Pseudogene repair driven by selection pressure applied in experimental evolution

被引:19
作者
Anand, Amitesh [1 ]
Olson, Connor A. [1 ]
Yang, Laurence [1 ]
Sastry, Anand V. [1 ]
Catoiu, Edward [1 ]
Choudhary, Kumari Sonal [1 ]
Phaneuf, Patrick V. [1 ]
Sandberg, Troy E. [1 ]
Xu, Sibei [1 ]
Hefner, Ying [1 ]
Szubin, Richard [1 ]
Feist, Adam M. [1 ,2 ]
Palsson, Bernhard O. [1 ,2 ]
机构
[1] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA
[2] Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, Lyngby, Denmark
关键词
ESCHERICHIA-COLI; BACTERIAL; TRANSPORTER; GENES;
D O I
10.1038/s41564-018-0340-2
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Pseudogenes represent open reading frames that have been damaged by mutations, rendering the gene product nonfunctional. Pseudogenes are found in many genomes and are not always eliminated, even if they are potentially 'wasteful'. This raises a fundamental question about their prevalence. Here we report pseudogene efeU repair that restores the iron uptake system of Escherichia coli under a designed selection pressure during adaptive laboratory evolution.
引用
收藏
页码:386 / 389
页数:4
相关论文
共 31 条
[1]   Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants:: the Keio collection [J].
Baba, Tomoya ;
Ara, Takeshi ;
Hasegawa, Miki ;
Takai, Yuki ;
Okumura, Yoshiko ;
Baba, Miki ;
Datsenko, Kirill A. ;
Tomita, Masaru ;
Wanner, Barry L. ;
Mori, Hirotada .
MOLECULAR SYSTEMS BIOLOGY, 2006, 2 (1) :2006.0008
[2]   AfterQC: automatic filtering, trimming, error removing and quality control for fastq data [J].
Chen, Shifu ;
Huang, Tanxiao ;
Zhou, Yanqing ;
Han, Yue ;
Xu, Mingyan ;
Gu, Jia .
BMC BIOINFORMATICS, 2017, 18
[3]   Microbial laboratory evolution in the era of genome-scale science [J].
Conrad, Tom M. ;
Lewis, Nathan E. ;
Palsson, Bernhard O. .
MOLECULAR SYSTEMS BIOLOGY, 2011, 7
[4]   One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products [J].
Datsenko, KA ;
Wanner, BL .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (12) :6640-6645
[5]  
Deatherage DE, 2014, METHODS MOL BIOL, V1151, P165, DOI 10.1007/978-1-4939-0554-6_12
[6]   Confidence intervals that match Fisher's exact or Blaker's exact tests [J].
Fay, Michael P. .
BIOSTATISTICS, 2010, 11 (02) :373-374
[7]   REGULATION OF ENTEROBACTIN IRON TRANSPORT IN ESCHERICHIA-COLI - CHARACTERIZATION OF ENT-MU D(APR LAC) OPERON FUSIONS [J].
FLEMING, TP ;
NAHLIK, MS ;
MCINTOSH, MA .
JOURNAL OF BACTERIOLOGY, 1983, 156 (03) :1171-1177
[8]   A new ferrous iron-uptake transporter, EfeU (YcdN), from Escherichia coli [J].
Grosse, Cornelia ;
Scherer, Judith ;
Koch, Doreen ;
Otto, Markus ;
Taudte, Nadine ;
Grass, Gregor .
MOLECULAR MICROBIOLOGY, 2006, 62 (01) :120-131
[9]  
Katoh K, 2017, BRIEF BIOINFORM, Vbbx108, P1, DOI [10.1093/bib/bbx108, DOI 10.1093/BIB/BBX108]
[10]   The Extinction Dynamics of Bacterial Pseudogenes [J].
Kuo, Chih-Horng ;
Ochman, Howard .
PLOS GENETICS, 2010, 6 (08)