Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities

ISME Journal

Volumn 4, Issue 11, 2010, Pages 1398-1409

  Singer, Steven W ^a   Erickson, Brian K ^b,c   Verberkmoes, Nathan C ^b   Hwang, Mona ^a   Shah, Manesh B ^b   Hettich, Robert L ^b   Banfield, Jillian F ^b   Thelen, Michael P ^a  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

Author keywords

cytochrome; metagenomics; proteomics; redox; variation

Indexed keywords

CYTOCHROME; PROTEOME;

ACID MINE DRAINAGE; BACTERIUM; BIOCHEMISTRY; BIOFILM; CYTOCHROME; ENVIRONMENTAL FACTOR; GENE EXPRESSION; GENETIC ANALYSIS; LIFE CYCLE; MICROBIAL COMMUNITY; PROTEIN; REDOX CONDITIONS;

ARTICLE; BACTERIAL PHENOMENA AND FUNCTIONS; BIOFILM; CHEMISTRY; GENE DELETION; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; OXIDATION REDUCTION REACTION; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN PROCESSING;

BACTERIAL PHYSIOLOGICAL PHENOMENA; BIOFILMS; CYTOCHROMES; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENVIRONMENTAL MICROBIOLOGY; OXIDATION-REDUCTION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; SEQUENCE DELETION;

LEPTOSPIRILLUM;

EID: 77958494387     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.64     Document Type: Article

References (23)

1. Bond PL, Smriga SP, Banfield JF (2000). Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl Environ Microbiol 66: 3842-3849.
2. Bradford MM. (1976). Rapid and sensitive method for quantitation of microgram quantities of protein-utilizing principle of protein-dye binding. Anal Biochem 72: 248-254.
3. Castelle C, Guiral M, Malarte G, Ledgham F, Leroy G, Brugna M et al. (2008). A new iron-oxidizing/ O2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans. J Biol Chem 283: 25803-25811.
4. Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC et al. (2010a). Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci USA 107: 2383-2390.
5. Denef VJ, Mueller RS, Banfield JF. (2010b). AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4: 599-610.
6. Denef VJ, VerBerkmoes NC, ShahMB, AbrahamP, Lefsrud M, Hettich RL et al. (2009). Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol 11: 313-325.
7. Francis RT, Becker RR. (1984). Specific indication of hemoproteins in polyacrylamide gels using a doublestaining process. Anal Biochem 136: 509-514.
8. Goltsman DSA, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS et al. (2009). Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing 'leptospirillum rubarum' (group ii) and 'leptospirillum ferrodiazotrophum' (group iii) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 75: 4599-4615.
9. Haveman SA, Holmes DE, Ding YHR,Ward JE, DiDonato RJ, Lovley DR. (2006). c-Type cytochromes in Pelobacter carbinolicus. Appl Environ Microbiol 72: 6980-6985.
10. Jeans C, Singer SW, Chan CS, VerBerkmoes NC, Shah M, Hettich RL et al. (2008). Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J 2: 542-550.
11. Laemmli UK. (1970). Cleavage of structural proteins during assembly of head of bacteriophage-T4. Nature 227: 680-685.
12. Lo I, Denef VJ, VerBerkmoes NC, Shah MB, Goltsman D, DiBartolo G et al (2007). Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446: 537-541.
13. Ram RJ, VerBerkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC et al. (2005). Community proteomics of a natural microbial biofilm. Science 308: 1915-1920.
14. Schrenk MO, Edwards KJ, Goodman RM, Hamers RJ, Banfield JF. (1998). Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans: implications for generation of acid mine drainage. Science 279: 1519-1522.
15. Simmons SL, DiBartolo G, Denef VJ, Goltsman DSA, Thelen MP, Banfield JF. (2008). Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLOS Biol 6: 1427-1442.
16. Singer SW, Chan CS, Zemla A, VerBerkmoes NC, Hwang M, Hettich RL et al. (2008). Characterization of cytochrome 579, an unusual cytochrome isolated from an ironoxidizing microbial community. Appl Environ Microbiol 74: 4454-4462.
17. Southey-Pillig CJ, Davies DG, Sauer K. (2005). Characterization of temporal protein production in Pseudomonas aeruginosa biofilms. J Bacteriol 187: 8114-8126.
18. Taha TM, Kanao T, Takeuchi F, Sugio T. (2008). Reconstitution of iron oxidase from sulfur-grown Acidithiobacillus ferrooxidans. Appl Environ Microbiol 74: 6808-6810.
19. Teal TK, Lies DP, Wold BJ, Newman DK. (2006). Spatiometabolic stratification of Shewanella oneidensis biofilms. Appl Environ Microbiol 72: 7324-7330.
20. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM et al. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
21. VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. (2009). SYSTEMS BIOLOGY functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 7: 196-205.
22. Wilmes P, Remis JP, Hwang M, Auer M, Thelen MP, Banfield JF. (2009a). Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME J 3: 266-270.
23. Wilmes P, Simmons SL, Denef VJ, Banfield JF. (2009b). The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev 33: 109-132.