Characterization of DNA ligase from the fungus Coprinus cinereus

The multi-replication protein A (RPA) system--a new perspective

Replication protein A (RPA) complex has been shown, using both in vivo and in vitro approaches, to be required for most aspects of eukaryotic DNA metabolism: replication, repair, telomere maintenance and homologous recombination. Here, we review recent data concerning the function and biological importance of the multi-RPA complex. There are distinct complexes of RPA found in the biological kingdoms, although for a long time only one type of RPA complex was believed to be present in eukaryotes. Each complex probably serves a different role. In higher plants, three distinct large and medium subunits are present, but only one species of the smallest subunit. Each of these protein subunits forms stable complexes with their respective partners. They are paralogs as complex. Humans possess two paralogs and one analog of RPA. The multi-RPA system can be regarded as universal in eukaryotes. Among eukaryotic kingdoms, paralogs, orthologs, analogs and heterologs of many DNA synthesis-related factors, including RPA, are ubiquitous. Convergent evolution seems to be ubiquitous in these processes. Using recent findings, we review the composition and biological functions of RPA complexes.

Two X family DNA polymerases, λ and μ, in meiotic tissues of the basidiomycete, Coprinus cinereus

The X family DNA polymerases lambda (CcPollambda) and mu (CcPolmu) were shown to be expressed during meiotic prophase in the basidiomycete, Coprinus cinereus. These two polymerases are the only members of the X family in the C. cinereus genome. The open reading frame of CcPollambda encoded a predicted product of 800 amino acid residues and that of CcPolmicro of 621 amino acid residues. Both CcPollambda and CcPolmicro required Mn(2+) ions for activity, and both were strongly inhibited by dideoxythymidine triphosphate. Unlike their mammalian counterparts, CcPollambda and CcPolmicro had no terminal deoxynucleotidyl transferase activity. Immunostaining analysis revealed that CcPollambda was present at meiotic prophase nuclei in zygotene and pachytene cells, which is the period when homologous chromosomes pair and recombine. CcPolmicro was present in a slightly wider range of cell stages, zygotene to diplotene. In analyses using D-loop recombination intermediate substrates, we found that both CcPollambda and CcPolmicro could promote primer extension of an invading strand in a D-loop structure. Moreover, both polymerases could fully extend the primer in the D-loop substrate, suggesting that D-loop extension is an activity intrinsic to CcPollambda and CcPolmicro. Based on these data, we discuss the possible roles of these polymerases in meiosis.

DNA ligase IV from a basidiomycete, Coprinus cinereus, and its expression during meiosis

DNA ligase IV is thought to be involved in DNA double-strand break repair and DNA non-homologous end-joining pathways, but these mechanisms are still unclear. To investigate the roles of DNA ligase IV from a biologically functional viewpoint, the authors studied its relationship to meiosis in a basidiomycete, Coprinus cinereus, which shows a highly synchronous meiotic cell cycle. The C. cinereus cDNA homologue of DNA ligase IV (CcLIG4) was successfully cloned. The 3.2 kb clone including the ORF encoded a predicted product of 1025 amino acid residues with a molecular mass of 117 kDa. A specific inserted sequence composed of 95 amino acids rich in aspartic acid and glutamic acid could be detected between tandem BRCT domains. The inserted sequence had no sequence identity with other eukaryotic counterparts of DNA ligase IV or with another aspartic acid and glutamic acid rich sequence inserted in C. cinereus proliferating cell nuclear antigen (CcPCNA), although the length and the percentages of aspartic and glutamic acids were similar. In addition, the recombinant CcLIG4 protein not only showed ATP-dependent ligase activity, but also used (dT)(16)/poly(dA) and (dT)(16)/poly(rA) as substrates, and had double-strand ligation activity, like human DNA ligase IV. Northern hybridization analysis and in situ hybridization indicated that CcLIG4 was expressed not only at the pre-meiotic S phase but also at meiotic prophase I. Intense signals were observed in leptotene and zygotene. Based on these observations, the possible role(s) of C. cinereus DNA ligase IV during meiosis are discussed.

Coprinus cinereus DNA ligase I during meiotic development

DNA ligase I is thought to be essential for DNA replication, repair and recombination, at least in the mitotic cell cycle, but whether this is also the case during the meiotic cell cycle is still obscure. To investigate the role of DNA ligase I during the meiotic cell cycle, we cloned the Coprinus cinereus DNA ligase I cDNA (CcLIG1). Northern blotting analysis indicated that CcLIG1 is expressed not only in the premeiotic S-phase but also during the meiotic cell cycle itself. Especially, intense signals were observed in the leptotene and zygotene stages. Western blotting analysis indicated that CcLIG1 is expressed through the meiotic cell cycle and immunofluorescence also showed CcLIG1 protein staining in meiotic cells. Interestingly, the patterns was similar to that for the C. cinereus proliferating cell nuclear antigen gene (CcPCNA) and immunoprecipitation analysis suggested that CcPCNA binds to CcLIG1 in crude extracts of meiotic prophase I tissues. Based on these observations, relationships and roles during the meiotic cell cycle are discussed.

Dynamic mechanism of nick recognition by DNA ligase

DNA ligases are the enzymes responsible for the repair of single-stranded and double-stranded nicks in dsDNA. DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNA has yet to be solved. DNA ligases share common structural elements with DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase-dsDNA interactions, we propose a mechanism for recognition of a single-stranded nick by DNA ligase. According to this mechanism, ligase induces a B-to-A DNA helix transition of the enzyme-bound dsDNA motif, which results in DNA contraction, bending and unwinding. For non-nicked dsDNA, this transition is reversible, leading to dissociation of the enzyme. For a nicked dsDNA substrate, the contraction of the enzyme-bound DNA motif (a) triggers an opened-closed conformational change of the enzyme, and (b) forces the motif to accommodate the strained A/B-form hybrid conformation, in which the nicked strand tends to retain a B-type helix, while the non-nicked strand tends to form a shortened A-type helix. We propose that this conformation is the catalytically competent transition state, which leads to the formation of the DNA-AMP intermediate and to the subsequent sealing of the nick.

Leucine aminopeptidase during meiotic development

We found a leucine aminopeptidase (LAP; EC 3.4.11.1) to be abundant in meiotic prophase tissue of a basidiomycete, Coprinus cinereus. After direct purification of the aminopeptidase component from meiocytes, we cloned the gene by degenerate PCR using partial amino-acid sequences of the purified enzyme and 5' and 3' RACE. It was homologous to the eukaryotic leucine aminopeptidase gene. The recombinant protein possesses the characteristic activities of a Coprinus leucine aminopeptidase (CoLAP) with a molecular mass of 52.4 kDa, and forms a homohexamer. Northern blot and spatial distribution analysis by immunohistochemical staining indicated CoLAP to be abundant in meiotic prophase cells and the supporting cells around meiocytes, but scarce in mycelium cells. Interestingly, from zygotene to pachytene, CoLAP was mostly present in supporting cells around meiocytes, but from diplotene onwards, it was plentiful in meiocytes themselves, suggesting that its expression is required to control some of the biochemical events at meiotic prophase. Moreover, the strong expression of CoLAP mRNA immediately after treatment with methyl methanesulfonate in mycelium implies that CoLAP has a role in somatic DNA repair.

Kinetic mechanism of the Mg2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases

The Mg(2+)-dependent adenylylation of the T4 DNA and RNA ligases was studied in the absence of a DNA substrate using transient optical absorbance and fluorescence spectroscopy. The concentrations of Mg(2+), ATP, and pyrophosphate were systematically varied, and the results led to the conclusion that the nucleotidyl transfer proceeds according to a two-metal ion mechanism. According to this mechanism, only the di-magnesium-coordinated form Mg(2)ATP(0) reacts with the enzyme forming the covalent complex E.AMP. The reverse reaction (ATP synthesis) occurs between the mono-magnesium-coordinated pyrophosphate form MgP(2)O(7)(2-) and the enzyme.MgAMP complex. The nucleotide binding rate decreases in the sequence ATP(4-) > MgATP(2-) > Mg(2)ATP(0), indicating that the formation of the non-covalent enzyme.nucleotide complex is driven by electrostatic interactions. T4 DNA ligase shows notably higher rates of ATP binding and of subsequent adenylylation compared with RNA ligase, in part because it decreases the K(d) of Mg(2+) for the enzyme-bound Mg(2)ATP(0) more than 10-fold. To elucidate the role of Mg(2+) in the nucleotidyl transfer catalyzed by T4 DNA and RNA ligases, we propose a transition state configuration, in which the catalytic Mg(2+) ion coordinates to both reacting nucleophiles: the lysyl moiety of the enzyme that forms the phosphoramidate bond and the alpha-beta-bridging oxygen of ATP.

Proliferating cell nuclear antigen from a basidiomycete, Coprinus cinereus. Alternative truncation and expression in meiosis

The primary purpose of the present study was to investigate whether DNA replication at meiotic prophase also requires replication factors, especially proliferating cell nuclear antigen (PCNA). We cloned PCNA cDNAs (CoPCNA) from a cDNA library made from basidia of the basidiomycete, Coprinus cinereus. Interestingly, although CoPCNA is a single-copy gene in the genome, two different PCNA cDNA species were isolated using degenerate primers and a meiotic cDNA library, and were designated as CoPCNA-alpha and CoPCNA-beta. CoPCNA-beta was made by truncating at specific sites in CoPCNA-alpha mRNA, 5'-AAGAAGGAGAAG-3' and 5'-GAAGAGGAAGAA-3'. Both of these sequences were present in exon IV in the genomic sequence, and interestingly the former was the same as the inverse sequence of the latter. CoPCNA-alpha was 107 amino acids larger than human PCNA, and so the 107 amino-acid sequence was inserted in a loop, the so-called D2E2 loop, in human PCNA. Northern blotting analysis indicated that CoPCNA was expressed not only at premeiotic S but also at the meiotic prophase stages such as leptotene and early zygotene, just before and when karyogamy occurs and the homologous chromosomes pair. Western blotting analysis using anti-(CoPCNA-alpha) Ig revealed that at least two CoPCNA mRNAs before and after truncation were translated at the meiotic prophase as CoPCNA-alpha and CoPCNA-beta.

Substrate recognition and fidelity of strand joining by an archaeal DNA ligase

We have previously identified a DNA ligase (LigTk) from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. The enzyme is the only characterized ATP-dependent DNA ligase from a hyperthermophile, and allows the analysis of enzymatic DNA ligation reactions at temperatures above the melting point of the substrates. Here we have focused on the interactions of LigTk with various DNA substrates, and its specificities toward metal cations. LigTk could utilize Mg2+, Mn2+, Sr2+ and Ca2+ as a metal cation, but not Co2+, Zn2+, Ni2+, or Cu2+. The enzyme displayed typical Michaelis-Menten steady-state kinetics with an apparent Km of 1.4 microm for nicked DNA. The kcat value of the enzyme was 0.11*s-1. Using various 3' hydroxyl group donors (L-DNA) and 5' phosphate group donors (R-DNA), we could detect ligation products as short as 16 nucleotides, the products of 7 + 9 nucleotide or 8 + 8 nucleotide combinations at 40 degrees C. An elevation in temperature led to a decrease in reaction efficiency when short oligonucleotides were used, suggesting that the formation of a nicked, double-stranded DNA substrate preceded enzyme-substrate recognition. LigTk was not inhibited by the addition of excess duplex DNA, implying that the enzyme did not bind strongly to the double-stranded ligation product after nick-sealing. In terms of reaction fidelity, LigTk was found to ligate various substrates with mismatched base-pairing at the 5' end of the nick, but did not show activity towards the 3' mismatched substrates. LigTk could not seal substrates with a 1-nucleotide or 2-nucleotide gap. Small amounts of ligation products were detected with DNA substrates containing a single nucleotide insertion, relatively more with the 5' insertions. The results revealed the importance of proper base-pairing at the 3' hydroxyl side of the nick for the ligation reaction by LigTk.

Strand exchange reaction in vitro and DNA-dependent ATPase activity of recombinant LIM15/DMC1 and RAD51 proteins from Coprinus cinereus

We previously cloned recA-homolog genes from a basidiomycete, Coprinus cinereus, and obtained the recombinant proteins (Nara et al., Mol. Gen. Genet. 262, 781-789, 1999, see Ref. 1; Nara and Sakaguchi, Biochem. Biophys. Res. Commun. 275, 97-102, 2000, see Ref. 2). The primary purpose of the present study was to characterize the biochemical properties of the recombinant LIM15/DMC1 (CoLIM15) and RAD51 (CoRAD51) proteins. We purified the recombinant proteins, and their molecular masses were 37 and 35 kDa, respectively. Both enzymes showed DNA-dependent ATPase activity and ATP-dependent strand exchange reaction in vitro. CoRad51 was a five- to sixfold stronger DNA-dependent ATPase and showed greater dependency on single-stranded DNA than CoLim15. In meiosis, both enzymes were highly accumulated in the meiotic tissue at leptotene and zygotene stages at which the homologous chromosomes pair, but disappeared just before the pachytene stage at which they recombine. From these and the previously reported results, we discuss here the relationships between the enzymes and meiosis.

Characterization of interaction of C- and N-terminal domains in LIM15/DMC1 and RAD51 from a basidiomycetes, Coprinus cinereus

Both LIM15/DMC1 and RAD51 are thought to be essential for meiosis in which homologous chromosomes pair and recombine. The primary purpose of the present study was to investigate the homotypic and heterotypic interactions among their terminal domains. We prepared cDNAs and recombinant proteins of the full-length, N-terminal, and the C-terminal domains of LIM15/DMC1 (CoLIM15) and RAD51 (CoRAD51) from the basidiomycete Coprinus cinereus. In both two-hybrid assay in vivo and pull-down assay in vitro, either CoLim15 or CoRad51 interacted homotypically between the C-terminal domains, respectively, but no heterotypic interaction was observed between CoLim15 and CoRad51. The N-terminal domain of CoLim15 bound to ssDNA and dsDNA, while the C-terminal domain of CoRad51 appeared to interact weakly with ssDNA. Based on these results, the interaction among the strand-exchange proteins and meiosis was discussed.

Life history and developmental processes in the basidiomycete Coprinus cinereus

Coprinus cinereus has two main types of mycelia, the asexual monokaryon and the sexual dikaryon, formed by fusion of compatible monokaryons. Syngamy (plasmogamy) and karyogamy are spatially and temporally separated, which is typical for basidiomycetous fungi. This property of the dikaryon enables an easy exchange of nuclear partners in further dikaryotic-monokaryotic and dikaryotic-dikaryotic mycelial fusions. Fruiting bodies normally develop on the dikaryon, and the cytological process of fruiting-body development has been described in its principles. Within the specialized basidia, present within the gills of the fruiting bodies, karyogamy occurs in a synchronized manner. It is directly followed by meiosis and by the production of the meiotic basidiospores. The synchrony of karyogamy and meiosis has made the fungus a classical object to study meiotic cytology and recombination. Several genes involved in these processes have been identified. Both monokaryons and dikaryons can form multicellular resting bodies (sclerotia) and different types of mitotic spores, the small uninucleate aerial oidia, and, within submerged mycelium, the large thick-walled chlamydospores. The decision about whether a structure will be formed is made on the basis of environmental signals (light, temperature, humidity, and nutrients). Of the intrinsic factors that control development, the products of the two mating type loci are most important. Mutant complementation and PCR approaches identified further genes which possibly link the two mating-type pathways with each other and with nutritional regulation, for example with the cAMP signaling pathway. Among genes specifically expressed within the fruiting body are those for two galectins, beta-galactoside binding lectins that probably act in hyphal aggregation. These genes serve as molecular markers to study development in wild-type and mutant strains. The isolation of genes for potential non-DNA methyltransferases, needed for tissue formation within the fruiting body, promises the discovery of new signaling pathways, possibly involving secondary fungal metabolites.

Non-histone chromosomal proteins HMG1 and 2 enhance ligation reaction of DNA double-strand breaks

DNA ligase IV in a complex with XRCC4 is responsible for DNA end-joining in repair of DNA double-strand breaks (DSB) and V(D)J recombination. We found that non-histone chromosomal high mobility group (HMG) proteins 1 and 2 enhanced the ligation of linearized pUC119 DNA with DNA ligase IV from rat liver nuclear extract. Intra-molecular and inter-molecular ligations of cohesive-ended and blunt-ended DNA were markedly stimulated by HMG1 and 2. Recombinant HMG2-domain A, B, and (A + B) polypeptides were similarly, but non-identically, effective for the stimulation of DSB ligation reaction. Ligation of single-strand breaks (nicks) was only slightly activated by the HMG proteins. The DNA end-binding Ku protein singly or in combination with the catalytic component of DNA-dependent protein kinase (DNA-PK) as the DNA-PK holoenzyme was ineffective for the ligation of linearized pUC119 DNA. Although the stimulatory effect of HMG1 and 2 on ligation of DSB in vitro was not specific to DNA ligase IV, these results suggest that HMG1 and 2 are involved in the final ligation step in DNA end-joining processes of DSB repair and V(D)J recombination.

A structure-specific endonuclease from cauliflower (Brassica oleracea var. botrytis) inflorescence

A protein with structure-specific endonuclease activity has been purified to near homogeneity from cauliflower ( Brassica oleracea var. botrytis) inflorescence through five successive column chromatographies. The protein is a single polypeptide with a molecular mass of 40 kDa. Using three different branched DNA structures (flap, pseudo-Y and stem-loop) we found that the enzyme, a cauliflower structure-specific endonuclease, cleaved the single-stranded tail in the 5'-flap and 5'-pseudo-Y structures, whereas it could not incise the 3'-flap and 3'-pseudo-Y structures. The incision points occur around the single strand-duplex junction in these DNA substrates and the enzyme leaves 5'-PO4 and 3'-OH termini on DNA. The protein also endonucleolytically cleaves on the 3'-side of the single-stranded region at the junction of unpaired and duplex DNA in the stem-loop structure. The structure-specific endonuclease activity is stimulated by Mg2+ and by Mn2+, but not by Ca2+. Like mammalian FEN-1, the protein has weak 5'-->3' double-stranded DNA-specific exonuclease activity. These results indicate that the cauliflower protein is a plant structure-specific endonuclease like mammalian FEN-1 or may be the plant alternative.

A DNA polymerase alpha catalytic subunit is purified independently from the tissues at meiotic prometaphase I of a basidiomycete, Coprinus cinereus

A 135kDa DNA polymerase alpha lacking primase activity has been purified to near homogeneity from Coprinus meiotic tissues. The activity of the DNA polymerase was sensitive to aphidicolin and N-ethylmaleimide, but was insensitive to dideoxythymidine triphosphate. DNA synthesis was proceeded with a low processivity. Neither activity nor processivity were affected by PCNA in the presence or absence of KCI. Monovalent cation inhibited its activity. These biochemical properties are almost identical to those of Coprinus DNA polymerase alpha -primase complex. However, the 135kDa DNA polymerase did not use activated DNA as a template-primer, inconsistent with Coprinus DNA polymerase alpha-primase complex. The 135kDa DNA polymerase was purified from the tissues at meiotic pro-metaphase I, suggesting that the alpha- DNA polymerase-primase complex dissociates as the meiotic cell cycle progresses and only the catalytic subunit remains at this stage.