the 11 most important signal transducers in response to internal and external stress conditions. Despite the 12 conserved secondary structure of the class I anti-σ factor domain (ASDI) that binds and inhibits the 13 ECF under non-inducing conditions, the binding interface between ECFs and ASDIs is surprisingly 14 variable between the published co-crystal structures. In this work, we provide a comprehensive 15 computational analysis of the ASDI protein family and study the different contact themes between 16ECFs and ASDIs. To this end, we harness the co-evolution of these diverse protein families and 17 predict covarying amino acid residues as likely candidates of an interaction interface. As a result, we 18 find two common binding interfaces linking the first α-helix of the ASDI to the DNA binding region in 19 the σ 4 domain of the ECF, and the fourth α-helix of the ASDI to the RNA polymerase (RNAP) binding 20 region of the σ 2 domain. The conservation of these two binding interfaces contrasts with the apparent 21 quaternary structure diversity of the ECF/ASDI complexes, partially explaining the high specificity 22between cognate ECF and ASDI pairs. Furthermore, we suggest that the dual inhibition of RNAP-and 23 DNA-binding interfaces are likely a universal feature of other ECF anti-σ factors, preventing the 24 formation of non-functional trimeric complexes between σ/anti-σ factors and RNAP or DNA. 25 26Significance 27In the bacterial world, extracytoplasmic function σ factors (ECFs) are the most widespread family of 28 alternative σ factors, mediating many cellular responses to environmental cues, such as stress. This 29 work uses a computational approach to investigate how these σ factors interact with class I anti-σ 30 factorsthe most abundant regulators of ECF activity. By comprehensively classifying the anti-σs 31 into phylogenetic groups and by comparing this phylogeny to the one of the cognate ECFs, the study 32 shows how these protein families have co-evolved to maintain their interaction over evolutionary time. 33These results shed light on the common contact residues that link ECFs and anti-σs in different 34 phylogenetic families and set the basis for the rational design of anti-σs to specifically target certain 35ECFs. This will help to prevent the cross-talk between heterologous ECF/anti-σ pairs, allowing their 36 use as orthogonal regulators for the construction of genetic circuits in synthetic biology. 37 38 factors, which, under non-inducing conditions, sequester ECF into inactive complexes via their anti-σ 48 domain (ASD). Under inducing conditions, anti-σ factors releases their ECFs by various mechanisms, 49including anti-σ proteolysis (4-6), conformational change (7, 8) or sequestration by ECF-mimicking 50 anti-anti-σ factors (9, 10). Given that bacteria harbor an average of 10 ECFs, and some species 51...

show abstract

“…2E). We interpret the successive changes in [6][7][8]. As a first step to assess whether the difference in s-finger length and sequence for ECF s factors vs. primary s factors affects the mechanism of initiation-factor displacement, we have performed an analysis analogous to that in Fig.…”

Section: Rnamentioning

confidence: 99%

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

Molodtsov

Lin

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

All organisms--bacteria, archaea, and eukaryotes--have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription-initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription-initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate, and define details of, stepwise, RNA-extension-driven displacement of the "s finger" of the bacterial transcription initiation factor s. The structures reveal that--for both the primary s factor and extracytoplasmic (ECF) s factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA--the "s finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ~5 nt to ~10 nt.

show abstract

Structural basis for transcription initiation by bacterial ECF σ factors

Cited by 59 publications

References 60 publications

Crl activates transcription by stabilizing the active conformation of the master stress factor σ^S

Crl activates transcription by stabilizing the active conformation of the master stress factor σ^S

Co-evolutionary analysis reveals a conserved dual binding interface between extracytoplasmic function (ECF) σ factors and class I anti-σ factors

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

Contact Info

Product

Resources

About

Structural basis for transcription initiation by bacterial ECF σ factors

Cited by 59 publications

References 60 publications

Crl activates transcription by stabilizing the active conformation of the master stress factor σS

Crl activates transcription by stabilizing the active conformation of the master stress factor σS

Co-evolutionary analysis reveals a conserved dual binding interface between extracytoplasmic function (ECF) σ factors and class I anti-σ factors

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

Contact Info

Product

Resources

About

Crl activates transcription by stabilizing the active conformation of the master stress factor σ^S

Crl activates transcription by stabilizing the active conformation of the master stress factor σ^S