RNAseq‐based transcriptome assembly of <i>Clostridium acetobutylicum</i> for functional genome annotation and discovery

Ralston, Matthew T.; Papoutsakis, E. T.

doi:10.1002/aic.16396

Cited by 6 publications

(7 citation statements)

References 68 publications

(149 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To establish the abundance of raiA motif RNAs relative to other transcripts, we analyzed previously published C. acetobutylicum whole-transcriptome RNAseq data ( 49 ). Transcriptomics data were derived from cells collected 75 min past an OD 600 measurement of 1 and therefore represent cells at or near stationary phase.…”

Section: Resultsmentioning

confidence: 99%

Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation

Soares,

King,

Fernando

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Several structured noncoding RNAs in bacteria are essential contributors to fundamental cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities to uncover and explore biochemical mechanisms relevant to other major and potentially ancient processes. A candidate structured ncRNA named the “ raiA motif” has been found via bioinformatic analyses in over 2,500 bacterial species. The gene coding for the RNA typically resides between the raiA and comFC genes of many species of Bacillota and Actinomycetota. Structural probing of the raiA motif RNA from the Gram-positive anaerobe Clostridium acetobutylicum confirms key features of its sophisticated secondary structure model. Expression analysis of raiA motif RNA reveals that the RNA is constitutively produced but reaches peak abundance during the transition from exponential growth to stationary phase. The raiA motif RNA becomes the fourth most abundant RNA in C. acetobutylicum , excluding ribosomal RNAs and transfer RNAs. Genetic disruption of the raiA motif RNA causes cells to exhibit substantially decreased spore formation and diminished ability to aggregate. Restoration of normal cellular function in this knock-out strain is achieved by expression of a raiA motif gene from a plasmid. These results demonstrate that raiA motif RNAs normally participate in major cell differentiation processes by operating as a trans-acting factor.

show abstract

Section: Resultsmentioning

confidence: 99%

Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation

Soares,

King,

Fernando

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…This is comparable to the proposed regulation by SolB in C. acetobutylicum ( Jones et al, 2018 ). Furthermore, some reads antisense to the sol operon of C. acetobutylicum , consisting of adhE , ctfA , and ctfB , were identified by transcriptomics ( Ralston and Papoutsakis, 2018 ), but the transcript and its regulatory role were not further investigated. In addition, the authors mention over 400 possible antisense interactions for other metabolic pathways ( Ralston and Papoutsakis, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, some reads antisense to the sol operon of C. acetobutylicum , consisting of adhE , ctfA , and ctfB , were identified by transcriptomics ( Ralston and Papoutsakis, 2018 ), but the transcript and its regulatory role were not further investigated. In addition, the authors mention over 400 possible antisense interactions for other metabolic pathways ( Ralston and Papoutsakis, 2018 ). This was also found in the transcriptomic data of C. saccharoperbutylacetonicum , e.g., transcripts antisense of the butyryl-CoA synthesis operon (Cspa_c04330 to Cspa_c04370) or the pta-ack operon (Cspa_c13010 and Cspa_c13020) (data not shown).…”

Section: Discussionmentioning

confidence: 99%

Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation

et al. 2022

View full text Add to dashboard Cite

Solvents such as butanol are important platform chemicals and are often produced from petrochemical sources. Production of butanol and other compounds from renewable and sustainable resources can be achieved by solventogenic bacteria, such as the hyper-butanol producer Clostridium saccharoperbutylacetonicum. Its sol operon consists of the genes encoding butyraldehyde dehydrogenase, CoA transferase, and acetoacetate decarboxylase (bld, ctfA, ctfB, adc) and the gene products are involved in butanol and acetone formation. It is important to understand its regulation to further optimize the solvent production. In this study, a new long non-coding antisense transcript complementary to the complete sol operon, now called Assolrna, was identified by transcriptomic analysis and the regulatory mechanism of Assolrna was investigated. For this purpose, the promoter-exchange strain C. saccharoperbutylacetonicum ΔPasr::Pasr** was constructed. Additionally, Assolrna was expressed plasmid-based under control of the native Pasr promoter and the lactose-inducible PbgaL promoter in both the wild type and the promoter-exchange strain. Solvent formation was strongly decreased for all strains based on C. saccharoperbutylacetonicum ΔPasr::Pasr** and growth could not be restored by plasmid-based complementation of the exchanged promoter. Interestingly, very little sol mRNA expression was detected in the strain C. saccharoperbutylacetonicum ΔPasr::Pasr** lacking Assolrna expression. Butanol titers were further increased for the overexpression strain C. saccharoperbutylacetonicum [pMTL83151_asr_PbgaL] compared to the wild type. These results suggest that Assolrna has a positive effect on sol operon expression. Therefore, a possible stabilization mechanism of the sol mRNA by Assolrna under physiological concentrations is proposed.

show abstract

“…Most importantly 3 -UTR confer stability to the mRNA (Zhao et al, 2018). Although, there are very limited studies related to 3 -UTR regions in Clostridium, the presence of transcripts with long 3 -UTR is confirmed in Clostridium (Ralston and Papoutsakis, 2018). Although several RNAseq studies were reported in the Clostridium, only few studies show the data related to regulation of mRNA based on 5 -and 3 -UTRs, leaderless transcripts and non-coding RNA (Soutourina et al, 2013;Wilson et al, 2013;Sedlar et al, 2018).…”

Section: Synthetic Srna and Untranslated Region Engineering As Potentmentioning

confidence: 99%

Synthetic Biology Tools for Genome and Transcriptome Engineering of Solventogenic Clostridium

Kwon¹,

Paari²,

Malaviya³

et al. 2020

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

Strains of Clostridium genus are used for production of various value-added products including fuels and chemicals. Development of any commercially viable production process requires a combination of both strain and fermentation process development strategies. The strain development in Clostridium sp. could be achieved by random mutagenesis, and targeted gene alteration methods. However, strain improvement in Clostridium sp. by targeted gene alteration method was challenging due to the lack of efficient tools for genome and transcriptome engineering in this organism. Recently, various synthetic biology tools have been developed to facilitate the strain engineering of solventogenic Clostridium. In this review, we consolidated the recent advancements in toolbox development for genome and transcriptome engineering in solventogenic Clostridium. Here we reviewed the genome-engineering tools employing mobile group II intron, pyrE alleles exchange, and CRISPR/Cas9 with their application for strain development of Clostridium sp. Next, transcriptome engineering tools such as untranslated region (UTR) engineering and synthetic sRNA techniques were also discussed in context of Clostridium strain engineering. Application of any of these discussed techniques will facilitate the metabolic engineering of clostridia for development of improved strains with respect to requisite functional attributes. This might lead to the development of an economically viable butanol production process with improved titer, yield and productivity.

show abstract

RNAseq‐based transcriptome assembly of Clostridium acetobutylicum for functional genome annotation and discovery

Cited by 6 publications

References 68 publications

Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation

Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation

Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation

Synthetic Biology Tools for Genome and Transcriptome Engineering of Solventogenic Clostridium

Contact Info

Product

Resources

About