The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential

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  • Parizzi, Lucas P
    • Other Affiliation: Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas
  • Grassi, Maria Carolina B
    • Other Affiliation: Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas
  • Llerena, Luige A
    • Other Affiliation: Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas
  • Carazzolle, Marcelo F
    • Other Affiliation: Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas
  • Queiroz, Verônica L
    • Other Affiliation: Braskem S.A, CP 6192, Campinas
  • Lunardi, Inês
    • Other Affiliation: Braskem S.A, CP 6192, Campinas
  • Zeidler, Ane F
    • Other Affiliation: Braskem S.A, CP 6192, Campinas
  • Teixeira, Paulo JPL
    • Other Affiliation: Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas
  • Mieczkowski, Piotr
    • Affiliation: School of Medicine, Department of Genetics
  • Rincones, Johana
    • Other Affiliation: Braskem S.A, CP 6192, Campinas
  • Pereira, Gonçalo AG
    • Other Affiliation: Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas
Abstract
  • Background Synthetic biology allows the development of new biochemical pathways for the production of chemicals from renewable sources. One major challenge is the identification of suitable microorganisms to hold these pathways with sufficient robustness and high yield. In this work we analyzed the genome of the propionic acid producer Actinobacteria Propionibacterium acidipropionici (ATCC 4875). Results The assembled P. acidipropionici genome has 3,656,170 base pairs (bp) with 68.8% G + C content and a low-copy plasmid of 6,868 bp. We identified 3,336 protein coding genes, approximately 1000 more than P. freudenreichii and P. acnes, with an increase in the number of genes putatively involved in maintenance of genome integrity, as well as the presence of an invertase and genes putatively involved in carbon catabolite repression. In addition, we made an experimental confirmation of the ability of P. acidipropionici to fix CO2, but no phosphoenolpyruvate carboxylase coding gene was found in the genome. Instead, we identified the pyruvate carboxylase gene and confirmed the presence of the corresponding enzyme in proteome analysis as a potential candidate for this activity. Similarly, the phosphate acetyltransferase and acetate kinase genes, which are considered responsible for acetate formation, were not present in the genome. In P. acidipropionici, a similar function seems to be performed by an ADP forming acetate-CoA ligase gene and its corresponding enzyme was confirmed in the proteome analysis. Conclusions Our data shows that P. acidipropionici has several of the desired features that are required to become a platform for the production of chemical commodities: multiple pathways for efficient feedstock utilization, ability to fix CO2, robustness, and efficient production of propionic acid, a potential precursor for valuable 3-carbon compounds.
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Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Lucas P Parizzi et al.; licensee BioMed Central Ltd.
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Journal title
  • BMC Genomics
Journal volume
  • 13
Journal issue
  • 1
Page start
  • 562
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1471-2164
Bibliographic citation
  • BMC Genomics. 2012 Oct 19;13(1):562
Publisher
  • BioMed Central Ltd
Access right
  • Open Access
Date uploaded
  • January 2, 2013

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file details 1471-2164-13-562.pdf 2019-05-06 Public Download
file details Table S1. P. acidipropionici proteins identified by UPLC-ESI-Q_TOF. List of proteins identified using UPLC-ESI-Q_TOF experiments. 2019-05-06 Public Download
file details 1471-2164-13-562.xml 2019-05-06 Public Download
file details Table S2. Transporter proteins comparison. Complete list of transporter families identified by annotation with TCDB classification. 2019-05-06 Public Download
file details Table S3. PTS protein-coding genes. List of annotated genes related to phosphotransferase system in P.acidipropionici genome. 2019-05-06 Public Download
file details Figures S1 to S5. 2019-05-06 Public Download