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1.
Nucleic Acids Res ; 48(18): 10142-10156, 2020 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-32976577

RESUMO

B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.


Assuntos
DNA Polimerase beta/química , DNA Polimerase beta/classificação , Eucariotos/enzimologia , Evolução Molecular , Archaea/enzimologia , Bactérias/enzimologia , Vírus de DNA/enzimologia , Bases de Dados de Proteínas
2.
Nucleic Acids Res ; 40(3): 1118-30, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22006845

RESUMO

Linear chromosomes and linear plasmids of Streptomyces are capped by terminal proteins that are covalently bound to the 5'-ends of DNA. Replication is initiated from an internal origin, which leaves single-stranded gaps at the 3'-ends. These gaps are patched by terminal protein-primed DNA synthesis. Streptomyces contain five DNA polymerases: one DNA polymerase I (Pol I), two DNA polymerases III (Pol III) and two DNA polymerases IV (Pol IV). Of these, one Pol III, DnaE1, is essential for replication, and Pol I is not required for end patching. In this study, we found the two Pol IVs (DinB1 and DinB2) to be involved in end patching. dinB1 and dinB2 could not be co-deleted from wild-type strains containing a linear chromosome, but could be co-deleted from mutant strains containing a circular chromosome. The resulting ΔdinB1 ΔdinB2 mutants supported replication of circular but not linear plasmids, and exhibited increased ultraviolet sensitivity and ultraviolet-induced mutagenesis. In contrast, the second Pol III, DnaE2, was not required for replication, end patching, or ultraviolet resistance and mutagenesis. All five polymerase genes are relatively syntenous in the Streptomyces chromosomes, including a 4-bp overlap between dnaE2 and dinB2. Phylogenetic analysis showed that the dinB1-dinB2 duplication occurred in a common actinobacterial ancestor.


Assuntos
DNA Polimerase III/fisiologia , DNA Polimerase beta/fisiologia , Replicação do DNA , Streptomyces/enzimologia , Streptomyces/genética , Telômero/metabolismo , Actinobacteria/genética , Alquilação , Cromossomos Bacterianos/química , Conjugação Genética , DNA/metabolismo , Dano ao DNA , DNA Polimerase III/classificação , DNA Polimerase III/genética , DNA Polimerase beta/classificação , DNA Polimerase beta/genética , Reparo do DNA , Deleção de Genes , Duplicação Gênica , Transferência Genética Horizontal , Filogenia , Plasmídeos/biossíntese , Sintenia , Raios Ultravioleta
3.
Biochem Biophys Res Commun ; 415(1): 193-9, 2011 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-22033415

RESUMO

While mammalian DNA polymerase ß (Pol ß), which is a member of the Pol X family, play important roles in base excision repair (BER) that efficiently removes DNA base lesions arising from both endogenous and exogenous agents, this protein has been found only a subset of animals. To understand natural evolution of this enzyme, we isolated and characterized Pol ß from jellyfish Aurelia sp.1. (AsPol ß). Despite of phylogenetic distance and environmental differences between jellyfish and mammals, in vitro assays showed biochemical characteristics of AsPol ß were very similar to those of a mammalian counterpart. We also searched two other homologs of mammalian genes that were involved in short patch (sp) BER in the nucleotide sequence database, and found that both of these homologs were encoded in the genomes of a lineage from Cnidarians through mammals and Arthropods. This study suggests that a DNA repair mechanism resembling mammalian sp-BER may be largely limited to a subset of animals. On the basis of our findings and previous reports, we discuss possible evolutional model of Pol ß and the other members of the Pol X family.


Assuntos
DNA Polimerase beta/metabolismo , Reparo do DNA , Cifozoários/enzimologia , Sequência de Aminoácidos , Animais , DNA Ligase Dependente de ATP , DNA Ligases/química , DNA Ligases/genética , DNA Ligases/metabolismo , DNA Polimerase beta/química , DNA Polimerase beta/classificação , DNA Polimerase beta/genética , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Evolução Molecular , Dados de Sequência Molecular , Filogenia , Proteínas de Ligação a Poli-ADP-Ribose , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteína 1 Complementadora Cruzada de Reparo de Raio-X , Proteínas de Xenopus
4.
Proc Natl Acad Sci U S A ; 103(12): 4540-5, 2006 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-16537396

RESUMO

Eukaryotes contain numerous transposable or mobile elements capable of parasite-like proliferation in the host genome. All known transposable elements in eukaryotes belong to two types: retrotransposons and DNA transposons. Here we report a previously uncharacterized class of DNA transposons called Polintons that populate genomes of protists, fungi, and animals, including entamoeba, soybean rust, hydra, sea anemone, nematodes, fruit flies, beetle, sea urchin, sea squirt, fish, lizard, frog, and chicken. Polintons from all these species are characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. In addition, Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Analogously to known transposable elements, Polintons exist as autonomous and nonautonomous elements. Our data suggest that Polintons have evolved from a linear plasmid that acquired a retroviral integrase at least 1 billion years ago. According to the model of Polinton transposition proposed here, a Polinton DNA molecule excised from the genome serves as a template for extrachromosomal synthesis of its double-stranded DNA copy by the Polinton-encoded DNA polymerase and is inserted back into genome by its integrase.


Assuntos
Elementos de DNA Transponíveis , Evolução Molecular , Fungos/genética , Genoma/genética , Urocordados/genética , Vertebrados/genética , Adenosina Trifosfatases/classificação , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Animais , Sequência de Bases , Cisteína Endopeptidases/classificação , Cisteína Endopeptidases/genética , Cisteína Endopeptidases/metabolismo , DNA Polimerase beta/classificação , DNA Polimerase beta/genética , DNA Polimerase beta/metabolismo , Fungos/enzimologia , Dados de Sequência Molecular , Filogenia , Urocordados/enzimologia , Vertebrados/metabolismo
5.
Nucleic Acids Res ; 34(4): 1102-11, 2006.
Artigo em Inglês | MEDLINE | ID: mdl-16488882

RESUMO

For many years, Taq polymerase has served as the stalwart enzyme in the PCR amplification of DNA. However, a major limitation of Taq is its inability to amplify damaged DNA, thereby restricting its usefulness in forensic applications. In contrast, Y-family DNA polymerases, such as Dpo4 from Sulfolobus solfataricus, can traverse a wide variety of DNA lesions. Here, we report the identification and characterization of five novel thermostable Dpo4-like enzymes from Acidianus infernus, Sulfolobus shibatae, Sulfolobus tengchongensis, Stygiolobus azoricus and Sulfurisphaera ohwakuensis, as well as two recombinant chimeras that have enhanced enzymatic properties compared with the naturally occurring polymerases. The Dpo4-like polymerases are moderately processive, can substitute for Taq in PCR and can bypass DNA lesions that normally block Taq. Such properties make the Dpo4-like enzymes ideally suited for the PCR amplification of damaged DNA samples. Indeed, by using a blend of Taq and Dpo4-like enzymes, we obtained a PCR amplicon from ultraviolet-irradiated DNA that was largely unamplifyable with Taq alone. The inclusion of thermostable Dpo4-like polymerases in PCRs, therefore, augments the recovery and analysis of lesion-containing DNA samples, such as those commonly found in forensic or ancient DNA molecular applications.


Assuntos
Archaea/enzimologia , DNA Polimerase beta/metabolismo , DNA/biossíntese , Reação em Cadeia da Polimerase , Temperatura , Proteínas Arqueais/classificação , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Sequência de Bases , Clonagem Molecular , Dano ao DNA , Impressões Digitais de DNA , DNA Polimerase beta/classificação , DNA Polimerase beta/genética , Estabilidade Enzimática , Genes Arqueais , Humanos , Células K562 , Dados de Sequência Molecular , Paleontologia , Filogenia , Sulfolobaceae/genética , Moldes Genéticos
6.
DNA Repair (Amst) ; 4(12): 1358-67, 2005 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-16213194

RESUMO

DNA polymerase lambda is a member of the X family of polymerases that is implicated in non-homologous end-joining of double-strand breaks in DNA and in base excision repair of DNA damage. To better understand the roles of DNA polymerase lambda in these repair pathways, here we review its structure and biochemical properties, with emphasis on its gap-filling polymerization activity, its dRP lyase activity and its unusual DNA synthetic (in)fidelity.


Assuntos
DNA Polimerase beta/química , DNA Polimerase beta/metabolismo , DNA Polimerase beta/classificação , Humanos , Conformação de Ácido Nucleico , Fósforo-Oxigênio Liases/química , Fósforo-Oxigênio Liases/metabolismo , Estrutura Terciária de Proteína , Relação Estrutura-Atividade
7.
Nucleic Acids Res ; 28(18): 3684-93, 2000 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-10982892

RESUMO

We describe here two novel mouse and human DNA polymerases: one (pol lambda) has homology with DNA polymerase beta while the other one (pol mu) is closer to terminal deoxynucleotidyltransferase. However both have DNA polymerase activity in vitro and share similar structural organization, including a BRCT domain, helix-loop-helix DNA-binding motifs and polymerase X domain. mRNA expression of pol lambda is highest in testis and fetal liver, while expression of pol mu is more lymphoid, with highest expression both in thymus and tonsillar B cells. An unusually large number of splice variants is observed for the pol mu gene, most of which affect the polymerase domain. Expression of mRNA of both polymerases is down-regulated upon treatment by DNA damaging agents (UV light, gamma-rays or H(2)O(2)). This suggests that their biological function may differ from DNA translesion synthesis, for which several DNA polymerase activities have been recently described. Possible functions are discussed.


Assuntos
DNA Polimerase Dirigida por DNA/química , Processamento Alternativo , Sequência de Aminoácidos , Animais , Linhagem Celular , Clonagem Molecular , Dano ao DNA , DNA Polimerase beta/química , DNA Polimerase beta/classificação , DNA Complementar/isolamento & purificação , DNA Polimerase Dirigida por DNA/classificação , DNA Polimerase Dirigida por DNA/isolamento & purificação , Escherichia coli , Regulação Enzimológica da Expressão Gênica , Humanos , Camundongos , Dados de Sequência Molecular , Filogenia , Conformação Proteica , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Distribuição Tecidual , Células Tumorais Cultivadas
8.
Nucleic Acids Res ; 27(7): 1609-18, 1999 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-10075991

RESUMO

A detailed analysis of the polbeta superfamily of nucleotidyltransferases was performed using computer methods for iterative database search, multiple alignment, motif analysis and structural modeling. Three previously uncharacterized families of predicted nucleotidyltransferases are described. One of these new families includes small proteins found in all archaea and some bacteria that appear to consist of the minimal nucleotidyltransferase domain and may resemble the ancestral state of this superfamily. Another new family that is specifically related to eukaryotic polyA polymerases is typified by yeast Trf4p and Trf5p proteins that are involved in chromatin remodeling. The TRF family is represented by multiple members in all eukaryotes and may be involved in yet unknown nucleotide polymerization reactions required for maintenance of chromatin structure. Another new family of bacterial and archaeal nucleotidyltransferases is predicted to function in signal transduction since, in addition to the nucleotidyltransferase domain, these proteins contain ligand-binding domains. It is further shown that the catalytic domain of gamma proteobacterial adenylyl cyclases is homologous to the polbeta superfamily nucleotidyltransferases which emphasizes the general trend for the origin of signal-transducing enzymes from those involved in replication, repair and RNA processing. Classification of the polbeta superfamily into distinct families and examination of their phyletic distribution suggests that the evolution of this type of nucleotidyltransferases may have included bursts of rapid divergence linked to the emergence of new functions as well as a number of horizontal gene transfer events.


Assuntos
Evolução Biológica , DNA Polimerase beta/genética , Família Multigênica , Adenilil Ciclases/química , Sequência de Aminoácidos , DNA Polimerase beta/classificação , DNA Polimerase beta/metabolismo , Dados de Sequência Molecular , Conformação Proteica , Homologia de Sequência de Aminoácidos , Transdução de Sinais
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