Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

Science ◽  
2013 ◽  
Vol 342 (6157) ◽  
pp. 475-479 ◽  
Author(s):  
D. B. Goodman ◽  
G. M. Church ◽  
S. Kosuri
Keyword(s):  
Codon Bias ◽  
Bacterial Genes ◽  
Terminal Codon

scholarly journals Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli

2018 ◽  
Vol 70 (5) ◽  
pp. 894-905.e5 ◽  
Author(s):  
Sanchari Bhattacharyya ◽  
William M. Jacobs ◽  
Bharat V. Adkar ◽  
Jin Yan ◽  
Wenli Zhang ◽  
...  
Keyword(s):  
Codon Bias ◽  
E Coli ◽  
Shine Dalgarno Sequence ◽  
Terminal Codon

scholarly journals Accessibility of the Shine–Dalgarno sequence dictates N-terminal codon bias in E. coli

2017 ◽  
Author(s):  
Sanchari Bhattacharyya ◽  
William M. Jacobs ◽  
Bharat V. Adkar ◽  
Jin Yan ◽  
Wenli Zhang ◽  
...  
Keyword(s):  
Codon Bias ◽  
Mrna Levels ◽  
Coding Region ◽  
Synonymous Substitutions ◽  
E Coli ◽  
Protein Levels ◽  
Shine Dalgarno Sequence ◽  
General Physical ◽  
Molecular Base ◽  
Terminal Codon

AbstractDespite considerable efforts, no physical mechanism has been shown to explain N-terminal codon bias in prokaryotic genomes. Using a systematic study of synonymous substitutions in two endogenous E. coli genes, we show that interactions between the coding region and the upstream Shine–Dalgarno (SD) sequence modulate the efficiency of translation initiation, affecting both intracellular mRNA and protein levels due to the inherent coupling of transcription and translation in E. coli. We further demonstrate that far-downstream mutations can also modulate mRNA levels by occluding the SD sequence through the formation of non-equilibrium secondary structures. By contrast, a non-endogenous RNA polymerase that decouples transcription and translation largely alleviates the effects of synonymous substitutions on mRNA levels. Finally, a complementary statistical analysis of the E. coli genome specifically implicates avoidance of intra-molecular base-pairing with the SD sequence. Our results provide general physical insights into the coding-level features that optimize protein expression in prokaryotes.

The gut microbiota resistome provides development of drug resistance in causative agents of human infectious diseases

2017 ◽  
pp. 20-32 ◽  
Author(s):  
Е.Н. Ильина ◽  
Е.И. Олехнович ◽  
А.В. Павленко
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Integrated Approach ◽  
Modern Medicine ◽  
Pathogenic Microorganisms ◽  
Human Pathogens ◽  
Potential Source ◽  
Causative Agents ◽  
Bacterial Genes

С течением времени подходы к изучению резистентности к антибиотикам трансформировались от сосредоточения на выделенных в виде чистой культуры патогенных микроорганизмах к исследованию резистентности на уровне микробных сообществ, составляющих биотопы человека и окружающей среды. По мере того, как продвигается изучение устойчивости к антибиотикам, возникает необходимость использования комплексного подхода для улучшения информирования мирового сообщества о наблюдаемых тенденциях в этой области. Все более очевидным становится то, что, хотя не все гены резистентности могут географически и филогенетически распространяться, угроза, которую они представляют, действительно серьезная и требует комплексных междисциплинарных исследований. В настоящее время резистентность к антибиотикам среди патогенов человека стала основной угрозой в современной медицине, и существует значительный интерес к определению ниши, в которых бактерии могут получить гены антибиотикорезистентности, и механизмов их передачи. В данном обзоре мы рассматриваем проблемы, возникшие на фоне широкого использования человечеством антибактериальных препаратов, в свете формирования микрофлорой кишечника резервуара генов резистентности. Over the time, studies of antibiotic resistance have transformed from focusing on pathogenic microorganisms isolated as a pure culture to analysis of resistance at the level of microbial communities that constitute human and environmental biotopes. Advancing studies of antibiotic resistance require an integrated approach to enhance availability of information about observed tendencies in this field to the global community. It becomes increasingly obvious that, even though not all resistance genes can geographically and phylogenetically spread, the threat they pose is indeed serious and requires complex interdisciplinary research. Currently, the antibiotic resistance of human pathogens has become a challenge to modern medicine, which is now focusing on determining a potential source for bacterial genes of drug resistance and mechanisms for the gene transmission. In this review, we discussed problems generated by the widespread use of antibacterial drugs in the light of forming a reservoir of resistance genes by gut microflora.

Analysis of Nuclear Gene Codon Bias on Soybean Genome and Transcriptome

2011 ◽  
Vol 37 (6) ◽  
pp. 965-974 ◽  
Author(s):  
Le ZHANG ◽  
Long-Guo JIN ◽  
Ling LUO ◽  
Yue-Ping WANG ◽  
Zhi-Min DONG ◽  
...  
Keyword(s):  
Codon Bias ◽  
Nuclear Gene ◽  
Soybean Genome

Analysis of Codon Bias of NAD-ME Gene in Amaranthus hypochondriacus*

2011 ◽  
Vol 17 (1) ◽  
pp. 12-17
Author(s):  
Ping Li ◽  
Yunfeng BAI ◽  
Ruiyun FENG ◽  
Yuanyuan WANG ◽  
Weifeng ZHANG
Keyword(s):  
Codon Bias ◽  
Amaranthus Hypochondriacus

scholarly journals Mating Type in Chlamydomonas Is Specified by mid, the Minus-Dominance Gene

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 859-869 ◽  
Author(s):  
Patrick J Ferris ◽  
Ursula W Goodenough
Keyword(s):  
Transcription Factor ◽  
Mating Type ◽  
Codon Bias ◽  
Leucine Zipper ◽  
Laboratory Strain ◽  
Leucine Zipper Motif ◽  
Type Locus ◽  
Diploid Cells ◽  
Necessary And Sufficient

Diploid cells of Chlamydomonas reinhardtii that are heterozygous at the mating-type locus (mt  +/mt  –) differentiate as minus gametes, a phenomenon known as minus dominance. We report the cloning and characterization of a gene that is necessary and sufficient to exert this minus dominance over the plus differentiation program. The gene, called mid, is located in the rearranged (R) domain of the mt  – locus, and has duplicated and transposed to an autosome in a laboratory strain. The imp11 mt  – mutant, which differentiates as a fusion-incompetent plus gamete, carries a point mutation in mid. Like the fus1 gene in the mt  + locus, mid displays low codon bias compared with other nuclear genes. The mid sequence carries a putative leucine zipper motif, suggesting that it functions as a transcription factor to switch on the minus program and switch off the plus program of gametic differentiation. This is the first sex-determination gene to be characterized in a green organism.

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