A Small RNA, UdsC, Interacts with the RpoHII mRNA and Affects the Motility and Stress Resistance of Rhodobacter sphaeroides

Spanka, Daniel-Timon; Grützner, Julian; Jäger, Andreas; Klug, Gabriele

doi:10.3390/ijms232415486

Cited by 3 publications

(2 citation statements)

References 49 publications

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“…E.g. sRNAs were shown to make important contributions to the regulated formation of the photosynthetic apparatus and to regulation of stress responses in R. sphaeroides ( Mank et al, 2012 ; Adnan et al, 2015 ; Billenkamp et al, 2015 ; Müller et al, 2016 ; Peng et al, 2016 ; Eisenhardt et al, 2018 , 2021 ; Reuscher and Klug, 2021 ; Spanka et al, 2022 ). Many sRNAs were detected in the R. capsulatus transcriptome ( Licht et al, 2020 ), which are still awaiting functional characterization.…”

Section: Resultsmentioning

confidence: 99%

Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus

Kretz,

Börner,

Friedrich

et al. 2024

Front. Microbiol.

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Bacteria use CRISPR Cas systems to defend against invading foreign nucleic acids, e.g., phage genomes, plasmids or mobile genetic elements. Some CRISPR Cas systems were reported to have physiological importance under a variety of abiotic stress conditions. We used physiological tests under different stress conditions and RNA-seq analyses to address the possible function of the RNA-targeting class 2 type VI CRISPR Cas system of the facultative phototrophic α-proteobacterium Rhodobacter capsulatus. Expression of the system was low under exponential non-stress conditions and high during oxidative stress, membrane stress and in stationary phase. Induction of the CRISPR Cas system in presence of a target protospacer RNA resulted in a growth arrest of R. capsulatus. RNA-seq revealed a strong alteration of the R. capsulatus transcriptome when cas13a was induced in presence of a target protospacer. RNA 5′ end mapping indicated that the CRISPR Cas-dependent transcriptome remodeling is accompanied by fragmentation of cellular RNAs, e.g., for mRNAs originating from a genomic locus which encodes multiple ribosomal proteins and the RNA polymerase subunits RpoA, RpoB and RpoC. The data suggest a function of this CRISPR Cas system in regulated growth arrest, which may prevent the spread of phages within the population.

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Section: Resultsmentioning

confidence: 99%

Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus

Kretz,

Börner,

Friedrich

et al. 2024

Front. Microbiol.

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“…For instance, the wild-type lac promoter from E. coli is reported to function poorly in R. sphaeroides (26). While no inducible promoters have been examined in N. aromaticivorans to our knowledge, promoters inducible by light, oxygen, crystal violet, and IPTG have been tested in R. sphaeroides (26)(27)(28)(29). Although these foreign promoters can respond to an array of possible inducers, some inducers inhibit R. sphaeroides growth (crystal violet) (26) or substantially alter physiological processes of interest (light, oxygen).…”

Section: Introductionmentioning

confidence: 99%

Tools for Genetic Engineering and Gene Expression Control inNovosphingobium aromaticivoransandRhodobacter sphaeroides

Hall,

Kinney

et al. 2023

Preprint

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Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts have the potential to form the backbone of the sustainable bioeconomy. Among the Alphaproteobacteria,Novosphingobium aromaticivorans,Rhodobacter sphaeroides, andZymomonas mobilis, show particular promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit forZ. mobilis,N. aromaticivoransandR. sphaeroidesstill need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools forN. aromaticivoransandR. sphaeroidesto address these issues. We demonstrate that Tn7transposition is an effective approach for introducing engineered DNA into the chromosome ofN. aromaticivoransandR. sphaeroides. We screen a synthetic promoter library to identify inducible promoters with strong, regulated activity in both organisms. Combining Tn7integration with promoters from our library, we establish CRISPR interference systems forN. aromaticivoransandR. sphaeroidesthat can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these industrially important species and other Alphaproteobacteria.IMPORTANCEIt is important to increase our understanding of the microbial world to improve health, agriculture, the environment and biotechnology. For example, building a sustainable bioeconomy depends on the efficient conversion of plant material to valuable biofuels and bioproducts by microbes. One limitation in this conversion process is that microbes with otherwise excellent properties for conversion are challenging to genetically engineer. Here, we report systems to overcome that barrier in the Alphaproteobacteria,Novosphingobium aromaticivoransandRhodobacter sphaeroides, by producing genetic tools that allow easy insertion of engineered pathways into their genomes and to precisely control gene expression by inducing genes with synthetic promoters or repressing genes using CRISPR interference. These tools can be used in future work to gain additional insight into these and other Alphaproteobacteria and to optimize yield of biofuels and bioproducts.

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sRNA molecules participate in hyperosmotic stress response regulation in Sphingomonas melonis TY

Wang,

Wang

et al. 2024

Appl Environ Microbiol

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Drought and salinity are ubiquitous environmental factors that pose hyperosmotic threats to microorganisms and impair their efficiency in performing environmental functions. However, bacteria have developed various responses and regulatory systems to cope with these abiotic challenges. Posttranscriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions can lead to the induction of specific small RNA molecules (sRNAs) that participate in stress response regulation. Here, we report a candidate functional sRNA landscape of Sphingomonas melonis TY under hyperosmotic stress, and 18 sRNAs were found with a clear response to hyperosmotic stress. These findings will help in the comprehensive analysis of sRNA regulation in Sphingomonas species. Weighted correlation network analysis revealed a 263 nucleotide sRNA, SNC251, which was transcribed from its own promoter and showed the most significant correlation with hyperosmotic response factors. Deletion of snc251 affected biofilm formation and multiple cellular processes, including ribosome-related pathways, aromatic compound degradation, and the nicotine degradation capacity of S. melonis TY, while overexpression of SNC251 facilitated biofilm formation by TY under hyperosmotic stress. Two genes involved in the TonB system were further verified to be activated by SNC251, which also indicated that SNC251 is a trans -acting sRNA. Briefly, this research reports a landscape of sRNAs participating in the hyperosmotic stress response in S. melonis and reveals a novel sRNA, SNC251, which contributes to the S. melonis TY biofilm formation and thus enhances its hyperosmotic stress response ability. IMPORTANCE Sphingomonas species play a vital role in plant defense and pollutant degradation and survive extensively under drought or salinity. Previous studies have focused on the transcriptional and translational responses of Sphingomonas under hyperosmotic stress, but the posttranscriptional regulation of small RNA molecules (sRNAs) is also crucial for quickly modulating cellular processes to adapt dynamically to osmotic environments. In addition, the current knowledge of sRNAs in Sphingomonas is extremely scarce. This research revealed a novel sRNA landscape of Sphingomonas melonis and will greatly enhance our understanding of sRNAs’ acting mechanisms in the hyperosmotic stress response.

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A Small RNA, UdsC, Interacts with the RpoHII mRNA and Affects the Motility and Stress Resistance of Rhodobacter sphaeroides

Cited by 3 publications

References 49 publications

Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus

Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus

Tools for Genetic Engineering and Gene Expression Control inNovosphingobium aromaticivoransandRhodobacter sphaeroides

sRNA molecules participate in hyperosmotic stress response regulation in Sphingomonas melonis TY

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