Effect of polyamines and basic proteins on cleavage of DNA by restriction endonucleases

Pingoud, Alfred; Urbanke, Claus; Alves, Jürgen; Ehbrecht, H J; Zabeau, Marc; Gualerzi, Claudio O.

doi:10.1021/bi00319a006

Cited by 52 publications

(31 citation statements)

References 30 publications

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“…A, competition EMSA analysis using the Nrf-2 binding element as the labeled probe. One g of nuclear extract from H157 cells (lanes 1-4) endonuclease activity (43)(44)(45).…”

Section: Discussionmentioning

confidence: 99%

The Identification of a Cis-element and a Trans-acting Factor Involved in the Response to Polyamines and Polyamine Analogues in the Regulation of the Human Spermidine/Spermine N 1-Acetyltransferase Gene Transcription

Wang¹,

Xiao²,

Thiagalingam³

et al. 1998

Journal of Biological Chemistry

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The superinduction of spermidine/spermine N 1 -acetyltransferase (SSAT) gene has been associated with a cytotoxic response to a new class of antineoplastic polyamine analogues. The initial mechanism of SSAT superinduction is an increase in transcription in response to analogue exposure. This increased transcription appears to be modulated through the association between a nuclear protein factor and a cis-element described here as the polyamine-responsive element (PRE). The PRE was identified as a 9-base pair sequence, 5-TATGACTAA-3, in the context of a 31-base pair stretch from -1522 to -1492 base pairs with respect to the SSAT transcriptional start site. This element binds a nuclear factor from polyamine analogue-responsive cells, but not from polyamine analogue-insensitive cells. The labeled PRE was used to clone and identify the transcription factor, Nrf-2, that binds constitutively to the PRE sequence. Although the PRE sequence shares homology to the originally identified Nrf-2 recognition sequence, the two sequences are not identical. The Nrf-2 transcription factor appears only to be present in cell types that are capable of expressing high amounts of SSAT. The results of these studies suggest that Nrf-2, bound to the PRE, plays an important regulatory role of expression of the human SSAT gene.The requirement for polyamines in growth and development is absolute in eukaryotic cells (1). Although this requirement has been well established, some of the precise molecular functions of the polyamines have only recently been elucidated. Several newly synthesized polyamine analogues have been examined for their potential as antitumor agents (2-4). These compounds have been designed to alter the regulation of polyamine metabolism and interfere with the normal functions of polyamines in tumor cells. Some of these compounds appear to act in an association with an ability to superinduce the expression of spermidine/spermine N 1 -acetyltransferase (SSAT), 1 the rate-limiting enzyme in polyamine catabolism (5-7). The superinduction of SSAT has been associated with a phenotypespecific sensitivity to some of the antitumor polyamine analogues, and there are several reports demonstrating superinduction of SSAT and tumor cell toxicity (8 -13). Therefore, there is considerable interest in elucidating the mechanisms that differentiate sensitive tumors from analogue-insensitive tumors and normal tissue.Control of the analogue-mediated superinduction of SSAT is initiated at the level of transcription (14, 15). The -fold induction of SSAT transcription by analogue exposure is relatively small (2-7-fold) compared with the ultimate induction of enzyme activity; however, this increased transcription is necessary for the downstream events, which can result in Ͼ1000-fold increases in SSAT activity (8,16,17). Here we identify a cis-element in the 5Ј regulatory region of the human SSAT and define it as a polyamine-responsive element (PRE). Further, electrophoretic mobility shift assay (EMSA) results demonstrate that the PRE is bound by a...

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“…A, competition EMSA analysis using the Nrf-2 binding element as the labeled probe. One g of nuclear extract from H157 cells (lanes 1-4) endonuclease activity (43)(44)(45).…”

Section: Discussionmentioning

confidence: 99%

The Identification of a Cis-element and a Trans-acting Factor Involved in the Response to Polyamines and Polyamine Analogues in the Regulation of the Human Spermidine/Spermine N 1-Acetyltransferase Gene Transcription

Wang¹,

Xiao²,

Thiagalingam³

et al. 1998

Journal of Biological Chemistry

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“…However, similar mechanisms are not known for the type II R-M systems. Genomes of γ-proteobacteria are com- plexed with polyamines and various nucleoid-associated proteins (NAPs), all of which bind in a nonspecific fashion to cause bending, wrapping, bridging, and/or coating of DNA, which, in turn, could affect various DNA transaction processes (29)(30)(31). To determine the mechanisms that operate to discriminate self vs. nonself at the noncanonical sequences, R.KpnI DNA cleavage activity was compared on "naked" DNA and DNA coated with polyamines or NAPs.…”

Section: Resultsmentioning

confidence: 99%

Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria

Vasu

Nagamalleswari

Nagaraja

2012

Proc. Natl. Acad. Sci. U.S.A.

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Most bacterial genomes harbor restriction–modification systems, encoding a REase and its cognate MTase. On attack by a foreign DNA, the REase recognizes it as nonself and subjects it to restriction. Should REases be highly specific for targeting the invading foreign DNA? It is often considered to be the case. However, when bacteria harboring a promiscuous or high-fidelity variant of the REase were challenged with bacteriophages, fitness was maximal under conditions of catalytic promiscuity. We also delineate possible mechanisms by which the REase recognizes the chromosome as self at the noncanonical sites, thereby preventing lethal dsDNA breaks. This study provides a fundamental understanding of how bacteria exploit an existing defense system to gain fitness advantage during a host–parasite coevolutionary “arms race.”

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“…Even in microorganisms producing antibiotics, these metabolites are actively excreted from the cell to avoid suicide (57). On the contrary, polyamines (putrescine, spermine, and spermidine), prokaryotic histone-like proteins NS1 and NS2 (27), and polyphosphate (28) are common bacterial cell constituents that inhibit restriction endonuclease-catalyzed DNA cleavage. Now we can add THPs to this list of substances.…”

Section: Discussionmentioning

confidence: 99%

“…Now we can add THPs to this list of substances. However, THPs exhibit a number of distinct features compared with those of polyamines: (i) DNA cleavage by restriction endonucleases is not activated by low concentrations of THPs as it is by spermine and spermidine; (ii) although polyamines bind to double-stranded DNA and stabilize it, binding of THPs to DNA was not detected, and THP(B) significantly destabilized DNA; (iii) THPs do not cause any apparent condensation or precipitation of DNA as do polyamines at concentrations of 0.2-0.3 mM (27). The intracellular concentration of THP(A), as shown for a number of Streptomyces strains, ranges from 15-20 mM at normal growth conditions to 50 -150 mM as a response to osmotic stress or to 38 -44 mM at elevated temperatures (7).…”

Section: Discussionmentioning

confidence: 99%

“…It has been demonstrated that the binding of ligands, such as antibiotics and dyes, reduces the activity and specificity of restriction endonucleases (26). It has also been shown that the constituents of bacterial cells, such as polyamines and basic proteins (27) or polyphosphate (28), are also capable of inhibiting the DNA cleavage by restriction endonucleases in vitro. Hence, the primary function of the restriction-modification system, aimed at protecting bacteria from phage infection or from other sources of foreign DNA, might be dependent on the composition of intracellular metabolites.…”

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confidence: 99%

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Effect of Tetrahydropyrimidine Derivatives on Protein-Nucleic Acids Interaction

Malin¹,

Iakobashvili

Lapidot

1999

Journal of Biological Chemistry

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2-Methyl-4-carboxy,5-hydroxy-3,4,5,6-tetrahydropyrimidine (THP(A) or hydroxyectoine) and 2-methyl,4-carboxy-3,4,5,6-tetrahydropyrimidine (THP(B) or ectoine) are now recognized as ubiquitous bacterial osmoprotectants. To evaluate the impact of tetrahydropyrimidine derivatives (THPs) on protein-DNA interaction and on restriction-modification systems, we have examined their effect on the cleavage of plasmid DNA by 10 type II restriction endonucleases. THP(A) completely arrested the cleavage of plasmid and bacteriophage DNA by EcoRI endonuclease at 0.4 mM and the oligonucleotide (d(CGCGAATTCGCG)) 2 at about 4.0 mM. THP(B) was 10-fold less effective than THP(A), whereas for betaine and proline, a notable inhibition was observed only at 100 mM. Similar effects of THP(A) were observed for all tested restriction endonucleases, except for SmaI and PvuII, which were inhibited only partially at 50 mM THP(A). No effect of THP(A) on the activity of DNase I, RNase A, and Taq DNA polymerase was noticed. Gelshift assays showed that THP(A) inhibited the EcoRI-(d-(CGCGAATTCGCG)) 2 complex formation, whereas facilitated diffusion of EcoRI along the DNA was not affected. Methylation of the carboxy group significantly decreased the activity of THPs, suggesting that their zwitterionic character is essential for the inhibition effect. Possible mechanisms of inhibition, the role of THPs in the modulation of the protein-DNA interaction, and the in vivo relevance of the observed phenomena are discussed.Two tetrahydropyrimidine derivatives identified in Streptomyces bacteria (1-3), one a previously unknown metabolite, THP(A), 1 and the other previously identified (as ectoine) in halophilic bacteria (4), THP(B), are now recognized as widely spread osmoprotectants within the bacterial world (5). The role and activities of THPs are of special interest as they represent a limited group of osmoprotectants that are synthesized de novo, in the bacterial cell, in contrast to those transported from the medium (6). Their synthesis in a number of Streptomyces strains as a response to increased salinity and elevated temperature was recently described (7). THPs are small molecules, highly soluble in water and neutral at physiological pH. NMR and x-ray crystallography data show that THPs are zwitterionic molecules with a delocalized charge in the NCN group (Fig. 1) and form the half-chair conformation (8).More information has been accumulated lately on THPs activity in living cells. It was found that exogenously provided ectoine (THP(B)) could reverse growth inhibition, caused by osmotic stress, in Escherichia coli (9), Corynebacterium glutamicum (10), and the soil bacterium Rhizobium meliloti (11). We demonstrated that exogenously provided THP(A), like THP(B), reversed inhibition of E. coli growth by osmotic stress, and moreover, both THP(A) and THP(B) could stimulate growth of E. coli at an elevated temperature (43°C) (7). Recently cloned genes for ectoine synthesis from Halomonas elongata (12) and from Marinococcus halophilus (13) were demonstrated ...

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Effect of polyamines and basic proteins on cleavage of DNA by restriction endonucleases

Cited by 52 publications

References 30 publications

The Identification of a Cis-element and a Trans-acting Factor Involved in the Response to Polyamines and Polyamine Analogues in the Regulation of the Human Spermidine/Spermine N 1-Acetyltransferase Gene Transcription

The Identification of a Cis-element and a Trans-acting Factor Involved in the Response to Polyamines and Polyamine Analogues in the Regulation of the Human Spermidine/Spermine N 1-Acetyltransferase Gene Transcription

Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria

Effect of Tetrahydropyrimidine Derivatives on Protein-Nucleic Acids Interaction

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