Open Access Research article

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

Dmitry A Rodionov12, Chen Yang13, Xiaoqing Li1, Irina A Rodionova1, Yanbing Wang4, Anna Y Obraztsova47, Olga P Zagnitko5, Ross Overbeek5, Margaret F Romine6, Samantha Reed6, James K Fredrickson6, Kenneth H Nealson47 and Andrei L Osterman15*

Author Affiliations

1 Burnham Institute for Medical Research, La Jolla, California 92037, USA

2 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia

3 Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China

4 Department of Earth Sciences, University of Southern California, Los Angeles, California 90089, USA

5 Fellowship for Interpretation of Genomes, Burr Ridge, Illinois 60527, USA

6 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA

7 J. Craig Venter Institute, San Diego, California 92121, USA

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BMC Genomics 2010, 11:494  doi:10.1186/1471-2164-11-494

Published: 13 September 2010

Additional files

Additional file 1:

Collection of protein families involved in carbohydrate utilization in bacteria.

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Additional file 2:

Summary on distribution of carbohydrate utlization genes in Shewanella spp.

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Additional file 3:

Complete distribution of sugar catabolome genes in Shewanella genomes.

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Additional file 4:

Description of rare sugar utilization pathways in Shewanella.

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Additional file 5:

Predicted novel functional roles for isofunctional protein families from Shewanella sugar catabolome.

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Additional file 6:

Experimental verification of novel enzymes, transporters, and regulators involved in sugar utilization in Shewanella. A. Phenotypic characterization of glcPMal (Shewana3_2310) for its involvement in glucose utilization in Shewanella sp. ANA-3; B. Phenotypic characterization of nagP (SO3503) for its involvement in N-acetylglucosamine (Nag) utilization in Shewanella oneidensis MR-1; C. Phenotypic characterization of grtP (SO1771) for its involvement in D-glycerate; D. Complementation of the E. coli cellobiose utilization by the bglA-bglT (Sbal_1133-1132) genes from S. baltica OS155; E. Substrate specificity of Shewanella baltica OS155 GlkII (Sbal_1134) kinase; F. Growth of E. coli DH5a strain (Scr-) containing heterologously expressed sucrose utilization genes scrTII-scrP (Sfri_3989-3990) from S. frigidimarina.

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Additional file 7:

Growth phenotypes of Shewanella on various carbon sources determined by manual assay.

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Additional file 8:

Growth phenotypes of Shewanella on various carbon sources determined by microplate assay using Bioscreen C MBR system.

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Additional file 9:

Comparison of reconstructed sugar utilization pathways in Shewanella and Enterobacteria. A. N-acetylglucosamine (Nag) and chitin utilization pathways; B. D-glycerate (Grt) and glucarate/galactarate utilization pathways; C. β-glucoside (Bgl) utilization pathway; D. Sucrose (Scr) utilization pathway; E. L-arabinose (Ara) and arabinosides utilization pathways.

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Additional file 10:

The gluconate (A) and ribose (B) utilization gene loci in some closely related Shewanella strains and other γ-proteobacteria.

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