Marine Microbial Bioprospecting References 323
Part B | 11
C.J. Bult, J.F. Tomb, B.A. Dougherty, J.M. Merrick,
K. McKenney, G. Sutton, W. FitzHugh, C. Fields,
J.D. Gocayne, J. Scott, R. Shirley, L.-I. Liu,
A. Glodek, J.M. Kelley, J.F. Weidman, C.A. Phillips,
T. Spriggs, E. Hedblom, M.D. Cotton, T.R. Utterback, M.C. Hanna, D.T. Nguyen, D.M. Saudek,
R.C. Brandon, L.D. Fine, J.L. Fritchman,
J.L. Fuhrmann, N.S.M. Geoghagen, C.L. Gnehm,
L.A. McDonald, K.V. Small, C.M. Fraser, H.O. Smith,
J.C. Venter: Whole-genome random sequencing
and assembly of Haemophilus influenzae Rd,
Science 269, 496–512 (1995)
11.85
K. Lagesen, D.W. Ussery, T.M. Wassenaar: Genome
update: The 1000th genome – a cautionary tale,
Microbiology 156, 603–608 (2010)
11.86
E. Mardis, J. McPherson, R. Martienssen, R.K. Wilson, W.R. McCombie: What is finished, and why
does it matter, Genome Res. 12, 669–671 (2002)
11.87
D. MacLean, J.D.G. Jones, D.J. Studholme: Application of “next-generation” sequencing technologies to microbial genetics, Nat. Rev. Microbiol. 7, 287–296 (2009)
11.88
N. Ricker, H. Qian, R.R. Fulthorpe: The limitations
of draft assemblies for understanding prokaryotic
adaptation and evolution, Genomics 100, 167–175
(2012)
11.89
J. Jiang, J. Li, H.S. Kwan, C.H. Au, P.T.W. Law, L. Li,
K.M. Kam, J.M.L. Ling, F.C. Leung: A cost-effective
and universal strategy for complete prokaryotic
genomic sequencing proposed by computer simulation, BMC Res. Notes 5, 80 (2012)
11.90
S.B. Zotchev, O.N. Sekurova, L. Katz: Genomebased bioprospecting of microbes for new therapeutics, Current Opin. Biotechnol. 23, 941–947
(2012)
11.91
D.W. Udwary, L. Zeigler, R.N. Asolkar, V. Singan,
A. Lapidus, W. Fenical, P.R. Jensen, B.S. Moore:
Genome sequencing reveals complex secondary
metabolome in the marine actinomycete Salinispora tropica, Proc. Natl. Acad. Sci. USA 104,
10376–10381 (2007)
11.92
N. Ziemert, S. Podell, K. Penn, J.H. Badger,
E. Allen, P.R. Jensen: The natural product domain
seeker NaPDoS: A phylogeny based bioinformatic
tool to classify secondary metabolite gene diversity, PLoS One 7, e34064 (2012)
11.93
S.G. Van Lanen, B. Shen: Microbial genomics for
the improvement of natural product discovery,
Current Opin. Microbiol. 9, 252–260 (2006)
11.94
R. Madupu, A. Richter, R.J. Dodson, L. Brinkac,
D. Harkins, S. Durkin, S. Shrivastava, G. Sutton,
D. Haft: CharProtDB: A database of experimentally
characterized protein annotations, Nucleic Acids
Res. 40, D237–D241 (2012)
11.95
J.E. Velásquez, W.A. van der Donk: Genome mining for ribosomally synthesized natural products,
Current Opin. Chem. Biol. 15, 11–21 (2011)
11.96
A.J. Wargacki, E. Leonard, M.N. Win, D.D. Regitsky,
C.N.S. Santos, P.B. Kim, S.R. Cooper, R.M. Raisner, A. Herman, A.B. Sivitz, A. Lakshmanaswamy,
Y. Kashiyama, D. Baker, Y. Yoshikuni: An engineered microbial platform for direct biofuel production from brown macroalgae, Science 335,
308–313 (2012)
11.97
B. Li, D. Sher, L. Kelly, Y. Shi, K. Huang, P.J. Knerr,
I. Joewono, D. Rusch, S.W. Chisholm, W.A. van der
Donk: Catalytic promiscuity in the biosynthesis of
cyclic peptide secondary metabolites in planktonic marine cyanobacteria, Proc. Natl. Acad. Sci.
USA 107, 10430–10435 (2010)
11.98
V.R. de Berardinis, M. Durot, J. Weissenbach,
M. Salanoubat: Acinetobacter baylyi ADP1 as
a model for metabolic system biology, Current
Opin. Microbiol. 12, 568–576 (2009)
11.99
W. Zhang, F. Li, L. Nie: Integrating multiple
“omics” analysis for microbial biology: application and methodologies, Microbiology 156, 287–
301 (2010)
11.100 M.J. Filiatrault: Progress in prokaryotic transcriptomics, Current Opin. Microbiol. 14, 579–586
(2011)
11.101 A.H.M. Van Vliet: Next generation sequencing of microbial transcriptomes: challenges and
opportunities, FEMS Microbiol. Lett. 302, 1–7
(2009)
11.102 S.J. Cordwell: Microbial proteomics: How far have
we come?, Microb. Aust. 32, 169–173 (2011)
11.103 S.Y. Ow, P.C. Wright: Current trends in high
throughput proteomics in cyanobacteria, FEBS
Lett. 583, 1744–1752 (2009)
11.104 J. Liu, L. Chen, J. Wang, J. Qiao, W. Zhang:
Proteomic analysis reveals resistance mechanism
against biofuel hexane in Synechocystis sp., PCC
6803, Biotechnol. Biofuels 5, 68 (2012)
11.105 J. Qiao, J. Wang, L. Chen, X. Tian, S. Huang,
X. Ren, W. Zhang: quantitative iTRAQ LC-MS/MS
proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis
sp. PCC 6803, J. Proteome Res. 11, 5286–5300
(2012)
11.106 W.M. van Gulik: Fast sampling for quantitative
microbial metabolomics, Current Opin. Biotechnol. 21, 27–34 (2010)
11.107 F.S.O. Fritzsch, C. Dusny, O. Frick, A. Schmid:
Single-cell analysis in biotechnology, systems biology, and biocatalysis, Annu. Rev. Chem. Biomol.
Eng. 3, 129–155 (2012)
11.108 K.E.J. Tyo, K. Kocharin, J. Nielsen: Toward designbased engineering of industrial microbes, Current
Opin. Microbiol. 13, 255–262 (2010)
11.109 S. Ishii, K. Tago, K. Senoo: Single-cell analysis
and isolation for microbiology and biotechnology: Methods and applications, Appl. Microbiol.
Biotechnol. 86, 1281–1292 (2010)
11.110 Y. Kang, M.H. Norris, J. Zarzycki-Siek, W.C. Nierman, S.P. Donachie, T.T. Hoang: Transcript amplification from single bacterium for transcriptome
analysis, Genome Res. 21, 925–935 (2011)
Part B | 11
C.J. Bult, J.F. Tomb, B.A. Dougherty, J.M. Merrick,
K. McKenney, G. Sutton, W. FitzHugh, C. Fields,
J.D. Gocayne, J. Scott, R. Shirley, L.-I. Liu,
A. Glodek, J.M. Kelley, J.F. Weidman, C.A. Phillips,
T. Spriggs, E. Hedblom, M.D. Cotton, T.R. Utterback, M.C. Hanna, D.T. Nguyen, D.M. Saudek,
R.C. Brandon, L.D. Fine, J.L. Fritchman,
J.L. Fuhrmann, N.S.M. Geoghagen, C.L. Gnehm,
L.A. McDonald, K.V. Small, C.M. Fraser, H.O. Smith,
J.C. Venter: Whole-genome random sequencing
and assembly of Haemophilus influenzae Rd,
Science 269, 496–512 (1995)
11.85
K. Lagesen, D.W. Ussery, T.M. Wassenaar: Genome
update: The 1000th genome – a cautionary tale,
Microbiology 156, 603–608 (2010)
11.86
E. Mardis, J. McPherson, R. Martienssen, R.K. Wilson, W.R. McCombie: What is finished, and why
does it matter, Genome Res. 12, 669–671 (2002)
11.87
D. MacLean, J.D.G. Jones, D.J. Studholme: Application of “next-generation” sequencing technologies to microbial genetics, Nat. Rev. Microbiol. 7, 287–296 (2009)
11.88
N. Ricker, H. Qian, R.R. Fulthorpe: The limitations
of draft assemblies for understanding prokaryotic
adaptation and evolution, Genomics 100, 167–175
(2012)
11.89
J. Jiang, J. Li, H.S. Kwan, C.H. Au, P.T.W. Law, L. Li,
K.M. Kam, J.M.L. Ling, F.C. Leung: A cost-effective
and universal strategy for complete prokaryotic
genomic sequencing proposed by computer simulation, BMC Res. Notes 5, 80 (2012)
11.90
S.B. Zotchev, O.N. Sekurova, L. Katz: Genomebased bioprospecting of microbes for new therapeutics, Current Opin. Biotechnol. 23, 941–947
(2012)
11.91
D.W. Udwary, L. Zeigler, R.N. Asolkar, V. Singan,
A. Lapidus, W. Fenical, P.R. Jensen, B.S. Moore:
Genome sequencing reveals complex secondary
metabolome in the marine actinomycete Salinispora tropica, Proc. Natl. Acad. Sci. USA 104,
10376–10381 (2007)
11.92
N. Ziemert, S. Podell, K. Penn, J.H. Badger,
E. Allen, P.R. Jensen: The natural product domain
seeker NaPDoS: A phylogeny based bioinformatic
tool to classify secondary metabolite gene diversity, PLoS One 7, e34064 (2012)
11.93
S.G. Van Lanen, B. Shen: Microbial genomics for
the improvement of natural product discovery,
Current Opin. Microbiol. 9, 252–260 (2006)
11.94
R. Madupu, A. Richter, R.J. Dodson, L. Brinkac,
D. Harkins, S. Durkin, S. Shrivastava, G. Sutton,
D. Haft: CharProtDB: A database of experimentally
characterized protein annotations, Nucleic Acids
Res. 40, D237–D241 (2012)
11.95
J.E. Velásquez, W.A. van der Donk: Genome mining for ribosomally synthesized natural products,
Current Opin. Chem. Biol. 15, 11–21 (2011)
11.96
A.J. Wargacki, E. Leonard, M.N. Win, D.D. Regitsky,
C.N.S. Santos, P.B. Kim, S.R. Cooper, R.M. Raisner, A. Herman, A.B. Sivitz, A. Lakshmanaswamy,
Y. Kashiyama, D. Baker, Y. Yoshikuni: An engineered microbial platform for direct biofuel production from brown macroalgae, Science 335,
308–313 (2012)
11.97
B. Li, D. Sher, L. Kelly, Y. Shi, K. Huang, P.J. Knerr,
I. Joewono, D. Rusch, S.W. Chisholm, W.A. van der
Donk: Catalytic promiscuity in the biosynthesis of
cyclic peptide secondary metabolites in planktonic marine cyanobacteria, Proc. Natl. Acad. Sci.
USA 107, 10430–10435 (2010)
11.98
V.R. de Berardinis, M. Durot, J. Weissenbach,
M. Salanoubat: Acinetobacter baylyi ADP1 as
a model for metabolic system biology, Current
Opin. Microbiol. 12, 568–576 (2009)
11.99
W. Zhang, F. Li, L. Nie: Integrating multiple
“omics” analysis for microbial biology: application and methodologies, Microbiology 156, 287–
301 (2010)
11.100 M.J. Filiatrault: Progress in prokaryotic transcriptomics, Current Opin. Microbiol. 14, 579–586
(2011)
11.101 A.H.M. Van Vliet: Next generation sequencing of microbial transcriptomes: challenges and
opportunities, FEMS Microbiol. Lett. 302, 1–7
(2009)
11.102 S.J. Cordwell: Microbial proteomics: How far have
we come?, Microb. Aust. 32, 169–173 (2011)
11.103 S.Y. Ow, P.C. Wright: Current trends in high
throughput proteomics in cyanobacteria, FEBS
Lett. 583, 1744–1752 (2009)
11.104 J. Liu, L. Chen, J. Wang, J. Qiao, W. Zhang:
Proteomic analysis reveals resistance mechanism
against biofuel hexane in Synechocystis sp., PCC
6803, Biotechnol. Biofuels 5, 68 (2012)
11.105 J. Qiao, J. Wang, L. Chen, X. Tian, S. Huang,
X. Ren, W. Zhang: quantitative iTRAQ LC-MS/MS
proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis
sp. PCC 6803, J. Proteome Res. 11, 5286–5300
(2012)
11.106 W.M. van Gulik: Fast sampling for quantitative
microbial metabolomics, Current Opin. Biotechnol. 21, 27–34 (2010)
11.107 F.S.O. Fritzsch, C. Dusny, O. Frick, A. Schmid:
Single-cell analysis in biotechnology, systems biology, and biocatalysis, Annu. Rev. Chem. Biomol.
Eng. 3, 129–155 (2012)
11.108 K.E.J. Tyo, K. Kocharin, J. Nielsen: Toward designbased engineering of industrial microbes, Current
Opin. Microbiol. 13, 255–262 (2010)
11.109 S. Ishii, K. Tago, K. Senoo: Single-cell analysis
and isolation for microbiology and biotechnology: Methods and applications, Appl. Microbiol.
Biotechnol. 86, 1281–1292 (2010)
11.110 Y. Kang, M.H. Norris, J. Zarzycki-Siek, W.C. Nierman, S.P. Donachie, T.T. Hoang: Transcript amplification from single bacterium for transcriptome
analysis, Genome Res. 21, 925–935 (2011)