Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase

Kurkela, Juha; Fredman, Julia; Salminen, Tiina A.; Tyystjärvi, Taina

doi:10.1111/mmi.14603

Cited by 17 publications

(22 citation statements)

References 90 publications

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“…The C397*/WT ratios of peptides derived from transcription elongation factors GreA, GreB, Mfd, NusA, NusG, and RapA ranged from 1 to 1.4, whereas Rho was an outlier, with ~1.9‐fold enrichment in the C397* sample; σ 70 was slightly less abundant in the mutant (Figure 5a). The results were similar between replicate experiments with the exception of σ S (Figure 5a); an apparent increase in σ S levels (observed in only one sample) is consistent with preferential binding of alternative σ factors to ω‐less RNAP; reviewed in (Kurkela et al, 2021). These results indicate that defects in Rho‐dependent termination cannot be explained by the reduced affinity of C397* RNAP to Rho and Nus factors.…”

Section: Resultssupporting

confidence: 85%

“…The loss of β’ peptide encompassing residues 1356‐1369 is expected due to its absence in the mutant protein. We also observed changes in abundance of peptides derived from the α2 helix of ω, which makes polar contacts to β’D in structures of E. coli , Thermus thermophilus , and Mycobacterium tuberculosis enzymes (Kurkela et al, 2021), and in the ω α3 helix. These changes could result from either direct interactions between ω and the C397* tail or from changes in ω that are induced by these contacts, but are relatively modest.…”

Section: Resultsmentioning

confidence: 58%

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A non‐native C‐terminal extension of the β’ subunit compromises RNA polymerase and Rho functions

Mittermeier

Wang

Said

et al. 2022

Molecular Microbiology

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Escherichia coli RfaH abrogates Rho‐mediated polarity in lipopolysaccharide core biosynthesis operons, and ΔrfaH cells are hypersensitive to antibiotics, bile salts, and detergents. Selection for rfaH suppressors that restore growth on SDS identified a temperature‐sensitive mutant in which 46 C‐terminal residues of the RNA polymerase (RNAP) β’ subunit are replaced with 23 residues carrying a net positive charge. Based on similarity to rpoC397, which confers a temperature‐sensitive phenotype and resistance to bacteriophages, we named this mutant rpoC397*. We show that SDS resistance depends on a single nonpolar residue within the C397* tail, whereas basic residues are dispensable. In line with its mimicry of RfaH, C397* RNAP is resistant to Rho but responds to pause signals, NusA, and NusG in vitro similarly to the wild‐type enzyme and binds to Rho and Nus factors in vivo. Strikingly, the deletion of rpoZ, which encodes the ω “chaperone” subunit, restores rpoC397* growth at 42°C but has no effect on SDS sensitivity. Our results suggest that the C397* tail traps the ω subunit in an inhibitory state through direct contacts and hinders Rho‐dependent termination through long‐range interactions. We propose that the dynamic and hypervariable β’•ω module controls RNA synthesis in response to niche‐specific signals.

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Section: Resultssupporting

confidence: 85%

Section: Resultsmentioning

confidence: 58%

A non‐native C‐terminal extension of the β’ subunit compromises RNA polymerase and Rho functions

Mittermeier

Wang

Said

et al. 2022

Molecular Microbiology

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“…In contrast, the rpoZ gene product, encoding the omega subunit of the RNA polymerase, is upregulated in all three bacterial species. Omega is the only nonessential subunit of RNA polymerase, yet it has an important regulatory function, including in stress responses [ 62 ], thus its overrepresentation may illustrate the cell’s ability to combat stress that relates to osmotic challenges.…”

Section: Resultsmentioning

confidence: 99%

Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach

Kłoska

Cech

Nowicki

et al. 2022

IJMS

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Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.

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“…The largest subunit, β′, houses the active site that catalyzes RNA synthesis. The ω subunit promotes RNA polymerase activity in other bacteria (Mathew and Chatterji, 2006;Kurkela et al, 2020); however, its role in the B. burgdorferi RNA polymerase has yet to be characterized.…”

Section: Rna Polymerasementioning

confidence: 99%

Gene Regulation and Transcriptomics

Samuels¹,

Lybecker²,

Yang³

et al. 2022

Current Issues in Molecular Biology

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Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma (σ) factor cascade, the Hk1/Rrp1 twocomponent system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or finetuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by highthroughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each. caister.com/cimb 223 Curr. Issues Mol. Biol. Vol. 42 Curr. Issues Mol. Biol. 42: 223-266. caister.com/cimb Gene Regulation and Transcriptomics Samuels et al.Figure 2. A model of the RpoN-RpoS σ factor cascade. During tick feeding and mammalian infection, environmental and host signals activate the RpoN-RpoS σ factor cascade. Activation of RpoN requires phosphorylation of Rrp2 and accumulation of BosR. Rrp2 is the sole prokaryotic enhancer-binding protein present in B. burgdorferi that is required for RpoN (σ 54 ) activation. Phosphorylation of Rrp2 not only is required for RpoN-RpoS activation, but also is indispensable for cell survival, presumably replication. Levels of BosR respond to environmental signals and accumulation of BosR activates rpoS at its RpoN-dependent promoter via an unknown mechanism. BadR represses rpoS transcription by directly binding near the RpoN-dependent promoter region. In addition to the major rpoS mRNA species transcribed from the RpoN-dependent promoter, a longer rpoS transcript is produced at low cell density from an RpoN-independent promoter located within the upstream flgJ gene. The sRNA DsrABb regulates the efficiency of long rpoS mRNA species translation in response to temperature. DDB18 can regulate RpoS (σ S ) levels at the post-transcriptional level. Accumulation of rpoS transcript leads to the production of OspC, DbpA, DbpB, BBK32, and other mammalian infection-associated proteins.

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Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase

Cited by 17 publications

References 90 publications

A non‐native C‐terminal extension of the β’ subunit compromises RNA polymerase and Rho functions

A non‐native C‐terminal extension of the β’ subunit compromises RNA polymerase and Rho functions

Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach

Gene Regulation and Transcriptomics

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