Analysis of putative DNA amplification genes in the element AUD1 of Streptomyces lividans 66

Piendl, Wolfgang; Eichenseer, Christa; Viel, Petra; Altenbuchner, Josef; Cullum, John

doi:10.1007/bf00286697

Cited by 16 publications

(20 citation statements)

References 28 publications

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“…Significant cross-matches between the two groups were detected with the more sensitive profile-based technique and corroborated with a recently introduced robust significance test (Hofmann & Bucher, 1995). With a profile made from the larger eukaryotic subfamily, we obtained a significant match ( P < to one of the GOaserelated repeats in the AUDl protein (Piendl et al, 1994). With a profile made from all members of the second subfamily, we obtained significant matches to the human milk fat globule ( P < IOp5) and to the C2 repeat of bovine factor V ( P < Both profiles also identified a significant match ( P < lo-') in Clostridium pefringerzs Mu toxin, shown to possess hyaluronidase activity (Canard et al, 1994).…”

supporting

confidence: 77%

“…This domain was previously found to be similar to noncatalytic extensions of two bacterial sialidases (Bork & Doolittle, 1994). It is also relatively closely related to three internal repeats in ORF 4.7 of AUDI, an amplifiable DNA element from Streptomyces lividans (Piendl et al, 1994). In addition, we found homologous sequences in Mu toxin of Clostridium perjiringens (Canard et al, 1994) and migA of D. discoideurn (Escalante et al, 1997) "_""""""""""""""""""" CAMP and slug migration.…”

supporting

confidence: 67%

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The discoidin domain family revisited: New members from prokaryotes and a homology‐based fold prediction

Hofmann²,

et al. 1998

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Abstract:Members of the discoidin (DS) domain family, which includes the CI and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been implicated in cell-adhesion or developmental processes. So far, no three-dimensional structure of a known example of this extracellular module has been determined, limiting the usefulness of identifying a new sequence as member of this family. Here, we present results of a recent search of the protein sequence database for new DS domains using generalized profiles, a sensitive multiple alignment-based search technique. Several previously unrecognized DS domains could be identified by this method, including the first examples from prokaryotic species. More importantly, we present statistical, structural, and functional evidence that the Dl domain of galactose oxidase whose three-dimensional structure has been determined at 1.7 A resolution, is a distant member of this family. Taken together, these findings significantly expand the concept of the DS domain, by extending its taxonomic range and by implying a fold prediction for all its members. The proposed alignment with the galactose oxidase sequence makes it possible to construct homology-based three-dimensional models for the most interesting examples, as illustrated by an accompanying paper on the CI and C2 domains of factor V.

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supporting

confidence: 77%

supporting

confidence: 67%

The discoidin domain family revisited: New members from prokaryotes and a homology‐based fold prediction

Hofmann²,

et al. 1998

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“…It exhibits 65% identity to ORF-Sl, the LacI/GalR-like protein of S. limosus (41a), and 55% identity to Streptomyces ORFs found in regions of chromosomal instability in S. ambofaciens and S. lividans (1,33,47). Reg1 has 31% identity with CcpA, the carbon catabolite repressor of Bacillus subtilis (16).…”

Section: Resultsmentioning

confidence: 99%

Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene

et al. 1997

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A regulatory gene, reg1, was identified in Streptomyces lividans. It encodes a 345-amino-acid protein (Reg1) which contains a helix-turn-helix DNA-binding motif in the N-terminal region. Reg1 exhibits similarity with the LacI/GalR family members over the entire sequence. It displays 95% identity with MalR (the repressor of malE in S. coelicolor), 65% identity with ORF-Sl (a putative regulatory gene of ␣-amylase of S. limosus), and 31% identity with CcpA (the carbon catabolite repressor in Bacillus subtilis). In S. lividans, the chromosomal disruption of reg1 affected the expression of several genes. The production of ␣-amylases of S. lividans and that of the ␣-amylase of S. limosus in S. lividans were enhanced in the reg1 mutant strains and relieved of carbon catabolite repression. As a result, the transcription level of the ␣-amylase of S. limosus was noticeably increased in the reg1 mutant strain. Moreover, the induction of chitinase production in S. lividans was relieved of carbon catabolite repression by glucose in the reg1 mutant strain, while the induction by chitin was lost. Therefore, reg1 can be regarded as a pleiotropic regulatory gene in S. lividans.Streptomyces species, gram-positive soil bacteria with a high GC content, have the capacity to produce a vast array of secondary metabolites and extracellular proteins. The latter comprise many hydrolytic enzymes such as cellulases, chitinases, amylases, and xylanases allowing Streptomyces to grow on polymeric substrates (12). Genes encoding these enzymes are generally induced by degradation products of their polymeric substrates and repressed by readily metabolizable carbon sources such as glucose by a process known as catabolite repression. Several cis-acting sequences, displaying no apparent similarity, have been shown to be involved in the regulation of genes encoding such hydrolytic enzymes in various species of Streptomyces (10,11,44,49). However, no specific regulatory gene among those encoding extracellular proteins has so far been characterized for Streptomyces.␣-Amylases are secreted by several species of Streptomyces and catalyze the cleavage of the ␣-1,4 linkage of starch, yielding short linear maltodextrins which are finally converted to glucose. The highest ␣-amylase production was obtained when the ␣-amylase gene aml of Streptomyces limosus was cloned in S. lividans, which has a negligible ␣-amylase activity (43). In S. lividans, aml expression was induced by maltose and repressed by glucose. The regulation occurs at the level of transcription from the unique promoter. This led to the assumption that a regulatory protein(s) in S. lividans controlling the expression of aml might exist. A putative repressor, called open reading frame R (ORFR) in the present work, which is homologous to the regulatory proteins LacI and GalR of Escherichia coli has been located upstream of the ␣-amylase gene of S. venezuelae (45) and is also present upstream of the ␣-amylase genes of S. limosus (27) and S. griseus (42). Therefore, it was assumed that an ORF homo...

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“…To our knowledge, DNA sequences of DRs of class II elements are available only from AUD1 of S. lividans (18) Nucleotide sequence accession number. The DNA sequence data from this study were submitted to GenBank and have been assigned accession number U05249.…”

mentioning

confidence: 99%

The very large amplifiable element AUD2 from Streptomyces lividans 66 has insertion sequence-like repeats at its ends

Eichenseer

Altenbuchner

1994

J Bacteriol

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In a spontaneous, chloramphenicol-sensitive (Cms), arginine-auxotrophic (Arg-) [DRs]) of 800 to 2,200 bp. The amplified DNA sequences (ADSs) consist of tandemly repeated units of one copy of the DR and one copy of the sequence flanked by the DRs. Class I amplifications arise within the same chromosomal region but differ in size and endpoints. Only a few, if any, directly or inverted repeated base pairs are found at the ends of the sequence used for amplification. Both types of amplifications are accompanied by deletions on one side of the amplified DNA. The deletions always occur on the same side of the amplified DNA. So far, it is unknown whether elements of the two classes amplify by the same mechanism, which enzymes and DNA structures are involved in the amplification process, and how it is correlated to the deletions.Streptomyces lividans is especially suitable for studying amplification processes. This species segregates chloramphenicolsensitive (Cms) mutants at an average frequency of 0.5% and in a second step arginine-auxotrophic mutants (Arg-) at a frequency of about 25% that of germinating spores (1). The mutants have extensive chromosomal deletions, and more than

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Analysis of putative DNA amplification genes in the element AUD1 of Streptomyces lividans 66

Cited by 16 publications

References 28 publications

The discoidin domain family revisited: New members from prokaryotes and a homology‐based fold prediction

The discoidin domain family revisited: New members from prokaryotes and a homology‐based fold prediction

Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene

The very large amplifiable element AUD2 from Streptomyces lividans 66 has insertion sequence-like repeats at its ends

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