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Cited by 16Microbial Metabolic Engineering and BioproductionBacterial Genetics and BiotechnologyGene Regulatory Network Analysis

Integrative characterization of the near‐minimal bacterium Mesoplasma florum

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Matteau, Dominick, Lachance, Jean‐Christophe, Grenier, Frédéric, Gauthier, Samuel, Daubenspeck, James M, Dybvig, Kevin, Garneau, Daniel, Knight, Thomas F +2 more·2020·Molecular Systems Biology
DOI 10.15252/msb.20209844PMC PMC7745072
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Abstract

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.

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  • The discrepancy in spherical cell size is consistent with observations for similar organisms, where cell sizes can vary by hundreds of nanometers depending on the imaging method and sample preparation.

    “but this discrepancy is consistent with observations for similar organisms, where cell sizes can vary by hundreds of nanometers depending on the imaging method and sample preparation.35”

    From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [35]

  • Gene /0412 is a putative secDF protein export enhancing membrane component.

    “we have further support to annotate /0412 as a putative secDF protein export enhancing membrane component.”

    From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [34]

    The Results section on protein expression describes M. florum gene annotations generally, but does not identify /0412 as SecDF or assign it a protein-export function. Searches for “secDF,” “mfl412,” and protein-export membrane components found no passage addressing that annotation in our copy; page numbers were not available. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • Each of the SecD and SecF regions contains conserved sequence motifs observed across a variety of organisms.

    “Each of these two regions contains conserved sequence motifs that have been observed for both SecD and SecF across a variety of organisms,81 that previously supported the putative assignment of the analogous gene in M. florum L1 as secDF-like.34”

    From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [34]

    The Results section on genome-wide identification of promoters discusses conserved promoter motifs, not sequence motifs in SecD or SecF. Searches of our copy for SecD, SecF, secDF-like, and the putative M. florum gene assignment found no passage addressing either point. In the citing sentence, the motif claim is attached to citation 81, while this source is cited for the gene assignment. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • Gene /0412 is secDF, a protein translocase subunit involved in cell membrane.

    “secDF/0412 | cell membrane | protein translocase subunit”

    From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [34]

    The Results section’s overview of expressed cellular functions lists a membrane-transport category and a secretion-system category, but does not identify secDF or gene /0412. Searches for “secDF,” “0412,” and “protein translocase” found no passage in our copy establishing the claimed gene identity, function, or membrane association. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

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Authors
Matteau, D., Lachance, J., Grenier, F., Gauthier, S., Daubenspeck, J. M., Dybvig, K., Garneau, D., Knight, T. F., Jacques, P., & Rodrigue, S.
Affiliations
  • Université de Sherbrooke (CA)
  • University of Alabama at Birmingham (US)
  • Ginkgo Bioworks, Inc. (United States) (US)
Corresponding author
Rodrigue, Sébastien
ORCID
Venue
Molecular Systems Biology
Publisher
Springer Science and Business Media LLC
Published
2020-12-01
Volume
16
Issue
12
Pages
e9844-e9844
ISSN
1744-4292 (ISSN-L)
DOI
10.15252/msb.20209844
PMC
PMC7745072
OpenAlex
W3112226911
Cited by
16
References
168
Citations by year
2026: 2 · 2025: 3 · 2024: 3 · 2022: 3 · 2021: 4 · 2020: 1
FWCI
0.65
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Systems Biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Fonds de recherche du Québec – Nature et technologies (PR‐173580)
  • Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (386393)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
Mesoplasma florum, synthetic genomics, genome-scale metabolic models, genome-wide transcriptome, promoter elements, gene expression levels, cell size, growth kinetics, genome editing
MeSH terms
Base Sequence, Kinetics, Nucleic Acids, Promoter Regions, Genetic, Ribosomes, Temperature, Transcription, Genetic, Gene Expression Regulation, Bacterial, Open Reading Frames, Genome, Bacterial, Biomass, Transcription Initiation Site, Intracellular Space, Entomoplasmataceae, Macromolecular Substances

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