Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli

被引:44
作者
Avcilar-Kucukgoze, Irem [1 ]
Bartholomaeus, Alexander [1 ,2 ]
Varela, Juan A. Cordero [1 ]
Kaml, Robert Franz-Xaver [3 ]
Neubauer, Peter [3 ]
Budisa, Nediljko [4 ]
Ignatova, Zoya [1 ,2 ]
机构
[1] Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14467 Potsdam, Germany
[2] Univ Hamburg, Biochem & Mol Biol, Martin Luther King Pl 6, D-20146 Hamburg, Germany
[3] Tech Univ Berlin, Bioproc Engn, Ackerstr 76, D-13355 Berlin, Germany
[4] Tech Univ Berlin, Biocatalysis, Muller Breslau Str 10, D-10623 Berlin, Germany
关键词
AMINO-ACID STARVATION; CODON USAGE; IN-VIVO; GROWTH; SYNTHETASE; RIBOSOME; PROTEIN; SCALE; AMINOACYLATION; DEAMINASE;
D O I
10.1093/nar/gkw697
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth.
引用
收藏
页码:8324 / 8334
页数:11
相关论文
共 56 条
[51]   High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP [J].
Woolstenhulme, Christopher J. ;
Guydosh, Nicholas R. ;
Green, Rachel ;
Buskirk, Allen R. .
CELL REPORTS, 2015, 11 (01) :13-21
[52]   INTRACELLULAR CONDITION OF ESCHERICHIA COLI TRANSFER RNA [J].
YEGIAN, CD ;
STENT, GS ;
MARTIN, EM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1966, 55 (04) :839-&
[53]   Folding at the birth of the nascent chain: coordinating translation with co-translational folding [J].
Zhang, Gong ;
Ignatova, Zoya .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2011, 21 (01) :25-31
[54]   Global and local depletion of ternary complex limits translational elongation [J].
Zhang, Gong ;
Fedyunin, Ivan ;
Miekley, Oskar ;
Valleriani, Angelo ;
Moura, Alessandro ;
Ignatova, Zoya .
NUCLEIC ACIDS RESEARCH, 2010, 38 (14) :4778-4787
[55]   Transient ribosomal attenuation coordinates protein synthesis and co-translational folding [J].
Zhang, Gong ;
Hubalewska, Magdalena ;
Ignatova, Zoya .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2009, 16 (03) :274-280
[56]   Deficiency in L-Serine Deaminase Interferes with One-Carbon Metabolism and Cell Wall Synthesis in Escherichia coli K-12 [J].
Zhang, Xiao ;
El-Hajj, Ziad W. ;
Newman, Elaine .
JOURNAL OF BACTERIOLOGY, 2010, 192 (20) :5515-5525