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Escherichia coli and Salmonella 2000: the View From Here

Moselio Schaechter
2004 EcoSal Plus  
From the E. coli point of view, does this part of the intestine resemble well-aerated Luria-Bertani broth?  ...  THE GENOME The chromosome of the K-12 strain of E. coli is made up of nearly 4,400 genes.  ... 
doi:10.1128/ecosalplus.1.4 pmid:26443369 fatcat:aoxfdrxgybax3d3rrnng3vlbby

Escherichia coli and Salmonella 2000: the View From Here

M. Schaechter, The View From Here Group
2001 Microbiology and Molecular Biology Reviews  
From the E. coli point of view, does this part of the intestine resemble well-aerated Luria-Bertani broth?  ...  THE GENOME The chromosome of the K-12 strain of E. coli is made up of nearly 4,400 genes.  ... 
doi:10.1128/mmbr.65.1.119-130.2001 pmid:11238988 pmcid:PMC99021 fatcat:pguhox576naajecyk2svcp3ksq

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli

Denis Thieffry, Araceli M. Huerta, Ernesto Pérez-Rueda, Julio Collado-Vides
1998 Bioessays  
regulatory networks, at least in the case of some of the best-characterized organisms.This paper presents a global characterization of the transcriptional regulation in Escherichia coli on the basis of  ...  genes regulating a given regulated gene.  ...  We also acknowledge Heladia Salgado for her contribution to the collection of regulatory information. This work was supported by grants from DGAPA-UNAM and Conacyt (to J. C.-V.).  ... 
doi:10.1002/(sici)1521-1878(199805)20:5<433::aid-bies10>3.0.co;2-2 pmid:9670816 fatcat:bzzlrdakxzdbzd7fhcen6xmlka

Biodegradation of Tetralin: Genomics, Gene Function and Regulation

Belén Floriano, Eduardo Santero, Francisca Reyes-Ramírez
2019 Genes  
Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain.  ...  A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory  ...  Conflicts of Interest: The authors declare no conflict of interest. Genes 2019, 10, 339  ... 
doi:10.3390/genes10050339 pmid:31064110 pmcid:PMC6563040 fatcat:hmk55rh76ng3xjfqyr45ly7avi

Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

Morgan N Price, Paramvir S Dehal, Adam P Arkin
2008 Genome Biology  
To understand how the regulation of these acquired genes evolved, we examined the evolutionary histories of transcription factors and of regulatory interactions from the model bacterium Escherichia coli  ...  Most bacterial genes were acquired by horizontal gene transfer from other bacteria instead of being inherited by continuous vertical descent from an ancient ancestor.  ...  We examined the highest Basic Local Alignment Search Tool (BLAST) scores of homologs within groups of genomes at increasing distances from Escherichia coli.  ... 
doi:10.1186/gb-2008-9-1-r4 pmid:18179685 pmcid:PMC2395238 fatcat:egjfaqr5nnh7vffgcrlgj2uajm

Conserved units of co-expression in bacterial genomes: an evolutionary insight into gene regulation [article]

Ivan Junier, Olivier Rivoire
2014 bioRxiv   pre-print
Genome-wide measurements of transcriptional activity in bacteria indicate that the transcription of successive genes is strongly correlated beyond the scale of operons.  ...  Here, we identify supra-operonic segments of consecutive genes by comparing gene proximity in thousands of bacterial genomes.  ...  The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement n609989.  ... 
doi:10.1101/012526 fatcat:o5e7e6nv65cupmddtvj2lvsbjq

Gene Regulation by H-NS as a Function of Growth Conditions Depends on Chromosomal Position in Escherichia coli

Elisa Brambilla, Bianca Sclavi
2015 G3: Genes, Genomes, Genetics  
Although in eukaryotic cells genomic position is known to play an important role in regulation of gene expression, it remains to be established whether in bacterial cells there is an influence of chromosomal  ...  Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins.  ...  Upstream of the promoter and down-stream of the yfp gene T1 terminators from the Escherichia coli rrnB coding sequence were added to stop transcription from RNA polymerases coming from neighboring genes  ... 
doi:10.1534/g3.114.016139 pmid:25701587 pmcid:PMC4390576 fatcat:hokti4xjybemvpvgio34mlkvye

A genome-wide screen for identifying all regulators of a target gene

Guillaume Baptist, Corinne Pinel, Caroline Ranquet, Jérôme Izard, Delphine Ropers, Hidde de Jong, Johannes Geiselmann
2013 Nucleic Acids Research  
We apply the method to identify the genes that control the expression of the gene acs, encoding the acetyl coenzyme A synthetase, in Escherichia coli.  ...  We confirm most of the known genetic regulators, including CRP-cAMP, IHF and components of the phosphotransferase system.  ...  Laure Giannone helped with the analysis of the data.  ... 
doi:10.1093/nar/gkt655 pmid:23892289 pmcid:PMC3783194 fatcat:akaijvklgzdqhomorltem574vq

Genome organization and long-range regulation of gene expression by enhancers

Andrea Smallwood, Bing Ren
2013 Current Opinion in Cell Biology  
Mapping these interactions and understanding how the 3D landscape of the genome constrains such interactions is fundamental to our understanding of mammalian gene regulation.  ...  It is now well accepted that cell-type specific gene regulation is under the purview of enhancers.  ...  Acknowledgments We thank members of the Ren lab, in particular Jesse Dixon and Feng Yue, for comments during the preparation of this manuscript.  ... 
doi:10.1016/j.ceb.2013.02.005 pmid:23465541 pmcid:PMC4180870 fatcat:wup6q2bborboppteezp4b5i57a

Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes

Porfirio Quintero-Cadena, Paul W. Sternberg
2016 G3: Genes, Genomes, Genetics  
By reanalyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size.  ...  We propose that enhancer sharing is commonplace among eukaryotes, and that EP distance is an important layer of information in gene regulation. KEYWORDS  ...  Our work was supported by the Howard Hughes Medical Institute, of which P.W.S. is an investigator. Author contributions: P.Q.C. performed the experiments and analyzed the data.  ... 
doi:10.1534/g3.116.036228 pmid:27799341 pmcid:PMC5144984 fatcat:rqbw5yjef5dvbocas3n6ndiuaa

Genome-Wide Identification of Genes Regulated by the Rcs Phosphorelay System inErwinia amylovora

Dongping Wang, Mingsheng Qi, Bernarda Calla, Schuyler S. Korban, Steven J. Clough, Peter J. A. Cock, George W. Sundin, Ian Toth, Youfu Zhao
2012 Molecular Plant-Microbe Interactions  
The e-Xtra logo stands for "electronic extra" and indicates that three supplementary tables and one supplementary figure are published online. e-Xtra *  ...  This project was supported by the Agriculture and Food Research Initiative Competitive Grants Program grant no. 2010-65110-20497 from the United States Department of Agriculture National Institute of Food  ...  Pritchard of the James Hutton Institute, Invergowrie, U.K. for helping design and for sharing the microarray.  ... 
doi:10.1094/mpmi-08-11-0207 pmid:21936662 fatcat:vynxddqwdndx5kdjt6q5ei3k74

Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation

I. Zwir, H. Huang, E. A. Groisman
2005 Bioinformatics  
Motivation: A critical challenge of the post-genomic era is to understand how genes are differentially regulated even when they belong to a given network.  ...  Results: Application of this method to the enteric bacteria Escherichia coli and Salmonella enterica uncovered novel members, as well as regulatory interactions in the regulon controlled by the PhoP protein  ...  This work was supported, in part, by the grant AI49561 from the National Institutes of Health to E.A.G., who is an Investigator of the Howard Hughes Medical Institute.  ... 
doi:10.1093/bioinformatics/bti672 pmid:16159917 fatcat:6a4sdsxl6fhrhj4unzyd5naq5a

A Cluster of ABA-Regulated Genes on Arabidopsis thaliana BAC T07M07

Ming Li Wang, Stephen Belmonte, Ulandt Kim, Maureen Dolan, John W. Morris, Howard M. Goodman
1999 Genome Research  
Most putative genes were confirmed by gel-based RNA profiling and a cluster of ABA-regulated genes was identified. One of the 24 genes, designatedPP2C5, encodes a putative protein phosphatase 2C.  ...  The encoded protein was expressed in Escherichia coli, and its enzyme activity in vitro was confirmed.[The sequence data described in this paper have been submitted to GenBank under accession no.  ...  Rather than studying a single gene's function and expression, with the use of sequence arrays one can view the genome as a whole to study multiple genes' function and expression (functional genomics)  ... 
doi:10.1101/gr.9.4.325 fatcat:aco76lgyivewxplqzdnoy7vyp4

Prediction of functional modules based on gene distributions in microbial genomes

Hongwei Wu, Fenglou Mao, Zhengchang Su, Victor Olman, Ying Xu
2005 Genome Informatics Series  
We then apply a threshold-based clustering algorithm to this gene network, and obtain modules for each of which the number of genes is bounded from above by a pre-specified value and the component genes  ...  We present a computational method for prediction of functional modules that can be directly applied to the newly sequenced microbial genomes for predicting gene functions and the component genes of biological  ...  When MaxSize is set at 10 (which corresponds to viewing the functional relatedness among genes at a much finer resolution level), 49 of these 92 Escherichia coli K12 genes are predicted to belong to 15  ... 
pmid:16901107 fatcat:hunqz5sclbal3pzissb67jgtcu

Genome-Wide Expression Analysis Indicates that FNR of Escherichia coli K-12 Regulates a Large Number of Genes of Unknown Function

Y. Kang, K. D. Weber, Y. Qiu, P. J. Kiley, F. R. Blattner
2005 Journal of Bacteriology  
The major regulator controlling the physiological switch between aerobic and anaerobic growth conditions in Escherichia coli is the DNA binding protein FNR.  ...  Ninety-one genes with no presently defined function were also altered in expression, including seven of the most highly anaerobically induced genes, six of which we found to be directly regulated by FNR  ...  We also thank Karen Wassarman for the rpoSЈ-lacZ strain. This work was supported by National Institutes of Health Grants GM-45844 (to P.J.K.) and GM35682 (to F.R.B.).  ... 
doi:10.1128/jb.187.3.1135-1160.2005 pmid:15659690 pmcid:PMC545700 fatcat:uhtpairjbjgfnjgisjbvwchw3q
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