Global repositioning of transcription start sites in a plant-fermenting bacterium

Boutard, Magali; Ettwiller, Laurence; Cerisy, Tristan; Alberti, Adriana; Labadie, Karine; Salanoubat, Marcel; Schildkraut, Ira; Tolonen, Andrew C.

doi:10.1038/ncomms13783

Cited by 26 publications

(31 citation statements)

References 51 publications

(63 reference statements)

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“…Assimilation of galacturonic acid to pyruvate yields only 1 ATP (Fig. 7), and concomitantly, the primary fermentation product shifts to acetate (18), which boosts ATP production by 2 ATPs per sugar equivalent. C. phytofermentans can likely produce additional ATP using the F 1 F 0 -ATPase (Cphy3735-Cphy3742) to harness the ion gradient generated by the Rnf complex (Cphy0211-Cphy0216), which couples ferredoxin oxidation to NAD ϩ reduction to pump Na ϩ or H ϩ outside the cell (Fig.…”

Section: Discussionmentioning

confidence: 99%

ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans

et al. 2019

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The mechanisms by which bacteria uptake solutes across the cell membrane broadly impact their cellular energetics. Here, we use functional genomic, genetic, and biophysical approaches to reveal how Clostridium (Lachnoclostridium) phytofermentans, a model bacterium that ferments lignocellulosic biomass, uptakes plant hexoses using highly specific, nonredundant ATP-binding cassette (ABC) transporters. We analyze the transcription patterns of its 173 annotated sugar transporter genes to find those upregulated on specific carbon sources. Inactivation of these genes reveals that individual ABC transporters are required for uptake of hexoses and hexo-oligosaccharides and that distinct ABC transporters are used for oligosaccharides versus their constituent monomers. The thermodynamics of sugar binding shows that substrate specificity of these transporters is encoded by the extracellular solute-binding subunit. As sugars are not phosphorylated during ABC transport, we identify intracellular hexokinases based on in vitro activities. These mechanisms used by Clostridia to uptake plant hexoses are key to understanding soil and intestinal microbiomes and to engineer strains for industrial transformation of lignocellulose. IMPORTANCE Plant-fermenting Clostridia are anaerobic bacteria that recycle plant matter in soil and promote human health by fermenting dietary fiber in the intestine. Clostridia degrade plant biomass using extracellular enzymes and then uptake the liberated sugars for fermentation. The main sugars in plant biomass are hexoses, and here, we identify how hexoses are taken in to the cell by the model organism Clostridium phytofermentans. We show that this bacterium uptakes hexoses using a set of highly specific, nonredundant ABC transporters. Once in the cell, the hexoses are phosphorylated by intracellular hexokinases. This study provides insight into the functioning of abundant members of soil and intestinal microbiomes and identifies gene targets to engineer strains for industrial lignocellulosic fermentation.

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Section: Discussionmentioning

confidence: 99%

ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans

et al. 2019

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“…PFOR and cytochrome c) likely regulate transcription and/or translation of their downstream genes and operons (Figure 6). Analysis of transcription start sites (TSS) in Clostridium phytofermentans have shown that the TSS of one pfor gene occurs 78 bp upstream of its start codon (45), a length similar to the putative TSS of the pfor operons in Leptospirillum sp. (Figure 6), while transcripts with long 5’ UTRs encoding putative ncRNAs and uORFs have been reported in Haloferax volcanii (46) and in Mycobacterium sp.…”

Section: Discussionmentioning

confidence: 99%

Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms

Goltsman

Hauser

Dasari

et al. 2019

Preprint

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“…We have developed ReCappable-seq ( Figure 1a) to comprehensively identify TSS of all eukaryotic genes transcribed by Pol-I, Pol-II, Pol-III and POLRMT RNA polymerases. We used the Vaccinia Capping Enzyme (VCE) which can add a biotinylated G-cap structure to either a 5' triphosphate or 5' diphosphate RNA and has been used previously to identify TSS and primary transcripts in prokaryotes [9] [12] [13]. In eukaryotes the 5' ends of transcripts derived from Pol-II are capped and therefore cannot be directly biotinylated with VCE.…”

Section: Recappable-seqmentioning

confidence: 99%

ReCappable Seq: Comprehensive Determination of Transcription Start Sites derived from all RNA polymerases

Yan

Tzertzinis

Schildkraut

et al. 2019

Preprint

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Methodologies for determining eukaryotic Transcription Start Sites (TSS) rely on the selection of the 5’ canonical cap structure of Pol-II transcripts and are consequently ignoring entire classes of TSS derived from other RNA polymerases which play critical roles in various cell functions. To overcome this limitation, we developed ReCappable-seq and identified TSS from Pol-ll and non-Pol-II transcripts at nucleotide resolution. Applied to the human transcriptome, ReCappable-seq identifies Pol-II TSS with higher specificity than CAGE and reveals a rich landscape of TSS associated notably with Pol-III transcripts which have been previously not possible to study on a genome-wide scale. Novel TSS consistent with non-Pol-II transcripts can be found in the nuclear and mitochondrial genomes. By identifying TSS derived from all RNA-polymerases, ReCappable-seq reveals distinct epigenetic marks among Pol-lI and non-Pol-II TSS and provides a unique opportunity to concurrently interrogate the regulatory landscape of coding and non-coding RNA.

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Global repositioning of transcription start sites in a plant-fermenting bacterium

Cited by 26 publications

References 51 publications

ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans

ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans

Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms

ReCappable Seq: Comprehensive Determination of Transcription Start Sites derived from all RNA polymerases

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