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

Lucas P Parizzi1,2†, Maria Carolina B Grassi1,2†, Luige A Llerena1, Marcelo F Carazzolle1, Verônica L Queiroz2, Inês Lunardi2, Ane F Zeidler2, Paulo JPL Teixeira1, Piotr Mieczkowski3, Johana Rincones2 and Gonçalo AG Pereira1*

1 Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, Campinas, 13083-970, São Paulo, Brazil

2 Braskem S.A, CP 6192, Campinas, 13083-970, São Paulo, Brazil

3 Department of Genetics, School of Medicine, Carolina Center for Genome Sciences, University of North Carolina, Wilson Hall, Rm 341, CB#3280, Chapel Hill, NC, 27599-3280, USA

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BMC Genomics 2012, 13:562 doi:10.1186/1471-2164-13-562

Published: 19 October 2012

Additional files

Additional file 1:

Table S1. P. acidipropionici proteins identified by UPLC-ESI-Q/TOF. List of proteins identified using UPLC-ESI-Q/TOF experiments.

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Additional file 2:

Figures S1 to S5.S1. Comparative protein clustering. Four-set Venn diagram with protein families including P. acidipropionici, P. acnes, P. freudenreichii and M. phosphovorus. S2. Catabolic Repression in P. acidipropionici. Growth of P. acidipropionici in different carbon sources with or without addition of the hexose analogous 2-deoxy-glucose (2-DG). Error bars represent standard errors of the mean. S3. Alignment of CcO subunit I with homologs. Alignment of cytochrome C oxidase subunit I proteins of Propionibacterium acidipropionici ATCC4875 (Pacidi_2fr), P. avidum ATCC25577 (Pavidum; ZP_08938124.1), P. acnes KPA171202 (Pacnes; YP_055417.1) and Microlunatus phosphovorus NM-1 (Mphosp; YP_004574620.1). S4. CcO subunit I frameshift region. Alignment of 454 and Illumina reads with the frameshift region of cytochrome C oxidase subunit I. The combination of both technologies avoids the commom 454 homopolimer error, supporting the existence of the frameshift. First ten reads are from 454 sequencing. Last ten reads are from Illumina sequencing. S5. Gene clusters comprising B12 biosynthesis genes. The small cluster (red) harbors genes responsible for providing aminolaevulinic acid and converting it to uroporphyrinogen III, as well as the interconversion of uroporphyrinogen III into haem. The large cluster (green) harbors genes responsible for cobalt transport and adenosylcobalamin synthesis from uroporphyrinogen III.

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Additional file 3:

Table S2. Transporter proteins comparison. Complete list of transporter families identified by annotation with TCDB classification.

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Additional file 4:

Table S3. PTS protein-coding genes. List of annotated genes related to phosphotransferase system in P.acidipropionici genome.

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