The bacterial enhancer-dependent RNA polymerase

Zhang, Nan; Darbari, Vidya C.; Glyde, R.; Zhang, Xiaodong; Buck, Martin

doi:10.1042/bcj20160741c

Cited by 41 publications

(29 citation statements)

References 70 publications

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“…In EBPs, this module is attached to a helix-turn-helix (HTH) motif that secures DNA-binding specificity. Finally, most EBPs have a hypervariable additional signal-reception domain that ultimately triggers the whole transcription initiation process (Zhang et al, 2016).…”

Section: Networking: Sigma54-dependent Promoters and Cognate Transcrimentioning

confidence: 99%

“…As mentioned above, many of the features found in r 54 -dependent systems might be conserved in all three domains of life, specifically in eukaryotic promoters dependent on RNAP II. In terms of evolution, ancestors of r 54 domains may have been part of an early transcription repression system meant to keep the RNAP in check, even acting globally and in trans to genes before the RpoN domain was co-opted for promoter-specific binding and specific gene expression (Zhang et al, 2016). In these, TFs bind DNA sequences that are also distant from the promoter and DNA looping allows the activator to contact the sigma factor.…”

Section: Networking: Sigma54-dependent Promoters and Cognate Transcrimentioning

confidence: 99%

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Omnipresent Maxwell's demons orchestrate information management in living cells

Boël

Danot

Lorenzo

et al. 2019

Microbial Biotechnology

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Summary The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information‐managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy‐efficient way that is vastly better than our contemporary computers.

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Section: Networking: Sigma54-dependent Promoters and Cognate Transcrimentioning

confidence: 99%

Section: Networking: Sigma54-dependent Promoters and Cognate Transcrimentioning

confidence: 99%

Omnipresent Maxwell's demons orchestrate information management in living cells

Boël

Danot

Lorenzo

et al. 2019

Microbial Biotechnology

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“…In the AA strain, mutation of this gene causes a serine to phenylalanine substitution at position 366. The σ 54 transcriptional factor has already been well described in several bacterial species and contains three major domains (12) (Fig. 2a).…”

Section: Resultsmentioning

confidence: 94%

σ⁵⁴ (σ^L) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii

Hocq

Bouilloux-Lafont

Ferreira

et al. 2018

Preprint

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9Microbial production of butanol and isopropanol, two high value-added chemicals, is 10 naturally occurring in the solventogenic Clostridium beijerinckii DSM 6423. Despite its 11 ancient discovery, the precise mechanisms controlling alcohol synthesis in this 12 microorganism are poorly understood. In this work, an allyl alcohol tolerant strain 13 obtained by random mutagenesis was characterized. This strain, designated as the AA 14 mutant, shows a dominant production of acids, a severely diminished butanol synthesis 15 capacity, and produces acetone instead of isopropanol. Interestingly, this solvent-16 deficient strain was also found to have a limited consumption of two carbohydrates and 17 to be still able to form spores, highlighting its particular phenotype. Sequencing of the 18 AA mutant revealed point mutations in several genes including CIBE_0767 (sigL), which 19 encodes the σ 54 sigma factor. Complementation with the wild-type sigL gene fully 20 restored solvent production and sugar assimilation, demonstrating that σ 54 plays a 21 central role in regulating these pathways in C. beijerinckii DSM 6423. Genomic 22 comparison with other strains further revealed that these functions are probably 23 conserved among the C. beijerinckii strains. The importance of σ 54 in C. beijerinckii was 24 further assessed by the characterization of a sigL deletion mutant of the model strain 25 NCIMB 8052 obtained with a CRISPR/Cas9 tool. The resulting mutant exhibited 26 phenotypic traits similar to the AA strain, and was subsequently complemented with the 27 sigL gene from either the wild type or the AA strains. The results of this experiment 28 confirmed the crucial role of σ 54 in the regulation of both solventogenesis and sugar 29 consumption pathways in C. beijerinckii. 30 3 Importance 31Clostridium beijerinckii shows a significant potential for producing valuable biochemicals 32 and biofuels. One of the major hurdles impeding its widespread usage is its low 33 endogenous production of alcohols, which could be alleviated by metabolic engineering 34 approaches. Despite its former long-time use in the industrial acetone-butanol-ethanol 35 process, the molecular mechanisms controlling solventogenesis in the Clostridium 36 genus still remain elusive, preventing genetic engineering approaches for strain 37 enhancement. In this context, our study provides novel insights into the crucial role of 38 the σ 54 transcriptional factor in solvent synthesis regulation in two C. beijerinckii strains. 39Furthermore, we show that this sigma factor also controls sugar consumption and is 40 therefore a key controller of carbon metabolism in this species. 41 42 80 highly conserved DNA-binding region of the encoded protein. We hypothesize that this 81 mutation results in the loss of nucleic acid binding capacity and thus impedes 82 transcription of the σ 54 regulon. According to in silico analyses, this regulon is apparently 83 conserved in other C. beijerinckii strains. To confirm this hypothesis, sigL (Cbei_0595) 84was deleted in the acet...

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“…Unlike in many other bacteria cyanobacteria do not contain σ 54 type σ factors. These σ factors are not close homologs of σ 70 factors, and RNAP holoenzymes bearing σ 54 type σ factors require an activator protein and ATP to proceed from close to open promoter conformation during transcription initiation (Zhang et al ).…”

Section: Cyanobacterial Transcription Machinerymentioning

confidence: 99%

Harnessing transcription for bioproduction in cyanobacteria

Stensjö

Vavitsas

Tyystjärvi

2017

Physiologia Plantarum

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Sustainable production of biofuels and other valuable compounds is one of our future challenges. One tempting possibility is to use photosynthetic cyanobacteria as production factories. Currently, tools for genetic engineering of cyanobacteria are not good enough to exploit the full potential of cyanobacteria. A wide variety of expression systems will be required to adjust both the expression of heterologous enzyme(s) and metabolic routes to the best possible balance, allowing the optimal production of a particular substance. In bacteria, transcription, especially the initiation of transcription, has a central role in adjusting gene expression and thus also metabolic fluxes of cells according to environmental cues. Here we summarize the recent progress in developing tools for efficient cyanofactories, focusing especially on transcriptional regulation.

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The bacterial enhancer-dependent RNA polymerase

Cited by 41 publications

References 70 publications

Omnipresent Maxwell's demons orchestrate information management in living cells

Omnipresent Maxwell's demons orchestrate information management in living cells

σ⁵⁴ (σ^L) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii

Harnessing transcription for bioproduction in cyanobacteria

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The bacterial enhancer-dependent RNA polymerase

Cited by 41 publications

References 70 publications

Omnipresent Maxwell's demons orchestrate information management in living cells

Omnipresent Maxwell's demons orchestrate information management in living cells

σ54 (σL) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii

Harnessing transcription for bioproduction in cyanobacteria

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Resources

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σ⁵⁴ (σ^L) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii