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  • 1
    Electronic Resource
    Electronic Resource
    The Evolutionary History of Carbamoyltransferases: A Complex Set of Paralogous Genes Was Already Present in the Last Universal Common Ancestor (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 461-473 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Carbamoyltransferases — ATCase — OTCase — Protein evolution — Gene duplication — Paralogous proteins — Last universal common ancestor — Molecular phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Forty-four sequences of ornithine carbamoyltransferases (OTCases) and 33 sequences of aspartate carbamoyltransferases (ATCases) representing the three domains of life were multiply aligned and a phylogenetic tree was inferred from this multiple alignment. The global topology of the composite rooted tree (each enzyme family being used as an outgroup to root the other one) suggests that present-day genes are derived from paralogous ancestral genes which were already of the same size and argues against a mechanism of fusion of independent modules. A closer observation of the detailed topology shows that this tree could not be used to assess the actual order of organismal descent. Indeed, this tree displays a complex topology for many prokaryotic sequences, with polyphyly for Bacteria in both enzyme trees and for the Archaea in the OTCase tree. Moreover, representatives of the two prokaryotic Domains are found to be interspersed in various combinations in both enzyme trees. This complexity may be explained by assuming the occurrence of two subfamilies in the OTCase tree (OTC α and OTC β) and two other ones in the ATCase tree (ATC I and ATC II). These subfamilies could have arisen from duplication and selective losses of some differentiated copies during the successive speciations. We suggest that Archaea and Eukaryotes share a common ancestor in which the ancestral copies giving the present-day ATC II/OTC β combinations were present, whereas Bacteria comprise two classes: one containing the ATC II/OTC α combination and the other harboring the ATC I/OTC β combination. Moreover, multiple horizontal gene transfers could have occurred rather recently amongst prokaryotes. Whichever the actual history of carbamoyltransferases, our data suggest that the last common ancestor to all extant life possessed differentiated copies of genes coding for both carbamoyltransferases, indicating it as a rather sophisticated organism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006569
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  • 2
    Electronic Resource
    Electronic Resource
    Integration Host Factor (IHF) modulates the expression of the pyrimidine-specific promoter of the carAB operons of Escherichia coli K12 and Salmonella typhimurium LT2 (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 273-286 
    Details
    ISSN: 1617-4623
    Keywords: Integration Host Factor ; carAB ; Pyrimidine regulation ; Escherichia coli K12 ; Salmonella typhimurium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We report the identification of Integration Host Factor (IHF) as a new element involved in modulation of P1, the upstream pyrimidine-specific promoter of the Escherichia coli K12 and Salmonella typhimurium carAB operons. Band-shift assays, performed with S-30 extracts of the wild type and a himA, hip double mutant or with purified IHF demonstrate that, in vitro, this factor binds to a region 300 by upstream of the transcription initiation site of P1 in both organisms. This was confirmed by deletion analysis of the target site. DNase I, hydroxyl radical and dimethylsulphate footprinting experiments allowed us to allocate the IHF binding site to a 38 bp, highly A + T-rich stretch, centred around nucleotide −305 upstream of the transcription initiation site. Protein-DNA contacts are apparently spread over a large number of bases and are mainly located in the minor groove of the helix. Measurements of carbamoyl-phosphate synthetase (CPSase) and β-galactosidase specific activities from car-lacZ fusion constructs of wild type or IHF target site mutants introduced into several genetic backgrounds affected in the himA gene or in the pyrimidine-mediated control of P1 (carP6 or pyrH ±), or in both, indicate that, in vivo, IHF influences P1 activity as well as its control by pyrimidines. IHF stimulates P1 promoter activity in minimal medium, but increases the repressibility of this promoter by pyrimidines. These antagonistic effects result in a two- to threefold reduction in the repressibility of promoter P 1 by pyrimidines in the absence of IHF binding. IHF thus appears to be required for maximal expression as well as for establishment of full repression. IHF could exert this function by modulating the binding of a pyrimidine-specific regulatory molecule.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00282809
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    Paper (German National Licenses)
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