Ribonuclease E strongly impacts bacterial adaptation to different growth conditions

Börner, Janek; Friedrich, Tobias; Bartkuhn, Marek; Klug, Gabriele

doi:10.1080/15476286.2023.2195733

Cited by 9 publications

(8 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The RNA-Seq data processing was performed as described in Börner et al [23]. The alignment of the raw sequencing reads against the reference genome of R. sphaeroides (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) was performed using the READemption pipeline v.1.0.5 [45].…”

Section: Rna-seq Data Processingmentioning

confidence: 99%

“…com/article/10.3390/ijms24119515/s1. References [12,17,[23][24][25]41,[47][48][49] are cited in the supplementary materials Tables S1 and S2.…”

Section: Institutional Review Board Statement: Not Applicablementioning

confidence: 99%

“…The RIP-Seq analysis (CoIP) data are listed in GSE145045 [24] and in GSE230031. The RNA sequencing of the total RNA is listed in GSE200990 [23].…”

Section: Institutional Review Board Statement: Not Applicablementioning

confidence: 99%

“…In addition, a remarkable strong effect of the endoribonuclease RNase E on phototrophic but not on chemotrophic growth was observed [22]. RNase E was shown to differentially affect the stability of mRNAs for the important regulators AppA and PrrB under microaerobic and phototrophic growth conditions [23].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides

Grützner

Börner

Jäger

et al. 2023

IJMS

Self Cite

View full text Add to dashboard Cite

In natural habitats, bacteria frequently need to adapt to changing environmental conditions. Regulation of transcription plays an important role in this process. However, riboregulation also contributes substantially to adaptation. Riboregulation often acts at the level of mRNA stability, which is determined by sRNAs, RNases, and RNA-binding proteins. We previously identified the small RNA-binding protein CcaF1, which is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides. Rhodobacter is a facultative phototroph that can perform aerobic and anaerobic respiration, fermentation, and anoxygenic photosynthesis. Oxygen concentration and light conditions decide the pathway for ATP production. Here, we show that CcaF1 promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins. Levels of mRNAs for transcriptional regulators of photosynthesis genes are not affected by CcaF1. RIP-Seq analysis compares the binding of CcaF1 to RNAs during microaerobic and photosynthetic growth. The stability of the pufBA mRNA for proteins of the light-harvesting I complex is increased by CcaF1 during phototrophic growth but decreased during microaerobic growth. This research underlines the importance of RNA-binding proteins in adaptation to different environments and demonstrates that an RNA-binding protein can differentially affect its binding partners in dependence upon growth conditions.

show abstract

Section: Rna-seq Data Processingmentioning

confidence: 99%

“…com/article/10.3390/ijms24119515/s1. References [12,17,[23][24][25]41,[47][48][49] are cited in the supplementary materials Tables S1 and S2.…”

Section: Institutional Review Board Statement: Not Applicablementioning

confidence: 99%

“…The RIP-Seq analysis (CoIP) data are listed in GSE145045 [24] and in GSE230031. The RNA sequencing of the total RNA is listed in GSE200990 [23].…”

Section: Institutional Review Board Statement: Not Applicablementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides

Grützner

Börner

Jäger

et al. 2023

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although RNAseE has broad substrate specificity, various sequence features have been shown to increase its relative specific activity on individual mRNA species, including unstructured AU rich regions, and, most critically, the presence of a 5′-monophosphate (Bae et al, 2023;Callaghan et al, 2005;Richards & Belasco, 2023). However, other molecule-specific features, such as RNA-binding protein binding sites, codon usage, and secondary structure profiles can reduce RNAse E mediated turnover of endogenous mRNA (Börner et al, 2023;Roux et al, 2022). For protein production in E. coli, recombinant mRNA stability is commonly enhanced by using bacterial 5′ untranslated regions (UTRs) containing secondary structures that prevent RNAse binding (Viegas et al, 2018), however, these elements are incompatible with manufacture of synthetic mRNA for mammalian cell applications.…”

mentioning

confidence: 99%

Engineering an Escherichia coli based in vivo mRNA manufacturing platform

Curry,

Muir,

et al. 2024

Biotech & Bioengineering

View full text Add to dashboard Cite

Synthetic mRNA is currently produced in standardized in vitro transcription systems. However, this one‐size‐fits‐all approach has associated drawbacks in supply chain shortages, high reagent costs, complex product‐related impurity profiles, and limited design options for molecule‐specific optimization of product yield and quality. Herein, we describe for the first time development of an in vivo mRNA manufacturing platform, utilizing an Escherichia coli cell chassis. Coordinated mRNA, DNA, cell and media engineering, primarily focussed on disrupting interactions between synthetic mRNA molecules and host cell RNA degradation machinery, increased product yields >40‐fold compared to standard “unengineered” E. coli expression systems. Mechanistic dissection of cell factory performance showed that product mRNA accumulation levels approached theoretical limits, accounting for ~30% of intracellular total RNA mass, and that this was achieved via host‐cell's reallocating biosynthetic capacity away from endogenous RNA and cell biomass generation activities. We demonstrate that varying sized functional mRNA molecules can be produced in this system and subsequently purified. Accordingly, this study introduces a new mRNA production technology, expanding the solution space available for mRNA manufacturing.

show abstract

A comparative analysis of mycobacterial ribonucleases: Towards a therapeutic novel drug target

Jaiswal,

Singh,

Nayak

et al. 2024

Infection, Genetics and Evolution

View full text Add to dashboard Cite

Ribonuclease E strongly impacts bacterial adaptation to different growth conditions

Cited by 9 publications

References 80 publications

The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides

The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides

Engineering an Escherichia coli based in vivo mRNA manufacturing platform

A comparative analysis of mycobacterial ribonucleases: Towards a therapeutic novel drug target

Contact Info

Product

Resources

About