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Volumn 5, Issue , 2015, Pages

Essentiality drives the orientation bias of bacterial genes in a continuous manner

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENE; BACTERIAL GENOME; CORRELATION COEFFICIENT; DNA STRAND; ESSENTIAL GENE; QUANTITATIVE ANALYSIS; QUANTITATIVE STUDY; BACTERIAL CHROMOSOME; GENE EXPRESSION; GENE ORDER; REPRODUCTIVE FITNESS;

EID: 84946925898     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep16431     Document Type: Article
Times cited : (12)

References (33)
  • 1
    • 56949097722 scopus 로고    scopus 로고
    • Evolution of genome architecture
    • Koonin, E. V. Evolution of genome architecture. Int. J. Biochem. Cell. Biol. 41, 298-306 (2009).
    • (2009) Int. J. Biochem. Cell. Biol. , vol.41 , pp. 298-306
    • Koonin, E.V.1
  • 2
    • 0036567231 scopus 로고    scopus 로고
    • Pyrococcus genome comparison evidences chromosome shuffling-driven evolution
    • Zivanovic, Y., Lopez, P., Philippe, H. & Forterre, P. Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res. 30, 1902-1910 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1902-1910
    • Zivanovic, Y.1    Lopez, P.2    Philippe, H.3    Forterre, P.4
  • 3
    • 84902553494 scopus 로고    scopus 로고
    • Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: A new appraisal
    • Saha, S. K., Goswami, A. & Dutta, C. Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal. BMC Genomics. 15, 430 (2014).
    • (2014) BMC Genomics , vol.15 , pp. 430
    • Saha, S.K.1    Goswami, A.2    Dutta, C.3
  • 4
    • 0032417093 scopus 로고    scopus 로고
    • Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
    • McLean, M. J., Wolfe, K. H. & Devine, K. M. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes, J. Mol. Evol. 47, 691-696 (1998).
    • (1998) J. Mol. Evol. , vol.47 , pp. 691-696
    • McLean, M.J.1    Wolfe, K.H.2    Devine, K.M.3
  • 5
    • 20444485193 scopus 로고    scopus 로고
    • Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication
    • Price, M. N., Alm, E. J. & Arkin, A. P. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Res. 33, 3224-3234 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. 3224-3234
    • Price, M.N.1    Alm, E.J.2    Arkin, A.P.3
  • 6
    • 0036709941 scopus 로고    scopus 로고
    • Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?
    • Rocha, E. Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol. 10, 393-395 (2002).
    • (2002) Trends Microbiol. , vol.10 , pp. 393-395
    • Rocha, E.1
  • 7
    • 34447108347 scopus 로고    scopus 로고
    • Replication-associated purine asymmetry may contribute to strand-biased gene distribution
    • Hu, J., Zhao, X. & Yu, J. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Genomics 90, 186-194 (2007).
    • (2007) Genomics , vol.90 , pp. 186-194
    • Hu, J.1    Zhao, X.2    Yu, J.3
  • 8
    • 0042667165 scopus 로고    scopus 로고
    • Essentiality, not expressiveness, drives gene-strand bias in bacteria
    • Rocha, E. P. & Danchin, A. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nature genetics 34, 377 (2003).
    • (2003) Nature Genetics , vol.34 , pp. 377
    • Rocha, E.P.1    Danchin, A.2
  • 9
    • 77952744822 scopus 로고    scopus 로고
    • Functionality of essential genes drives gene strand-bias in bacterial genomes
    • Lin, Y., Gao, F. & Zhang, C. T. Functionality of essential genes drives gene strand-bias in bacterial genomes. Biochem. Biophys. Res. Commun. 396, 472-476 (2010).
    • (2010) Biochem. Biophys. Res. Commun. , vol.396 , pp. 472-476
    • Lin, Y.1    Gao, F.2    Zhang, C.T.3
  • 10
    • 84867696427 scopus 로고    scopus 로고
    • Essential genes as antimicrobial targets and cornerstones of synthetic biology
    • Juhas, M., Eberl, L. & Church, G. M. Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol. 30, 601-607 (2012).
    • (2012) Trends Biotechnol. , vol.30 , pp. 601-607
    • Juhas, M.1    Eberl, L.2    Church, G.M.3
  • 11
    • 84876808409 scopus 로고    scopus 로고
    • From essential to persistent genes: A functional approach to constructing synthetic life
    • Acevedo-Rocha, C. G., Fang, G., Schmidt, M., Ussery, D. W. & Danchin, A. From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet. 29, 273-279 (2013).
    • (2013) Trends Genet. , vol.29 , pp. 273-279
    • Acevedo-Rocha, C.G.1    Fang, G.2    Schmidt, M.3    Ussery, D.W.4    Danchin, A.5
  • 12
    • 84922259838 scopus 로고    scopus 로고
    • Novel essential gene involved in 16S rRNA processing in Escherichia coli
    • Kurata, T. et al. Novel essential gene involved in 16S rRNA processing in Escherichia coli. J. Mol. Biol. 427, 955-965 (2015).
    • (2015) J. Mol. Biol. , vol.427 , pp. 955-965
    • Kurata, T.1
  • 13
    • 31544450286 scopus 로고    scopus 로고
    • Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
    • Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
    • (2006) Mol. Syst. Biol. , vol.2
    • Baba, T.1
  • 14
    • 42949142245 scopus 로고    scopus 로고
    • A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1
    • de Berardinis, V. et al. A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol. Syst. Biol. 4, 174 (2008).
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 174
    • De Berardinis, V.1
  • 15
    • 33644504829 scopus 로고    scopus 로고
    • An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants
    • Liberati, N. T. et al. An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc. Natl. Acad. Sci. USA 103, 2833-2838 (2006).
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 2833-2838
    • Liberati, N.T.1
  • 16
    • 33846504443 scopus 로고    scopus 로고
    • A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate
    • Gallagher, L. A. et al. A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate. Proc. Natl. Acad. Sci. USA 104, 1009-1014 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 1009-1014
    • Gallagher, L.A.1
  • 17
    • 0346494858 scopus 로고    scopus 로고
    • DEG: A database of essential genes
    • Zhang, R., Ou, H. Y. & Zhang, C. T. DEG: a database of essential genes. Nucleic Acids Res 32, D271-D272 (2004).
    • (2004) Nucleic Acids Res , vol.32 , pp. D271-D272
    • Zhang, R.1    Ou, H.Y.2    Zhang, C.T.3
  • 18
    • 84902449498 scopus 로고    scopus 로고
    • Predicting bacterial essential genes using only sequence composition information
    • Ning, L. W. et al. Predicting bacterial essential genes using only sequence composition information. Genet. Mol. Res. 13, 4564-4572 (2014).
    • (2014) Genet. Mol. Res. , vol.13 , pp. 4564-4572
    • Ning, L.W.1
  • 19
    • 33749075731 scopus 로고    scopus 로고
    • In silico prediction of yeast deletion phenotypes
    • Saha, S. & Heber, S. In silico prediction of yeast deletion phenotypes. Genet. Mol. Res. 5, 224-232 (2006).
    • (2006) Genet. Mol. Res. , vol.5 , pp. 224-232
    • Saha, S.1    Heber, S.2
  • 21
    • 77955077532 scopus 로고    scopus 로고
    • Identifying essential genes in bacterial metabolic networks with machine learning methods
    • Plaimas, K., Eils, R. & Konig, R. Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Syst. Biol. 4, 56 (2010).
    • (2010) BMC Syst. Biol. , vol.4 , pp. 56
    • Plaimas, K.1    Eils, R.2    Konig, R.3
  • 22
    • 79951573994 scopus 로고    scopus 로고
    • Investigating the predictability of essential genes across distantly related organisms using an integrative approach
    • Deng, J. et al. Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res. 39, 795-807 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. 795-807
    • Deng, J.1
  • 23
    • 84881583820 scopus 로고    scopus 로고
    • Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny
    • Wei, W., Ning, L. W., Ye, Y. N. & Guo, F. B. Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny. PloS ONE 8, e72343 (2013).
    • (2013) PloS ONE , vol.8
    • Wei, W.1    Ning, L.W.2    Ye, Y.N.3    Guo, F.B.4
  • 24
    • 84987678568 scopus 로고    scopus 로고
    • IFIM: A database of integrated fitness information for microbial genes
    • Wei, W. et al. IFIM: a database of integrated fitness information for microbial genes. Database (Oxford) 11, pii:bau052 (2014).
    • (2014) Database (Oxford) , vol.11
    • Wei, W.1
  • 25
    • 84905974513 scopus 로고    scopus 로고
    • Variation in the fitness effects of mutations with population density and size in Escherichia coli
    • Cao, H., Butler, K., Hossain, M. & Lewis, J. D. Variation in the fitness effects of mutations with population density and size in Escherichia coli. PLoS One 9, e105369 (2014).
    • (2014) PLoS One , vol.9
    • Cao, H.1    Butler, K.2    Hossain, M.3    Lewis, J.D.4
  • 26
    • 84861552714 scopus 로고    scopus 로고
    • High-throughput comparison of gene fitness among related bacteria
    • Canals, R. et al. High-throughput comparison of gene fitness among related bacteria. BMC Genomics 13, 212 (2012).
    • (2012) BMC Genomics , vol.13 , pp. 212
    • Canals, R.1
  • 27
    • 84866916315 scopus 로고    scopus 로고
    • The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces
    • Mao, X., Zhang, H., Yin, Y. & Xu, Y. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. Nucleic Acids Res. 40, 8210-8218 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. 8210-8218
    • Mao, X.1    Zhang, H.2    Yin, Y.3    Xu, Y.4
  • 28
    • 84875609978 scopus 로고    scopus 로고
    • Accelerated gene evolution through replication-transcription conflicts
    • Paul, S., Million-Weaver, S., Chattopadhyay, S., Sokurenko, E. & Merrikh, H. Accelerated gene evolution through replication-transcription conflicts. Nature 495, 512-515 (2013).
    • (2013) Nature , vol.495 , pp. 512-515
    • Paul, S.1    Million-Weaver, S.2    Chattopadhyay, S.3    Sokurenko, E.4    Merrikh, H.5
  • 29
    • 84892535526 scopus 로고    scopus 로고
    • Why are genes encoded on the lagging strand of the bacterial genome?
    • Chen, X. & Zhang, J. Why are genes encoded on the lagging strand of the bacterial genome? Genome Biol. Evol. 5, 2436-2439 (2013).
    • (2013) Genome Biol. Evol. , vol.5 , pp. 2436-2439
    • Chen, X.1    Zhang, J.2
  • 30
    • 84891786814 scopus 로고    scopus 로고
    • DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements
    • Luo, H., Lin, Y., Gao, F., Zhang, C. T. & Zhang, R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res 42, D574-D580 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. D574-D580
    • Luo, H.1    Lin, Y.2    Gao, F.3    Zhang, C.T.4    Zhang, R.5
  • 31
    • 84874271270 scopus 로고    scopus 로고
    • NCBI GEO: Archive for functional genomics data sets-update
    • Barrett, T. et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 41, 991-995 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. 991-995
    • Barrett, T.1
  • 32
    • 84876566990 scopus 로고    scopus 로고
    • DoriC 5.0: An updated database of oriC regions in both bacterial and archaeal genomes
    • Gao, F., Luo, H. & Zhang, C. T. DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res. 41, 90-93 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. 90-93
    • Gao, F.1    Luo, H.2    Zhang, C.T.3
  • 33
    • 34547912489 scopus 로고    scopus 로고
    • DoriC: A database of oriC regions in bacterial genomes
    • Gao, F. & Zhang, C. T. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 23, 1866-1867 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1866-1867
    • Gao, F.1    Zhang, C.T.2


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