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Author(s): Ivica Tamas, Svetlana N. Dedysh, Werner Liesack,
Matthew B. Stott, Maqsudul Alam, J. Colin Murrell, and Peter F.
Dunfield
Article Title: Complete Genome Sequence of Beijerinckia indica subsp.
indica
Year of publication: 2010
Link to published article: http://dx.doi.org/10.1128/JB.00656-10
Publisher statement: None
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GENOME ANNOUNCEMENT
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Complete Genome Sequence of Beijerinckia indica subsp. indica
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Ivica Tamas 1, Svetlana N. Dedysh 2, Werner Liesack 3, Matthew B. Stott 4, Maqsudul
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Alam 5, J. Colin Murrell 6, Peter F. Dunfield 1
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Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4 Canada
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Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany.
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GNS Science, Wairakei Research Institute, Taupo, New Zealand
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Department of Microbiology, University of Hawaii, Honolulu, HI 96822, USA
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Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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*Correspondence: Peter F. Dunfield, Department of Biological Sciences, University of
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Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4 Canada. Phone: 403-
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220-2469. Fax: 403-289-9311 E-mail: [email protected]
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Abstract
Beijerinckia indica subsp. indica is an aerobic, acidophilic, N2-fixing soil
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bacterium known for its abundant production of exoheteropolysaccharide. It is a
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chemoorganotroph that is phylogenetically closely related to facultative and obligate
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methanotrophs of the genera Methylocella and Methylocapsa. Here we report the full
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genome sequence of this bacterium.
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Beijerinckia indica subsp. indica ATCC 9039 is the type strain of the genus
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Beijerinckia (Starkey and De, 1939), a member of the Rhizobiales order of the
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Alphaproteobacteria. Beijerinckia spp. are commonly found as free-living bacteria in
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acidic soils, and also in plant rhizosphere and phyllosphere environments (Kennedy,
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2005). Research on Beijerinckia has suffered from chronic taxonomic confusion, with
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some strains of Sphingomonas and Azotobacter being misidentified in the literature: e.g. a
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“Beijerinckia” reported to degrade PAH has been reclassified (Gibson, 1999). However,
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some Beijerinckia spp. have received research attention due to their potential plant-
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growth-promoting properties (Thuler 2003), and for their production of
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heteropolysaccharides with potential biotechnological uses (Scampanari 2000).
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Genomic DNA from Beijerinckia indica subsp. indica was used to create 3-Kb, 8-
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Kb, and 40-Kb DNA libraries. Sequencing, assembly, and automated annotation was
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performed at the Joint Genome Institute using standard procedures (U.S. Department of
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Energy; http://www.jgi.doe.gov/sequencing/strategy.html). The total number of paired-
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end shotgun Sanger reads in the assembly was 33870. In addition, 454 sequence data
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were included into the final assembly: large Newbler contigs were chopped into 4975
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overlapping fragments of 1000-bp and entered into the assembly as pseudo-reads.
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The genome of B. indica subsp. indica was 4,170,153 bp. In addition, two
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plasmids of 181,736 and 66,727 bp were present. There are a total of 3982 ORFs
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predicted using Glimmer, of which 3784 are predicted protein-coding genes and 2695
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(70%) have been assigned a predicted function based on BLASTP searches against the
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KEGG (Kyoto Encyclopedia of Genes and Genomes). There are 134 pseudogenes, 10
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rRNA genes and 52 tRNAs. The GC content is 57.0%.
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The genome lacks phosphofructokinase, the key enzyme of the Embden-
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Meyerhof pathway. Instead, it uses the Entner-Doudoroff or pentose phosphate pathways
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to catabolize sugars, which is typical of free-living Rhizobiales. The majority of the genes
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involved in N2-fixation are clustered in two genomic islands (10 Kb and 51 Kb), with the
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notable absence of the nifS gene encoding cysteine desulphurase.
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Beijerinckia indica is a metabolically versatile bacterium capable of growth on a
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variety of organic acids, sugars, and alcohols (Kennedy 2005). In contrast, its close
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phylogenetic cousins Methylocella and Methylocapsa are highly specialized
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methanotrophs capable of growth on very few substrates (Dedysh 2005). However, the
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genome size of Beijerinckia indica versus Methylocella silvestris (4.17 versus 4.30 Mbp)
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and the predicted protein-encoding genes (3788 versus 3917) are remarkably similar. A
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BLAST analysis indicated that the 57% of genes in the genome of B. indica have
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homologues in M. silvestris (stringency threshold expectation value (E) of 1e-50). Many
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key pathways of one-carbon metabolism (such as the serine, ribulose monophosphate,
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and tetrahydromethanopterin pathways of formaldehyde metabolism) present in M.
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silvestris are absent in B. indica, which confirm experiments showing that the organism is
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incapable of growth on one-carbon substrates (Dedysh et al 2005). However, an operon
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encoding a putative propane monooxygenase homologous to soluble propane/methane
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monooxygenases of Methylocella silvestris BL2 was identified. More in-depth
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comparison of these genomes will help elucidate what defines their very distinct lifestyles.
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Nucleotide sequence accession number. The genome sequence and annotation were
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deposited in Genbank with accession number CP001016.
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Acknowledgements
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This work was performed under the auspices of the US Department of Energy's
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Office of Science, Biological and Environmental Research Program, and by the
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University of California, Lawrence Livermore National Laboratory under
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Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under
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contract No. DE-AC02-05CH11231 and Los Alamos National Laboratory under
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contract No. DE-AC02-06NA25396. The work was supported in part by the Natural
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Sciences and Engineering Research Council of Canada Discovery Grant Program (PD).
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