Strong patterns in homooligomer tracts occurrences in non-coding and in potential regulatory sites in eukaryotic genomes

Previous studies of the dinucleotides flanking both the 5' and 3' ends of homooligomer tracts have shown that some flanks are consistently preferred over others (1,2). In the first preferred group, the homooligomer tracts are flanked by the same nucleotide and/or the complementary nucleotides, e.g.,ATAn,TTAn,CCGn, where n = 2-5. Runs flanked by nucleotides with which they cannot base pair are distinctly disfavored. (In this group An/Tn are flanked by C and/or G; Gn/Cn are flanked by A/T, e.g.,CGAn,TnGG,GnAT). The frequencies of runs flanked by A or T, and G or C ("mixed"group) are as expected. Here we seek the origin of this effect and its relevance to protein-DNA interactions. Surprisingly, within the first group, runs flanked by their complements with a pyrimidine-purine junction (e.g.,TTAn,CnGG) are greatly preferred. The frequencies of their purine-pyrimidine junction mirror-images is just as expected. This effect, as well as additional ones enumerated below, is seen universally in eukaryotes and in prokaryotes, although it is stronger in the former. Detailed analysis of regulatory regions shows these strong trends, particularly in GC sequences. The potential relationship to DNA conformation and DNA-protein interaction is discussed.     

Strong sequence patterns in eukaryotic promoter regions: Potential implications for DNA structure

• 1.1. Analysis of eukaryotic sequences reveals recurring trends in upstream regions. Oligomers composed of (G/C)_n and (A/T)_m blocks are preferentially flanked by (G/C)₂ doublets on their 3' rather than on their 5′ ends, that is (G/C)_nä(A/T)_m(G/C)₂ > (G/C)_n+2(A/T)_m.
• 2.2. These trends are stronger for larger n and smaller m. Additional trends are outlined below.
• 3.3. The trends are correlated with DNA structural parameters, in particular with twist and roll angles.
• 4.4. Generally, the trends hold if the base pair step joining the 5′ (G/C)₂ doublet to the (G/C)_n (A/T)_m oligomer is not undertwisted and is not strongly rolled into the major groove.
• 5.5. Other DNA parameters crucial for DNA-protein interactions are discussed as well.

     

Non-mutagenic and mutagenic post-replicative DNA repair in prokaryotic and eukaryotic cells

The review is devoted to mechanisms of repair gaps in DNA daughter strand, formed during the stall of moving replication forks and restart of replication in cells after the action of DNA damaging agents (predominantly--UV light). The repair of daughter DNA, or postreplication DNA repair (PRR), is realized by error-free (non-mutagenic) and error-prone (mutagenic) pathways. The former is a recombination repair, or recombination between two sister duplexes. By this way the major part of postreplication gaps is eliminated. The second way is related with the induction of SOS-response. In Escherichia coli cells mutagenic SOS-response is realized by proteins RecA, UmuD, UmuC, DNA-polymerase III holoenzyme and others. In E. coli some mutagenic enzymes--DNA-polymerase IV (the product of dinB gene) and DNA-polymerase V (the product of umuDC genes) have been recently discovered. In Saccharomyces cerevisiae cells postreplicative translesion synthesis is realized by newly discovered enzymes deoxycytidilmonophosphatetransferase (encoded by REV1 gene), DNA-polymerase zeta (encoded by REV3 gene), DNA-polymerase eta (encoded by RAD30 gene). All the three enzymes share a great homology with UmuC enzyme of E. coli. DNA polymerase eta correctly inserts adenine residues in the daughter strand opposite noncoded thymine residues in cyclobutane pyrimidine dimer. Based on RAD6 gene of S. cerevisiae, human cells hREV1, hREV3 and hRAD30A have been obtained to encode, respectively, deoxycytidiltransferase, DNA-polymerase zeta and DNA-polymerase eta. It has been shown that the defect of PRR DNA in xeroderma pigmentosum variant is associated with DNA-polymerase eta deficiency. This defect is corrected by the extract of intact HeLa cells. The importance of newly discovered enzymes in the system of mechanisms of DNA repair and replication is discussed.     

The ordering of nucleotides in the DNA: strong pyrimidine-purine patterns near homooligomer tracts

Here, we study the frequencies of occurrence of homooligomers flanked by one base, XnU or UXn, where X = A, C, G, T and U not equal to X. Specifically, we search for preferences (or discriminations) in their nearest neighbor doublet, VV. Extensive analysis of the data base reveals striking patterns in such VVUXn or UXn VV oligomers (V = A, C, G, T). With very few exceptions, if the VV and Xn are composed of complementary nucleotides, those oligomers having a pyrimidine (Y)-purine (R) junction are preferred over those with an RY one. If the VV and Xn nucleotides are not complementary, the RY junction oligomers are preferred over their YR counterparts. These trends are observed consistently in eukaryotic and prokaryotic sequences. They are particularly striking in the YR greater than RY oligomers containing complementary nucleotides. The general preferences and discriminations described here are in the same direction as our previous results for homooligomer tracts. These recurrences, along with some additional universal "rules", aid in our understanding of the ordering of nucleotides in the DNA.     

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.     

Co-polymer tracts in eukaryotic, prokaryotic, and organellar DNA.

Large variations in DNA base composition and noticeable strand asymmetries are known to occur between different organisms and within different regions of the genomes of single organisms. Apparently such composition and sequence biases occur to fulfill structural rather than informational requirements. Here we report the wide occurrence of a more subtle biasing of DNA sequence that can have structural consequences: an increase or a suppression of the number of long tracts of two-base co-polymers. Strong biases were observed when the DNA sequences of the longest eukaryotic, prokaryotic, and organellar entries in the GenBank data base (totaling 773 kilobases) were analyzed for the number of occurrences of tracts of the two-base co-polymers (A,T)n, (G,C)n, and (A,C)n as a function of tract length. (The expression (A,T)n is used here to denote an uninterrupted tract, n nucleotides in length, of A and T bases in any proportion or order, terminated at each end by a G or C residue.) Characteristic differences are also observed in tract biases of eukaryotic vs. prokaryotic organisms.     

Structural and functional relationships between prokaryotic and eukaryotic DNA polymerases.

The Bacillus subtilis phage luminal diameter 29 DNA polymerase, involved in protein-primed viral DNA replication, was inhibited by phosphonoacetic acid (PAA), a known inhibitor of alpha-like DNA polymerases, by decreasing the rate of elongation. Three highly conserved regions of amino acid homology, found in several viral alpha-like DNA polymerases and in the luminal diameter 29 DNA polymerase, one of them proposed to be the PAA binding site, were also found in the T4 DNA polymerase. This prokaryotic enzyme was highly sensitive to the drugs aphidicolin and the nucleotide analogues butylanilino dATP (BuAdATP) and butylphenyl dGTP (BuPdGTP), known to be specific inhibitors of eukaryotic alpha-like DNA polymerases. Two potential DNA polymerases from the linear plasmid pGKL1 from yeast and the S1 mitochondrial DNA from maize have been identified, based on the fact that they contain the three conserved regions of amino acid homology. Comparison of DNA polymerases from prokaryotic and eukaryotic origin showed extensive amino acid homology in addition to highly conserved domains. These findings reflect evolutionary relationships between hypothetically unrelated DNA polymerases.     

A putative signal peptidase recognition site and sequence in eukaryotic and prokaryotic signal peptides

Presecretory signal peptides of 39 proteins from diverse prokaryotic and eukaryotic sources have been compared. Although varying in length and amino acid composition, the labile peptides share a hydrophobic core of approximately 12 amino acids. A positively charged residue (Lys or Arg) usually precedes the hydrophobic core. Core termination is defined by the occurrence of a charged residue, a sequence of residues which may induce a beta-turn in a polypeptide, or an interruption in potential alpha-helix or beta-extended strand structure. The hydrophobic cores contain, by weight average, 37% Leu: 15% Ala: 10% Val: 10% Phe: 7% Ile plus 21% other hydrophobic amino acids arranged in a non-random sequence. Following the hydrophobic cores (aligned by their last residue) a highly non-random and localized distribution of Ala is apparent within the initial eight positions following the core: (formula; see text) Coincident with this observation, Ala-X-Ala is the most frequent sequence preceding signal peptidase cleavage. We propose the existence of a signal peptidase recognition sequence A-X-B with the preferred cleavage site located after the sixth amino acid following the core sequence. Twenty-two of the above 27 underlined Ala residues would participate as A or B in peptidase cleavage. Position A includes the larger aliphatic amino acids, Leu, Val and Ile, as well as the residues already found at B (principally Ala, Gly and Ser). Since a preferred cleavage site can be discerned from carboxyl and not amino terminal alignment of the hydrophobic cores it is proposed that the carboxyl ends are oriented inward toward the lumen of the endoplasmic reticulum where cleavage is thought to occur. This orientation coupled with the predicted beta-turn typically found between the core and the cleavage site implies reverse hairpin insertion of the signal sequence. The structural features which we describe should help identify signal peptides and cleavage sites in presumptive amino acid sequences derived from DNA sequences.     

Complimentary DNA sequence data analysis of prokaryotic systems

Complimentary DNA sequence data of Φ × 174, fd, f1, G4, Ml3, MS2, λ and T7 phages ofEscherichia coli are analysed at mono-, di-, tri- and tetranucleotide levels. Our analysis shows that, (i) mononucleotides have certain preferences to occur at specific positions X₁, X₂, X₃ of codon, (ii) These nucleotides interact nonlinearly to form dinucleotide and this dinucleotide also interacts nonlinearely with a third nucleotide to form codon, (iii) However, nonlinear interactions are negligible at tetranucleotide level suggesting that, coding regions of complimentary DNA are Markov chains of order two. Trinucleotide potential values in three frames have suggested that, at least thirteen different trinucleotides can be used as a marker to locate coding regions in DNA of prokaryotes. (iv) Parallel paired codons are expressed in such a way that one of the codons in the pair expresses with high frequency while the other with low frequency. On the other hand the complimentary codon pairs express with small frequency difference, (v) In the synonymous codon groups, codon ending with T are found to express with more frequency     

Protein length in eukaryotic and prokaryotic proteomes

We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. The magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended multi-functional and multi-domain proteins. Comparing Bacteria and Archaea, we determined that the small but significant length difference observed between their proteins results from a combination of three factors: (i) bacterial proteomes include a greater proportion than archaeal proteomes of longer proteins involved in metabolism or cellular processes, (ii) within most functional classes, protein families unique to Bacteria are generally longer than protein families unique to Archaea and (iii) within the same protein family, homologs from Bacteria tend to be longer than the corresponding homologs from Archaea. These differences are interpreted with respect to evolutionary trends and prevailing environmental conditions within the two prokaryotic groups.     

Homology between prokaryotic and eukaryotic ribonucleases

Summary There is homology between the amino acid sequences of the extracellular ribonucleases T1 and St, from the eukaryoteAspergillus oryzae and the prokaryoteStreptomyces erythreus, respectively. Together with other extracellular ribonucleases homologous to each, these enzymes make up a family of interest to evolutionary biology and useful in studies of protein structure and function.     

Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps.

The remarkable processivity of cellular replicative DNA polymerases derive their tight grip to DNA from a ring-shaped protein that encircles DNA and tethers the polymerase to the chromosome. The crystal structures of prototypical 'sliding clamps' of prokaryotes (beta subunit) and eukaryotes (PCNA) are ring shaped proteins for encircling DNA. Although beta is a dimer and PCNA is a trimer, their structures are nearly superimposable. Even though they are not hexamers, the sliding clamps have a pseudo 6-fold symmetry resulting from three globular domains comprising each beta monomer and two domains comprising each PCNA monomer. These domains have the same chain fold and are nearly identical in three-dimensions. The amino acid sequences of 11 beta and 13 PCNA proteins from different organisms have been aligned and studied to gain further insight into the relation between the structure and function of these sliding clamps. Furthermore, a putative embryonic form of PCNA is the size of beta and thus may encircle DNA as a dimer like the prokaryotic clamps.     

Cloning and DNA sequence analysis of the serC-aroA operon from Salmonella gallinarum; evolutionary relationships between the prokaryotic and eukaryotic aroA-encoded enzymes

The serC-aroA operon of Salmonella gallinarum was isolated from a gene library using a labelled oligonucleotide probe and by complementation of an aroA Escherichia coli strain. The nucleotide sequence of a 2.6 kbp fragment was determined. The predicted amino acid sequence of the aroA gene product was compared to the equivalent sequence from ten other organisms. Computer-generated evolutionary trees clearly divide the eleven sequences into four different groups: Gram-negative bacteria, Gram-positive bacteria, fungi and plants. These trees depict a close evolutionary relationship between the sequences from Gram-negative bacteria and higher plants.     

Active polypeptide fragments common to prokaryotic, eukaryotic, and mitochondrial DNA polymerases

With a procedure that allows the renaturation of the DNA polymerase catalytic activity in situ after SDS-polyacrylamide gel electrophoresis, we have compared the active polypeptides present in extracts from organisms covering a wide evolutionary range from prokaryotes to eukaryotes, namely: Escherichia coli, Oryza sativa, Daucus carota , Neurospora crassa, Dictyostelium discoideum, Saccharomyces cerevisiae, Ceratitis capitata, Leucophaea maderae , Xenopus laevis, rat tissues and human lymphoblastoid cells. Two main clusters of active peptides are visible in mammalian and adult insect tissues, characterized by a mol. wt. greater than 70000 and less than 50000, respectively. High mol. wt. peptides are heterogeneous in size and correspond to active fragments of DNA polymerase alpha, whereas low mol. wt. peptides show the same migration rate as purified DNA polymerase beta and are not generated by proteolysis of the high mol. wt. cluster, In the three species of fungi studied, only high mol. wt. peptides are found. The same is true in plant cells, where no DNA polymerase beta activity is detectable and the pattern of the high mol. wt. cluster is similar to that observed in E. coli extracts (which also lack low mol. wt. peptides). Also in mitochondria from higher and lower eukaryotes only high mol. wt. species are observed, and the active band(s) range from 70000 to 145000 daltons. Our results indicate that the structure of DNA polymerase has been highly conserved during evolution so that an active fragment of mol. wt. greater than or equal to 70 000 is always found in prokaryotic enzymes and in the replicative species of eukaryotic and mitochondrial DNA polymerases; at a certain stage in evolution, another species of low mol. wt. DNA polymerase (beta or beta-like) appears.     

gamma-Carboxyglutamic acid in eukaryotic and prokaryotic ribosomes.

γ-carboxyglutamic acid (GLA) has been assayed in ribosomes of wheat germ and E. coli, and in E. coli ribosomal sub-units, by amino acid analysis of total protein. Results, as nMoles GLA/mg protein, were 18.1 (wheat germ), 58.4 (E. coli), 39.6 and 81.5 (E. coli 30S and 50S sub-units, respectively.) Results for wheat germ and previously reported mammalian ribosomes were highly similar. Hence the level of GLA in eukaryotic ribosomes appears to be approximately constant, but low compared to bacterial (E. coli) ribosomes.     

A conserved 3'----5' exonuclease active site in prokaryotic and eukaryotic DNA polymerases

The 3'----5' exonuclease active site of E. coli DNA polymerase I is predicted to be conserved for both prokaryotic and eukaryotic DNA polymerases based on amino acid sequence homology. Three amino acid regions containing the critical residues in the E. coli DNA polymerase I involved in metal binding, single-stranded DNA binding, and catalysis of the exonuclease reaction are located in the amino-terminal half and in the same linear arrangement in several prokaryotic and eukaryotic DNA polymerases. Site-directed mutagenesis at the predicted exonuclease active site of the phi 29 DNA polymerase, a model enzyme for prokaryotic and eukaryotic alpha-like DNA polymerases, specifically inactivated the 3'----5' exonuclease activity of the enzyme. These results reflect a high evolutionary conservation of this catalytic domain. Based on structural and functional data, a modular organization of enzymatic activities in prokaryotic and eukaryotic DNA polymerases is also proposed.