Automated derivation and refinement of sequence length patterns for protein sequences using evolutionary computation.

Several stratagems are used in protein bioinformatics for the classification of proteins based on sequence, structure or function. We explore the concept of a minimal signature embedded in a sequence that defines the likely position of a protein in a classification. Specifically, we address the derivation of sparse profiles for the G-protein coupled receptor (GPCR) clan of integral membrane proteins. We present an evolutionary algorithm (EA) for the derivation of sparse profiles (signatures) without the need to supply a multiple alignment. We also apply an evolution strategy (ES) to the problem of pattern and profile refinement. Patterns were derived for the GPCR 'superfamily' and GPCR families 1-3 individually from starting populations of randomly generated signatures, using a database of integral membrane protein sequences and an objective function using a modified receiver operator characteristic (ROC) statistic. The signature derived for the family 1 GPCR sequences was shown to perform very well in a stringent cross-validation test, detecting 76% of unseen GPCR sequences at 5% error. Application of the ES refinement method to a signature developed by a previously described method [Sadowski, M.I., Parish, J.H., 2003. Automated generation and refinement of protein signatures: case study with G-protein coupled receptors. Bioinformatics 19, 727-734] resulted in a 6% increase of coverage for 5% error as measured in the validation test. We note that there might be a limit to this or any classification of proteins based on patterns or schemata.

Key residues approach to the definition of protein families and analysis of sparse family signatures.

We extend the concept of the motif as a tool for characterizing protein families and explore the feasibility of a sparse "motif" that is the length of the protein sequence itself. The type of motif discussed is a sparse family signature consisting of a set of N key residue positions (A1, A2...AN) preceded by gaps (G) thus G1A1G2A2. ...GNAN. Both a residue and gap can be variable. A signature is matched to a protein sequence and scored using a dynamic programming algorithm which permits variability in gap distance and residue type. Generating a signature involves identifying residues associated with points of contact in interactions between secondary structure elements. A raw signature consists of a set of positions with potential key structural roles sampled from a sequence alignment constructed with reference to this contact data. Raw signatures are refined by sampling different gap-residue pairs until the specificity of a signature for the family cannot be further improved. We summarize signatures for nine families of protein of diverse fold and function and present results of scans against the OWL protein sequence database. The implications of such signatures are discussed.

Mechanism of uptake of a cationic water-soluble pyridinium zinc phthalocyanine across the outer membrane of Escherichia coli.

Previous studies have shown that a cationic water-soluble pyridinium zinc phthalocyanine (PPC) is a powerful photosensitizer that is able to inactivate Escherichia coli. In the current work incubation of E. coli cells with PPC in the dark caused alterations in the outer membrane permeability barrier of the cells, rendering the bacteria much more sensitive to hydrophobic compounds, with little effect seen with hydrophilic compounds. Addition of Mg(2+) to the medium prior to incubation of the cells with PPC prevented these alterations in the outer membrane permeability barrier. The presence of Mg(2+) in the medium also prevented the photoinactivation of E. coli cells with PPC. These results are consistent with the hypothesis that PPC gains access across the outer membrane of E. coli cells via the self-promoted uptake pathway, a mechanism of uptake postulated for the uptake of other cationic compounds across the outer membranes of gram-negative bacteria.

Reactivities of flavonoids with different hydroxyl substituents for the cleavage of DNA in the presence of Cu(II).

DNA strand scission reactions of flavonoids in the presence of Cu(II) have been extended by using flavonoids with a variety of patterns of hydroxyl substitution. In particular we have examined for the first time a flavonoid (7,8-dihydroxyflavone) that lacks the possibility of forming a complex involving the oxygen at position 4. By comparing the reactivities of several flavonoids, including data from the literature, we draw generalizations for the correlation of structure and activity and present evidence for at least three different modes of action of flavonoids as genotoxic agents.

Alignment of a sparse protein signature with protein sequences: application to fold prediction for three small globulins.

A novel algorithm has been developed for scoring the match between an imprecise sparse signature and all the protein sequences in a sequence database. The method was applied to a specific problem: signatures were derived from the probable folding nucleus and positions obtained from the determined interactions that occur during the folding of three small globular proteins and points of inter-element contact and sequence comparison of the actual three-dimensional structures of the same three proteins. In the case of two of these, lysozyme and myoglobin, the residues in the folding nucleus corresponded well to the key residues spotted by examination of the structures and in the remaining case, barnase, they did not. The diagnostic performance of the two types of signatures were compared for all three proteins. The significance of this for the application of an understanding of the protein folding mechanisms for structure prediction is discussed. The algorithm is generic and could be applied to other user-defined problems of sequence analysis.

The genome and genes of Neurospora crassa.

Neurospora crassa is an organism with a 7-decade contribution to genetic research. in a genome of 42.9 Mb and just over 1000 map units, to date over 800 different genes have been identified by phenotype and/or map location, and 222 genes have been characterized by sequencing. Methods by which analysis of the genome has been carried out are discussed, including linkage, RFLP, and chromosome walking. Characterized centomeres, telomeres, the nucleolar organizer and the dispersed 5S rRNA genes are discussed. Analysis of the protein-encoding genes is undertaken, using new software for the querying of standard sequence databases. Gene analysis includes consensus sequences for transcription and RNA splicing and new insights into codon usage.

Oxygen is not required for degradation of DNA by glutathione and Cu(II).

Previous studies by others have shown that thiols, such as glutathione, cause cleavage of DNA in the presence of Cu(II) ions and that the hydroxyl radical derived from molecular oxygen is the major cleaving species. In this paper, we present several lines of evidence that strongly suggest that molecular oxygen is not essential for DNA cleavage and that thiyl radicals may also be involved. Indirect evidence is presented to indicate that glutathione may substitute oxygen as an electron acceptor. In addition, DNA degradation occurs to a significant extent under anaerobic conditions and no inhibition of single-strand cleavage of supercoiled plasmid DNA is seen in the presence of superoxide dismutase and catalase. In view of the ubiquitous presence of glutathione, these results could be of interest under certain diseased conditions where copper concentrations are elevated.

Photoinactivation of bacteria. Use of a cationic water-soluble zinc phthalocyanine to photoinactivate both gram-negative and gram-positive bacteria.

The photosensitization of microorganisms is potentially useful for sterilization and for the treatment of certain bacterial diseases. Until now, any broad spectrum approach has been inhibited because, although Gram-positive bacteria can be photoinactivated by a range of photosensitizers, Gram-negative bacteria have not usually been susceptible to photosensitized destruction. In the present work, it has been shown that the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, as well as the Gram-positive bacterium Enterococcus seriolicida, can be photoinactivated when illuminated in the presence of a cationic water-soluble zinc pyridinium phthalocyanine (PPC). The degree of photoinactivation is dependent on both the concentration of PPC and the illumination time. In contrast, the three bacteria are not photoinactivated by illumination in the presence of a neutral tetra-diethanolamine phthalocyanine (TDEPC) or negatively charged tetra-sulphonated phthalocyanine (TSPC). Uptake studies have revealed that the lack of activity of TSPC is due to the fact that it has very little affinity for any of the organisms. However, the issue appears to be more complex than simply the gross levels of cellular uptake, since TDEPC and PPC are both taken up by the organisms but only PPC shows activity. This indicates that the localization and subcellular distribution of the phthalocyanines may be a crucial factor in determining their cell killing potential. Further analysis of the uptake data has revealed a cell-bound photosensitizer fraction, which remains tightly associated after several washings, and another weakly bound fraction, which is removed by successive washings. Analysis of the cell killing curves, carried out after successive washings of E. coli exposed to PPC, has revealed that it is the tightly associated fraction that is involved in the photosensitization. Taken together with other data, these results suggest that cationic photosensitizers may have a broader application in the photoinactivation of bacterial cells than the anionic or neutral photosensitizers commonly used in photodynamic therapy.

Relationships between bacterial drug resistance pumps and other transport proteins.

We have used three reference sequences representative of bacterial drug resistance pumps and sugar transport proteins to collect the 91 most closely related sequences from a composite, nonredundant protein sequence database. Having eliminated certain very close relatives, the remainder were subjected to analysis and alignment by using two different similarity matrices: one of these was a matrix based on structural conservation of amino acid residues in proteins of known conformation and the other was based on the more familiar mutational matrix. Unrooted similarity trees for these proteins were constructed for each matrix and compared. A systematic analysis of the differences between these trees was undertaken and the sequences were analyzed for the presence or absence of certain sequence motifs. The results show that the clades created by the two methods are broadly comparable but that there are some clusters of sequences that are significantly different. Further analysis confirmed that (1) the sequences collected by this objective method are all known or putative 12-helix (in some cases reported as 14-helix) transmembrane proteins, (2) there is evidence for few cases of an origin based on gene duplication, (3) the bacterial drug resistance pumps are distributed in more than one clade and cannot be regarded as a definitive subset of these proteins, and that (4) the diversity is such that there is no evidence of a single ancestral protein. The possible extension of the methods to other cases of divergent protein sequences is discussed.

Free radical-induced fragmentation of proteins by quercetin.

The flavonoid, quercetin, is known to bind to DNA and, in the presence of Cu(II) and other ions, causes fragmentation of the molecule. We examined whether quercetin might bind to protein and cause similar fragmentation. By using UV spectroscopic and fluorescence quenching experiments we show that quercetin binds to bovine serum albumin and that the complex does, in the presence of Cu(II), lead to fragmentation of the protein. The binding involves binding to tryptophan residues in the albumin. The reaction is not detected in certain other tryptophan-containing proteins. We discuss the possible implications for protein damage by this and other radical-generating reagents.

Mode of binding of quercetin to DNA.

The difference spectrum of the quercetin--DNA complex versus quercetin alone was characterized by a peak at 395 nm. An increase in the magnitude of difference spectrum was seen with increased ionic strength. Spectrophotometric changes in absorbance and fluorescence of quercetin showed that ethidium bromide is able to displace quercetin from the quercetin--DNA complex. These results indicate that the binding of quercetin to DNA does not involve electrostatic interactions but may be intercalative in nature. Experiments using DNase I footprinting technique showed that the flavonoid does not possess any preferred sites of binding in DNA. Strand scission in DNA by the quercetin--Cu(II) system gave a generally uniform cutting pattern of internucleotide bonds. This led to the observation that the quercetin--Cu(II) cleavage reaction has the potential of being used as preferred DNA footprinting reagent.

Cloning and sequence analysis of the glucoamylase gene of Neurospora crassa.

A 1.0-kb DNA fragment, corresponding to an internal region of the Neurospora crassa glucoamylase gene, gla-1, was generated from genomic DNA by the polymerase chain reaction, using oligonucleotide primers which had been deduced from the known N-terminal amino-acid sequence or from consensus regions within the aligned amino-acid sequences of other fungal glucoamylases. The fragment was used to screen an N. crassa genomic DNA library. One clone contained the gene together with flanking regions and its sequence was determined. The gene was found to code for a preproprotein of 626 amino acids, 35 of which constitute a signal and propeptide region. The protein and the gene are compared with corresponding sequences in other fungi.

Cloning and sequence analysis of an Escherichia coli gene conferring bicyclomycin resistance.

We have cloned and sequenced DNA from Escherichia coli that, when present in a high-copy-number plasmid, confers resistance to the diketopiperazine antibiotic, bicyclomycin (Bc). The DNA includes a 378-amino-acid open reading frame (ORF), disruption of which results in the loss of Bc resistance. This ORF contains the BcR gene. Studies using the minicell expression system reveal that a polypeptide of 31 kDa is produced from this cloned region. The ORF maps at 47.1 min on the E. coli genome map. Sequence comparison between the translated ORF and a protein database reveal between 26.5 and 23.4% aa sequence homology to bacterial transmembrane (TM) proteins including those mediating chloramphenicol (Cm) and tetracycline (Tc) resistance and an arabinose-proton symport protein. Sequence analysis using the Diagon program showed the BcR gene product (BcR) had homology with the N-terminal regions of the CmR and TcR-encoded proteins and weak N-terminal homology with the arabinose-proton symport protein. Hydropathy profiles of the BcR protein and CmR products show a striking similarity, both having twelve predicted TM domains.

Activities of flavonoids for the cleavage of DNA in the presence of Cu(II): correlation with generation of active oxygen species.

The activities of several flavonoids and the related nonflavonoid compound epicatechin were compared with respect to Cu(II)-induced strand scission of DNA by using two different assays. The same series of compounds was used to study the stoichiometry of Cu(II) reduction in the absence of DNA. The compounds were compared for their ability to generate superoxide, hydrogen peroxide and the Cu(II)-dependent production of hydroxyl radicals. Flavonoids were examined to assess the production of a charge-transfer complex with Cu and the rate of decay of the complexes were compared. All the compounds tested had some ability to cause DNA strand scission in the presence of Cu(II), with myricetin being the most active and galangin the least active. The ability to cause such scission correlated with the rate of decay of the charge-transfer complex, the ability to generate active oxygen species and with the stoichiometry of Cu(II) binding. Analysis of the data in the light of the structural differences between the flavonoids led to a discussion of alternative Cu(II)-sequestering mechanisms.

Strand scission in DNA induced by dietary flavonoids: role of Cu(I) and oxygen free radicals and biological consequences of scission.

The naturally occurring flavonoid, quercetin, in the presence of Cu(II) and molecular oxygen caused breakage of calf thymus DNA, supercoiled pBR322 plasmid DNA and single stranded M13 phage DNA. In the case of the plasmid, the product(s) were relaxed circles or a mixture of these and linear molecules depending upon the conditions. For the breakage reaction, Cu(II) could be replaced by Fe(III) but not by other ions tested [Fe(II), Co(II), Ni(II), Mn(II) and Ca(II)]. Structurally related flavonoids, rutin, galangin, apigenin and fisetin were effective or less effective than quercetin in causing DNA breakage. In the case of the quercetin-Cu(II) reaction, Cu(I) was shown to be essential intermediate by using the Cu(I)-sequestering reagent, bathocuproine. By using Job plots we established that, in the absence of DNA, five Cu(II) ions were reduced by one quercetin molecule; in contrast two ions were reduced per quercetin molecule in the DNA breakage reaction. Equally neocuproine inhibited the DNA breakage reaction. The involvement of active oxygen in the reaction was established by the inhibition of DNA breakage by superoxide dismutase, iodide, mannitol, formate and catalase (the inhibition was complete in the last case). The strand scission reaction was shown to account for the biological activity of quercetin as assayed by bacteriophage inactivation. From these data we propose a mechanism for the DNA strand scission reaction of quercetin and related flavonoids.

Complexes involving quercetin, DNA and Cu(II).

The genotoxic flavonoid, quercetin, was shown to bind to both double-stranded and single-stranded DNA with concomitant changes in absorption spectrum and fluorescence emission spectrum of quercetin. Quercetin and Cu(II) were shown to form a charge transfer complex that decayed in oxygen-dependent reaction(s) and this decay was accelerated by DNA. Analysis of the three component system, DNA--querectin--Cu(II), led to a discussion of the complexes likely to be involved in the initial reactions that lead, ultimately, to strand scission of DNA.

Strand scission in DNA by quercetin and Cu(II): identification of free radical intermediates and biological consequences of scission.

Quercetin was shown to reduce oxygen to superoxide. In the presence of Cu(II), the hydroxyl radical was formed. The strand scission of DNA was shown to occur under conditions in which Cu(II), quercetin and either hydrogen peroxide or oxygen were present and superoxide was not a necessary intermediate. Strand scission involved the hydroxyl radical and a radical DNA intermediate. The strand scission reaction was shown to account for the biological activity of quercetin as assayed by bacteriophage inactivation.

Effect of 5-fluorouracil combination therapy on RNA processing in human colonic carcinoma cells.

We have evaluated the RNA-directed cytotoxicity of 5-fluorouracil (5-FU) in human colonic carcinoma cells. The mode of action of 5-FU and its effects on human pre-rRNA processing were then examined. From these data, possible reasons why the disruption of pre-rRNA maturation could induce cytotoxic effects are considered. The results imply that inhibition of thymidylate synthase is not the sole primary cytotoxic lesion in this cell line. First, exogenous thymidine (dTHd) enchanced cytotoxicity. Second, addition of dThd to the cells was found to enhance incorporation of 5-FU into total cellular RNA. Third, 5-FU disrupted rRNA processing by a different mechanism from actinomycin D and methotrexate (MTX), suggesting that the inhibition was not just a consequence of cell death. Finally, the addition of dThd was found to enhance the disruption of rRNA processing consistent with an increase in concentration of 5-FU. These data are discussed in the light of literature reports and their potential for optimising 5-FU protocols.

Strand scission in DNA induced by quercetin and Cu(II): role of Cu(I) and oxygen free radicals.

The naturally occurring flavonoid, quercetin, in the presence of Cu(II) and molecular oxygen caused breakage of calf thymus DNA, supercoiled pBR322 plasmid DNA and single-stranded M13 phage DNA. In the case of the plasmid, the product(s) were relaxed circles or a mixture of these and linear molecules depending upon the conditions. For the breakage reaction, Cu(II) could be replaced by Fe(III) but not by other ions tested [Fe(II), Co(II), Ni(II) and Ca(II)]. Structurally related flavonoids, rutin, galangin, apigenin and fisetin, were ineffective or less effective than quercetin in causing DNA breakage. In the case of the quercetin--Cu(II) reaction, Cu(I) was shown to be an essential intermediate by using the Cu(I)-sequestering reagents, neocuproine and bathocuproine. By using Job plots we established that, in the absence of DNA, five Cu(II) ions can be reduced by one quercetin molecule; in contrast, two ions were reduced per quercetin molecule in the DNA breakage reaction. Equally neocuproine inhibited the DNA breakage reaction. The involvement of active oxygen in the reaction was established by the inhibition of DNA breakage by superoxide dismutase, iodide, mannitol, formate and catalase (the inhibition was complete in the last case). From these data we propose a mechanism for the DNA strand scission reaction of quercetin and related flavonoids.