Abstract：
:The redundancy of the genetic code implies that most amino acids are encoded by multiple synonymous codons. In all domains of life, a biased frequency of synonymous codons is observed at the genome level, in functionally related genes (e.g., in operons), and within single genes. Other codon bias variants include biased codon pairs and codon co-occurrence. Although translation initiation is the key step in protein synthesis, it is generally accepted that codon bias contributes to translation efficiency by tuning the elongation rate of the process. Moreover, codon bias plays an important role in controlling a multitude of cellular processes, ranging from differential protein production to protein folding. Here we review currently known types of codon bias and how they may influence translation. We discuss how understanding the principles of codon bias and translation can contribute to improved protein production and developments in synthetic biology.
journal_name
Mol Celljournal_title
Molecular cellauthors
Quax TE,Claassens NJ,Söll D,van der Oost Jdoi
10.1016/j.molcel.2015.05.035subject
Has Abstractpub_date
2015-07-16 00:00:00pages
149-61issue
2eissn
1097-2765issn
1097-4164pii
S1097-2765(15)00402-5journal_volume
59pub_type
杂志文章,评审相关文献
MOLECULAR CELL文献大全abstract：:Trimethylation of histone H3 on lysine 4 (H3K4me3) localizes near the 5' region of genes and is tightly associated with active loci. Several proteins, such as CHD1, BPTF, JMJD2A, and the ING tumor suppressor family, directly recognize this lysine methyl mark. However, how H3K4me3 recognition participates in active tra...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2007.11.010
更新日期：2007-11-30 00:00:00
abstract：:Signaling by TGFbeta regulates the expression of hundreds of genes. The rapid repression of c-Myc stands out because of its roles in growth control and cancer. Recent work shows that c-Myc repression by TGFbeta is mediated by the nuclear translocation of a novel, preformed complex composed of Smad3, E2F4 or E2F5, and ...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/s1097-2765(02)00584-1
更新日期：2002-07-01 00:00:00
abstract：:The tumor suppressor BAP1 interacts with chromatin-associated proteins and regulates cell proliferation, but its mechanism of action and regulation remain poorly defined. We show that the ubiquitin-conjugating enzyme UBE2O multi-monoubiquitinates the nuclear localization signal of BAP1, thereby inducing its cytoplasmi...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2014.03.002
更新日期：2014-05-08 00:00:00
abstract：:In this issue, Song et al. (2014) describe how microtubules and the RAN GTPase/importin-β system collaborate to control timing of HURP action and its turnover via the anaphase promoting complex (APC)-proteasome system, thereby ensuring temporal control of late mitotic events. ...
journal_title：Molecular cell
pub_type： 评论,杂志文章
doi：10.1016/j.molcel.2014.01.007
更新日期：2014-01-23 00:00:00
abstract：:Networks of protein interactions coordinate cellular functions. We describe a bimolecular fluorescence complementation (BiFC) assay for determination of the locations of protein interactions in living cells. This approach is based on complementation between two nonfluorescent fragments of the yellow fluorescent protei...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/s1097-2765(02)00496-3
更新日期：2002-04-01 00:00:00
abstract：:Interphase chromatin is organized into topologically associating domains (TADs). Within TADs, chromatin looping interactions are formed between DNA regulatory elements, but their functional importance for the establishment of the 3D genome organization and gene regulation during development is unclear. Using high-reso...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2018.05.032
更新日期：2018-07-05 00:00:00
abstract：:A defining feature of centromeres is the presence of the histone H3 variant CENP-A(Cnp1). It is not known how CENP-A(Cnp1) is specifically delivered to, and assembled into, centromeric chromatin. Through a screen for factors involved in kinetochore integrity in fission yeast, we identified Sim3. Sim3 is homologous to ...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2007.10.010
更新日期：2007-12-28 00:00:00
abstract：:The histone methyltransferase PR-Set7/Set8 is the sole enzyme that catalyzes monomethylation of histone H4 at K20 (H4K20me1). Previous reports document disparate evidence regarding PR-Set7 expression during the cell cycle, the biological relevance of PR-Set7 interaction with PCNA, and its role in the cell. We find tha...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2010.10.011
更新日期：2010-11-12 00:00:00
abstract：:The SMN complex assembles Sm cores on snRNAs, a key step in the biogenesis of snRNPs, the spliceosome's major components. Here, using SMN complex inhibitors identified by high-throughput screening and a ribo-proteomic strategy on formaldehyde crosslinked RNPs, we dissected this pathway in cells. We show that protein s...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2010.03.014
更新日期：2010-05-28 00:00:00
abstract：:We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-beta-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, inc...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2010.06.021
更新日期：2010-07-30 00:00:00
abstract：:Alternative mRNA splicing of the fibronectin EDI exon is controlled by a purine-rich exonic splicing enhancer (ESE), postulated as a binding site for SR proteins. By using a transient expression alternative splicing assay combined with promoter swapping, we have demonstrated that the promoter can also control EDI spli...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/s1097-2765(00)80372-x
更新日期：1999-08-01 00:00:00
abstract：:Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in prokaryotes. The system preserves memories of prior infections by integrating short segments of foreign DNA, termed spacers, into the CRISPR array in a process termed adaptati...
journal_title：Molecular cell
pub_type： 杂志文章,评审
doi：10.1016/j.molcel.2016.01.030
更新日期：2016-03-17 00:00:00
abstract：:Environmental cues provoke rapid transitions in gene expression to support growth and cellular plasticity through incompletely understood mechanisms. Lin28 RNA-binding proteins have evolutionarily conserved roles in post-transcriptional coordination of pro-growth gene expression, but signaling pathways allowing trophi...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2016.12.025
更新日期：2017-02-02 00:00:00
abstract：:The mRNA cap structure is bound by either the nuclear (CBC) or the cytoplasmic (eIF4F) cap binding complex. Following mRNA export, CBC must be exchanged for eIF4F in the cytoplasm. It is not known how this exchange occurs or how this RNP remodeling event is integrated with mRNA function. Here we report genetic and bio...
journal_title：Molecular cell
pub_type： 杂志文章
doi：
更新日期：2000-07-01 00:00:00
abstract：:The genomes of mammalian neurons contain uniquely high levels of non-CG DNA methylation that can be bound by the Rett syndrome protein, MeCP2, to regulate gene expression. How patterns of non-CG methylation are established in neurons and the mechanism by which this methylation works with MeCP2 to control gene expressi...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2019.10.033
更新日期：2020-01-16 00:00:00
abstract：:Identifying DNA fragile sites is crucial to reveal hotspots of genomic rearrangements, yet their precise mapping has been a challenge. A new study in this issue of Molecular Cell (Canela et al., 2016) introduces a highly sensitive and accurate method to detect DNA breaks in vivo that can be adapted to various experime...
journal_title：Molecular cell
pub_type： 评论,杂志文章
doi：10.1016/j.molcel.2016.08.012
更新日期：2016-09-01 00:00:00
abstract：:The tumor suppressor protein, p53, plays a critical role in mediating cellular response to stress signals by regulating genes involved in cell cycle arrest and apoptosis. p53 is believed to be inactive for DNA binding unless its C terminus is modified or structurally altered. We show that unmodified p53 actively binds...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/s1097-2765(01)00283-0
更新日期：2001-07-01 00:00:00
abstract：:MeCP2 is an essential transcriptional repressor that mediates gene silencing through binding to methylated DNA. Binding specificity has been thought to depend on hydrophobic interactions between cytosine methyl groups and a hydrophobic patch within the methyl-CpG-binding domain (MBD). X-ray analysis of a methylated DN...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2007.12.028
更新日期：2008-02-29 00:00:00
abstract：:How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains unanswered today. Early biochemical and microscopic studies revealed the existence of chromatin domains and loops as a pervasive feature of interphase chromosomes, but the biological implications of such organizational features were...
journal_title：Molecular cell
pub_type： 杂志文章,评审
doi：10.1016/j.molcel.2016.05.018
更新日期：2016-06-02 00:00:00
abstract：:Nucleosomes are barriers to transcription in vitro; however, their effects on RNA polymerase in vivo are unknown. Here we describe a simple and general strategy to comprehensively map the positions of elongating and arrested RNA polymerase II (RNAPII) at nucleotide resolution. We find that the entry site of the first ...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2014.02.014
更新日期：2014-03-06 00:00:00
abstract：:RNA polymerases (RNAPs) are core components of the cellular transcriptional machinery. Progress with functional studies of eukaryotic RNAPs has been delayed by the fact that it has not yet been possible to assemble active enzymes from individual subunits. Archaeal RNAPs are directly comparable to eukaryotic RNAPII in ...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/s1097-2765(02)00629-9
更新日期：2002-09-01 00:00:00
abstract：:Mutations in Hnf-1alpha are the most common Mendelian cause of diabetes mellitus. To elucidate the molecular function of a mutational hotspot, we cocrystallized human HNF-1alpha 83-279 with a high-affinity promoter and solved the structure of the complex. Two identical protein molecules are bound to the promoter. Each...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/s1097-2765(02)00704-9
更新日期：2002-11-01 00:00:00
abstract：:Despite the importance of retinoic acid (RA) signaling and histone monoubiquitination in determining cell fate, the underlying mechanism linking the two processes is poorly explored. We describe that additional sex comb-like 1 (ASXL1) represses RA receptor activity by cooperating with BRCA1-associated protein 1 (BAP1)...
journal_title：Molecular cell
pub_type： 杂志文章,收录出版
doi：10.1016/j.molcel.2013.06.005
更新日期：2013-07-25 00:00:00
abstract：:Epigenetic silencing of transposons by Piwi-interacting RNAs (piRNAs) constitutes an RNA-based genome defense mechanism. Piwi endonuclease action amplifies the piRNA pool by generating new piRNAs from target transcripts by a poorly understood mechanism. Here, we identified mouse Fkbp6 as a factor in this biogenesis pa...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2012.07.019
更新日期：2012-09-28 00:00:00
abstract：:Rad51 is a DNA recombinase functioning in the repair of DNA double-strand breaks and the generation of genetic diversity by homologous recombination (HR). In the presence of ATP, Rad51 self-assembles into an extended polymer on single-stranded DNA to catalyze strand exchange. Inappropriate HR causes genomic instabilit...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2009.05.026
更新日期：2009-07-10 00:00:00
abstract：:Eukaryotic neurotransmitter:sodium symporters (NSSs), targets for antidepressants and psychostimulants, terminate neurotransmission by sodium-driven reuptake. The crystal structure of LeuT(Aa), a prokaryotic NSS homolog, revealed an occluded state in which one leucine and two Na(+) ions are bound, but provided limited...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2008.05.008
更新日期：2008-06-20 00:00:00
abstract：:DNA replication is initiated by assembly of the kinase cell division cycle 7 (CDC7) with its regulatory activation subunit, activator of S-phase kinase (ASK), to activate DNA helicase. However, the mechanism underlying regulation of CDC7-ASK complex is unclear. Here, we show that ADP generated from CDC7-mediated MCM p...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2018.09.007
更新日期：2018-11-15 00:00:00
abstract：:Poly-ubiquitin chains direct protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 during ATP-dependent substrate degradation. Rapid deubiquitination is required for efficient degradation but must be restricted to committed substrates that are engaged with the ATPase motor to pre...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2017.07.023
更新日期：2017-09-07 00:00:00
abstract：:X chromosome inactivation (XCI) depends on a noncoding sense-antisense transcript pair, Xist and Tsix. At the onset of XCI, Xist RNA accumulates on one of two Xs, coating and silencing the chromosome in cis. The molecular basis for monoallelic Xist upregulation is not known, though evidence predominantly supports a po...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2006.01.028
更新日期：2006-03-03 00:00:00
abstract：:The proteolytic activation of the membrane-associated transcription factor pro-sigma(K) is controlled by a signal transduction pathway during sporulation in the bacterium Bacillus subtilis. The pro-sigma(K) processing enzyme SpoIVFB, a membrane-embedded metalloprotease, is held inactive by two other integral-membrane ...
journal_title：Molecular cell
pub_type： 杂志文章
doi：10.1016/j.molcel.2006.05.019
更新日期：2006-07-07 00:00:00
