Comparative analysis of FUR regulons in gamma-proteobacteria

Panina, Ekaterina M.; Миронов, А.; Gelfand, Mikhail S.

doi:10.1093/nar/29.24.5195

Cited by 91 publications

(84 citation statements)

References 58 publications

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“…Together, these data demonstrate that Fur binds to the iha promoter at the site predicted by Panina et. al [20].…”

Section: Interaction Of the Iha Promoter With Furmentioning

confidence: 98%

“…al, who identified a putative Fur binding site upstream of iha that contains 13 of the 19 bases of the consensus site [20] and spans the −35 locus. To test this hypothesis, we first examined iha transcriptional regulation by constructing single copy chromosomal transcriptional fusions of approximately 1.6 kb of iha with the firefly luc reporter gene.…”

Section: Iha Is Repressed By Ironmentioning

confidence: 99%

“…This hypothesis is based on the presence of a ferric uptake regulator protein (Fur) binding site predicted upstream of the iha coding region [20].…”

Section: Introductionmentioning

confidence: 99%

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Expression of the Escherichia coli IrgA homolog adhesin is regulated by the ferric uptake regulation protein

Rashid

Tarr

Moseley

2006

Microbial Pathogenesis

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The IrgA homologue adhesin (Iha) is an adherence-conferring outer membrane protein of Escherichia coli associated with enterohemorrhagic and uropathogenic strains. Here, we used primer extension analysis to identify iha promoters in O157:H7 and uropathogenic E. coli strains. Transcriptional fusions demonstrated that iha transcription is repressed by iron. Gel shifts using purified ferric uptake regulator protein (Fur) demonstrated that repression involves a direct interaction between Fur and the iha promoter. We identified strain-dependent differences in iha expression and determined that single nucleotide polymorphisms upstream of the iha promoter, in particular position −85, contribute to differences in expression levels.

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“…Together, these data demonstrate that Fur binds to the iha promoter at the site predicted by Panina et. al [20].…”

Section: Interaction Of the Iha Promoter With Furmentioning

confidence: 98%

Section: Iha Is Repressed By Ironmentioning

confidence: 99%

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Expression of the Escherichia coli IrgA homolog adhesin is regulated by the ferric uptake regulation protein

Rashid

Tarr

Moseley

2006

Microbial Pathogenesis

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“…Although this is extremely difficult most of the time due to the low degree of sequence conservation in prokaryotic operating regions, some apparently successful attempts (based on the simultaneous analysis of several gamma proteobacterial genomes) have been reported already for regulons of highly structurally conserved regulators, including Fur. In Y. pestis, the presence of upstream Fur-boxes has lead to the identification of several previously characterized Furcontrolled operons (including, very surprisingly, the psaEF operon that is discussed above), as well as potentially new operons (Panina et al, 2001a). Similar studies have also been performed in Y. pestis with other regulators, such those of aromatic amino acid, ribose, arabinose, and xylose metabolism (Laikova et al, 2001;Panina et al, 2001b).…”

mentioning

confidence: 88%

Transcriptional Regulation inYersinia: An UpdateYersinia: An Update

2005

Current Issues in Molecular Biology

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In response to the ever-present need to adapt to environmental stress, bacteria have evolved complex (and often overlapping) regulatory networks that respond to various changes in growth conditions, including entry into the host. The expression of most bacterial virulence factors is regulated; thus the question of how bacteria orchestrate this process has become a recurrent research theme for every bacterial pathogen, and the three pathogenic Yersinia are no exception. The earliest studies of regulation in these species were prompted by the characterization of plasmid-encoded virulence determinants, and those conducted since have continued to focus on the principal aspects of virulence in these pathogens. Most Yersinia virulence factors are thermally regulated, and are active at either 28°C (the optimal growth temperature) or 37°C (the host temperature). However, regulation by this omnipresent thermal stimulus occurs through a wide variety of mechanisms, which generally act in conjunction with (or are modulated by) additional controls for other environmental cues such as pH, ion concentration, nutrient availability, osmolarity, oxygen tension and DNA damage. Yersinia's recent entry into the genome sequencing era has given scientists the opportunity to study these regulators on a genome-wide basis. This has prompted the first attempts to establish links between the presence or absence of regulatory elements and the three pathogenic species' respective lifestyles and degrees of virulence. IntroductionCompared to cells of multicellular organisms, microorganisms face a significant additional challenge: they encounter a wide array of sudden, intense and sometimes even life-threatening environmental changes, and must therefore rapidly modify their structure and metabolism accordingly. Although other mechanisms exist, these changes in bacterial physiology mainly occur by regulating the production of the appropriate structural proteins and enzymes. Adaptation of gene expression in response to such situations appears to be essential for bacterial survival, and thus the regulators involved in these processes should be treated as being as important as the effectors themselves. In bacterial pathogens like those of the Yersinia genus, most outside-to-inside stressinduced responses lead to changes in the expression of virulence factors. In fact, most of the known Yersinia virulence genes are regulated, and elements controlling their expression are thus also virulence factors.All regulatory systems have a common purpose: to create an interface between the perception of one or several stimuli and to activate or repress expression of their cognate effectors. As we will see by reviewing what is known about Yersinia, the means used to regulate the production of a given bacterial factor range from very simple mechanisms (where the DNA-binding properties of the transcriptional regulator are directly altered by the stimulus) to extremely complex systems which sometimes require lengthy signal transduction cascades and/or simul...

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“…The multiple gene, single species approach recognizes motifs because they recur with few changes in the promoters of multiple genes within a single genome (Stormo and Hartzell, 1989;Lawrence et al, 1993;Hertz and Stormo, 1999;Bailey et al, 2006;Elemento et al, 2007). In contrast, the single gene, multiple species-or phylogenetic footprinting-approach recognizes motifs in a single promoter region by their conservation across species, which is assumed to be greater than that of the surrounding background sequence (Gelfand, 1999;McGuire et al, 2000;McCue et al, 2001;Panina et al, 2001;Rajewsky et al, 2002;Frazer et al, 2003;Panina et al, 2003;Marchal et al, 2004). These methods work because binding sites are typically under selective pressure and therefore mutate more slowly than the surrounding sequence.…”

Section: Introductionmentioning

confidence: 99%

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs

Ihuegbu

Stormo

Buhler

2012

Journal of Computational Biology

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Regulatory sites that control gene expression are essential to the proper functioning of cells, and identifying them is critical for modeling regulatory networks. We have developed Magma (Multiple Aligner of Genomic Multiple Alignments), a software tool for multiple species, multiple gene motif discovery. Magma identifies putative regulatory sites that are conserved across multiple species and occur near multiple genes throughout a reference genome. Magma takes as input multiple alignments that can include gaps. It uses efficient clustering methods that make it about 70 times faster than PhyloNet, a previous program for this task, with slightly greater sensitivity. We ran Magma on all non-coding DNA conserved between Caenorhabditis elegans and five additional species, about 70 Mbp in total, in < 4 h. We obtained 2,309 motifs with lengths of 6-20 bp, each occurring at least 10 times throughout the genome, which collectively covered about 566 kbp of the genomes, approximately 0.8% of the input. Predicted sites occurred in all types of non-coding sequence but were especially enriched in the promoter regions. Comparisons to several experimental datasets show that Magma motifs correspond to a variety of known regulatory motifs.

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Comparative analysis of FUR regulons in gamma-proteobacteria

Cited by 91 publications

References 58 publications

Expression of the Escherichia coli IrgA homolog adhesin is regulated by the ferric uptake regulation protein

Expression of the Escherichia coli IrgA homolog adhesin is regulated by the ferric uptake regulation protein

Transcriptional Regulation inYersinia: An UpdateYersinia: An Update

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs

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