Regulation of antimicrobial resistance by extracytoplasmic function (ECF) sigma factors

Woods, Emily; McBride, Shonna M.

doi:10.1016/j.micinf.2017.01.007

“…On average, bacterial genomes encode six ECF σ factors; the given number for a particular bacterium will vary according to its genome size and environmental complexity 9 , 10 . ECF σ factors enable bacteria to rapidly respond to a variety of stresses 9 , 11 , 12 and are known to be essential for the pathogenicity of several disease-causing bacteria 13 , 14 . Mycobacterium tuberculosis has 10 ECF σ factors (σ C , σ D , σ E , σ G , σ H , σ I , σ J , σ K , σ L , and σ M ); deletion of ECF σ factors from M. tuberculosis results in attenuated disease progression (e.g., sigC and sigD ) or in alleviated virulence (e.g., sigE and sigH ) 15 , 16 .…”

Section: Introductionmentioning

confidence: 99%

Structural basis for transcription initiation by bacterial ECF σ factors

Li

¹

,

Fang

²

,

Zhuang

³

et al. 2019

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Bacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σH (σH-RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σH-RNAP (σH-RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σH and RNAP that are essential for σH-RNAP holoenzyme assembly as well as the interactions between σH-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding.

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“…On average, bacterial genomes encode six ECF σ factors; the given number for a particular bacterium will vary according to its genome size and environmental complexity 9,10 . ECF σ factors enable bacteria to rapidly respond to a variety of stresses 9,11,12 and are known to be essential for the pathogenicity of several disease-causing bacteria 13,14 .…”

Section: Introductionmentioning

confidence: 99%

Structural basis for transcription initiation by bacterial ECF σ factors

Li

¹

,

Fang

²

,

Zhuang

³

et al. 2019

Preprint

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Bacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σ H (σ H -RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σ H -RNAP (σ H -RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σ H and RNAP that are essential for σ H -RNAP holoenzyme assembly as well as the interactions between σ H -RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding. elements: the domain σ4 forms sequence-specific interactions with exposed bases in the major groove of the -35 dsDNA 21 ; the σ2.5 and σ3.1 domains reach into the major groove of the extended -10 element and make base-specific contacts 22, 23 ; the σ2 and σ1.2 domains recognize and then unwind the -10 element dsDNA 3, 24 .During the process of promoter unwinding, a tryptophan dyad of σ2 (W256/W257 in T. aquaticus σ A or W433/W434 in E. coli σ 70 ) forms a chair-like structure that functions as a wedge to separate the dsDNA at the (-12)/(-11) junction 22, 23 . The group-2 σ factors use the same set of residues to unwind promoter DNA; but the melting residues of group-3 σ factors are not conserved 25 . Subsequently the base moieties of the unwound nucleotides at position -11 and -7 of the nontemplate strand-A(-11)(nt) and T(-7)(nt)-are flipped out and inserted into pre-formed pockets by σ2 and σ1.2 3, 24 . Domain σ1.2 also recognizes the discriminator element by flipping out the guanine base of G(-6)(nt) and inserting it into a pocket 24 . Although σ3.2 does not read the promoter sequence directly, it is essential for transcription initiation. Domain σ3.2 reaches into the RNAP active site cleft and "pre-organizes" template ssDNA 24 . Domain σ3.2 also blocks the path of the extending RNA chain (> 5nt) 26,27 thereby contributing to both initial transcription pausing 28 and promoter escape 29,30 .Each category of known ECF σ factors recognizes promoters bearing a unique sequence signature at the -35 and the -10 elements 10,31 . In contrast to the high tolerance to sequence variation at the -35 and the -10 promoter elements exhibited by the primary σ factor, the ECF σ factors have stringent requirements for sequence identity in the -35 and the -10 elements and for spacer length between these two elements through an unknown mechanism 8, 32 .Although both the primary and ECF σ factors recognize the -35 element via σ4 and recognize the -10 element via σ2, the protein sequences of these two domains are not well conserved, and the c...

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“…The sigW genes were annotated on the basis of sigW present in Bacillus subtilis , which have been suggested to be involved in mediating resistance to certain antibiotics, e.g . fosfomycin 67 . The cnrH genes were predicted as homologs of cnrH present in Cupriavidus metallidurans CH34 where it is part of a circuit regulating resistance to metals, in particular nickel 68,69 .…”

Section: Discussionmentioning

confidence: 99%

Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

Behra

¹

,

Pettersson

²

,

Ramesh

³

et al. 2019

Sci Rep

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Nontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern “omics” approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, MmucT, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.

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Regulation of antimicrobial resistance by extracytoplasmic function (ECF) sigma factors

Cited by 34 publications

References 147 publications

Structural basis for transcription initiation by bacterial ECF σ factors

Structural basis for transcription initiation by bacterial ECF σ factors

Structural basis for transcription initiation by bacterial ECF σ factors

Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

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