Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast

Nucleic Acids Research

Volumn 40, Issue 20, 2012, Pages 10375-10383

  Tagwerker, Christian ^a   Dupont, Christopher L ^a   Karas, Bogumil J ^a   Ma, Li ^a   Chuang, Ray Yuan ^a   Benders, Gwynedd A ^a   Ramon, Adi ^a,d   Novotny, Mark ^a   Montague, Michael G ^a   Venepally, Pratap ^a   Brami, Daniel ^b   Schwartz, Ariel ^b   Andrews Pfannkoch, Cynthia ^a   Gibson, Daniel G ^a,b   Glass, John I ^a   Smith, Hamilton O ^a,b   Venter, J Craig ^a,b,c   Hutchison, Clyde A ^a,b  

^a J CRAIG VENTER INSTITUTE   (United States)

^b Synthetic Genomics Inc   (United States)

^c Department of Synthetic Biology and Bioenergy ^*  (United States)

^d SG Biofuels Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARTICLE; AT RICH SEQUENCE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; CODON; CONTROLLED STUDY; DNA BASE COMPOSITION; FRAMESHIFT MUTATION; GENE EXPRESSION; GENETIC CODE; GROWTH RATE; MISSENSE MUTATION; MOLECULAR CLONING; MUTATIONAL ANALYSIS; MYCOPLASMA MYCOIDES; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROCHLOROCOCCUS; PROCHLOROCOCCUS MARINUS; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; STOP CODON;

CLONING, MOLECULAR; GENES, BACTERIAL; GENOME, BACTERIAL; MUTATION; PROCHLOROCOCCUS; REPLICATION ORIGIN; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; MYCOPLASMA; MYCOPLASMA MYCOIDES; PROCHLOROCOCCUS; PROCHLOROCOCCUS MARINUS; SACCHAROMYCES CEREVISIAE;

EID: 84868275346     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks823     Document Type: Article

References (38)

1. DiTullio, G.R., Geesey, M.E., Jones, D.R., Daly, K.L., Campbell, L. and Smith, W. Jr (2003) Phytoplankton assemblage structure and primary productivity along 170W in the South Pacific Ocean. Mar. Ecol. Prog. Ser., 255, 55-80.
2. Chisholm, S.W., Olson, R.J., Zettler, E.R., Goericke, R., Waterbury, J.B. and Welschmeyer, N.A. (1988) A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature, 334, 340-343.
3. Partensky, F., Hess, W.R. and Vaulot, D. (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev., 63, 106-127.
4. Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., Arellano, A., Coleman, M., Hauser, L., Hess, W.R. et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature, 424, 1042-1047.
5. Williamson, S.J., Rusch, D.B., Yooseph, S., Halpern, A.L., Heidelberg, K.B., Glass, J.I., Andrews-Pfannkoch, C., Fadrosh, D., Miller, C.S., Sutton, G. et al. (2008) The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS one, 3, e1456.
6. Rusch, D.B., Martiny, A.C., Dupont, C.L., Halpern, A.L. and Venter, J.C. (2010) Characterization of Prochlorococcus clades from iron-depleted oceanic regions. Proc. Natl Acad. Sci. USA, 107, 16184-16189.
7. Tolonen, A.C., Liszt, G.B. and Hess, W.R. (2006) Genetic manipulation of Prochlorococcus strain MIT9313: green fluorescent protein expression from an RSF1010 plasmid and Tn5 transposition. Appl. Environ. Microbiol., 72, 7607-7613.
8. Coleman, M.L., Sullivan, M.B., Martiny, A.C., Steglich, C., Barry, K., Delong, E.F. and Chisholm, S.W. (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science, 311, 1768-1770.
9. Kettler, G.C., Martiny, A.C., Huang, K., Zucker, J., Coleman, M.L., Rodrigue, S., Chen, F., Lapidus, A., Ferriera, S., Johnson, J. et al. (2007) Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet., 3, e231.
10. Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison, C.A. III, Smith, H.O. and Venter, J.C. (2007) Genome transplantation in bacteria: changing one species to another. Science, 317, 632-638.
11. Lartigue, C., Vashee, S., Algire, M.A., Chuang, R.-Y., Benders, G.A., Ma, L., Noskov, V.N., Denisova, E.A., Gibson, D.G., Assad- Garcia, N. et al. (2009) Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science, 325, 1693-1696.
12. Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A. et al. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science, 319, 1215-1220.
13. Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R.-Y., Algire, M.A., Benders, G.A., Montague, M.G., Ma, L., Moodie, M.M. et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329, 52-56.
14. Benders, G., Noskov, V.N., Denisova, E.A., Lartigue, C., Gibson, D.G., Assad-Garcia, N., Chuang, R.-Y., Carrera, W., Moodie, M., Algire, M.A. et al. (2010) Cloning whole bacterial genomes in yeast. Nucleic Acids Res., 38, 2558-2569.
15. Noskov, V.N., Segall-Shapiro, T.H. and Chuang, R.-Y. (2010) Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast. Nucleic Acids Res., 38, 2570-2576.
16. Kouprina, N. and Larionov, V. (2008) Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat. Protoc., 3, 371-377.
17. Noskov, V.N., Chuang, R.-Y., Gibson, D.G., Leem, S.-H., Larionov, V. and Kouprina, N. (2010) Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies. Nat. Protoc., 6, 89-96.
18. Karas, B.J., Tagwerker, C., Yonemoto, I.T., Hutchison, C.A. III and Smith, H.O. (2012) Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid. ACS Synth. Biol., 1, 22-28.
19. Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C. and Salzberg, S.L. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
20. Palzkill, T.G. and Newlon, C.S. (1988) A yeast replication origin consists of multiple copies of a small conserved sequence. Cell, 53, 441-450.
21. Celniker, S.E., Sweder, K., Srienc, F., Bailey, J.E. and Campbell, J.L. (1984) Deletion mutations affecting autonomously replicating sequence ARSI of Saccharomyces cerevisiae. Construction, 4, 2455-2466.
22. Nieduszynski, C.A., Knox, Y. and Donaldson, A.D. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev., 20, 1874-1879.
23. Theis, J.F. and Newlon, C.S. (1997) The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc. Natl Acad. Sci. USA, 94, 10786-10791.
24. Wyrick, J.J., Aparicio, J.G., Chen, T., Barnett, J.D., Jennings, E.G., Young, R.A., Bell, S.P. and Aparicio, O.M. (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science, 294, 2357-2360.
25. Xu, W., Aparicio, J.G., Aparicio, O.M. and Tavaré, S. (2006) Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics, 7, 276.
26. Noskov, V.N., Karas, B.J., Young, L., Chuang, R.-Y., Gibson, D.G., Lin, Y.-C., Stam, J., Yonemoto, I.T., Suzuki, Y., Andrews- Pfannkoch, C. et al. (2012) Assembly of large, high G+C bacterial DNA fragments in yeast. ACS Synth. Biol., 1, 267-273.
27. Osburne, M.S., Holmbeck, B.M., Frias-Lopez, J., Steen, R., Huang, K., Kelly, L., Coe, A., Waraska, K., Gagne, A. and Chisholm, S.W. (2010) UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase. Environ. Microbiol., 12, 1978-1988.
28. Vogel, J., Axmann, I., Herzel, H. and Hess, W. (2003) Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res., 31, 2890-2899.
29. Sweetser, D., Nonet, M. and Young, R.A. (1987) Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc. Natl Acad. Sci. USA, 84, 1192-1196.
30. Singer, V., Wobbe, C. and Struhl, K. (1990) A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev., 4, 636-645.
31. Romanos, M., Scorer, C. and Clare, J. (1992) Foreign gene expression in yeast: a review. Yeast, 8, 423-488.
32. Romanos, M. and Makoff, A. (1991) Expression of tetanus toxin fragment C in yeast: gene synthesis is required to eliminate fortuitous polyadenylation sites in AT-rich DNA. Nucleic Acids Res., 19, 1461-1467.
33. Guo, Z. and Sherman, F. (1995) 3'-end-forming signals of yeast mRNA. Mol. Cell. Biol., 15, 5983-5990.
34. Weinberg, Z., Barrick, J.E., Yao, Z., Roth, A., Kim, J.N., Gore, J., Wang, J.X., Lee, E.R., Block, K., Sudarsan, N. et al. (2007) The CMfinder comparative genomics pipeline discovers 22 novel putative RNAs in bacteria. Supplementary Data: diagrams of all motifs. Nucleic Acids Res., 35, 4809-4819.
35. Karlin, S. and Mrazek, J. (2000) Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol., 182, 5238-5250.
36. Kozak, M. (1999) Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187-208.
37. Gibson, D.G., Benders, G.A., Axelrod, K.C., Zaveri, J., Algire, M.A., Moodie, M., Montague, M.G., Venter, J.C., Smith, H.O. and Hutchison, C.A.III. (2008) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc. Natl Acad. Sci. USA, 105, 20404-20409.
38. Fuhrmann, M., Hausherr, A., Ferbitz, L., Schödl, T., Heitzer, M. and Hegemann, P. (2004) Monitoring dynamic expression of nuclear genes in Chlamydomonas reinhardtii by using a synthetic luciferase reporter gene. Plant Mol. Biol., 55, 869-881.