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Improved genome annotation for Zymomonas mobilis

Nature Biotechnology volume 27, pages 893–894 (2009)Cite this article

To the Editor:

The first genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4 was reported in your journal five years ago1. Because of its productivity, high level of ethanol tolerance and ability to be genetically manipulated2, Z. mobilis is a promising industrial bacterium for fermenting lignocellulosic biomass into ethanol, which is being advanced as an alternative to petroleum-derived transportation fuels3. Strains of the bacterium have been developed to ferment both hexoses and pentoses into ethanol4, and the genome sequence will provide further opportunities for strain developments as well as providing more fundamental insights5. We have observed many differences between the primary annotation and one performed by the J. Craig Venter Institute (JCVI) and have detected differential gene expression in genes predicted by JCVI (http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?org=ntzm01) that were absent from the primary annotation in our previous work6. We present here an improved version of the ZM4 genome annotation based on the original primary genome sequence, new experimental data generated by 454 pyrosequencing and mass spectrometry–based proteomics, a novel gene prediction algorithm called Prodigal (prokaryotic dynamic programming genefinding algorithm) that is incorporated into an annotation pipeline, and manual curation (Supplementary Table 1). Prodigal has been used to annotate all microorganisms submitted to GenBank by the Department of Energy (DOE) Joint Genome Institute (JGI; Walnut Creek, CA, USA) since November 2007 and is freely available (http://compbio.ornl.gov/prodigal/).

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References

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Acknowledgements

We thank A. Savidor for making his six-frame translation proteomics search scripts available, L. Goodwin (US DOE JGI) for management of plasmid sequencing and O. Chertkov (JGI–Los Alamos National Laboratory) for plasmid sequence improvement and finishing. Research sponsored in part by the Laboratory Directed Research and Development Program of ORNL, managed by UT-Battelle, LLC for the US Department of Energy under contract no. DE-AC05-00OR22725; the BioEnergy Science Center, a US DOE Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science; and the DOE JGI managed by the University of California, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract no. DE-AC52-07NA27344 and Los Alamos National Laboratory under contract no. DE-AC02-06NA25396.

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Authors and Affiliations

  1. Biosciences Division Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

    Shihui Yang, Loren J Hauser, Miriam L Land, Gwo-Liang Chen, Dale A Pelletier, Dawn M Klingeman, Yun-Juan Chang & Steven D Brown

  2. BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

    Shihui Yang, Loren J Hauser, Miriam L Land, Chongle Pan, Dawn M Klingeman & Steven D Brown

  3. Department of Genetics & Biotechnology, University of Athens, Athens, Greece

    Katherine M Pappas, Vassili N Kouvelis & Milton A Typas

  4. Chemical Sciences Division Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

    Gregory B Hurst

  5. Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

    Chongle Pan & Nagiza F Samatova

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  1. Shihui Yang
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  2. Katherine M Pappas
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  8. Vassili N Kouvelis
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  9. Milton A Typas
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  10. Dale A Pelletier
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  13. Nagiza F Samatova
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  14. Steven D Brown
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Corresponding authors

Correspondence to Katherine M Pappas or Steven D Brown.

Supplementary information

Supplementary Text and Figures

Supplementary Fig. 1 (PDF 111 kb)

Supplemental Table 1

ZM4 differences. (HTM 830 kb)

Supplemental Table 2

ZM4 pseudogenes converted into full length CDS. (XLS 28 kb)

Supplemental Table 3

Newly described ZM4 chromosomal genes. (XLS 25 kb)

Supplemental Table 4

Gene-by-gene comparison or primary and ORNL annotations. (XLS 177 kb)

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Yang, S., Pappas, K., Hauser, L. et al. Improved genome annotation for Zymomonas mobilis. Nat Biotechnol 27, 893–894 (2009). https://doi.org/10.1038/nbt1009-893

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