scholarly journals Position preference of essential genes in prokaryotic operons

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250380
Author(s):  
Tao Liu ◽  
Hao Luo ◽  
Feng Gao
Keyword(s):  
General Rule ◽  
Essential Genes ◽  
Position Preference ◽  
Bacterial Genomes ◽  
Average Position

Essential genes, which form the basis of life activities, are crucial for the survival of organisms. Essential genes tend to be located in operons, but how they are distributed in operons is still unclear for most prokaryotes. In order to clarify the general rule of position preference of essential genes in operons, an index of the average position of genes in an operon was proposed, and the distributions of essential and non-essential genes in operons in 51 bacterial genomes and two archaeal genomes were analyzed based on this new index. Consequently, essential genes were found to preferentially occupy the front positions of the operons, which tend to be expressed at higher levels.

A statistical feature of Hurst exponents of essential genes in bacterial genomes

2011 ◽  
Vol 4 (1) ◽  
pp. 93-98 ◽  
Author(s):  
Xiao Liu ◽  
Shi-Yuan Wang ◽  
Jia Wang
Keyword(s):  
Essential Genes ◽  
Bacterial Genomes ◽  
Statistical Feature ◽  
Hurst Exponents

scholarly journals Identification of Conserved Amino Acid Residues of the Salmonella σS Chaperone Crl Involved in Crl-σS Interactions

2009 ◽  
Vol 192 (4) ◽  
pp. 1075-1087 ◽  
Author(s):  
Véronique Monteil ◽  
Annie Kolb ◽  
Jacques D'Alayer ◽  
Pierre Beguin ◽  
Françoise Norel
Keyword(s):  
General Rule ◽  
Site Directed Mutagenesis ◽  
Ferric Uptake Regulator ◽  
Amino Acid Residues ◽  
Bacterial Genomes ◽  
E Coli ◽  
Core Enzyme ◽  
Serovar Typhimurium ◽  
Σ Factor ◽  
The Relationship

ABSTRACT Proteins that bind σ factors typically attenuate the function of the σ factor by restricting its access to the RNA polymerase (RNAP) core enzyme. An exception to this general rule is the Crl protein that binds the stationary-phase sigma factor σS (RpoS) and enhances its affinity for the RNAP core enzyme, thereby increasing expression of σS-dependent genes. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than rpoS. Seventeen residues are conserved in all members of the Crl family. Site-directed mutagenesis of the crl gene from Salmonella enterica serovar Typhimurium and complementation of a Δcrl mutant of Salmonella indicated that substitution of the conserved residues Y22, F53, W56, and W82 decreased Crl activity. This conclusion was further confirmed by promoter binding and abortive transcription assays. We also used a bacterial two-hybrid system (BACTH) to show that the four substitutions in Crl abolish Crl-σS interaction and that residues 1 to 71 in σS are dispensable for Crl binding. In Escherichia coli, it has been reported that Crl also interacts with the ferric uptake regulator Fur and that Fur represses crl transcription. However, the Salmonella Crl and Fur proteins did not interact in the BACTH system. In addition, a fur mutation did not have any significant effect on the expression level of Crl in Salmonella. These results suggest that the relationship between Crl and Fur is different in Salmonella and E. coli.

scholarly journals Using bacterial genomes and essential genes for the development of new antibiotics

2017 ◽  
Vol 134 ◽  
pp. 74-86 ◽  
Author(s):  
Francisco R. Fields ◽  
Shaun W. Lee ◽  
Michael J. McConnell
Keyword(s):  
Essential Genes ◽  
Bacterial Genomes ◽  
New Antibiotics

scholarly journals The tRNAargGene andengAAre Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

2012 ◽  
Vol 195 (2) ◽  
pp. 202-212 ◽  
Author(s):  
George diCenzo ◽  
Branislava Milunovic ◽  
Jiujun Cheng ◽  
Turlough M. Finan
Keyword(s):  
Brucella Abortus ◽  
Sinorhizobium Meliloti ◽  
Essential Genes ◽  
Host Bacterium ◽  
Synteny Analysis ◽  
Related Strain ◽  
Bacterial Genomes ◽  
Content Type ◽  
Sinorhizobium Medicae ◽  
Ancestral Strain

ABSTRACTBacterial genomes with two (or more) chromosome-like replicons are known, and these appear to be particularly frequent in alphaproteobacteria. The genome of the N2-fixing alfalfa symbiontSinorhizobium meliloti1021 contains a 3.7-Mb chromosome and 1.4-Mb (pSymA) and 1.7-Mb (pSymB) megaplasmids. In this study, the tRNAargandengAgenes, located on the pSymB megaplasmid, are shown to be essential for growth. These genes could be deleted from pSymB when copies were previously integrated into the chromosome. However, in the closely related strainSinorhizobium frediiNGR234, the tRNAargandengAgenes are located on the chromosome, in a 69-kb region designated theengA-tRNAarg-rmlCregion. This region includesbacA, a gene that is important for intracellular survival during host-bacterium interactions forS. melilotiand the related alphaproteobacteriumBrucella abortus. TheengA-tRNAarg-rmlCregion lies between thekdgKanddppF2(NGR_c24410) genes on theS. frediichromosome. Synteny analysis showed thatkdgKanddppF2orthologues are adjacent to each other on the chromosomes of 15 sequenced strains ofS. melilotiandSinorhizobium medicae, whereas the 69-kbengA-tRNAarg-rmlCregion is present on the pSymB-equivalent megaplasmids. This and other evidence strongly suggests that theengA-tRNAarg-rmlCregion translocated from the chromosome to the progenitor of pSymB in an ancestor common toS. melilotiandS. medicae. To our knowledge, this work represents one of the first experimental demonstrations that essential genes are present on a megaplasmid.

Application Of Electron Probe Analyses Of Minerals In Discussing The Relationship Between Ductile Deformation And Metamorphism

1990 ◽  
Vol 48 (2) ◽  
pp. 250-251
Author(s):  
Fan Guochuan ◽  
Sun Zhongshi
Keyword(s):  
Chemical Composition ◽  
Shear Deformation ◽  
Electron Probe ◽  
General Rule ◽  
Granulite Facies ◽  
Ductile Deformation ◽  
Higher Temperature ◽  
Ductile Shear ◽  
The Relationship ◽  
Ductile Shear Deformation

Under influence of ductile shear deformation, granulite facies mineral paragenesis underwent metamorphism and changes in chemical composition. The present paper discusses some changes in chemical composition of garnet in hypers thene_absent felsic gnesiss and of hypersthene in rock in early and late granulite facies undergone increasing ductile shear deformation .In garnet fetsic geniss, band structures were formed because of partial melting and resulted in zoning from massive⟶transitional⟶melanocrate zones in increasing deformed sequence. The electron-probe analyses for garnet in these zones are listed in table 1 . The Table shows that Mno, Cao contents in garnet decrease swiftly from slightly to intensely deformed zones.In slightly and moderately deformed zones, Mgo contents keep unchanged and Feo is slightly lower. In intensely deformed zone, Mgo contents increase, indicating a higher temperature. This is in accord with the general rule that Mgo contents in garnet increase with rising temperature.

Natural products in complex microbiomes – Assembling multiple bacterial genomes directly through shotgun metagenomics

Planta Medica ◽  
2014 ◽  
Vol 80 (10) ◽  
Author(s):  
IJ Miller ◽  
T Weyna ◽  
C Mlot ◽  
SS Fong ◽  
K McPhail ◽  
...  
Keyword(s):  
Natural Products ◽  
Bacterial Genomes ◽  
Shotgun Metagenomics

From the “Judicialization of Politics” to the “Politicization of Justice” in the UK and Switzerland

2016 ◽  
Vol 6 (2) ◽  
pp. 118-135
Author(s):  
Lucia Della Torre
Keyword(s):  
General Rule ◽  
The State ◽  
The Other ◽  
Specific Field ◽  
Widespread Phenomenon ◽  
Judicialization Of Politics ◽  
The Uk ◽  
Migration Law

Not very long ago, scholars saw it fit to name a new and quite widespread phenomenon they had observed developing over the years as the “judicialization” of politics, meaning by it the expanding control of the judiciary at the expenses of the other powers of the State. Things seem yet to have begun to change, especially in Migration Law. Generally quite a marginal branch of the State's corpus iuris, this latter has already lent itself to different forms of experimentations which then, spilling over into other legislative disciplines, end up by becoming the new general rule. The new interaction between the judiciary and the executive in this specific field as it is unfolding in such countries as the UK and Switzerland may prove to be yet another example of these dynamics.

ON CONSTRUCT OF THE RIGHT OF PRE-EMPTION IN RESPECT OF PARTICIPATORY INTEREST (SHARES)

2020 ◽  
Vol 20 (4) ◽  
pp. 94-219
Author(s):  
I.S. CHUPRUNOV
Keyword(s):  
General Rule ◽  
Constitutive Theory ◽  
Freedom Of Contract ◽  
Legal Nature ◽  
Public Corporation ◽  
Russian Law ◽  
Right Of First Refusal ◽  
The Right

The paper provides analysis of the legal nature and the mechanism for exercise of the right of pre-emption (right of first refusal) in respect of execution of a contract taking as an example of right of first refusal to purchase a stake in a non-public corporation, and also examines the boundaries of parties’ autonomy and freedom of contract in this area. The author comes to the conclusion that the key elements of the construction of the right of pre-emption are the transformation powers that belong to the right holder. The author also demonstrates that, notwithstanding their dominance in Russian law, the views, which suggest that exercise of the right of pre-emption leads to “transfer of rights and obligations of a purchaser” (the translative theory), should be rejected. These views must be replaced with the constitutive theory, according to which exercise of the right of pre-emption results in a new contract between the right holder and the seller (as a general rule, on the same terms that were agreed between the seller and the purchaser).

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