Core proteome of the minimal cell: Comparative proteomics of three mollicute species

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Fisunov, Gleb Y ^a   Alexeev, Dmitry G ^a,c   Bazaleev, Nicolay A ^a   Ladygina, Valentina G ^a   Galyamina, Maria A ^a   Kondratov, Ilya G ^a   Zhukova, Nadezhda A ^b   Serebryakova, Marina V ^a   Demina, Irina A ^a   Govorun, Vadim M ^a,b,c  

^a FEDERAL RESEARCH AND CLINICAL CENTER OF PHYSICAL CHEMICAL MEDICINE OF FEDERAL MEDICAL BIOLOGICAL AGENCY   (Russian Federation)

^b KURCHATOV INSTITUTE   (Russian Federation)

^c MOSCOW INSTITUTE OF PHYSICS AND TECHNOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CORE PROTEOME; FTSK PROTEIN; FTSZ PROTEIN; PROTEOME; RIBOSOME PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; UVRA PROTEIN; UVRB PROTEIN; UVRC PROTEIN; UVRD PROTEIN; COMPLEMENTARY RNA;

ACHOLEPLASMA LAIDLAWII; ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; GENETIC TRANSCRIPTION; GENOME ANALYSIS; MOLLICUTES; MYCOPLASMA GALLISEPTICUM; MYCOPLASMA MOBILE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; SPECIES COMPARISON; COMPARATIVE STUDY; CYTOLOGY; GENETICS; METABOLISM; METHODOLOGY; MYCOPLASMA; PROTEIN BINDING; PROTEOMICS; SPECIES DIFFERENCE;

MOLLICUTES; MYCOPLASMA; MYCOPLASMA GALLISEPTICUM; MYCOPLASMA MOBILE; MYCOPLASMATALES; PROKARYOTA;

BACTERIAL PROTEINS; GENOME, BACTERIAL; MYCOPLASMA; OPEN READING FRAMES; PROTEIN BINDING; PROTEOME; PROTEOMICS; RNA, ANTISENSE; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC;

EID: 79960454302     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021964     Document Type: Article

References (34)

1. Koonin EV, Wolf YI, (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic acids research 36: 6688-719.
2. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
3. Mushegian AR, Koonin EV, (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93: 10268-10273.
4. Harris JK, Kelley ST, Spiegelman GB, Pace NR, (2003) The Genetic Core of the Universal Ancestor. Genome Research 13: 407-412.
5. Koonin EV, Mushegian AR, Bork P, (1996) Non-orthologous gene displacement. Trends Genet 12: 334-6.
6. Hutchison CA III, (1999) Global Transposon Mutagenesis and a Minimal Mycoplasma Genome. Science 286: 2165-2169.
7. Glass JI, Assad-garcia N, Alperovich N, Yooseph S, Lewis MR, et al. (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103: 425-430.
8. Zhang R, Lin Y, (2009) DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic acids research 37: D455-8.
9. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, et al. (2003) Essential Bacillus subtilis genes. Proceedings of the National Academy of Sciences of the United States of America 100: 4678-83.
10. Fang G, Rocha E, Danchin A, (2005) How essential are nonessential genes? Molecular biology and evolution 22: 2147-56.
11. Forster AC, Church GM, (2006) Towards synthesis of a minimal cell. Molecular Systems Biology.
12. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Molecular systems biology 2: 2006.0008.
13. Sassetti CM, Boyd DH, Rubin EJ, (2003) Genes required for mycobacterial growth defined by high density mutagenesis. Molecular microbiology 48: 77-84.
14. Rasmussen S, Nielsen HB, Jarmer H, (2009) The transcriptionally active regions in the genome of Bacillus subtilis. Molecular microbiology 73: 1043-57.
15. Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, et al. (2008) Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome research 18: 1133-42.
16. Callister SJ, McCue LA, Turse JE, Monroe ME, Auberry KJ, et al. (2008) Comparative Bacterial Proteomics: Analysis of the Core Genome Concept. PLoS One 3: e1542.
17. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, et al. (2004) The complete genome and proteome of Mycoplasma mobile. Genome research 14: 1447-61.
18. Laemmli UK, (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
19. Shevchenko A, Wilm M, Vorm O, Mann M, (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68: 850-8.
20. Jensen ON, Wilm M, Shevchenko A, Mann M, (1999) Sample preparation methods for mass spectrometric peptide mapping directly from 2-DE gels. \ Methods Mol. Biol 112: 513-530.
21. Beck M, Claassen M, Aebersold R, (2010) Comprehensive proteomics. Current opinion in biotechnology 1-6.
22. Kühner S, Noort V van, Betts MJ, Leo-Macias A, Batisse C, et al. (2009) Proteome organization in a genome-reduced bacterium. Science (New York, N.Y.) 326: 1235-40.
23. Demina IA, Serebryakova MV, Ladygina VG, Rogova MA, Zgoda VG, et al. (2009) Proteome of the bacterium Mycoplasma gallisepticum. Biochemistry (Moscow) 74: 165-174.
24. Güell M, Noort V van, Yus E, Chen W-H, Leigh-Bell J, et al. (2009) Transcriptome complexity in a genome-reduced bacterium. Science (New York, N.Y.) 326: 1268-71.
25. Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, et al. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Molecular & cellular proteomics: MCP 8: 1350-60.
26. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, et al. (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-6.
27. Pereyre S, Sirand-Pugnet P, Beven L, Charron A, Renaudin H, et al. (2009) Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas. PLoS genetics 5: e1000677.
28. Gitai Z, (2005) The new bacterial cell biology: moving parts and subcellular architecture. Cell 120: 577-86.
29. Jain R, Rivera MC, Lake JA, (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proceedings of the National Academy of Sciences of the United States of America 96: 3801-6.
30. Peterson SN, Fraser CM, (2001) The Complexity of Simplicity. Genome Biol 2.
31. Eisen JA, (1998) A phylogenomic study of the MutS family of proteins. Nucleic acids research 26: 4291-300.
32. Lartigue C, Vashee S, Algire MA, Chuang R-Y, Benders GA, et al. (2009) Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science (New York, N.Y.) 325: 1693-6.
33. Pennisi E, (2004) Searching for the Genome's Second Code. Science 306: 632-635.
34. Grundy FJ, Henkin TM, (2006) From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements. Crit Rev Biochem Mol Biol 41: 329-38.