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Category:GO:0070475 ! rRNA base methylation

2011-04-06T18:29:51Z

165.91.51.6: New GO term category page

PMID:19786035

2010-05-11T17:36:03Z

165.91.51.6: Fill PMID: Page!

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 '''Jeong, H, Barbe, V, Lee, CH, Vallenet, D, Yu, DS, Choi, SH, Couloux, A, Lee, SW, Yoon, SH, Cattolico, L, Hur, CG, Park, HS, Ségurens, B, Kim, SC, Oh, TK, Lenski, RE, Studier, FW, Daegelen, P and Kim, JF''' (2009) Genome sequences of Escherichia coli B strains REL606 and BL21(DE3).''J. Mol. Biol.'' '''394''':644-52

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|{{TableHeadingColor}} |'''Abstract''' || <protect>Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19786035 PubMed]
Online version:[http://dx.doi.org/10.1016/j.jmb.2009.09.052 10.1016/j.jmb.2009.09.052]
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{| id="K4be99583a84ce" class=" tableEdit GO_table_reference"
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!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171987.K4be99583a84ce&page=171987&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
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PMID:19786035

2010-05-11T17:36:03Z

165.91.51.6: New PMID: Page!

PMID: 19786035

2010-05-11T17:36:03Z

165.91.51.6: New PMID: Page!

#REDIRECT [[PMID:19786035]]

PMID:19696877

2010-05-11T17:13:11Z

165.91.51.6: Fill PMID: Page!

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 '''Ndifon, W, Plotkin, JB and Dushoff, J''' (2009) On the accessibility of adaptive phenotypes of a bacterial metabolic network.''PLoS Comput. Biol.'' '''5''':e1000472

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|{{TableHeadingColor}} |'''Abstract''' || <protect>The mechanisms by which adaptive phenotypes spread within an evolving population after their emergence are understood fairly well. Much less is known about the factors that influence the evolutionary accessibility of such phenotypes, a pre-requisite for their emergence in a population. Here, we investigate the influence of environmental quality on the accessibility of adaptive phenotypes of Escherichia coli's central metabolic network. We used an established flux-balance model of metabolism as the basis for a genotype-phenotype map (GPM). We quantified the effects of seven qualitatively different environments (corresponding to both carbohydrate and gluconeogenic metabolic substrates) on the structure of this GPM. We found that the GPM has a more rugged structure in qualitatively poorer environments, suggesting that adaptive phenotypes could be intrinsically less accessible in such environments. Nevertheless, on average approximately 74% of the genotype can be altered by neutral drift, in the environment where the GPM is most rugged; this could allow evolving populations to circumvent such ruggedness. Furthermore, we found that the normalized mutual information (NMI) of genotype differences relative to phenotype differences, which measures the GPM's capacity to transmit information about phenotype differences, is positively correlated with (simulation-based) estimates of the accessibility of adaptive phenotypes in different environments. These results are consistent with the predictions of a simple analytic theory that makes explicit the relationship between the NMI and the speed of adaptation. The results suggest an intuitive information-theoretic principle for evolutionary adaptation; adaptation could be faster in environments where the GPM has a greater capacity to transmit information about phenotype differences. More generally, our results provide insight into fundamental environment-specific differences in the accessibility of adaptive phenotypes, and they suggest opportunities for research at the interface between information theory and evolutionary biology.</protect>
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|{{TableHeadingColor}} nowrap |'''Links''' ||
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19696877 PubMed]
Online version:[http://dx.doi.org/10.1371/journal.pcbi.1000472 10.1371/journal.pcbi.1000472]
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</protect>
==Significance {{HelpIcon|Help:Literature}} ==
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== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
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==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="F4be990272d605" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171985.F4be990272d605&page=171985&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
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==References==
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PMID:19696877

2010-05-11T17:13:11Z

165.91.51.6: New PMID: Page!