Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

BMC Systems Biology

Volumn 8, Issue 1, 2014, Pages

  Ong, Wai K ^a   Vu, Trang T ^a   Lovendahl, Klaus N ^a   Llull, Jenna M ^a   Serres, Margrethe H ^b   Romine, Margaret F ^c   Reed, Jennifer L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b MARINE BIOLOGICAL LABORATORY   (United States)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Constraint based model; Electron acceptors; FBA; Phenotype

Indexed keywords

CARBON;

ARTICLE; BACTERIAL GENE; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPARATIVE STUDY; ELECTRON TRANSPORT; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; PHENOTYPE; SHEWANELLA; SPECIES DIFFERENCE;

CARBON; CLUSTER ANALYSIS; ELECTRON TRANSPORT; GENES, BACTERIAL; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; MUTATION; PHENOTYPE; SHEWANELLA; SPECIES SPECIFICITY;

EID: 84899131429     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-8-31     Document Type: Article

References (21)

1. Nealson KH, Scott J. Ecophysiology of the Genus Shewanella. Prokaryotes: A Handbook on the Biology of Bacteria, Vol 6. Third edition 2006, 1133-1151. New York, NY: Springer.
2. Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JLM, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. Towards environmental systems biology of Shewanella. Nat Rev Microbiol 2008, 6:592-603. 10.1038/nrmicro1947, 18604222.
3. Rodionov DA, Yang C, Li XQ, Rodionova IA, Wang YB, Obraztsova AY, Zagnitko OP, Overbeek R, Romine MF, Reed S, Fredrickson JK, Nealson KH, Osterman AL. Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics 2010, 11:494. 10.1186/1471-2164-11-494, 2996990, 20836887.
4. Deutschbauer A, Price MN, Wetmore KM, Shao WJ, Baumohl JK, Xu ZC, Nguyen M, Tamse R, Davis RW, Arkin AP. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. Plos Genetics 2011, 7(11):e1002385. 10.1371/journal.pgen.1002385, 3219624, 22125499.
5. Nealson KH, Belz A, McKee B. Breathing metals as a way of life: geobiology in action. Anton Leeuw Int J G 2002, 81:215-222.
6. Gorby YA, Lovley DR. Enzymatic uranium precipitation. Environ Sci Technol 1992, 26:205-207.
7. Hau HH, Gralnick JA. Ecology and biotechnology of the genus Shewanella. Annu Rev Microbiol 2007, 61:237-258. 10.1146/annurev.micro.61.080706.093257, 18035608.
8. Flynn JM, Ross DE, Hunt KA, Bond DR, Gralnick JA. Enabling unbalanced fermentations by using engineered electrode-interfaced bacteria. MBio 2010, 1. doi: 10.1128/mBio.00190-10.
9. Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics 2011, 12(Suppl 1):S3.
10. Rodrigues JL, Serres MH, Tiedje JM. Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level. Appl Environ Microbiol 2011, 77:5352-5360. 10.1128/AEM.00097-11, 3147445, 21642407.
11. Pinchuk GE, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, Osterman A, Scott JH, Reed SB, Romine MF, Konopka AE, Beliaev AS, Fredrickson JK, Reed JL. Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol 2010, 6:e1000822. 10.1371/journal.pcbi.1000822, 2891590, 20589080.
12. Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, Brown RN, Lipton MS, Osterman A, Fredrickson JK, Konopka AE, Beliaev AS, Reed JL. Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput Biol 2012, 8:e1002460. 10.1371/journal.pcbi.1002460, 3329150, 22529767.
13. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40:D109-D114. 10.1093/nar/gkr988, 3245020, 22080510.
14. Hamilton JJ, Reed JL. Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. PLoS One 2012, 7:e34670. 10.1371/journal.pone.0034670, 3359066, 22666308.
15. Konstantinidis KT, Serres MH, Romine MF, Rodrigues JL, Auchtung J, McCue LA, Lipton MS, Obraztsova A, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc Natl Acad Sci USA 2009, 106:15909-15914. 10.1073/pnas.0902000106, 2747217, 19805231.
16. Romine MF, Carlson TS, Norbeck AD, McCue LA, Lipton MS. Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome. Appl Environ Microbiol 2008, 74:3257-3265. 10.1128/AEM.02720-07, 2394961, 18378659.
17. Romine MF. Genome-wide protein localization prediction strategies for gram negative bacteria. BMC Genomics 2011, 12(Suppl 1):S1.
18. Orth JD, Thiele I, Palsson B. What is flux balance analysis?. Nat Biotechnol 2010, 28:245-248. 10.1038/nbt.1614, 3108565, 20212490.
19. Vinogradov E, Korenevsky A, Beveridge TJ. The structure of the rough-type lipopolysaccharide from Shewanella oneidensis MR-1, containing 8-amino-8-deoxy-Kdo and an open-chain form of 2-acetamido-2-deoxy-D-galactose. Carbohydr Res 2003, 338:1991-1997. 10.1016/S0008-6215(03)00325-2, 14499575.
20. Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson B, Agarwalla S. Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol 2006, 188:8259-8271. 10.1128/JB.00740-06, 1698209, 17012394.
21. Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson B. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci USA 2013, 110:20338-20343. 10.1073/pnas.1307797110, 3864276, 24277855.