Mesoplasma florum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA35297 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12068546.fastq.gz | Fastqsanger.gz | |||
| SRR12068547_1.fastq.gz | Fastqsanger.gz | |||
| SRR12068547_2.fastq.gz | Fastqsanger.gz | |||
| SRR12068548_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Mesoplasma florum is a small-genome fast-growing mollicute that is an attractive model for systems and synthetic genomics studies. We report the complete 825,824-bp genome sequence of a second representative of this species, M. florum strain W37, which contains 733 predicted open reading frames and 35 stable RNAs.
| S-EPMC3869320 | biostudies-literature
Project description:The near-minimal bacterium Mesoplasma florum is an interesting model for synthetic genomics and systems biology due to its small genome (~ 800 kb), fast growth rate, and lack of pathogenic potential. However, fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. We investigated several physical and physiological parameters of this bacterium, including cell size, growth kinetics, and biomass composition of the cell. We also performed the first genome-wide analysis of its transcriptome and proteome, notably revealing a conserved promoter motif, the organization of transcription units, and the transcription and protein expression levels of all protein-coding sequences. We converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts provide a strong experimental foundation for the development of a genome-scale model for M. florum and will guide future genome engineering endeavors in this simple organism.
| S-EPMC7745072 | biostudies-literature
Project description:The near-minimal bacterium Mesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. However, the lack of genetic engineering tools for this microorganism has limited our capacity to understand its basic biology and modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first generation of artificial plasmids able to replicate in this bacterium. Selected regions of the predicted M. florum chromosomal origin of replication (oriC) were used to create different plasmid versions that were tested for their transformation frequency and stability. Using polyethylene glycol-mediated transformation, we observed that plasmids harboring both rpmH-dnaA and dnaA-dnaN intergenic regions, interspaced or not with a copy of the dnaA gene, resulted in a frequency of ∼4.1 × 10-6 transformants per viable cell and were stably maintained throughout multiple generations. In contrast, plasmids containing only one M. florumoriC intergenic region or the heterologous oriC region of Mycoplasma capricolum, Mycoplasma mycoides, or Spiroplasma citri failed to produce any detectable transformants. We also developed alternative transformation procedures based on electroporation and conjugation from Escherichia coli, reaching frequencies up to 7.87 × 10-6 and 8.44 × 10-7 transformants per viable cell, respectively. Finally, we demonstrated the functionality of antibiotic resistance genes active against tetracycline, puromycin, and spectinomycin/streptomycin in M. florum Taken together, these valuable genetic tools will facilitate efforts toward building an M. florum-based near-minimal cellular chassis for synthetic biology.IMPORTANCEMesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. M. florum is closely related to the mycoides cluster of mycoplasmas, which has become a model for whole-genome cloning, genome transplantation, and genome minimization. However, M. florum shows higher growth rates than other Mollicutes, has no known pathogenic potential, and possesses a significantly smaller genome that positions this species among some of the simplest free-living organisms. So far, the lack of genetic engineering tools has limited our capacity to understand the basic biology of M. florum in order to modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first artificial plasmids and transformation methods for this bacterium. This represents a strong basis for ongoing genome engineering efforts using this near-minimal microorganism.
| S-EPMC5359490 | biostudies-literature
Project description:Mesoplasma florum Genome sequencing and assembly
| PRJNA412852 | ENA
Project description:The near-minimal bacterium Mesoplasma florum constitutes an interesting model for synthetic genomics and systems biology studies due to its small genome, fast growth rate, and lack of pathogenic potential. However, some fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. More specifically, we investigated several physical and physiological aspects of this bacterium, and performed the first genome-wide analysis of its transcriptome and proteome using RNA sequencing techniques and two-dimensional liquid chromatography-tandem mass spectrometry. These analyses notably revealed the M. florum consensus promoter, a first experimental cartography of transcription units, as well as the transcription and expression levels of all annotated genes. We also converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts will provide an experimental foundation for the development of a genome-scale metabolic model for M. florum and will guide future genome engineering endeavours in this simple organism.
2020-11-16 | PXD019922 | Pride
Project description:The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species? On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal genomes could help reveal different gene compositions and strategies that can support life, even within closely related species.
| S-EPMC5893858 | biostudies-literature
Project description:Mesoplasma florum W37 Genome sequencing
| PRJNA222289 | ENA
Project description:Mesoplasma florum is a near-minimal bacterium belonging to the Mollicutes class particularly characterized by its small genome, fast growth rate, and lack of pathogenic potential. Here, we report the first genome-wide transcriptomic analysis of this microorganism using directional RNA sequencing (RNA-Seq) and 5'-rapid amplification of cDNA ends (5'-RACE). 5'-RACE sequencing reads were used to identify 605 putative transcription start sites (TSSs), of which more than 400 could be associated to a conserved promoter sequence. Along with terminator predictions, these TSSs allowed the reconstruction of M. florum transcription units, covering more than 90% of annotated genes. We evaluated the expression level of all M. florum protein coding genes using paired-end RNA-Seq reads according to the number of fragments per kilobase per million of mapped reads (FPKM). FPKM values were converted to absolute transcript abundances using biomass quantification data. These efforts aim at reaching a deep understanding of global cellular mechanisms in M. florum and will guide future genome engineering projects in this simple organism.
2020-11-02 | GSE152985 | GEO
Project description:Mesoplasma florum rep-seq raw sequence reads
| PRJNA285998 | ENA
Project description:Mutation-accumulation Lines of Mesoplasma florum L1
| PRJNA256337 | ENA